Datasets:

codeparrot

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codeparrot-clean-valid

like 8

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CodeParrot 108

amolenaar/gaphor

gaphor/core/modeling/coremodel.py

1

2200

# This file is generated by codegen.py. DO NOT EDIT! from __future__ import annotations import uuid from typing import TYPE_CHECKING, Callable, List, Optional from gaphor.core.modeling.element import Element from gaphor.core.modeling.properties import ( association, attribute, derived, derivedunion, enumeration, redefine, relation_many, relation_one, ) if TYPE_CHECKING: from gaphor.UML import Dependency, Namespace # 8: override Element # defined above # 11: override NamedElement # Define extra attributes defined in UML model class NamedElement(Element): name: attribute[str] qualifiedName: derived[List[str]] namespace: relation_one[Namespace] clientDependency: relation_many[Dependency] supplierDependency: relation_many[Dependency] class PackageableElement(NamedElement): pass # 55: override Diagram # defined in gaphor.core.modeling.diagram # 46: override Presentation # defined in gaphor.core.modeling.presentation class Comment(Element): body: attribute[str] annotatedElement: relation_many[Element] # 40: override StyleSheet # defined in gaphor.core.modeling.presentation NamedElement.name = attribute("name", str) Comment.body = attribute("body", str) # 43: override StyleSheet.styleSheet # defined in gaphor.core.modeling.presentation # 52: override Presentation.subject # defined in gaphor.core.modeling.presentation # 49: override Element.presentation # defined in gaphor.core.modeling.presentation Comment.annotatedElement = association( "annotatedElement", Element, opposite="ownedComment" ) Element.ownedComment = association("ownedComment", Comment, opposite="annotatedElement") # 20: override NamedElement.qualifiedName(NamedElement.namespace): derived[List[str]] def _namedelement_qualifiedname(self) -> List[str]: """ Returns the qualified name of the element as a tuple """ if self.namespace: return _namedelement_qualifiedname(self.namespace) + [self.name] else: return [self.name] NamedElement.qualifiedName = derived( NamedElement, "qualifiedName", List[str], 0, 1, lambda obj: [_namedelement_qualifiedname(obj)], )

lgpl-2.1

rackerlabs/deuce-client

deuceclient/auth/rackspaceauth.py

1

2721

""" Deuce Rackspace Authentication API """ import logging import deuceclient.auth import deuceclient.auth.openstackauth def get_identity_apihost(datacenter): if datacenter in ('us', 'uk', 'lon', 'iad', 'dfw', 'ord'): return 'https://identity.api.rackspacecloud.com/v2.0' elif datacenter in ('hkg', 'syd'): return'https://{0:}.identity.api.rackspacecloud.com/v2.0'.\ format(datacenter) else: raise deuceclient.auth.AuthenticationError( 'Unknown Data Center: {0:}'.format(datacenter)) class RackspaceAuthentication( deuceclient.auth.openstackauth.OpenStackAuthentication): """Rackspace Identity Authentication Support Only difference between this and OpenStackAuthentication is that this can know the servers without one being specified. """ def __init__(self, userid=None, usertype=None, credentials=None, auth_method=None, datacenter=None, auth_url=None): # If an authentication url is not provided then create one using # Rackspace's Identity Service for the specified datacenter if auth_url is None: if datacenter is None: raise deuceclient.auth.AuthenticationError( 'Required Parameter, datacenter, not specified.') auth_url = get_identity_apihost(datacenter) log = logging.getLogger(__name__) log.debug('No AuthURL specified. Using {0:}'.format(auth_url)) super(RackspaceAuthentication, self).__init__(userid=userid, usertype=usertype, credentials=credentials, auth_method=auth_method, datacenter=datacenter, auth_url=auth_url) @staticmethod def _management_url(*args, **kwargs): # NOTE(TheSriram): kwarg region_name is the datacenter supplied # when instantiating RackspaceAuthentication class return get_identity_apihost(kwargs['region_name']) @staticmethod def patch_management_url(): from keystoneclient.service_catalog import ServiceCatalog ServiceCatalog.url_for = RackspaceAuthentication._management_url def get_client(self): """Retrieve the Rackspace Client """ # NOTE(TheSriram): The exceptions thrown if any, would still # bear OpenstackAuthentication class in the message. RackspaceAuthentication.patch_management_url() return super(RackspaceAuthentication, self).get_client()

apache-2.0

lambdaloop/CIT-biosignals

pygame/present_images_pygame.py

1

1565

import pygame from pygame.locals import * from constants import * from generate_images import * import time import pandas as pd from pylsl import StreamInfo, StreamOutlet import random pygame.init() #pygame.mouse.set_visible(False) from screen import screen from drawstuff import * study_time = int(time.time()) print(study_time) info = StreamInfo('Ganglion_EEG', 'Markers', 1, 0.0, 'int32', 'marker') outlet = StreamOutlet(info) images = gen_images() def check_for_key(key=K_ESCAPE): while True: event = pygame.event.poll() if event.type == 0: return False elif event.dict.get('key', -1) == key: return True def check_for_escape(): return check_for_key(K_ESCAPE) def finish_stuff(early=False): return text_slide("""Start recording and press space to continue""") while not check_for_key(K_SPACE): pass focus_slide() outlet.push_sample([-1], time.time()) time.sleep(0.5) images = [(path, pygame.image.load(path)) for path in images] t = time.time() for image_path, img in images: # if d['is_shown'] != 1: # continue # word = d['word'] print(time.time() - t) t = time.time() print(image_path, hash(image_path)) image_slide(img) outlet.push_sample([hash(image_path)], time.time()) time.sleep(4) if check_for_escape(): finish_stuff(early=True) exit() focus_slide() outlet.push_sample([-1], time.time()) time.sleep(2.0) if check_for_escape(): finish_stuff(early=True) exit()

mit

Metruption/hophacks17project

src/analysis.py

1

2022

""" analysis.py: A wrapper for the Bark Partner API Copyright (C) 2016 Aaron Thomas This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. """ import json import pybark from bark_config import BARK_TOKEN def check_message(message): ''' preconditions: @param message is a string postconditions: returns a boolean True of the message is abusive False if the message is not abusive ''' resp = pybark.woof(BARK_TOKEN, message) resp = json.loads(resp) power_level = [resp['abusive'],resp['results']['sentiment'] in ["VERY_NEGATIVE", "NEGATIVE"]] bad_varname = ["profanity", "cyberbullying"] power_level = power_level + [resp['results'][i]['abusive'] for i in bad_varname] return sum(power_level) >=2 def find_handle(message): ''' preconditions: @param message is a string postconditions: returns a tuple containing all of the twitter ids of any @handles given in the text of the direct message returns a tuple containing all of the twitter @handles given in the text of the direct message example outputs: () none given (aaron_the_king,,@hack,@hateishate_) three given (@aaron_the_king,@jack) two (@aaron_the_king) one given ''' words = message.split(" ") handles = (word for word in words if word.startswith('@')) return handles

gpl-3.0

yadt/yadt-config-rpm-maker

src/config_rpm_maker/token/treenode.py

1

1209

# yadt-config-rpm-maker # Copyright (C) 2011-2013 Immobilien Scout GmbH # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. class NameNotAcceptedException(Exception): def __init__(self, name): self.name = name def __str__(self): return "name '%s' is not accepted, must not be empty or null" % self.name class TreeNode: def __init__(self, name, children=None): if children is None: children=[] if name is None or len(name) == 0: raise NameNotAcceptedException(name) self.name = name self.children = set(children)

gpl-3.0

cfobel/camip

camip/bin/vpr_net_to_df.py

1

2970

import sys from collections import OrderedDict import numpy as np import pandas as pd from path_helpers import path from vpr_netfile_parser.VprNetParser import cVprNetFileParser try: profile except NameError: profile = lambda f: f INPUT_DRIVER_PIN = 0 LOGIC_DRIVER_PIN = 4 LOGIC_BLOCK = 0 INPUT_BLOCK = 1 OUTPUT_BLOCK = 2 CLOCK_PIN = 5 CONNECTION_CLOCK = 5 CONNECTION_DRIVER = 200 CONNECTION_SINK = 100 CONNECTION_CLOCK_DRIVER = 30 # Connection type = DRIVER_TYPE + 10 * SINK_TYPE DELAY_IO_TO_IO = INPUT_BLOCK + 10 * OUTPUT_BLOCK DELAY_FB_TO_FB = LOGIC_BLOCK + 10 * LOGIC_BLOCK DELAY_IO_TO_FB = INPUT_BLOCK + 10 * LOGIC_BLOCK DELAY_FB_TO_IO = LOGIC_BLOCK + 10 * OUTPUT_BLOCK @profile def vpr_net_to_df(net_file_path): parser = cVprNetFileParser(net_file_path) block_labels = pd.Series(parser.block_labels) net_labels = pd.Series(parser.net_labels) type_labels = pd.Series(['.clb', '.input', '.output'], index=[LOGIC_BLOCK, INPUT_BLOCK, OUTPUT_BLOCK]) type_keys = pd.DataFrame(range(type_labels.shape[0]), dtype='uint32', index=type_labels, columns=['type_key']) block_type_keys = type_keys.loc[parser.block_type, 'type_key'].reset_index(drop=True) block_to_net_ids = parser.block_to_net_ids() net_key = np.concatenate(block_to_net_ids).astype('uint32') block_key = np.concatenate([[i] * len(v) for i, v in enumerate(block_to_net_ids)]).astype('uint32') pin_key = np.concatenate(parser.block_used_pins).astype('uint32') connections = pd.DataFrame(OrderedDict([('net_key', net_key), ('block_key', block_key), ('pin_key', pin_key)])) connections.insert(2, 'block_type', block_type_keys.iloc[connections.block_key].values) connections['net_label'] = net_labels.iloc[connections.net_key].values connections['block_label'] = block_labels.iloc[connections.block_key].values return connections.sort(['net_key', 'block_key']).reset_index(drop=True) def parse_args(argv=None): '''Parses arguments, returns (options, args).''' from argparse import ArgumentParser if argv is None: argv = sys.argv parser = ArgumentParser(description='Convert VPR netlist `.net` file to HDF ' 'connections `.h5` format.') parser.add_argument(dest='vpr_net_file', type=path) parser.add_argument(dest='hdf_file', type=path) args = parser.parse_args() return args if __name__ == '__main__': args = parse_args() df_netlist = vpr_net_to_df(args.vpr_net_file) df_netlist.to_hdf(str(args.hdf_file), '/connections', format='table', data_columns=df_netlist.columns, complib='zlib', complevel=6)

gpl-2.0

khchine5/xl

lino_xl/lib/ledger/fixtures/demo_bookings.py

1

4927

# -*- coding: UTF-8 -*- # Copyright 2012-2017 Luc Saffre # License: BSD (see file COPYING for details) """ Creates fictive demo bookings with monthly purchases. See also: - :mod:`lino_xl.lib.finan.fixtures.demo_bookings` - :mod:`lino_xl.lib.sales.fixtures.demo_bookings` - :mod:`lino_xl.lib.invoicing.fixtures.demo_bookings` """ from __future__ import unicode_literals import datetime from dateutil.relativedelta import relativedelta as delta from decimal import Decimal from django.conf import settings from lino.utils import Cycler from lino.utils.dates import AMONTH from lino.api import dd, rt from lino_xl.lib.vat.mixins import myround # from lino.core.requests import BaseRequest REQUEST = settings.SITE.login() # BaseRequest() MORE_THAN_A_MONTH = datetime.timedelta(days=40) from lino_xl.lib.vat.choicelists import VatAreas, VatRules from lino_xl.lib.ledger.choicelists import TradeTypes def objects(): Journal = rt.models.ledger.Journal PaymentTerm = rt.models.ledger.PaymentTerm Company = rt.models.contacts.Company USERS = Cycler(settings.SITE.user_model.objects.all()) def func(): # qs = Company.objects.filter(sepa_accounts__iban__isnull=False) qs = Company.objects.exclude(vat_regime='').filter( country__isnull=False) for p in qs.order_by('id'): # if Journal.objects.filter(partner=p).exists(): # continue # if not p.vat_regime: # continue va = VatAreas.get_for_country(p.country) if va is None: continue rule = VatRules.get_vat_rule( va, TradeTypes.purchases, p.vat_regime, default=False) if rule: yield p PROVIDERS = Cycler(func()) if len(PROVIDERS) == 0: raise Exception("No providers.") JOURNAL_P = Journal.objects.get(ref="PRC") if dd.is_installed('ana'): ANA_ACCS = Cycler(rt.models.ana.Account.objects.all()) ACCOUNTS = Cycler(JOURNAL_P.get_allowed_accounts()) AMOUNTS = Cycler([Decimal(x) for x in "20 29.90 39.90 99.95 199.95 599.95 1599.99".split()]) AMOUNT_DELTAS = Cycler([Decimal(x) for x in "0 0.60 1.10 1.30 2.50".split()]) DATE_DELTAS = Cycler((1, 2, 3, 4, 5, 6, 7)) INFLATION_RATE = Decimal("0.02") """"purchase stories" : each story represents a provider who sends monthly invoices. """ PURCHASE_STORIES = [] for i in range(7): # provider, (account,amount) story = (PROVIDERS.pop(), []) story[1].append((ACCOUNTS.pop(), AMOUNTS.pop())) if i % 3: story[1].append((ACCOUNTS.pop(), AMOUNTS.pop())) PURCHASE_STORIES.append(story) START_YEAR = dd.plugins.ledger.start_year date = datetime.date(START_YEAR, 1, 1) end_date = settings.SITE.demo_date(-10) # + delta(years=-2) # end_date = datetime.date(START_YEAR+1, 5, 1) # print(20151216, START_YEAR, settings.SITE.demo_date(), end_date - date) PAYMENT_TERMS = Cycler(PaymentTerm.objects.all()) if len(PAYMENT_TERMS) == 0: raise Exception("No PAYMENT_TERMS.") while date < end_date: for story in PURCHASE_STORIES: vd = date + delta(days=DATE_DELTAS.pop()) if dd.is_installed('ana'): cl = rt.models.ana.AnaAccountInvoice else: cl = rt.models.vat.VatAccountInvoice invoice = cl( journal=JOURNAL_P, partner=story[0], user=USERS.pop(), voucher_date=vd, payment_term=PAYMENT_TERMS.pop(), entry_date=vd + delta(days=1)) yield invoice for account, amount in story[1]: kwargs = dict() if dd.is_installed('ana'): if account.needs_ana: kwargs.update(ana_account=ANA_ACCS.pop()) model = rt.models.ana.InvoiceItem else: model = rt.models.vat.InvoiceItem amount += amount + \ (amount * INFLATION_RATE * (date.year - START_YEAR)) item = model(voucher=invoice, account=account, total_incl=myround(amount) + AMOUNT_DELTAS.pop(), **kwargs) try: item.total_incl_changed(REQUEST) except Exception as e: msg = "20171006 {} in ({} {!r})".format( e, invoice.partner, invoice.vat_regime) # raise Exception(msg) dd.logger.warning(msg) else: item.before_ui_save(REQUEST) yield item invoice.register(REQUEST) invoice.save() date += AMONTH

bsd-2-clause

AeroNotix/django-timetracker

tracker/management/commands/approval_reminders.py

1

1376

''' Simple module to aid in command-line debugging of notification related issues. ''' from django.core.management.base import BaseCommand, CommandError from django.conf import settings from django.core.mail import EmailMessage from timetracker.overtime.models import PendingApproval, Tbluser def send_approval_digest(market): approvals = PendingApproval.objects.filter(closed=False, approver__market=market) if not len(approvals): return if len({entry.approver for entry in approvals}) > 1: error_log.critical( "Cannot send e-mails as a clear approval chain cannot be established." ) return message = "Hi,\n\n" \ "You have %d approvals pending in the timetracker." \ "\n\n" \ "Kind Regards,\n" \ "Timetracker team" message = message % len(approvals) email = EmailMessage(from_email='[email protected]') email.body = message email.to = approvals[0].entry.user.get_manager_email() email.subject = "Pending Approvals in the Timetracker." email.send() class Command(BaseCommand): def handle(self, *args, **options): for market in Tbluser.MARKET_CHOICES: if settings.SENDING_APPROVAL_DIGESTS.get(market[0]): send_approval_digest(market[0])

bsd-3-clause

digitalhealthhack/is_it_good_for_me

data_scripts/get_studies.py

1

3019

from requests import get as get_page from bs4 import BeautifulSoup import csv import codecs import cStringIO TOPIC = 'chocolate' def _get_study_url(url): # Receives the url of a cochrane search result and returns the url for the # study result_page = get_page(url) result_soup = BeautifulSoup(result_page.text) study_url = result_soup \ .find(id='node_review_full_group_research') \ .find_all('a')[0] \ .get('href') return study_url def _get_info_for_study(study_url): study_page = get_page(study_url) soup = BeautifulSoup(study_page.text) study_title = soup.find(class_='articleTitle').span.text abstract_html = soup.find(id='mrwFulltext').div.find_all(['p', 'div']) abstract_text = u'' authors_conclusions = u'' is_capturing = False for html in abstract_html: if is_capturing and html.name != 'p' and html.text != 'Authors\' conclusions': is_capturing = False break abstract_text += unicode(html.text) if is_capturing: authors_conclusions += unicode(html.text) if html.name != 'p' and html.text == 'Authors\' conclusions': is_capturing = True return (study_title, authors_conclusions, abstract_text) def main(search_query=''): req = get_page( 'http://summaries.cochrane.org/search/site/{}'.format(search_query), ) soup = BeautifulSoup(req.text) results = soup.find_all(class_='search-result') studies = [] for result in results: result_url = result.a.get('href') if result_url: study_url = _get_study_url(result_url) study_title, study_conclusion, study_abstract = \ _get_info_for_study(study_url) studies.append([study_title, study_conclusion, study_abstract]) filename = 'studies.csv' with open(filename, 'w') as csv_file: for study in studies: spamwriter = UnicodeWriter(csv_file) spamwriter.writerow(study) class UnicodeWriter: """ A CSV writer which will write rows to CSV file "f", which is encoded in the given encoding. """ def __init__(self, f, dialect=csv.excel, encoding="utf-8", **kwds): # Redirect output to a queue self.queue = cStringIO.StringIO() self.writer = csv.writer(self.queue, dialect=dialect, **kwds) self.stream = f self.encoder = codecs.getincrementalencoder(encoding)() def writerow(self, row): self.writer.writerow([s.encode("utf-8") for s in row]) # Fetch UTF-8 output from the queue ... data = self.queue.getvalue() data = data.decode("utf-8") # ... and reencode it into the target encoding data = self.encoder.encode(data) # write to the target stream self.stream.write(data) # empty queue self.queue.truncate(0) def writerows(self, rows): for row in rows: self.writerow(row) main(TOPIC)

mit

EliCDavis/PyChart

src/ColorSelector.py

1

1167

import math import random class ColorSelector: def __init__(self): self._colors_for_selection = ['F94F48', 'FF6A41', 'B4B4B4', 'D5D5D5', 'E973F5', '237FEA', 'F2B838', '19EC5A', '2395DE', 'D4B57F', 'FFD700'] self._colors_already_selected = [] def get_random_color(self): index = math.floor(random.random()*len(self._colors_for_selection)) index_has_been_found = False # Keep trying to find an index until we're successful # TODO this needs to be way more efficient while index_has_been_found is False: if index not in self._colors_already_selected: index_has_been_found = True else: index = math.floor(random.random()*len(self._colors_for_selection)) # Finally get our color color = self._colors_for_selection[index] self._colors_already_selected.append(index) # If we've used all the colors then start all over if len(self._colors_already_selected) == len(self._colors_for_selection): self._colors_already_selected = [] return color

mit

justb4/GeoHealthCheck

GeoHealthCheck/app.py

1

38830

# ================================================================= # # Authors: Tom Kralidis <[email protected]> # Just van den Broecke <[email protected]> # # Copyright (c) 2014 Tom Kralidis # # Permission is hereby granted, free of charge, to any person # obtaining a copy of this software and associated documentation # files (the "Software"), to deal in the Software without # restriction, including without limitation the rights to use, # copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following # conditions: # # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES # OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT # HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, # WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR # OTHER DEALINGS IN THE SOFTWARE. # # ================================================================= import base64 import csv import json import logging from io import StringIO from flask import (abort, flash, g, jsonify, redirect, render_template, request, url_for) from flask_babel import gettext from flask_login import (LoginManager, login_user, logout_user, current_user, login_required) from flask_migrate import Migrate from itertools import chain import views from __init__ import __version__ from enums import RESOURCE_TYPES from factory import Factory from init import App from models import Resource, Run, ProbeVars, CheckVars, Tag, User, Recipient from resourceauth import ResourceAuth from util import send_email, geocode, format_checked_datetime, \ format_run_status, format_obj_value # Module globals for convenience LOGGER = logging.getLogger(__name__) APP = App.get_app() CONFIG = App.get_config() DB = App.get_db() BABEL = App.get_babel() MIGRATE = Migrate(APP, DB) LOGIN_MANAGER = LoginManager() LOGIN_MANAGER.init_app(APP) LANGUAGES = ( ('en', 'English'), ('fr', 'Français'), ('de', 'German'), ('nl_NL', 'Nederlands (Nederland)'), ('es_BO', 'Español (Bolivia)'), ('hr_HR', 'Croatian (Croatia)') ) # Should GHC Runner be run within GHC webapp? if CONFIG['GHC_RUNNER_IN_WEBAPP'] is True: LOGGER.info('Running GHC Scheduler in WebApp') from scheduler import start_schedule # Start scheduler start_schedule() else: LOGGER.info('NOT Running GHC Scheduler in WebApp') # commit or rollback shorthand def db_commit(): err = None try: DB.session.commit() except Exception: DB.session.rollback() # finally: # DB.session.close() return err @APP.before_request def before_request(): g.user = current_user if request.args and 'lang' in request.args and request.args['lang'] != '': g.current_lang = request.args['lang'] if not hasattr(g, 'current_lang'): g.current_lang = 'en' if CONFIG['GHC_REQUIRE_WEBAPP_AUTH'] is True: # Login is required to access GHC Webapp. # We need to pass-through static resources like CSS. if any(['/static/' in request.path, request.path.endswith('.ico'), g.user.is_authenticated(), # This is from Flask-Login (request.endpoint is not None and getattr(APP.view_functions[request.endpoint], 'is_public', False))]): return # Access granted else: return redirect(url_for('login')) # Marks (endpoint-) function as always to be accessible # (used for GHC_REQUIRE_WEBAPP_AUTH) def public_route(decorated_function): decorated_function.is_public = True return decorated_function @APP.teardown_appcontext def shutdown_session(exception=None): DB.session.remove() @BABEL.localeselector def get_locale(): return g.get('current_lang', 'en') # return request.accept_languages.best_match(LANGUAGES.keys()) @LOGIN_MANAGER.user_loader def load_user(identifier): return User.query.get(int(identifier)) @LOGIN_MANAGER.unauthorized_handler def unauthorized_callback(): if request.query_string: url = '%s%s?%s' % (request.script_root, request.path, request.query_string) else: url = '%s%s' % (request.script_root, request.path) return redirect(url_for('login', lang=g.current_lang, next=url)) @LOGIN_MANAGER.request_loader def load_user_from_request(request): # Try to login using Basic Auth # Inspiration: https://flask-login.readthedocs.io # /en/latest/#custom-login-using-request-loader basic_auth_val = request.headers.get('Authorization') if basic_auth_val: basic_auth_val = basic_auth_val.replace('Basic ', '', 1) authenticated = False try: username, password = base64.b64decode(basic_auth_val).split(':') user = User.query.filter_by(username=username).first() if user: authenticated = user.authenticate(password) finally: # Ignore errors, they should all fail the auth attempt pass if not authenticated: LOGGER.warning('Unauthorized access for user=%s' % username) abort(401) else: return user # TODO: may add login via api-key or token here # finally, return None if both methods did not login the user return None @APP.template_filter('cssize_reliability') def cssize_reliability(value, css_type=None): """returns CSS button class snippet based on score""" number = int(value) if CONFIG['GHC_RELIABILITY_MATRIX']['red']['min'] <= number <= \ CONFIG['GHC_RELIABILITY_MATRIX']['red']['max']: score = 'danger' panel = 'red' elif (CONFIG['GHC_RELIABILITY_MATRIX']['orange']['min'] <= number <= CONFIG['GHC_RELIABILITY_MATRIX']['orange']['max']): score = 'warning' panel = 'yellow' elif (CONFIG['GHC_RELIABILITY_MATRIX']['green']['min'] <= number <= CONFIG['GHC_RELIABILITY_MATRIX']['green']['max']): score = 'success' panel = 'green' else: # should never really get here score = 'info' panel = 'blue' if css_type is not None and css_type == 'panel': return panel else: return score @APP.template_filter('cssize_reliability2') def cssize_reliability2(value): """returns CSS panel class snippet based on score""" return cssize_reliability(value, 'panel') @APP.template_filter('round2') def round2(value): """rounds a number to 2 decimal places except for values of 0 or 100""" if value in [0.0, 100.0]: return int(value) return round(value, 2) @APP.context_processor def context_processors(): """global context processors for templates""" rtc = views.get_resource_types_counts() tags = views.get_tag_counts() return { 'app_version': __version__, 'resource_types': RESOURCE_TYPES, 'resource_types_counts': rtc['counts'], 'resources_total': rtc['total'], 'languages': LANGUAGES, 'tags': tags, 'tagnames': list(tags.keys()) } @APP.route('/') def home(): """homepage""" response = views.get_health_summary() return render_template('home.html', response=response) @APP.route('/csv', endpoint='csv') @APP.route('/json', endpoint='json') def export(): """export resource list as JSON""" resource_type = None if request.args.get('resource_type') in RESOURCE_TYPES.keys(): resource_type = request.args['resource_type'] query = request.args.get('q') response = views.list_resources(resource_type, query) if request.url_rule.rule == '/json': json_dict = {'total': response['total'], 'resources': []} for r in response['resources']: try: ghc_url = '%s/resource/%s' % \ (CONFIG['GHC_SITE_URL'], r.identifier) last_run_report = '-' if r.last_run: last_run_report = r.last_run.report json_dict['resources'].append({ 'resource_type': r.resource_type, 'title': r.title, 'url': r.url, 'ghc_url': ghc_url, 'ghc_json': '%s/json' % ghc_url, 'ghc_csv': '%s/csv' % ghc_url, 'first_run': format_checked_datetime(r.first_run), 'last_run': format_checked_datetime(r.last_run), 'status': format_run_status(r.last_run), 'min_response_time': round(r.min_response_time, 2), 'average_response_time': round(r.average_response_time, 2), 'max_response_time': round(r.max_response_time, 2), 'reliability': round(r.reliability, 2), 'last_report': format_obj_value(last_run_report) }) except Exception as e: LOGGER.warning( 'JSON error resource id=%d: %s' % (r.identifier, str(e))) return jsonify(json_dict) elif request.url_rule.rule == '/csv': output = StringIO() writer = csv.writer(output) header = [ 'resource_type', 'title', 'url', 'ghc_url', 'ghc_json', 'ghc_csv', 'first_run', 'last_run', 'status', 'min_response_time', 'average_response_time', 'max_response_time', 'reliability' ] writer.writerow(header) for r in response['resources']: try: ghc_url = '%s%s' % (CONFIG['GHC_SITE_URL'], url_for('get_resource_by_id', identifier=r.identifier)) writer.writerow([ r.resource_type, r.title, r.url, ghc_url, '%s/json' % ghc_url, '%s/csv' % ghc_url, format_checked_datetime(r.first_run), format_checked_datetime(r.last_run), format_run_status(r.last_run), round(r.min_response_time, 2), round(r.average_response_time, 2), round(r.max_response_time, 2), round(r.reliability, 2) ]) except Exception as e: LOGGER.warning( 'CSV error resource id=%d: %s' % (r.identifier, str(e))) return output.getvalue(), 200, {'Content-type': 'text/csv'} @APP.route('/opensearch') def opensearch(): """generate OpenSearch description document""" content = render_template('opensearch_description.xml') return content, 200, {'Content-type': 'text/xml'} @APP.route('/resource/<identifier>/csv', endpoint='csv-resource') @APP.route('/resource/<identifier>/json', endpoint='json-resource') def export_resource(identifier): """export resource as JSON or CSV""" resource = views.get_resource_by_id(identifier) history_csv = '%s/resource/%s/history/csv' % (CONFIG['GHC_SITE_URL'], resource.identifier) history_json = '%s/resource/%s/history/json' % (CONFIG['GHC_SITE_URL'], resource.identifier) if 'json' in request.url_rule.rule: last_run_report = '-' if resource.last_run: last_run_report = resource.last_run.report json_dict = { 'identifier': resource.identifier, 'title': resource.title, 'url': resource.url, 'resource_type': resource.resource_type, 'owner': resource.owner.username, 'min_response_time': resource.min_response_time, 'average_response_time': resource.average_response_time, 'max_response_time': resource.max_response_time, 'reliability': resource.reliability, 'status': format_run_status(resource.last_run), 'first_run': format_checked_datetime(resource.first_run), 'last_run': format_checked_datetime(resource.last_run), 'history_csv': history_csv, 'history_json': history_json, 'last_report': format_obj_value(last_run_report) } return jsonify(json_dict) elif 'csv' in request.url_rule.rule: output = StringIO() writer = csv.writer(output) header = [ 'identifier', 'title', 'url', 'resource_type', 'owner', 'min_response_time', 'average_response_time', 'max_response_time', 'reliability', 'status', 'first_run', 'last_run', 'history_csv', 'history_json' ] writer.writerow(header) writer.writerow([ resource.identifier, resource.title, resource.url, resource.resource_type, resource.owner.username, resource.min_response_time, resource.average_response_time, resource.max_response_time, resource.reliability, format_run_status(resource.last_run), format_checked_datetime(resource.first_run), format_checked_datetime(resource.last_run), history_csv, history_json ]) return output.getvalue(), 200, {'Content-type': 'text/csv'} @APP.route('/resource/<identifier>/history/csv', endpoint='csv-resource-history') @APP.route('/resource/<identifier>/history/json', endpoint='json-resource-history') def export_resource_history(identifier): """export resource history as JSON or CSV""" resource = views.get_resource_by_id(identifier) if 'json' in request.url_rule.rule: json_dict = {'runs': []} for run in resource.runs: json_dict['runs'].append({ 'owner': resource.owner.username, 'resource_type': resource.resource_type, 'checked_datetime': format_checked_datetime(run), 'title': resource.title, 'url': resource.url, 'response_time': round(run.response_time, 2), 'status': format_run_status(run) }) return jsonify(json_dict) elif 'csv' in request.url_rule.rule: output = StringIO() writer = csv.writer(output) header = [ 'owner', 'resource_type', 'checked_datetime', 'title', 'url', 'response_time', 'status' ] writer.writerow(header) for run in resource.runs: writer.writerow([ resource.owner.username, resource.resource_type, format_checked_datetime(run), resource.title, resource.url, round(run.response_time, 2), format_run_status(run), ]) return output.getvalue(), 200, {'Content-type': 'text/csv'} @APP.route('/settings') def settings(): """settings""" pass @APP.route('/resources') def resources(): """lists resources with optional filter""" resource_type = None if request.args.get('resource_type') in RESOURCE_TYPES.keys(): resource_type = request.args['resource_type'] tag = request.args.get('tag') query = request.args.get('q') response = views.list_resources(resource_type, query, tag) return render_template('resources.html', response=response) @APP.route('/resource/<identifier>') def get_resource_by_id(identifier): """show resource""" response = views.get_resource_by_id(identifier) return render_template('resource.html', resource=response) @APP.route('/register', methods=['GET', 'POST']) def register(): """register a new user""" if not CONFIG['GHC_SELF_REGISTER']: msg1 = gettext('This site is not configured for self-registration') msg2 = gettext('Please contact') msg = '%s. %s %s' % (msg1, msg2, CONFIG['GHC_ADMIN_EMAIL']) flash('%s' % msg, 'danger') return render_template('register.html', errmsg=msg) if request.method == 'GET': return render_template('register.html') # Check for existing user or email user = User.query.filter_by(username=request.form['username']).first() email = User.query.filter_by(email=request.form['email']).first() if user or email: flash('%s' % gettext('Invalid username or email'), 'danger') return render_template('register.html') user = User(request.form['username'], request.form['password'], request.form['email']) DB.session.add(user) try: DB.session.commit() except Exception as err: DB.session.rollback() bad_column = err.message.split()[2] bad_value = request.form[bad_column] msg = gettext('already registered') flash('%s %s %s' % (bad_column, bad_value, msg), 'danger') return redirect(url_for('register', lang=g.current_lang)) return redirect(url_for('login', lang=g.current_lang)) @APP.route('/add', methods=['GET', 'POST']) @login_required def add(): """add resource""" if not g.user.is_authenticated(): return render_template('add.html') if request.method == 'GET': return render_template('add.html') resource_type = request.form['resource_type'] tags = request.form.getlist('tags') url = request.form['url'].strip() resources_to_add = [] from healthcheck import sniff_test_resource, run_test_resource sniffed_resources = sniff_test_resource(CONFIG, resource_type, url) if not sniffed_resources: msg = gettext("No resources detected") LOGGER.exception() flash(msg, 'danger') for (resource_type, resource_url, title, success, response_time, message, start_time, resource_tags,) in sniffed_resources: tags_to_add = [] for tag in chain(tags, resource_tags): tag_obj = tag if not isinstance(tag, Tag): tag_obj = Tag.query.filter_by(name=tag).first() if tag_obj is None: tag_obj = Tag(name=tag) tags_to_add.append(tag_obj) resource_to_add = Resource(current_user, resource_type, title, resource_url, tags=tags_to_add) resources_to_add.append(resource_to_add) probe_to_add = None checks_to_add = [] # Always add a default Probe and Check(s) # from the GHC_PROBE_DEFAULTS conf if resource_type in CONFIG['GHC_PROBE_DEFAULTS']: resource_settings = CONFIG['GHC_PROBE_DEFAULTS'][resource_type] probe_class = resource_settings['probe_class'] if probe_class: # Add the default Probe probe_obj = Factory.create_obj(probe_class) probe_to_add = ProbeVars( resource_to_add, probe_class, probe_obj.get_default_parameter_values()) # Add optional default (parameterized) # Checks to add to this Probe checks_info = probe_obj.get_checks_info() checks_param_info = probe_obj.get_plugin_vars()['CHECKS_AVAIL'] for check_class in checks_info: check_param_info = checks_param_info[check_class] if 'default' in checks_info[check_class]: if checks_info[check_class]['default']: # Filter out params for Check with fixed values param_defs = check_param_info['PARAM_DEFS'] param_vals = {} for param in param_defs: if param_defs[param]['value']: param_vals[param] = \ param_defs[param]['value'] check_vars = CheckVars( probe_to_add, check_class, param_vals) checks_to_add.append(check_vars) result = run_test_resource(resource_to_add) run_to_add = Run(resource_to_add, result) DB.session.add(resource_to_add) # prepopulate notifications for current user resource_to_add.set_recipients('email', [g.user.email]) if probe_to_add: DB.session.add(probe_to_add) for check_to_add in checks_to_add: DB.session.add(check_to_add) DB.session.add(run_to_add) try: DB.session.commit() msg = gettext('Services registered') flash('%s (%s, %s)' % (msg, resource_type, url), 'success') except Exception as err: DB.session.rollback() flash(str(err), 'danger') return redirect(url_for('home', lang=g.current_lang)) if len(resources_to_add) == 1: return edit_resource(resources_to_add[0].identifier) return redirect(url_for('home', lang=g.current_lang)) @APP.route('/resource/<int:resource_identifier>/update', methods=['POST']) @login_required def update(resource_identifier): """update a resource""" update_counter = 0 status = 'success' try: resource_identifier_dict = request.get_json() resource = Resource.query.filter_by( identifier=resource_identifier).first() for key, value in resource_identifier_dict.items(): if key == 'tags': resource_tags = [t.name for t in resource.tags] tags_to_add = set(value) - set(resource_tags) tags_to_delete = set(resource_tags) - set(value) # Existing Tags: create relation else add new Tag all_tag_objs = Tag.query.all() for tag in tags_to_add: tag_add_obj = None for tag_obj in all_tag_objs: if tag == tag_obj.name: # use existing tag_add_obj = tag_obj break if not tag_add_obj: # add new tag_add_obj = Tag(name=tag) DB.session.add(tag_add_obj) resource.tags.append(tag_add_obj) for tag in tags_to_delete: tag_to_delete = Tag.query.filter_by(name=tag).first() resource.tags.remove(tag_to_delete) update_counter += 1 elif key == 'probes': # Remove all existing ProbeVars for Resource for probe_var in resource.probe_vars: resource.probe_vars.remove(probe_var) # Add ProbeVars anew each with optional CheckVars for probe in value: LOGGER.info('adding Probe class=%s parms=%s' % (probe['probe_class'], str(probe))) probe_vars = ProbeVars(resource, probe['probe_class'], probe['parameters']) for check in probe['checks']: check_vars = CheckVars( probe_vars, check['check_class'], check['parameters']) probe_vars.check_vars.append(check_vars) resource.probe_vars.append(probe_vars) update_counter += 1 elif key == 'notify_emails': resource.set_recipients('email', [v for v in value if v.strip()]) elif key == 'notify_webhooks': resource.set_recipients('webhook', [v for v in value if v.strip()]) elif key == 'auth': resource.auth = value elif getattr(resource, key) != resource_identifier_dict[key]: # Update other resource attrs, mainly 'name' setattr(resource, key, resource_identifier_dict[key]) min_run_freq = CONFIG['GHC_MINIMAL_RUN_FREQUENCY_MINS'] if int(resource.run_frequency) < min_run_freq: resource.run_frequency = min_run_freq update_counter += 1 # Always update geo-IP: maybe failure on creation or # IP-address of URL may have changed. latitude, longitude = geocode(resource.url) if latitude != 0.0 and longitude != 0.0: # Only update for valid lat/lon resource.latitude = latitude resource.longitude = longitude update_counter += 1 except Exception as err: LOGGER.error("Cannot update resource: %s", err, exc_info=err) DB.session.rollback() status = str(err) update_counter = 0 # finally: # DB.session.close() if update_counter > 0: err = db_commit() if err: status = str(err) return jsonify({'status': status}) @APP.route('/resource/<int:resource_identifier>/test', methods=['GET', 'POST']) @login_required def test(resource_identifier): """test a resource""" resource = Resource.query.filter_by(identifier=resource_identifier).first() if resource is None: flash(gettext('Resource not found'), 'danger') return redirect(request.referrer) from healthcheck import run_test_resource result = run_test_resource( resource) if request.method == 'GET': if result.message == 'Skipped': msg = gettext('INFO') flash('%s: %s' % (msg, result.message), 'info') elif result.message not in ['OK', None, 'None']: msg = gettext('ERROR') flash('%s: %s' % (msg, result.message), 'danger') else: flash(gettext('Resource tested successfully'), 'success') return redirect(url_for('get_resource_by_id', lang=g.current_lang, identifier=resource_identifier)) elif request.method == 'POST': return jsonify(result.get_report()) @APP.route('/resource/<int:resource_identifier>/edit') @login_required def edit_resource(resource_identifier): """edit a resource""" resource = Resource.query.filter_by(identifier=resource_identifier).first() if resource is None: flash(gettext('Resource not found'), 'danger') return redirect(request.referrer) probes_avail = views.get_probes_avail(resource.resource_type, resource) suggestions = json.dumps(Recipient.get_suggestions('email', g.user.username)) return render_template('edit_resource.html', lang=g.current_lang, resource=resource, suggestions=suggestions, auths_avail=ResourceAuth.get_auth_defs(), probes_avail=probes_avail) @APP.route('/resource/<int:resource_identifier>/delete') @login_required def delete(resource_identifier): """delete a resource""" resource = Resource.query.filter_by(identifier=resource_identifier).first() if g.user.role != 'admin' and g.user.username != resource.owner.username: msg = gettext('You do not have access to delete this resource') flash(msg, 'danger') return redirect(url_for('get_resource_by_id', lang=g.current_lang, identifier=resource_identifier)) if resource is None: flash(gettext('Resource not found'), 'danger') return redirect(url_for('home', lang=g.current_lang)) resource.clear_recipients() DB.session.delete(resource) try: DB.session.commit() flash(gettext('Resource deleted'), 'success') return redirect(url_for('home', lang=g.current_lang)) except Exception as err: DB.session.rollback() flash(str(err), 'danger') return redirect(url_for(request.referrer)) @APP.route('/probe/<string:probe_class>/<int:resource_identifier>/edit_form') @APP.route('/probe/<string:probe_class>/edit_form') @login_required def get_probe_edit_form(probe_class, resource_identifier=None): """get the form to edit a Probe""" probe_obj = Factory.create_obj(probe_class) if resource_identifier: resource = views.get_resource_by_id(resource_identifier) if resource: probe_obj._resource = resource probe_obj.expand_params(resource) probe_info = probe_obj.get_plugin_vars() probe_vars = ProbeVars( None, probe_class, probe_obj.get_default_parameter_values()) # Get only the default Checks for this Probe class checks_avail = probe_obj.get_checks_info_defaults() checks_avail = probe_obj.expand_check_vars(checks_avail) for check_class in checks_avail: check_obj = Factory.create_obj(check_class) check_params = check_obj.get_default_parameter_values() probe_check_param_defs = \ probe_info['CHECKS_AVAIL'][check_class]['PARAM_DEFS'] for param in probe_check_param_defs: if 'value' in probe_check_param_defs[param]: check_params[param] = probe_check_param_defs[param]['value'] # Appends 'check_vars' to 'probe_vars' (SQLAlchemy) CheckVars(probe_vars, check_class, check_params) return render_template('includes/probe_edit_form.html', lang=g.current_lang, probe=probe_vars, probe_info=probe_info) @APP.route('/check/<string:check_class>/edit_form') @login_required def get_check_edit_form(check_class): """get the form to edit a Check""" check_obj = Factory.create_obj(check_class) check_info = check_obj.get_plugin_vars() check_vars = CheckVars( None, check_class, check_obj.get_default_parameter_values()) return render_template('includes/check_edit_form.html', lang=g.current_lang, check=check_vars, check_info=check_info) @APP.route('/login', methods=['GET', 'POST']) @public_route def login(): """login""" if request.method == 'GET': return render_template('login.html') username = request.form['username'] password = request.form['password'] registered_user = User.query.filter_by(username=username).first() authenticated = False if registered_user: # May not have upgraded to pw encryption: warn if len(registered_user.password) < 80: msg = 'Please upgrade GHC to encrypted passwords first, see docs!' flash(gettext(msg), 'danger') return redirect(url_for('login', lang=g.current_lang)) try: authenticated = registered_user.authenticate(password) finally: pass if not authenticated: flash(gettext('Invalid username and / or password'), 'danger') return redirect(url_for('login', lang=g.current_lang)) # Login ok login_user(registered_user) if 'next' in request.args: return redirect(request.args.get('next')) return redirect(url_for('home', lang=g.current_lang)) @APP.route('/logout') def logout(): """logout""" logout_user() flash(gettext('Logged out'), 'success') if request.referrer: return redirect(request.referrer) else: return redirect(url_for('home', lang=g.current_lang)) @APP.route('/reset_req', methods=['GET', 'POST']) @public_route def reset_req(): """ Reset password request handling. """ if request.method == 'GET': return render_template('reset_password_request.html') # Reset request form with email email = request.form['email'] registered_user = User.query.filter_by(email=email).first() if registered_user is None: LOGGER.warn('Invalid email for reset_req: %s' % email) flash(gettext('Invalid email'), 'danger') return redirect(url_for('reset_req', lang=g.current_lang)) # Generate reset url using user-specific token token = registered_user.get_token() reset_url = '%s/reset/%s' % (CONFIG['GHC_SITE_URL'], token) # Create message body with reset link msg_body = render_template('reset_password_email.txt', lang=g.current_lang, config=CONFIG, reset_url=reset_url, username=registered_user.username) try: from email.mime.text import MIMEText from email.utils import formataddr msg = MIMEText(msg_body, 'plain', 'utf-8') msg['From'] = formataddr((CONFIG['GHC_SITE_TITLE'], CONFIG['GHC_ADMIN_EMAIL'])) msg['To'] = registered_user.email msg['Subject'] = '[%s] %s' % (CONFIG['GHC_SITE_TITLE'], gettext('reset password')) from_addr = '%s <%s>' % (CONFIG['GHC_SITE_TITLE'], CONFIG['GHC_ADMIN_EMAIL']) to_addr = registered_user.email msg_text = msg.as_string() send_email(CONFIG['GHC_SMTP'], from_addr, to_addr, msg_text) except Exception as err: msg = 'Cannot send email. Contact admin: ' LOGGER.warn(msg + ' err=' + str(err)) flash(gettext(msg) + CONFIG['GHC_ADMIN_EMAIL'], 'danger') return redirect(url_for('login', lang=g.current_lang)) flash(gettext('Password reset link sent via email'), 'success') if 'next' in request.args: return redirect(request.args.get('next')) return redirect(url_for('home', lang=g.current_lang)) @APP.route('/reset/<token>', methods=['GET', 'POST']) @public_route def reset(token=None): """ Reset password submit form handling. """ # Must have at least a token to proceed. if token is None: return redirect(url_for('reset_req', lang=g.current_lang)) # Token received: verify if ok, may also time-out. registered_user = User.verify_token(token) if registered_user is None: LOGGER.warn('Cannot find User from token: %s' % token) flash(gettext('Invalid token'), 'danger') return redirect(url_for('login', lang=g.current_lang)) # Token and user ok: return reset form. if request.method == 'GET': return render_template('reset_password_form.html') # Valid token and user: change password from form-value password = request.form['password'] if not password: flash(gettext('Password required'), 'danger') return redirect(url_for('reset/%s' % token, lang=g.current_lang)) registered_user.set_password(password) DB.session.add(registered_user) try: DB.session.commit() flash(gettext('Update password OK'), 'success') except Exception as err: msg = 'Update password failed!' LOGGER.warn(msg + ' err=' + str(err)) DB.session.rollback() flash(gettext(msg), 'danger') # Finally redirect user to login page return redirect(url_for('login', lang=g.current_lang)) # # REST Interface Calls # @APP.route('/api/v1.0/summary') @APP.route('/api/v1.0/summary/') @APP.route('/api/v1.0/summary.<content_type>') def api_summary(content_type='json'): """ Get health summary for all Resources within this instance. """ health_summary = views.get_health_summary() # Convert Runs to dict-like structure for run in ['first_run', 'last_run']: run_obj = health_summary.get(run, None) if run_obj: health_summary[run] = run_obj.for_json() # Convert Resources failing to dict-like structure failed_resources = [] for resource in health_summary['failed_resources']: failed_resources.append(resource.for_json()) health_summary['failed_resources'] = failed_resources if content_type == 'json': result = jsonify(health_summary) else: result = '<pre>\n%s\n</pre>' % \ render_template('status_report_email.txt', lang=g.current_lang, summary=health_summary) return result @APP.route('/api/v1.0/probes-avail/') @APP.route('/api/v1.0/probes-avail/<resource_type>') @APP.route('/api/v1.0/probes-avail/<resource_type>/<int:resource_id>') def api_probes_avail(resource_type=None, resource_id=None): """ Get available (configured) Probes for this installation, optional for resource type """ resource = None if resource_id: resource = views.get_resource_by_id(resource_id) probes = views.get_probes_avail(resource_type=resource_type, resource=resource) return jsonify(probes) @APP.route('/api/v1.0/runs/<int:resource_id>') @APP.route('/api/v1.0/runs/<int:resource_id>.<content_type>') @APP.route('/api/v1.0/runs/<int:resource_id>/<int:run_id>') @APP.route('/api/v1.0/runs/<int:resource_id>/<int:run_id>.<content_type>') def api_runs(resource_id, run_id=None, content_type='json'): """ Get Runs (History of results) for Resource. """ if run_id: runs = [views.get_run_by_id(run_id)] else: runs = views.get_run_by_resource_id(resource_id) run_arr = [] for run in runs: run_dict = { 'id': run.identifier, 'success': run.success, 'response_time': run.response_time, 'checked_datetime': run.checked_datetime, 'message': run.message, 'report': run.report } run_arr.append(run_dict) runs_dict = {'total': len(run_arr), 'runs': run_arr} result = 'unknown' if content_type == 'json': result = jsonify(runs_dict) elif content_type == 'html': result = render_template('includes/runs.html', lang=g.current_lang, runs=runs_dict['runs']) return result if __name__ == '__main__': # run locally, for fun import sys HOST = '0.0.0.0' PORT = 8000 if len(sys.argv) > 1: HOST, PORT = sys.argv[1].split(':') APP.run(host=HOST, port=int(PORT), use_reloader=True, debug=True)

mit

openstates/openstates

openstates/az/__init__.py

1

15461

import lxml.html import re import requests from openstates.utils import State from .people import AZPersonScraper from .bills import AZBillScraper # from .committees import AZCommitteeScraper # from .events import AZEventScraper class Arizona(State): scrapers = { "people": AZPersonScraper, # 'committees': AZCommitteeScraper, # 'events': AZEventScraper, "bills": AZBillScraper, } legislative_sessions = [ { "_scraped_name": "2009 - Forty-ninth Legislature - First Regular Session", "classification": "primary", "end_date": "2009-07-01", "identifier": "49th-1st-regular", "name": "49th Legislature, 1st Regular Session (2009)", "start_date": "2009-01-12", }, { "_scraped_name": "2009 - Forty-ninth Legislature - First Special Session", "classification": "special", "end_date": "2009-01-31", "identifier": "49th-1st-special", "name": "49th Legislature, 1st Special Session (2009)", "start_date": "2009-01-28", }, { "_scraped_name": "2010 - Forty-ninth Legislature - Second Regular Session", "classification": "primary", "end_date": "2010-04-29", "identifier": "49th-2nd-regular", "name": "49th Legislature, 2nd Regular Session (2010)", "start_date": "2010-01-11", }, { "_scraped_name": "2009 - Forty-ninth Legislature - Second Special Session", "classification": "special", "end_date": "2009-05-27", "identifier": "49th-2nd-special", "name": "49th Legislature, 2nd Special Session (2009)", "start_date": "2009-05-21", }, { "_scraped_name": "2009 - Forty-ninth Legislature - Third Special Session", "classification": "special", "end_date": "2009-08-25", "identifier": "49th-3rd-special", "name": "49th Legislature, 3rd Special Session (2009)", "start_date": "2009-07-06", }, { "_scraped_name": "2009 - Forty-ninth Legislature - Fourth Special Session", "classification": "special", "end_date": "2009-11-23", "identifier": "49th-4th-special", "name": "49th Legislature, 4th Special Session (2009)", "start_date": "2009-11-17", }, { "_scraped_name": "2009 - Forty-ninth Legislature - Fifth Special Session", "classification": "special", "end_date": "2009-12-19", "identifier": "49th-5th-special", "name": "49th Legislature, 5th Special Session (2009)", "start_date": "2009-12-17", }, { "_scraped_name": "2010 - Forty-ninth Legislature - Sixth Special Session", "classification": "special", "end_date": "2010-02-11", "identifier": "49th-6th-special", "name": "49th Legislature, 6th Special Session (2010)", "start_date": "2010-02-01", }, { "_scraped_name": "2010 - Forty-ninth Legislature - Seventh Special Session", "classification": "special", "end_date": "2010-03-16", "identifier": "49th-7th-special", "name": "49th Legislature, 7th Special Session (2010)", "start_date": "2010-03-08", }, { "_scraped_name": "2010 - Forty-ninth Legislature - Eighth Special Session", "classification": "special", "end_date": "2010-04-01", "identifier": "49th-8th-special", "name": "49th Legislature, 8th Special Session (2010)", "start_date": "2010-03-29", }, { "_scraped_name": "2010 - Forty-ninth Legislature - Ninth Special Session", "classification": "special", "end_date": "2010-08-11", "identifier": "49th-9th-special", "name": "49th Legislature, 9th Special Session (2010)", "start_date": "2010-08-09", }, { "_scraped_name": "2011 - Fiftieth Legislature - First Regular Session", "classification": "primary", "end_date": "2011-04-20", "identifier": "50th-1st-regular", "name": "50th Legislature, 1st Regular Session (2011)", "start_date": "2011-01-10", }, { "_scraped_name": "2011 - Fiftieth Legislature - First Special Session", "classification": "special", "end_date": "2011-01-20", "identifier": "50th-1st-special", "name": "50th Legislature, 1st Special Session (2011)", "start_date": "2011-01-19", }, { "_scraped_name": "2012 - Fiftieth Legislature - Second Regular Session", "classification": "primary", "identifier": "50th-2nd-regular", "name": "50th Legislature, 2nd Regular Session (2012)", "start_date": "2012-01-09", "end_date": "2012-05-03", }, { "_scraped_name": "2011 - Fiftieth Legislature - Second Special Session", "classification": "special", "end_date": "2011-02-16", "identifier": "50th-2nd-special", "name": "50th Legislature, 2nd Special Session (2011)", "start_date": "2011-02-14", }, { "_scraped_name": "2011 - Fiftieth Legislature - Third Special Session", "classification": "special", "end_date": "2011-06-13", "identifier": "50th-3rd-special", "name": "50th Legislature, 3rd Special Session (2011)", "start_date": "2011-06-10", }, { "_scraped_name": "2011 - Fiftieth Legislature - Fourth Special Session", "classification": "special", "end_date": "2011-11-01", "identifier": "50th-4th-special", "name": "50th Legislature, 4th Special Session (2011)", "start_date": "2011-11-01", }, { "_scraped_name": "2013 - Fifty-first Legislature - First Regular Session", "classification": "primary", "identifier": "51st-1st-regular", "name": "51st Legislature - 1st Regular Session (2013)", "start_date": "2013-01-14", "end_date": "2013-06-14", }, { "_scraped_name": "2013 - Fifty-first Legislature - First Special Session", "classification": "primary", "identifier": "51st-1st-special", "name": "51st Legislature - 1st Special Session (2013)", "start_date": "2013-06-11", "end_date": "2013-06-14", }, { "_scraped_name": "2014 - Fifty-first Legislature - Second Regular Session", "classification": "primary", "identifier": "51st-2nd-regular", "name": "51st Legislature - 2nd Regular Session", "start_date": "2014-01-13", "end_date": "2014-04-24", }, { "_scraped_name": "2014 - Fifty-first Legislature - Second Special Session", "classification": "special", "identifier": "51st-2nd-special", "name": "51st Legislature - 2nd Special Session", "start_date": "2014-05-27", "end_date": "2014-05-29", }, { "_scraped_name": "2015 - Fifty-second Legislature - First Regular Session", "classification": "primary", "identifier": "52nd-1st-regular", "name": "52nd Legislature - 1st Regular Session", "start_date": "2015-01-12", "end_date": "2015-04-02", }, { "_scraped_name": "2015 - Fifty-second Legislature - First Special Session", "classification": "special", "identifier": "52nd-1st-special", "name": "52nd Legislature - 1st Special Session", "start_date": "2015-10-28", "end_date": "2015-10-30", }, { "_scraped_name": "2016 - Fifty-second Legislature - Second Regular Session", "classification": "primary", "identifier": "52nd-2nd-regular", "name": "52nd Legislature - 2nd Regular Session", "start_date": "2016-01-11", "end_date": "2016-05-07", }, { "_scraped_name": "2017 - Fifty-third Legislature - First Regular Session", "classification": "primary", "end_date": "2017-05-03", "identifier": "53rd-1st-regular", "name": "53rd Legislature - 1st Regular Session", "start_date": "2017-01-09", }, { "_scraped_name": "2018 - Fifty-third Legislature - First Special Session", "classification": "special", "identifier": "53rd-1st-special", "name": "53rd Legislature - 1st Special Session", "start_date": "2018-01-22", "end_date": "2018-01-26", }, { "_scraped_name": "2018 - Fifty-third Legislature - Second Regular Session", "classification": "primary", "identifier": "53rd-2nd-regular", "name": "53rd Legislature - 2nd Regular Session", "start_date": "2018-01-08", "end_date": "2018-05-03", }, { "_scraped_name": "2019 - Fifty-fourth Legislature - First Regular Session", "classification": "primary", "identifier": "54th-1st-regular", "name": "54th Legislature - 1st Regular Session", "start_date": "2019-01-14", "end_date": "2019-03-29", }, { "_scraped_name": "2020 - Fifty-fourth Legislature - Second Regular Session", "classification": "primary", "identifier": "54th-2nd-regular", "name": "54th Legislature - 2nd Regular Session", "start_date": "2020-01-13", }, ] ignored_scraped_sessions = [ "2008 - Forty-eighth Legislature - Second Regular Session", "2007 - Forty-eighth Legislature - First Regular Session", "2006 - Forty-seventh Legislature - First Special Session", "2006 - Forty-seventh Legislature - Second Regular Session", "2005 - Forty-seventh Legislature - First Regular Session", "2004 - Forty-sixth Legislature - Second Regular Session", "2003 - Forty-sixth Legislature - Second Special Session", "2003 - Forty-sixth Legislature - First Special Session", "2003 - Forty-sixth Legislature - First Regular Session", "2002 - Forty-fifth Legislature - Sixth Special Session", "2002 - Forty-fifth Legislature - Fifth Special Session", "2002 - Forty-fifth Legislature - Fourth Special Session", "2002 - Forty-fifth Legislature - Third Special Session", "2002 - Forty-fifth Legislature - Second Regular Session", "2001 - Forty-fifth Legislature - Second Special Session", "2001 - Forty-fifth Legislature - First Special Session", "2001 - Forty-fifth Legislature - First Regular Session", "2000 - Forty-fourth Legislature - Seventh Special Session", "2000 - Forty-fourth Legislature - Sixth Special Session", "2000 - Forty-fourth Legislature - Fifth Special Session", "2000 - Forty-fourth Legislature - Fourth Special Session", "2000 - Forty-fourth Legislature - Second Regular Session", "1999 - Forty-fourth Legislature - Third Special Session", "1999 - Forty-fourth Legislature - Second Special Session", "1999 - Forty-fourth Legislature - First Special Session", "1999 - Forty-fourth Legislature - First Regular Session", "1998 - Forty-third Legislature - Sixth Special Session", "1998 - Forty-third Legislature - Fifth Special Session", "1998 - Forty-third Legislature - Fourth Special Session", "1998 - Forty-third Legislature - Third Special Session", "1998 - Forty-third Legislature - Second Regular Session", "1997 - Forty-third Legislature - Second Special Session", "1997 - Forty-third Legislature - First Special Session", "1997 - Forty-third Legislature - First Regular Session", "1996 - Forty-second Legislature - Seventh Special Session", "1996 - Forty-second Legislature - Sixth Special Session", "1996 - Forty-second Legislature - Fifth Special Session", "1996 - Forty-second Legislature - Second Regular Session", "1995 - Forty-second Legislature - Fourth Special Session", "1995 - Forty-second Legislature - Third Special Session", "1995 - Forty-Second Legislature - Second Special Session", "1995 - Forty-Second Legislature - First Special Session", "1995 - Forty-second Legislature - First Regular Session", "1994 - Forty-first Legislature - Ninth Special Session", "1994 - Forty-first Legislature - Eighth Special Session", "1994 - Forty-first Legislature - Second Regular Session", "1993 - Forty-first Legislature - Seventh Special Session", "1993 - Forty-first Legislature - Sixth Special Session", "1993 - Forty-first Legislature - Fifth Special Session", "1993 - Forty-first Legislature - Fourth Special Session", "1993 - Forty-first Legislature - Third Special Session", "1993 - Forty-first Legislature - Second Special Session", "1993 - Forty-first Legislature - First Special Session", "1993 - Forty-first Legislature - First Regular Session", "1992 - Fortieth Legislature - Ninth Special Session", "1992 - Fortieth Legislature - Eighth Special Session", "1992 - Fortieth Legislature - Seventh Special Session", "1992 - Fortieth Legislature - Fifth Special Session", "1992 - Fortieth Legislature - Sixth Special Session", "1992 - Fortieth Legislature - Second Regular Session", "1991 - Fortieth Legislature - Fourth Special Session", "1991 - Fortieth Legislature - Third Special Session", "1991 - Fortieth Legislature - Second Special Session", "1991 - Fortieth Legislature - First Special Session", "1991 - Fortieth Legislature - First Regular Session", "1990 - Thirty-ninth Legislature - Fifth Special Session", "1990 - Thirty-ninth Legislature - Fourth Special Session", "1990 - Thirty-ninth Legislature - Third Special Session", "1990 - Thirty-ninth Legislature - Second Regular Session", "1989 - Thirty-ninth Legislature - Second Special Session", "1989 - Thirty-ninth Legislature - First Special Session", "1989 - Thirty-ninth Legislature - First Regular Session", ] def get_session_list(self): session = requests.Session() data = session.get("https://www.azleg.gov/") # TODO: JSON at https://apps.azleg.gov/api/Session/ doc = lxml.html.fromstring(data.text) sessions = doc.xpath("//select/option/text()") sessions = [re.sub(r"\(.+$", "", x).strip() for x in sessions] return sessions

gpl-3.0

jcsalterego/pynsour

src/bot.py

1

5843

"""Bot class""" import os import socket from parser import Parser from logger import Logger from sandbox import Sandbox import botcode MAX_CONSOLE_LEN = 50 BUFFER_SIZE = 1024 STATE_DISCONNECTED = 0 STATE_CONNECTING = 1 STATE_HANDSHAKE = 2 STATE_CONNECTED = 3 STATE_ONLINE = 4 class Bot: def __init__(self): """Constructor """ self.__state = STATE_DISCONNECTED self.__load_defaults() self.parser = Parser() self.logger = Logger() self.sandbox = Sandbox() def __load_defaults(self): """Loads default settings """ self.username = os.getlogin() self.password = None self.nicks = ["nick", "altnick"] self.realname = "Default pynsour user" self.handlers = [] self.localhost = 'localhost' self.on_connect = [] self.ops = [] self.name = "" def asDict(self): """Return object as dictionary Ignores doc variables """ info = {} for attr in dir(self): if attr[0] == "_" or attr[:2] == "__": continue i = getattr(self, attr) if type(i).__name__ == "instancemethod": continue else: info[attr] = i return info def connect(self): """Connect the bot to the IRC server """ self.__state = STATE_CONNECTING self.__connection = socket.socket(socket.AF_INET, socket.SOCK_STREAM) self.logger.console("+++ Connecting to %s:%s" % (self.hostname, self.port)) self.__connection.connect((self.hostname, self.port)) def event(self): """Event fire """ if self.__state == STATE_DISCONNECTED: return elif self.__state == STATE_CONNECTING: if self.password: self.write("PASS %s" % self.password) self.write("NICK %s" % self.nicks[0]) self.write("USER %s %s %s :%s" % (self.username, self.localhost, self.hostname, self.realname)) self.__state = STATE_HANDSHAKE elif self.__state == STATE_HANDSHAKE: pass self.read() self.ops += self.parser.parse() self.execute() def execute(self): """Execute botcode """ # Expand meta-ops, e.g. connect events new_ops = [] for operation in self.ops: if operation[0] == botcode.OP_EVENT_CONNECT: new_ops += self.on_connect self.__state = STATE_ONLINE elif operation[0] == botcode.OP_EVENT_PRIVMSG: sandbox_ops = self.filter_eval(operation[1]) if sandbox_ops: new_ops += self.sandbox.execute(sandbox_ops) else: new_ops.append(operation) self.ops = new_ops while len(self.ops) > 0: new_ops = [] for operation in self.ops: if operation[0] == botcode.OP_PONG: self.write("PONG :%s" % operation[1]) elif operation[0] == botcode.OP_JOIN: if len(operation) == 2: self.write("JOIN %s :%s" % operation[1]) elif len(operation) == 1: self.write("JOIN %s" % operation[1]) elif operation[0] == botcode.OP_MODE: self.write("MODE %s" % operation[1]) elif operation[0] == botcode.OP_PRIVMSG: self.write("PRIVMSG %s :%s" % operation[1:3]) elif operation[0] == botcode.OP_ERROR: self.logger.console("ERR\n" "%s" % operation[1]) self.ops = new_ops # self.ops will be empty by here def filter_eval(self, line): """Filter based on channel """ ops = [] words = line.split(":", 1) if len(words) == 1: return ops args, msg = words argv = args.split(" ") if len(argv) < 4: return ops sender, action, recipient = argv[:3] path = "%s/%s" % (self.name, recipient) for handler in self.handlers: re = handler['channel_re'] if re.match(path): # self.logger.console("F: %s %s" % (path, argv)) script_path = re.sub(handler['script'].replace("$", "\\"), path) ops += (botcode.OP_EVENT_SCRIPT, script_path, (sender, action, recipient, msg)), return ops def read(self): """Reading from connection """ if self.__state > STATE_DISCONNECTED: incoming = self.__connection.recv(BUFFER_SIZE) self.parser.append(incoming) read_bytes = len(incoming) first_line = incoming.split("\n")[0] if len(first_line) > MAX_CONSOLE_LEN: first_line = "%s..." % first_line[:MAX_CONSOLE_LEN] self.logger.console(" IN [%4d] %s" % (read_bytes, first_line)) def write(self, outgoing): """Writing to connection """ first_line = outgoing outgoing = "".join((outgoing, "\r\n")) write_bytes = len(outgoing) if len(first_line) > MAX_CONSOLE_LEN: first_line = "%s..." % first_line[:MAX_CONSOLE_LEN] self.logger.console("OUT [%4d] %s" % (write_bytes, first_line)) self.__connection.send(outgoing)

bsd-2-clause

mlecours/netman

tests/adapters/unified_tests/configured_test_case.py

1

3935

# Copyright 2015 Internap. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. import json import logging import unittest from functools import wraps from unittest import SkipTest from netman import raw_or_json from netman.main import app class ConfiguredTestCase(unittest.TestCase): switch_specs = None def setUp(self): tested_switch = type(self).switch_specs self.switch_hostname = tested_switch["hostname"] self.switch_port = tested_switch["port"] self.switch_type = tested_switch["model"] self.switch_username = tested_switch["username"] self.switch_password = tested_switch["password"] self.test_port = tested_switch["test_port_name"] def get(self, relative_url, fail_on_bad_code=True): with app.test_client() as http_client: r = http_client.get(**self.request(relative_url)) if fail_on_bad_code and r.status_code >= 400: raise AssertionError("Call to %s returned %s : %s" % (relative_url, r.status_code, r.data)) return json.loads(r.data) def post(self, relative_url, data=None, raw_data=None, fail_on_bad_code=True): with app.test_client() as http_client: r = http_client.post(data=raw_or_json(raw_data, data), **self.request(relative_url)) if fail_on_bad_code and r.status_code >= 400: raise AssertionError("Call to %s returned %s : %s" % (relative_url, r.status_code, r.data)) return r def put(self, relative_url, data=None, raw_data=None, fail_on_bad_code=True): with app.test_client() as http_client: r = http_client.put(data=raw_or_json(raw_data, data), **self.request(relative_url)) if fail_on_bad_code and r.status_code >= 400: raise AssertionError("Call to %s returned %s : %s" % (relative_url, r.status_code, r.data)) return r def delete(self, relative_url, fail_on_bad_code=True): with app.test_client() as http_client: r = http_client.delete(**self.request(relative_url)) if fail_on_bad_code and r.status_code >= 400: raise AssertionError("Call to %s returned %s : %s" % (relative_url, r.status_code, r.data)) return r def request(self, relative_url): logging.info("Querying " + ("http://netman.example.org%s" % relative_url.format(switch=self.switch_hostname, port=self.test_port))) headers = { 'Netman-Model': self.switch_type, 'Netman-Username': self.switch_username, 'Netman-Password': self.switch_password, 'Netman-Port': self.switch_port } return { "path": relative_url.format(switch=self.switch_hostname, port=self.test_port), "headers": headers } def get_vlan(self, number): data = self.get("/switches/{switch}/vlans") vlan = next((vlan for vlan in data if vlan["number"] == number), None) if not vlan: raise AssertionError("Vlan #{} not found".format(number)) return vlan def skip_on_switches(*to_skip): def resource_decorator(fn): @wraps(fn) def wrapper(self, *args, **kwargs): if not self.switch_type in to_skip: return fn(self, *args, **kwargs) else: raise SkipTest('Test not executed on Switch model %s' % self.switch_type) return wrapper return resource_decorator

apache-2.0

plucena24/OpenClos

jnpr/openclos/cli_parser.py

1

16382

#------------------------------------------------------------------------------ # cli_parser.py #------------------------------------------------------------------------------ ''' @author : rgiyer Date : October 20th, 2014 This module is responsible for parsing command model defined in cliCommands.yaml and providing functions for: - Validation of user-input - invoking execution handle for CLI commands or macro expansions - determine possible arg match for command auto-completion based on context ''' # Standard Python libraries import os import re import inspect import subprocess # Packages required for openclos import yaml # openclos classes import util # cli related classes from cli_handle_impl import CLIImplementor #------------------------------------------------------------------------------ #------------------------------------------------------------------------------ class CLICommand: def __init__ ( self, cmd_access, cmd_handle, cmd_macro, cmd_desc ): self.cmd_access = cmd_access self.cmd_handle = cmd_handle self.cmd_macro = cmd_macro self.cmd_desc = cmd_desc # end class CLICommand #------------------------------------------------------------------------------ #------------------------------------------------------------------------------ class CLIUtil: def __init__ ( self ): commandConfFile = os.path.join ( util.configLocation, 'cliCommands.yaml' ) self.yaml_file_stream = open ( commandConfFile, 'r' ) raw_graph = yaml.load ( self.yaml_file_stream ) self.cmd_graph = {} self.indentation = 8 self.dump_cmd ( raw_graph ) self.yaml_file_stream.close () #------------------------------------------------------------------------------ def get_implementor_handle ( self, class_instance, handle_name ): handles = inspect.getmembers ( class_instance, predicate = inspect.ismethod ) for function_tuple in handles: if ( handle_name == function_tuple [ 0 ] ): return function_tuple [ 1 ] # no match found return 0 #------------------------------------------------------------------------------ # Parse through the dictionary iteratively: def dump_cmd ( self, cmds, cmd_root="", cmd_access="READ", cmd_handle="", cmd_macro="", cmd_desc="" ): for cmd in cmds: if ( cmd_root == "" ): cmd_compound = cmd else: cmd_compound = cmd_root + "_" + cmd cmd_data = cmds [ cmd ] # Get command access if cmd_data.has_key ( "Access" ): cmd_access = cmd_data [ "Access" ] # Get command handler if cmd_data.has_key ( "Handle" ): cmd_handle = cmd_data [ "Handle" ] elif ( cmd_handle != "" ): cmd_handle = "" # Get command macro if cmd_data.has_key ( "Macro" ): cmd_macro = cmd_data [ "Macro" ] elif ( cmd_macro != "" ): cmd_macro = "" # Get command description if cmd_data.has_key ( "Desc" ): cmd_desc = cmd_data [ "Desc" ] elif ( cmd_desc != "" ): cmd_desc = "" # Parse the arguments if cmd_data.has_key ( "Args" ): cmd_args = cmd_data [ "Args" ] self.dump_cmd ( cmd_args, cmd_compound, cmd_access, cmd_handle, cmd_macro, cmd_desc ) if cmd_data.has_key ( "Handle" ): self.cmd_graph [ cmd_compound ] = CLICommand ( cmd_access, cmd_handle, cmd_macro, cmd_desc ) if ( len ( cmd_compound ) > self.indentation ): self.indentation = len ( cmd_compound ) #------------------------------------------------------------------------------ def normalize_command ( self, cmd ): return cmd.replace ( " ", "_" ) #------------------------------------------------------------------------------ def get_indentation ( self, cmd ): return ( self.indentation + 8 - len ( cmd ) ) #------------------------------------------------------------------------------ def suffix_macro_to_cmd ( self, macro_list, cmd ): ret_cmd = [] for macro in macro_list: ret_cmd.append ( self.normalize_command ( cmd + "_" + macro ) ) return ret_cmd #------------------------------------------------------------------------------ def get_macro_list ( self, class_instance, macro_txt, add_help=None ): fn_macro = self.get_implementor_handle ( class_instance, macro_txt ) return fn_macro ( add_help ) #------------------------------------------------------------------------------ def include_macro ( self, macro_list, ret_list ): for item in macro_list: ret_list.append ( item ) #------------------------------------------------------------------------------ def string_has_enter ( self, string ): if ( re.search ( "<enter>", string ) != None ): return 1 else: return 0 #------------------------------------------------------------------------------ def add_enter_instruction ( self, result_list ): if ( len ( result_list ) ): string = result_list [ 0 ] if ( self.string_has_enter ( string ) == 1 ): return 0 result_list.insert ( 0, " <enter>" + " " * self.get_indentation ( "<enter" ) + "Execute the current command" ) #------------------------------------------------------------------------------ def match_macro ( self, macro_list, needle, ret_list ): for haystack in macro_list: if ( len ( needle ) == len ( haystack ) ): if ( re.match ( needle, haystack ) != None ): self.add_enter_instruction ( ret_list ) elif ( len ( needle ) < len ( haystack ) ): if ( re.match ( needle, haystack ) != None ): ret_list.append ( haystack ) else: print "" #------------------------------------------------------------------------------ def option_exists ( self, consider_option, ret_list ): for option in ret_list: if ( re.match ( option, consider_option ) != None ): return 1 return 0 #------------------------------------------------------------------------------ def complete_command ( self, part_cmd, full_cmd, end_index, cmd_helper, ret_list ): unmatched_string = full_cmd [ end_index: ] # This is an adjustment for "<space>" before tab / ? keypress if ( part_cmd [ -1 ] == "_" ): part_cmd = part_cmd [ 0:-1 ] unmatched_string = "_" + unmatched_string if ( unmatched_string [ 0 ] == "_" ): # attach possible matches possible_option = unmatched_string.replace ( "_", " " ) + ( " " * self.get_indentation ( full_cmd ) ) possible_option = possible_option + "<" + cmd_helper.cmd_desc + ">" ret_list.append ( possible_option ) else: # Get part of the command from part_cmd match_object = re.search ( "_", part_cmd ) while ( match_object != None ): part_cmd = part_cmd [ match_object.end (): ] match_object = re.search ( "_", part_cmd ) # Get rest of the command from unmatched_string match_object = re.search ( "_", unmatched_string ) if ( match_object != None ): unmatched_string = unmatched_string [ :(match_object.end()-1)] complete_word = part_cmd + unmatched_string if ( self.option_exists ( complete_word, ret_list ) == 0 ): ret_list.append ( complete_word ) return ret_list #------------------------------------------------------------------------------ def get_all_cmds ( self ): ret_list = [] for cmd in self.cmd_graph: cmd_str = cmd.replace ( "_", " " ) cmd_str = cmd_str + ( " " * self.get_indentation ( cmd ) ) + "<" + self.cmd_graph [ cmd ].cmd_desc + ">" ret_list.append ( cmd_str ) return ret_list #------------------------------------------------------------------------------ # Lot of reference here to needle and haystack, needle being the current # command context of the CLI, and haystack being the command model dict # created during CLIUtil instantiation #------------------------------------------------------------------------------ def get_match ( self, cmd ): if ( len ( cmd ) == 0 or re.search ( "[a-z|A-Z|0-9]", cmd ) == None ): return self.get_all_cmds () # chomp input string if ( cmd [ -1 ] == " " ): cmd = cmd [ 0:-1 ] needle = self.normalize_command ( cmd ) ret_list = [] for haystack in self.cmd_graph: len_haystack = len ( haystack ) len_needle = len ( needle ) cmd_helper = self.cmd_graph [ haystack ] # Case 1: Full command is provided, without macro expansion if ( len_needle == len_haystack ): # check if we have a match if ( re.match ( needle, haystack ) != None ): if ( cmd_helper.cmd_macro != "" ): self.include_macro ( self.get_macro_list ( CLIImplementor (), cmd_helper.cmd_macro, "add help" ), ret_list ) else: self.add_enter_instruction ( ret_list ) # Case 2: Full command is provided with macro expansion elif ( len_needle > len_haystack ): match_object = re.match ( haystack, needle ) if ( match_object != None ): # Match exists - so get the macro cmd_macro = needle [ match_object.end (): ] if ( cmd_macro [ 0 ] == "_" and len ( cmd_macro ) > 1 ): cmd_macro = cmd_macro [ 1: ] if ( cmd_helper.cmd_macro != "" ): cmd_macro_list = self.get_macro_list ( CLIImplementor(), cmd_helper.cmd_macro ) self.match_macro ( cmd_macro_list, cmd_macro, ret_list ) # Case 3: Part command is provided elif ( len_needle < len_haystack ): match_object = re.match ( needle, haystack ) if ( match_object != None ): # Match exists - get rest of the command balance_cmd = haystack [ match_object.end (): ] self.complete_command ( needle, haystack, match_object.end (), self.cmd_graph [ haystack ], ret_list ) return ret_list #------------------------------------------------------------------------------ def chomp ( self, token ): match_object = re.search ( "[a-z|A-Z|0-9]", token ) if ( match_object != None ): token = token [ ( match_object.end () - 1): ] token = token [ ::-1 ] match_object = re.search ( "[a-z|A-Z|0-9]", token ) if ( match_object != None ): token = token [ ( match_object.end () - 1): ] token = token [ ::-1 ] return token #------------------------------------------------------------------------------ def validate_command_and_execute ( self, full_cmd_context ): # We will do the validation again in case this function is called # outside the CLI context best_cmd_match = "" best_cmd_args = "" best_cmd_handle = None for command in self.cmd_graph: match_object = re.match ( command, self.normalize_command ( full_cmd_context ) ) if ( match_object != None ): # Okay - we found a match. Get macros if included command_args = "" # TODO - different impl here for multiple args support if ( len ( full_cmd_context ) > len ( command ) ): command_args = self.chomp ( full_cmd_context [ match_object.end (): ] ) if ( len ( best_cmd_match ) < len ( command ) ): best_cmd_match = command best_cmd_args = command_args best_cmd_handle = self.get_implementor_handle ( CLIImplementor (), self.cmd_graph [ command ].cmd_handle ) if ( best_cmd_handle != 0 ): return best_cmd_handle ( best_cmd_args ) else: print self.cmd_graph [ best_cmd_match ].cmd_handle + " not implemented" #------------------------------------------------------------------------------ def print_results ( self, result_list ): for result in result_list: print "\t" + result #------------------------------------------------------------------------------ def print_command_graph ( self, cmd_dict ): for keys in cmd_dict: print keys + "=>" cmd = cmd_dict [ keys ] if ( cmd.cmd_desc != "" ): print " " + cmd.cmd_desc print " " + cmd.cmd_access if ( cmd.cmd_macro != "" ): fn_macro = self.get_implementor_handle ( CLIImplementor (), cmd.cmd_macro ) if ( fn_macro != 0 ): print fn_macro () else: print " Macro not implemented" if ( cmd.cmd_handle != "" ): fn_handle = self.get_implementor_handle ( CLIImplementor (), cmd.cmd_handle ) if ( fn_handle != 0 ): fn_handle () else: print " Handler not implemented" # end class CLIUtil #------------------------------------------------------------------------------ #------------------------------------------------------------------------------ #------------------------------------------------------------------------------ # MAIN #------------------------------------------------------------------------------ cli_util = CLIUtil () match_options = [ "create cabling", # "create cabling-plan", # "create cabling-", # "create cabling", # "create cabling-plan pod", # "create cabling-plan pod pod_2", # "create", # "create dev", # "create device-config", # "create device-config p", # "create device-config pod", # "create device-config pod pod_1", # "run", # "update password", # "run r", # "run RE", # "create cab", "create pods", "create pods from", "create pods from-file", "" ] if __name__ == '__main__': for match in match_options: print "Matching results for " + match + " is:" cli_util.print_results ( cli_util.get_match ( match ) ) print "------------------------------------------------------"

apache-2.0

xapple/plumbing

plumbing/scraping/blockers.py

1

1536

#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Written by Lucas Sinclair. MIT Licensed. Contact at www.sinclair.bio """ # Built-in modules # # Internal modules # # First party modules # from autopaths.file_path import FilePath ################################################################################ def check_blocked_request(tree): """ Check if the request was denied by the server. And raise an exception if it was. """ # Modules # from lxml import etree # Did we get a filepath? # if isinstance(tree, FilePath): if tree.count_bytes > 1000000: return tree = tree.contents # Did we get a tree or raw text? # if isinstance(tree, str): tree = etree.HTML(tree) # By default we are good # blocked = False # Try Incapsula # blocked = blocked or check_incapsula(tree) # If we were indeed blocked, we can stop here # if blocked: raise Exception("The request was flagged and blocked by the server.") ################################################################################ def check_incapsula(tree): # By default we are good # blocked = False # Result type 1 from Incapsula # meta = tree.xpath("//head/meta[@name='ROBOTS']") if meta and 'NOINDEX' in meta[0].get('content'): blocked = True # Result type 2 from Incapsula # meta = tree.xpath("//head/meta[@name='robots']") if meta and 'noindex' in meta[0].get('content'): blocked = True # If we were indeed blocked, we can stop here # return blocked

mit

OCA/account-invoicing

purchase_stock_picking_return_invoicing/tests/test_purchase_stock_picking_return_invoicing.py

1

7543

# Copyright 2019 Eficent Business and IT Consulting Services # Copyright 2017-2018 Tecnativa - Pedro M. Baeza # License AGPL-3.0 or later (http://www.gnu.org/licenses/agpl). from odoo import fields from odoo.tests.common import Form, SavepointCase class TestPurchaseStockPickingReturnInvoicing(SavepointCase): at_install = False post_install = True @classmethod def setUpClass(cls): """Add some defaults to let the test run without an accounts chart.""" super(TestPurchaseStockPickingReturnInvoicing, cls).setUpClass() cls.journal = cls.env["account.journal"].create( {"name": "Test journal", "type": "purchase", "code": "TEST_J"} ) cls.account_payable_type = cls.env["account.account.type"].create( { "name": "Payable account type", "type": "payable", "internal_group": "liability", } ) cls.account_expense_type = cls.env["account.account.type"].create( { "name": "Expense account type", "type": "other", "internal_group": "expense", } ) cls.payable_account = cls.env["account.account"].create( { "name": "Payable Account", "code": "PAY", "user_type_id": cls.account_payable_type.id, "reconcile": True, } ) cls.expense_account = cls.env["account.account"].create( { "name": "Expense Account", "code": "EXP", "user_type_id": cls.account_expense_type.id, "reconcile": False, } ) cls.partner = cls.env["res.partner"].create( {"name": "Test partner", "is_company": True} ) cls.partner.property_account_payable_id = cls.payable_account cls.product_categ = cls.env["product.category"].create( {"name": "Test category"} ) cls.product = cls.env["product.product"].create( { "name": "test product", "categ_id": cls.product_categ.id, "uom_id": cls.env.ref("uom.product_uom_unit").id, "uom_po_id": cls.env.ref("uom.product_uom_unit").id, "default_code": "tpr1", } ) cls.product.property_account_expense_id = cls.expense_account cls.po = cls.env["purchase.order"].create( { "partner_id": cls.partner.id, "order_line": [ ( 0, 0, { "name": cls.product.name, "product_id": cls.product.id, "product_qty": 5.0, "product_uom": cls.product.uom_id.id, "price_unit": 10, "date_planned": fields.Datetime.now(), }, ) ], } ) cls.po_line = cls.po.order_line cls.po.button_confirm() def check_values( self, po_line, qty_returned, qty_received, qty_refunded, qty_invoiced, invoice_status, ): self.assertAlmostEqual(po_line.qty_returned, qty_returned, 2) self.assertAlmostEqual(po_line.qty_received, qty_received, 2) self.assertAlmostEqual(po_line.qty_refunded, qty_refunded, 2) self.assertAlmostEqual(po_line.qty_invoiced, qty_invoiced, 2) self.assertEqual(po_line.order_id.invoice_status, invoice_status) def test_initial_state(self): self.check_values(self.po_line, 0, 0, 0, 0, "no") def test_purchase_stock_return_1(self): """Test a PO with received, invoiced, returned and refunded qty. Receive and invoice the PO, then do a return of the picking. Check that the invoicing status of the purchase, and quantities received and billed are correct throughout the process. """ # receive completely pick = self.po.picking_ids pick.move_lines.write({"quantity_done": 5}) pick.button_validate() self.check_values(self.po_line, 0, 5, 0, 0, "to invoice") # Make invoice ctx = self.po.action_view_invoice()["context"] active_model = self.env["account.move"].with_context(ctx) view_id = "account.view_move_form" with Form(active_model, view=view_id) as f: f.partner_id = self.partner f.purchase_id = self.po inv_1 = f.save() self.check_values(self.po_line, 0, 5, 0, 5, "invoiced") self.assertAlmostEqual(inv_1.amount_untaxed_signed, -50, 2) # Return some items, after PO was invoiced return_wizard = self.env["stock.return.picking"].create({"picking_id": pick.id}) return_wizard._onchange_picking_id() return_wizard.product_return_moves.write({"quantity": 2, "to_refund": True}) return_pick = pick.browse(return_wizard.create_returns()["res_id"]) return_pick.move_lines.write({"quantity_done": 2}) return_pick.button_validate() self.check_values(self.po_line, 2, 3, 0, 5, "to invoice") # Make refund ctx = self.po.action_view_invoice_refund()["context"] active_model = self.env["account.move"].with_context(ctx) view_id = "account.view_move_form" with Form(active_model, view=view_id) as f: f.partner_id = self.partner f.purchase_id = self.po inv_2 = f.save() self.check_values(self.po_line, 2, 3, 2, 3, "invoiced") self.assertAlmostEqual(inv_2.amount_untaxed_signed, 20, 2) action = self.po.action_view_invoice() self.assertEqual(action["res_id"], inv_1.id) action2 = self.po.action_view_invoice_refund() self.assertEqual(action2["res_id"], inv_2.id) def test_purchase_stock_return_2(self): """Test a PO with received and returned qty, and invoiced after. Receive the PO, then do a partial return of the picking. Create a new invoice to get the bill for the remaining qty. Check that the invoicing status of the purchase, and quantities received and billed are correct throughout the process. """ pick = self.po.picking_ids pick.move_lines.write({"quantity_done": 5}) pick.button_validate() # Return some items before PO was invoiced return_wizard = self.env["stock.return.picking"].create({"picking_id": pick.id}) return_wizard._onchange_picking_id() return_wizard.product_return_moves.write({"quantity": 2, "to_refund": True}) return_pick = pick.browse(return_wizard.create_returns()["res_id"]) return_pick.move_lines.write({"quantity_done": 2}) return_pick.button_validate() self.check_values(self.po_line, 2, 3, 0, 0, "to invoice") # Make invoice ctx = self.po.action_view_invoice()["context"] active_model = self.env["account.move"].with_context(ctx) view_id = "account.view_move_form" with Form(active_model, view=view_id) as f: f.partner_id = self.partner f.purchase_id = self.po inv_1 = f.save() self.check_values(self.po_line, 2, 3, 0, 3, "invoiced") self.assertAlmostEqual(inv_1.amount_untaxed_signed, -30, 2)

agpl-3.0

juja256/tasks_manager

des/perm.py

1

1503

from bitarray import * class Permutation: def __init__(self, l): # if sorted(l) != range(1, len(l)+1): # raise ValueError("List is not valid!") self.__bare = [i - 1 for i in l] def Get(self): return self.__bare def Reverse(self): rev = [0] * len(self.__bare) for i in range(0, len(self.__bare)): rev[self.__bare[i]] = i + 1 return Permutation(rev) def Substitude(self, msg): """ Substitudes all bits in input message """ bits = bitarray() if type(msg) == str or type(msg) == bytes: bits.frombytes(msg) elif type(msg) == bitarray: bits = msg else: raise ValueError("Not valid type of input data") res = bitarray(bits.length() * [0]) size = len(self.__bare) for i in range(0, bits.length()): res[i] = bits[(i // size) * size + self.__bare[i % size]] return res def Reduce(self, block, size): """ Shrinks or extends block to specified size with permutation """ bits = bitarray() if type(block) == str or type(block) == bytes: bits.frombytes(block) elif type(block) == bitarray: bits = block else: raise ValueError("Not valid type of input data") res = bitarray(size * [0]) for i in range(0, size): res[i] = bits[self.__bare[i]] return res

gpl-2.0

lzkelley/sne

scripts/import.py

1

293386

#!/usr/local/bin/python3.5 import csv import os import re import urllib import requests import calendar import sys import json import codecs import resource import argparse import gzip import io import shutil import statistics import warnings from datetime import timedelta, datetime from glob import glob from hashlib import md5 from html import unescape from cdecimal import Decimal from astroquery.vizier import Vizier from astroquery.simbad import Simbad from astroquery.irsa_dust import IrsaDust from copy import deepcopy from astropy import constants as const from astropy import units as un from astropy.io import fits from astropy.time import Time as astrotime from astropy.cosmology import Planck15 as cosmo, z_at_value from collections import OrderedDict, Sequence from math import log10, floor, sqrt, isnan, ceil from bs4 import BeautifulSoup, Tag, NavigableString from string import ascii_letters from photometry import * from tq import * from digits import * from repos import * from events import * parser = argparse.ArgumentParser(description='Generate a catalog JSON file and plot HTML files from SNE data.') parser.add_argument('--update', '-u', dest='update', help='Only update catalog using live sources.', default=False, action='store_true') parser.add_argument('--verbose', '-v', dest='verbose', help='Print more messages to the screen.', default=False, action='store_true') parser.add_argument('--refresh', '-r', dest='refresh', help='Ignore most task caches.', default=False, action='store_true') parser.add_argument('--full-refresh', '-f', dest='fullrefresh', help='Ignore all task caches.', default=False, action='store_true') parser.add_argument('--archived', '-a', dest='archived', help='Always use task caches.', default=False, action='store_true') parser.add_argument('--travis', '-tr', dest='travis', help='Run import script in test mode for Travis.', default=False, action='store_true') parser.add_argument('--refreshlist', '-rl', dest='refreshlist', help='Comma-delimited list of caches to clear.', default='') args = parser.parse_args() tasks = OrderedDict([ ("deleteoldevents", {"nicename":"Deleting old events", "update": False}), ("internal", {"nicename":"%pre metadata and photometry", "update": False}), ("radio", {"nicename":"%pre radio data", "update": False}), ("xray", {"nicename":"%pre X-ray data", "update": False}), ("simbad", {"nicename":"%pre SIMBAD", "update": False}), ("vizier", {"nicename":"%pre VizieR", "update": False}), ("donations", {"nicename":"%pre donations", "update": False}), ("pessto-dr1", {"nicename":"%pre PESSTO DR1", "update": False}), ("scp", {"nicename":"%pre SCP", "update": False}), ("ascii", {"nicename":"%pre ASCII", "update": False}), ("cccp", {"nicename":"%pre CCCP", "update": False, "archived": True}), ("suspect", {"nicename":"%pre SUSPECT", "update": False}), ("cfa", {"nicename":"%pre CfA archive photometry", "update": False}), ("ucb", {"nicename":"%pre UCB photometry", "update": False, "archived": True}), ("sdss", {"nicename":"%pre SDSS photometry", "update": False}), ("csp", {"nicename":"%pre CSP photometry", "update": False}), ("itep", {"nicename":"%pre ITEP", "update": False}), ("asiago", {"nicename":"%pre Asiago metadata", "update": False}), ("tns", {"nicename":"%pre TNS metadata", "update": True, "archived": True}), ("rochester", {"nicename":"%pre Latest Supernovae", "update": True, "archived": False}), ("lennarz", {"nicename":"%pre Lennarz", "update": False}), ("fermi", {"nicename":"%pre Fermi", "update": False}), ("gaia", {"nicename":"%pre GAIA", "update": True, "archived": False}), ("ogle", {"nicename":"%pre OGLE", "update": True, "archived": False}), ("snls", {"nicename":"%pre SNLS", "update": False}), ("psthreepi", {"nicename":"%pre Pan-STARRS 3π", "update": True, "archived": False}), ("psmds", {"nicename":"%pre Pan-STARRS MDS", "update": False}), ("crts", {"nicename":"%pre CRTS", "update": True, "archived": False}), ("snhunt", {"nicename":"%pre SNhunt", "update": True, "archived": False}), ("nedd", {"nicename":"%pre NED-D", "update": False}), ("cpcs", {"nicename":"%pre CPCS", "update": True, "archived": False}), ("ptf", {"nicename":"%pre PTF", "update": False, "archived": False}), ("des", {"nicename":"%pre DES", "update": False, "archived": False}), ("asassn", {"nicename":"%pre ASASSN", "update": True }), #("asiagospectra", {"nicename":"%pre Asiago spectra", "update": True }), #("wiserepspectra", {"nicename":"%pre WISeREP spectra", "update": False}), #("cfaspectra", {"nicename":"%pre CfA archive spectra", "update": False}), #("snlsspectra", {"nicename":"%pre SNLS spectra", "update": False}), #("cspspectra", {"nicename":"%pre CSP spectra", "update": False}), #("ucbspectra", {"nicename":"%pre UCB spectra", "update": True, "archived": True}), #("suspectspectra", {"nicename":"%pre SUSPECT spectra", "update": False}), #("snfspectra", {"nicename":"%pre SNH spectra", "update": False}), #("superfitspectra", {"nicename":"%pre Superfit spectra", "update": False}), #("mergeduplicates", {"nicename":"Merging duplicates", "update": False}), #("setprefnames", {"nicename":"Setting preferred names", "update": False}), ("writeevents", {"nicename":"Writing events", "update": True }) ]) oscbibcode = '2016arXiv160501054G' oscname = 'The Open Supernova Catalog' oscurl = 'https://sne.space' cfaack = ("This research has made use of the CfA Supernova Archive, " "which is funded in part by the National Science Foundation " "through grant AST 0907903.") clight = const.c.cgs.value km = (1.0 * un.km).cgs.value planckh = const.h.cgs.value keV = (1.0 * un.keV).cgs.value travislimit = 10 currenttask = '' eventnames = [] events = OrderedDict() warnings.filterwarnings('ignore', r'Warning: converting a masked element to nan.') with open('type-synonyms.json', 'r') as f: typereps = json.loads(f.read(), object_pairs_hook=OrderedDict) with open('source-synonyms.json', 'r') as f: sourcereps = json.loads(f.read(), object_pairs_hook=OrderedDict) with open('non-sne-types.json', 'r') as f: nonsnetypes = json.loads(f.read(), object_pairs_hook=OrderedDict) nonsnetypes = [x.upper() for x in nonsnetypes] repbetterquantity = { 'redshift', 'ebv', 'velocity', 'lumdist', 'discoverdate', 'maxdate' } maxbands = [ ['B', 'b', 'g'], # B-like bands first ['V', 'G'], # if not, V-like bands ['R', 'r'] # if not, R-like bands ] def uniq_cdl(values): return ','.join(list(OrderedDict.fromkeys(values).keys())) def event_attr_priority(attr): if attr == 'photometry': return 'zzzzzzzy' if attr == 'spectra': return 'zzzzzzzz' if attr == 'name': return 'aaaaaaaa' if attr == 'sources': return 'aaaaaaab' if attr == 'alias': return 'aaaaaaac' return attr prefkinds = ['heliocentric', 'cmb', 'spectroscopic', 'photometric', 'host', 'cluster', ''] def frame_priority(attr): if 'kind' in attr: if attr['kind'] in prefkinds: return prefkinds.index(attr['kind']) else: return len(prefkinds) return len(prefkinds) def alias_priority(name, attr): if name == attr: return 0 return 1 def ct_priority(name, attr): aliases = attr['source'].split(',') max_source_year = -10000 vaguetypes = ['CC', 'I'] if attr['value'] in vaguetypes: return -max_source_year for alias in aliases: if alias == 'D': continue source = get_source_by_alias(name, alias) if 'bibcode' in source: source_year = get_source_year(source) if source_year > max_source_year: max_source_year = source_year return -max_source_year def get_source_year(source): if 'bibcode' in source: if is_number(source['bibcode'][:4]): return int(source['bibcode'][:4]) else: return -10000 raise(ValueError('No bibcode available for source!')) def name_clean(name): newname = name.strip(' ;,*') if newname.startswith('MASJ'): newname = newname.replace('MASJ', 'MASTER OT J', 1) if newname.startswith('MASTER') and is_number(newname[7]): newname = newname.replace('MASTER', 'MASTER OT J', 1) if newname.startswith('MASTER OT J '): newname = newname.replace('MASTER OT J ', 'MASTER OT J', 1) if newname.startswith('Psn'): newname = newname.replace('Psn', 'PSN', 1) if newname.startswith('PSNJ'): newname = newname.replace('PSNJ', 'PSN J', 1) if newname.startswith('TCPJ'): newname = newname.replace('TCPJ', 'TCP J', 1) if newname.startswith('SMTJ'): newname = newname.replace('SMTJ', 'SMT J', 1) if newname.startswith('PSN20J'): newname = newname.replace('PSN20J', 'PSN J', 1) if newname.startswith('ASASSN') and newname[6] != '-': newname = newname.replace('ASASSN', 'ASASSN-', 1) if newname.startswith('ROTSE3J'): newname = newname.replace('ROTSE3J', 'ROTSE3 J', 1) if newname.startswith('SNHunt'): newname = newname.replace('SNHunt', 'SNhunt', 1) if newname.startswith('ptf'): newname = newname.replace('ptf', 'PTF', 1) if newname.startswith('PTF '): newname = newname.replace('PTF ', 'PTF', 1) if newname.startswith('iPTF '): newname = newname.replace('iPTF ', 'iPTF', 1) if newname.startswith('SNHunt'): newname = newname.replace('SNHunt', 'SNhunt', 1) if newname.startswith('PESSTOESO'): newname = newname.replace('PESSTOESO', 'PESSTO ESO ', 1) if newname.startswith('snf'): newname = newname.replace('snf', 'SNF', 1) if newname.startswith('SNF') and is_number(newname[3:]) and len(newname) >= 12: newname = 'SNF' + newname[3:11] + '-' + newname[11:] if newname.startswith(('MASTER OT J', 'ROTSE3 J')): prefix = newname.split('J')[0] coords = newname.split('J')[-1].strip() decsign = '+' if '+' in coords else '-' coordsplit = coords.replace('+','-').split('-') if '.' not in coordsplit[0] and len(coordsplit[0]) > 6 and '.' not in coordsplit[1] and len(coordsplit[1]) > 6: newname = (prefix + 'J' + coordsplit[0][:6] + '.' + coordsplit[0][6:] + decsign + coordsplit[1][:6] + '.' + coordsplit[1][6:]) if newname.startswith('Gaia ') and is_number(newname[3:4]) and len(newname) > 5: newname = newname.replace('Gaia ', 'Gaia', 1) if len(newname) <= 4 and is_number(newname): newname = 'SN' + newname + 'A' if len(newname) > 4 and is_number(newname[:4]) and not is_number(newname[4:]): newname = 'SN' + newname if newname.startswith('sn') and is_number(newname[2:6]) and len(newname) > 6: newname = newname.replace('sn', 'SN', 1) if newname.startswith('SN ') and is_number(newname[3:7]) and len(newname) > 7: newname = newname.replace('SN ', 'SN', 1) if newname.startswith('SN') and is_number(newname[2:6]) and len(newname) == 7 and newname[6].islower(): newname = 'SN' + newname[2:6] + newname[6].upper() elif (newname.startswith('SN') and is_number(newname[2:6]) and (len(newname) == 8 or len(newname) == 9) and newname[6:].isupper()): newname = 'SN' + newname[2:6] + newname[6:].lower() newname = (' '.join(newname.split())).strip() return newname def get_aliases(name, includename = True): if 'alias' in events[name]: aliases = [x['value'] for x in events[name]['alias']] if includename and name not in aliases: return [name] + aliases return aliases if includename: return [name] return [] def add_event(name, load = True, delete = True, source = '', loadifempty = True): if loadifempty and args.update and not len(events): load_stubs() newname = name_clean(name) if newname not in events or 'stub' in events[newname]: match = '' if newname not in events: for event in events: aliases = get_aliases(event) if (len(aliases) > 1 and newname in aliases and ('distinctfrom' not in events[event] or newname not in events[event]['distinctfrom'])): match = event break if match: newname = match if load: loadedname = load_event_from_file(name = newname, delete = delete) if loadedname: if 'stub' in events[loadedname]: raise(ValueError('Failed to find event file for stubbed event')) return loadedname if match: return match events[newname] = OrderedDict() events[newname]['name'] = newname if source: add_quantity(newname, 'alias', newname, source) if args.verbose and 'stub' not in events[newname]: tprint('Added new event ' + newname) return newname else: return newname def event_exists(name): if name in events: return True for ev in events: if name in get_aliases(ev): return True return False def get_preferred_name(name): if name not in events: matches = [] for event in events: aliases = get_aliases(event) if len(aliases) > 1 and name in aliases: return event return name else: return name def snname(string): newstring = string.replace(' ', '').upper() if (newstring[:2] == "SN"): head = newstring[:6] tail = newstring[6:] if len(tail) >= 2 and tail[1] != '?': tail = tail.lower() newstring = head + tail return newstring def add_source(name, refname = '', reference = '', url = '', bibcode = '', secondary = '', acknowledgment = ''): nsources = len(events[name]['sources']) if 'sources' in events[name] else 0 if not refname: if not bibcode: raise(ValueError('Bibcode must be specified if name is not.')) if bibcode and len(bibcode) != 19: raise(ValueError('Bibcode "' + bibcode + '" must be exactly 19 characters long')) refname = bibcode if refname.upper().startswith('ATEL') and not bibcode: refname = refname.replace('ATEL', 'ATel').replace('Atel', 'ATel').replace('ATel #', 'ATel ').replace('ATel#', 'ATel').replace('ATel', 'ATel ') refname = ' '.join(refname.split()) atelnum = refname.split()[-1] if is_number(atelnum) and atelnum in atelsdict: bibcode = atelsdict[atelnum] if refname.upper().startswith('CBET') and not bibcode: refname = refname.replace('CBET', 'CBET ') refname = ' '.join(refname.split()) cbetnum = refname.split()[-1] if is_number(cbetnum) and cbetnum in cbetsdict: bibcode = cbetsdict[cbetnum] if refname.upper().startswith('IAUC') and not bibcode: refname = refname.replace('IAUC', 'IAUC ') refname = ' '.join(refname.split()) iaucnum = refname.split()[-1] if is_number(iaucnum) and iaucnum in iaucsdict: bibcode = iaucsdict[iaucnum] for rep in sourcereps: if refname in sourcereps[rep]: refname = rep break if 'sources' not in events[name] or (refname not in [x['name'] for x in events[name]['sources']] and (not bibcode or bibcode not in [x['bibcode'] if 'bibcode' in x else '' for x in events[name]['sources']])): source = str(nsources + 1) newsource = OrderedDict() newsource['name'] = refname if url: newsource['url'] = url if reference: newsource['reference'] = reference if bibcode: newsource['bibcode'] = bibcode if acknowledgment: newsource['acknowledgment'] = acknowledgment newsource['alias'] = source if secondary: newsource['secondary'] = True events[name].setdefault('sources',[]).append(newsource) else: if refname in [x['name'] for x in events[name]['sources']]: source = [x['alias'] for x in events[name]['sources']][ [x['name'] for x in events[name]['sources']].index(refname)] elif bibcode and bibcode in [x['bibcode'] if 'bibcode' in x else '' for x in events[name]['sources']]: source = [x['alias'] for x in events[name]['sources']][ [x['bibcode'] if 'bibcode' in x else '' for x in events[name]['sources']].index(bibcode)] else: raise(ValueError("Couldn't find source that should exist!")) return source def get_source_by_alias(name, alias): for source in events[name]['sources']: if source['alias'] == alias: return source raise(ValueError('Source alias not found!')) def same_tag_str(photo, val, tag): issame = ((tag not in photo and not val) or (tag in photo and not val) or (tag in photo and photo[tag] == val)) return issame def same_tag_num(photo, val, tag, canbelist = False): issame = ((tag not in photo and not val) or (tag in photo and not val) or (tag in photo and ((not canbelist and Decimal(photo[tag]) == Decimal(val)) or (canbelist and ((isinstance(photo[tag], str) and isinstance(val, str) and Decimal(photo[tag]) == Decimal(val)) or (isinstance(photo[tag], list) and isinstance(val, list) and photo[tag] == val)))))) return issame def add_photometry(name, time = "", u_time = "MJD", e_time = "", telescope = "", instrument = "", band = "", magnitude = "", e_magnitude = "", source = "", upperlimit = False, system = "", observatory = "", observer = "", host = False, includeshost = False, survey = "", flux = "", fluxdensity = "", e_flux = "", e_fluxdensity = "", u_flux = "", u_fluxdensity = "", frequency = "", u_frequency = "", counts = "", e_counts = "", nhmw = "", photonindex = "", unabsorbedflux = "", e_unabsorbedflux = "", energy = "", u_energy = "", e_lower_magnitude = "", e_upper_magnitude = ""): if (not time and not host) or (not magnitude and not flux and not fluxdensity and not counts and not unabsorbedflux): warnings.warn('Time or brightness not specified when adding photometry, not adding.') tprint('Name : "' + name + '", Time: "' + time + '", Band: "' + band + '", AB magnitude: "' + magnitude + '"') return if (not host and not is_number(time)) or (not is_number(magnitude) and not is_number(flux) and not is_number(fluxdensity) and not is_number(counts)): warnings.warn('Time or brightness not numerical, not adding.') tprint('Name : "' + name + '", Time: "' + time + '", Band: "' + band + '", AB magnitude: "' + magnitude + '"') return if ((e_magnitude and not is_number(e_magnitude)) or (e_flux and not is_number(e_flux)) or (e_fluxdensity and not is_number(e_fluxdensity)) or (e_counts and not is_number(e_counts))): warnings.warn('Brightness error not numerical, not adding.') tprint('Name : "' + name + '", Time: "' + time + '", Band: "' + band + '", AB error: "' + e_magnitude + '"') return if e_time and not is_number(e_time): warnings.warn('Time error not numerical, not adding.') tprint('Name : "' + name + '", Time: "' + time + '", Time error: "' + e_time + '"') return if (flux or fluxdensity) and ((not u_flux and not u_fluxdensity) or (not frequency and not band and not energy)): warnings.warn('Unit and band/frequency must be set when adding photometry by flux or flux density, not adding.') tprint('Name : "' + name + '", Time: "' + time) return if not source: ValueError('Photometry must have source before being added!') if is_erroneous(name, 'photometry', source): return # Do some basic homogenization sband = bandrepf(band) sinstrument = instrument ssystem = system stelescope = telescope if not sinstrument: sinstrument = bandmetaf(sband, 'instrument') if not stelescope: stelescope = bandmetaf(sband, 'telescope') if not ssystem: ssystem = bandmetaf(sband, 'system') # Look for duplicate data and don't add if duplicate if 'photometry' in events[name]: for photo in events[name]['photometry']: if (same_tag_str(photo, sband, 'band') and same_tag_str(photo, u_time, 'u_time') and same_tag_num(photo, time, 'time', canbelist = True) and same_tag_num(photo, magnitude, 'magnitude') and (('host' not in photo and not host) or ('host' in photo and host)) and same_tag_num(photo, flux, 'flux') and same_tag_num(photo, unabsorbedflux, 'unabsorbedflux') and same_tag_num(photo, fluxdensity, 'fluxdensity') and same_tag_num(photo, counts, 'counts') and same_tag_num(photo, energy, 'energy') and same_tag_num(photo, frequency, 'frequency') and same_tag_num(photo, photonindex, 'photonindex') and same_tag_num(photo, e_magnitude, 'e_magnitude') and same_tag_num(photo, e_lower_magnitude, 'e_lower_magnitude') and same_tag_num(photo, e_upper_magnitude, 'e_upper_magnitude') and same_tag_num(photo, e_flux, 'e_flux') and same_tag_num(photo, e_unabsorbedflux, 'e_unabsorbedflux') and same_tag_num(photo, e_fluxdensity, 'e_fluxdensity') and same_tag_num(photo, e_counts, 'e_counts') and same_tag_num(photo, u_flux, 'u_flux') and same_tag_num(photo, u_fluxdensity, 'u_fluxdensity') and same_tag_num(photo, u_frequency, 'u_frequency') and same_tag_num(photo, u_energy, 'u_energy') and same_tag_str(photo, ssystem, 'system') ): return photoentry = OrderedDict() if time: photoentry['time'] = time if isinstance(time, list) or isinstance(time, str) else str(time) if e_time: photoentry['e_time'] = str(e_time) if u_time: photoentry['u_time'] = u_time if sband: photoentry['band'] = sband if ssystem: photoentry['system'] = ssystem if magnitude: photoentry['magnitude'] = str(magnitude) if e_magnitude: photoentry['e_magnitude'] = str(e_magnitude) if e_lower_magnitude: photoentry['e_lower_magnitude'] = str(e_lower_magnitude) if e_upper_magnitude: photoentry['e_upper_magnitude'] = str(e_upper_magnitude) if frequency: photoentry['frequency'] = frequency if isinstance(frequency, list) or isinstance(frequency, str) else str(frequency) if u_frequency: photoentry['u_frequency'] = u_frequency if energy: photoentry['energy'] = energy if isinstance(energy, list) or isinstance(energy, str) else str(energy) if u_energy: photoentry['u_energy'] = u_energy if flux: photoentry['flux'] = str(flux) if e_flux: photoentry['e_flux'] = str(e_flux) if unabsorbedflux: photoentry['unabsorbedflux'] = str(unabsorbedflux) if e_unabsorbedflux: photoentry['e_unabsorbedflux'] = str(e_unabsorbedflux) if u_flux: photoentry['u_flux'] = str(u_flux) if photonindex: photoentry['photonindex'] = str(photonindex) if fluxdensity: photoentry['fluxdensity'] = str(fluxdensity) if e_fluxdensity: photoentry['e_fluxdensity'] = str(e_fluxdensity) if u_fluxdensity: photoentry['u_fluxdensity'] = str(u_fluxdensity) if counts: photoentry['counts'] = str(counts) if e_counts: photoentry['e_counts'] = str(e_counts) if upperlimit: photoentry['upperlimit'] = upperlimit if host: photoentry['host'] = host if includeshost: photoentry['includeshost'] = includeshost if observer: photoentry['observer'] = observer if survey: photoentry['survey'] = survey if observatory: photoentry['observatory'] = observatory if stelescope: photoentry['telescope'] = stelescope if sinstrument: photoentry['instrument'] = sinstrument if nhmw: photoentry['nhmw'] = nhmw if source: photoentry['source'] = source events[name].setdefault('photometry',[]).append(photoentry) def trim_str_arr(arr, length = 10): return [str(round_sig(float(x), length)) if (len(x) > length and len(str(round_sig(float(x), length))) < len(x)) else x for x in arr] def add_spectrum(name, waveunit, fluxunit, wavelengths = "", fluxes = "", u_time = "", time = "", instrument = "", deredshifted = "", dereddened = "", errorunit = "", errors = "", source = "", snr = "", telescope = "", observer = "", reducer = "", filename = "", observatory = "", data = ""): if is_erroneous(name, 'spectra', source): return spectrumentry = OrderedDict() if 'spectra' in events[name]: for si, spectrum in enumerate(events[name]['spectra']): if 'filename' in spectrum and spectrum['filename'] == filename: # Copy exclude info if 'exclude' in spectrum: spectrumentry['exclude'] = spectrum['exclude'] # Don't add duplicate spectra if 'data' in spectrum: return del(events[name]['spectra'][si]) break if not waveunit: warnings.warn('No error unit specified, not adding spectrum.') return if not fluxunit: warnings.warn('No flux unit specified, not adding spectrum.') return if not data or (not wavelengths or not fluxes): ValueError('Spectrum must have wavelengths and fluxes set, or data set.') if not source: ValueError('Spectrum must have source before being added!') if deredshifted != '': spectrumentry['deredshifted'] = deredshifted if dereddened != '': spectrumentry['dereddened'] = dereddened if instrument: spectrumentry['instrument'] = instrument if telescope: spectrumentry['telescope'] = telescope if observatory: spectrumentry['observatory'] = observatory if u_time: spectrumentry['u_time'] = u_time if time: spectrumentry['time'] = time if snr: spectrumentry['snr'] = snr if observer: spectrumentry['observer'] = observer if reducer: spectrumentry['reducer'] = reducer if filename: spectrumentry['filename'] = filename spectrumentry['waveunit'] = waveunit spectrumentry['fluxunit'] = fluxunit if data: spectrumentry['data'] = data else: if errors and max([float(x) for x in errors]) > 0.: if not errorunit: warnings.warn('No error unit specified, not adding spectrum.') return spectrumentry['errorunit'] = errorunit data = [trim_str_arr(wavelengths), trim_str_arr(fluxes), trim_str_arr(errors)] else: data = [trim_str_arr(wavelengths), trim_str_arr(fluxes)] spectrumentry['data'] = [list(i) for i in zip(*data)] if source: spectrumentry['source'] = source events[name].setdefault('spectra',[]).append(spectrumentry) def is_erroneous(name, field, sources): if 'errors' in events[name]: for alias in sources.split(','): source = get_source_by_alias(name, alias) if ('bibcode' in source and source['bibcode'] in [x['value'] for x in events[name]['errors'] if x['kind'] == 'bibcode' and x['extra'] == field]): return True if ('name' in source and source['name'] in [x['value'] for x in events[name]['errors'] if x['kind'] == 'name' and x['extra'] == field]): return True return False def add_quantity(name, quantity, value, sources, forcereplacebetter = False, lowerlimit = '', upperlimit = '', error = '', unit = '', kind = '', extra = ''): if not quantity: raise(ValueError('Quantity must be specified for add_quantity.')) if not sources: raise(ValueError('Source must be specified for quantity before it is added.')) if not isinstance(value, str) and (not isinstance(value, list) or not isinstance(value[0], str)): raise(ValueError('Quantity must be a string or an array of strings.')) if is_erroneous(name, quantity, sources): return svalue = value.strip() serror = error.strip() skind = kind.strip() sunit = '' if not svalue or svalue == '--' or svalue == '-': return if serror and (not is_number(serror) or float(serror) < 0.): raise(ValueError('Quanta error value must be a number and positive.')) #Set default units if not unit and quantity == 'velocity': unit = 'km/s' if not unit and quantity == 'ra': unit = 'hours' if not unit and quantity == 'dec': unit = 'degrees' if not unit and quantity in ['lumdist', 'comovingdist']: unit = 'Mpc' #Handle certain quantity if quantity == 'alias': svalue = name_clean(svalue) if 'distinctfrom' in events[name]: if svalue in [x['value'] for x in events[name]['distinctfrom']]: return if quantity in ['velocity', 'redshift', 'ebv', 'lumdist', 'comovingdist']: if not is_number(svalue): return if quantity == 'host': if is_number(svalue): return if svalue.lower() in ['anonymous', 'anon.', 'anon', 'intergalactic']: return if svalue.startswith('M ') and is_number(svalue[2:]): svalue.replace('M ', 'M', 1) svalue = svalue.strip("()").replace(' ', ' ', 1) svalue = svalue.replace("Abell", "Abell ", 1) svalue = svalue.replace("APMUKS(BJ)", "APMUKS(BJ) ", 1) svalue = svalue.replace("ARP", "ARP ", 1) svalue = svalue.replace("CGCG", "CGCG ", 1) svalue = svalue.replace("HOLM", "HOLM ", 1) svalue = svalue.replace("IC", "IC ", 1) svalue = svalue.replace("Intergal.", "Intergalactic", 1) svalue = svalue.replace("MCG+", "MCG +", 1) svalue = svalue.replace("MCG-", "MCG -", 1) svalue = svalue.replace("M+", "MCG +", 1) svalue = svalue.replace("M-", "MCG -", 1) svalue = svalue.replace("MGC ", "MCG ", 1) svalue = svalue.replace("Mrk", "MRK", 1) svalue = svalue.replace("MRK", "MRK ", 1) svalue = svalue.replace("NGC", "NGC ", 1) svalue = svalue.replace("PGC", "PGC ", 1) svalue = svalue.replace("SDSS", "SDSS ", 1) svalue = svalue.replace("UGC", "UGC ", 1) if len(svalue) > 4 and svalue.startswith("PGC "): svalue = svalue[:4] + svalue[4:].lstrip(" 0") if len(svalue) > 4 and svalue.startswith("UGC "): svalue = svalue[:4] + svalue[4:].lstrip(" 0") if len(svalue) > 5 and svalue.startswith(("MCG +", "MCG -")): svalue = svalue[:5] + '-'.join([x.zfill(2) for x in svalue[5:].strip().split("-")]) if len(svalue) > 5 and svalue.startswith("CGCG "): svalue = svalue[:5] + '-'.join([x.zfill(3) for x in svalue[5:].strip().split("-")]) if (len(svalue) > 1 and svalue.startswith("E")) or (len(svalue) > 3 and svalue.startswith('ESO')): if svalue[0] == "E": esplit = svalue[1:].split("-") else: esplit = svalue[3:].split("-") if len(esplit) == 2 and is_number(esplit[0].strip()): if esplit[1].strip()[0] == 'G': parttwo = esplit[1][1:].strip() else: parttwo = esplit[1].strip() if is_number(parttwo.strip()): svalue = 'ESO ' + esplit[0].lstrip('0') + '-G' + parttwo.lstrip('0') svalue = ' '.join(svalue.split()) if (not skind and ((svalue.lower().startswith('abell') and is_number(svalue[5:].strip())) or 'cluster' in svalue.lower())): skind = 'cluster' elif quantity == 'claimedtype': isq = False svalue = svalue.replace('young', '') if '?' in svalue: isq = True svalue = svalue.strip(' ?') for rep in typereps: if svalue in typereps[rep]: svalue = rep break if isq: svalue = svalue + '?' elif quantity in ['ra', 'dec', 'hostra', 'hostdec']: if unit == 'floatdegrees': deg = float('%g' % Decimal(svalue)) sig = get_sig_digits(svalue) if 'ra' in quantity: flhours = deg / 360.0 * 24.0 hours = floor(flhours) minutes = floor((flhours - hours) * 60.0) seconds = (flhours * 60.0 - (hours * 60.0 + minutes)) * 60.0 if seconds > 60.0: raise(ValueError('Invalid seconds value for ' + quantity)) svalue = str(hours).zfill(2) + ':' + str(minutes).zfill(2) + ':' + zpad(pretty_num(seconds, sig = sig - 1)) elif 'dec' in quantity: fldeg = abs(deg) degree = floor(fldeg) minutes = floor((fldeg - degree) * 60.0) seconds = (fldeg * 60.0 - (degree * 60.0 + minutes)) * 60.0 if seconds > 60.0: raise(ValueError('Invalid seconds value for ' + quantity)) svalue = (('+' if deg >= 0.0 else '-') + str(degree).strip('+-').zfill(2) + ':' + str(minutes).zfill(2) + ':' + zpad(pretty_num(seconds, sig = sig - 1))) elif unit == 'nospace' and 'ra' in quantity: svalue = svalue[:2] + ':' + svalue[2:4] + ((':' + zpad(svalue[4:])) if len(svalue) > 4 else '') elif unit == 'nospace' and 'dec' in quantity: if svalue.startswith(('+', '-')): svalue = svalue[:3] + ':' + svalue[3:5] + ((':' + zpad(svalue[5:])) if len(svalue) > 5 else '') else: svalue = '+' + svalue[:2] + ':' + svalue[2:4] + ((':' + zpad(svalue[4:])) if len(svalue) > 4 else '') else: svalue = svalue.replace(' ', ':') if 'dec' in quantity: valuesplit = svalue.split(':') svalue = (('-' if valuesplit[0].startswith('-') else '+') + valuesplit[0].strip('+-').zfill(2) + (':' + valuesplit[1].zfill(2) if len(valuesplit) > 1 else '') + (':' + zpad(valuesplit[2]) if len(valuesplit) > 2 else '')) if 'ra' in quantity: sunit = 'hours' elif 'dec' in quantity: sunit = 'degrees' # Correct case of arcseconds = 60.0. valuesplit = svalue.split(':') if len(valuesplit) == 3 and valuesplit[-1] in ["60.0", "60.", "60"]: svalue = valuesplit[0] + ':' + str(Decimal(valuesplit[1]) + Decimal(1.0)) + ':' + "00.0" # Strip trailing dots. svalue = svalue.rstrip('.') elif quantity == 'maxdate' or quantity == 'discoverdate': # Make sure month and day have leading zeroes sparts = svalue.split('/') if len(sparts) >= 2: svalue = sparts[0] + '/' + sparts[1].zfill(2) if len(sparts) == 3: svalue = svalue + '/' + sparts[2].zfill(2) if quantity in events[name]: for i, ct in enumerate(events[name][quantity]): # Only add dates if they have more information if len(ct['value'].split('/')) > len(svalue.split('/')): return if is_number(svalue): svalue = '%g' % Decimal(svalue) if serror: serror = '%g' % Decimal(serror) if quantity in events[name]: for i, ct in enumerate(events[name][quantity]): if ct['value'] == svalue and sources: if 'kind' in ct and skind and ct['kind'] != skind: return for source in sources.split(','): if source not in events[name][quantity][i]['source'].split(','): events[name][quantity][i]['source'] += ',' + source if serror and 'error' not in events[name][quantity][i]: events[name][quantity][i]['error'] = serror return if not sunit: sunit = unit quantaentry = OrderedDict() quantaentry['value'] = svalue if serror: quantaentry['error'] = serror if sources: quantaentry['source'] = sources if skind: quantaentry['kind'] = skind if sunit: quantaentry['unit'] = sunit if lowerlimit: quantaentry['lowerlimit'] = lowerlimit if upperlimit: quantaentry['upperlimit'] = upperlimit if extra: quantaentry['extra'] = extra if (forcereplacebetter or quantity in repbetterquantity) and quantity in events[name]: newquantities = [] isworse = True if quantity in ['discoverdate', 'maxdate']: for ct in events[name][quantity]: ctsplit = ct['value'].split('/') svsplit = svalue.split('/') if len(ctsplit) < len(svsplit): isworse = False continue elif len(ctsplit) < len(svsplit) and len(svsplit) == 3: if max(2,get_sig_digits(ctsplit[-1].lstrip('0'))) < max(2,get_sig_digits(svsplit[-1].lstrip('0'))): isworse = False continue newquantities.append(ct) else: newsig = get_sig_digits(svalue) for ct in events[name][quantity]: if 'error' in ct: if serror: if float(serror) < float(ct['error']): isworse = False continue newquantities.append(ct) else: if serror: isworse = False continue oldsig = get_sig_digits(ct['value']) if oldsig >= newsig: newquantities.append(ct) if newsig >= oldsig: isworse = False if not isworse: newquantities.append(quantaentry) events[name][quantity] = newquantities else: events[name].setdefault(quantity,[]).append(quantaentry) def load_cached_url(url, filepath, timeout = 120, write = True): filemd5 = '' filetxt = '' if not args.refresh and os.path.isfile(filepath): with codecs.open(filepath, 'r', encoding='utf8') as f: filetxt = f.read() if args.update: filemd5 = md5(filetxt.encode('utf-8')).hexdigest() try: session = requests.Session() response = session.get(url, timeout = timeout) if any([x.status_code == 307 for x in response.history]): raise txt = response.text newmd5 = md5(txt.encode('utf-8')).hexdigest() #tprint(filemd5 + ":" + newmd5) if args.update and newmd5 == filemd5: tprint('Skipping file in "' + currenttask + '," local and remote copies identical [' + newmd5 + '].') return False except: return filetxt else: if write: with codecs.open(filepath, 'w', encoding='utf8') as f: f.write(txt) return txt def make_date_string(year, month = '', day = ''): if not year: raise ValueError('At least the year must be specified when constructing date string') datestring = str(year) if month: datestring = datestring + '/' + str(month).zfill(2) if day: datestring = datestring + '/' + str(day).zfill(2) return datestring def get_max_light(name): if 'photometry' not in events[name]: return (None, None, None, None) eventphoto = [(x['u_time'], x['time'], Decimal(x['magnitude']), x['band'] if 'band' in x else '', x['source']) for x in events[name]['photometry'] if ('magnitude' in x and 'time' in x and 'u_time' in x and 'upperlimit' not in x)] if not eventphoto: return (None, None, None, None) mlmag = None for mb in maxbands: leventphoto = [x for x in eventphoto if x[3] in mb] if leventphoto: mlmag = min([x[2] for x in leventphoto]) eventphoto = leventphoto break if not mlmag: mlmag = min([x[2] for x in eventphoto]) mlindex = [x[2] for x in eventphoto].index(mlmag) mlband = eventphoto[mlindex][3] mlsource = eventphoto[mlindex][4] if eventphoto[mlindex][0] == 'MJD': mlmjd = float(eventphoto[mlindex][1]) return (astrotime(mlmjd, format='mjd').datetime, mlmag, mlband, mlsource) else: return (None, mlmag, mlband, mlsource) def get_first_light(name): if 'photometry' not in events[name]: return (None, None) eventphoto = [(Decimal(x['time']) if isinstance(x['time'], str) else Decimal(min(float(y) for y in x['time'])), x['source']) for x in events[name]['photometry'] if 'upperlimit' not in x and 'time' in x and 'u_time' in x and x['u_time'] == 'MJD'] if not eventphoto: return (None, None) flmjd = min([x[0] for x in eventphoto]) flindex = [x[0] for x in eventphoto].index(flmjd) flmjd = float(flmjd) flsource = eventphoto[flindex][1] return (astrotime(flmjd, format='mjd').datetime, flsource) def set_first_max_light(name): if 'maxappmag' not in events[name]: (mldt, mlmag, mlband, mlsource) = get_max_light(name) if mldt: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'maxdate', make_date_string(mldt.year, mldt.month, mldt.day), uniq_cdl([source,mlsource])) if mlmag: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'maxappmag', pretty_num(mlmag), uniq_cdl([source,mlsource])) if mlband: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'maxband', mlband, uniq_cdl([source,mlsource])) if 'discoverdate' not in events[name] or max([len(x['value'].split('/')) for x in events[name]['discoverdate']]) < 3: (fldt, flsource) = get_first_light(name) if fldt: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'discoverdate', make_date_string(fldt.year, fldt.month, fldt.day), uniq_cdl([source,flsource])) if 'discoverdate' not in events[name] and 'spectra' in events[name]: minspecmjd = float("+inf") for spectrum in events[name]['spectra']: if 'time' in spectrum and 'u_time' in spectrum: if spectrum['u_time'] == 'MJD': mjd = float(spectrum['time']) elif spectrum['u_time'] == 'JD': mjd = float(jd_to_mjd(Decimal(spectrum['time']))) else: continue if mjd < minspecmjd: minspecmjd = mjd minspecsource = spectrum['source'] if minspecmjd < float("+inf"): fldt = astrotime(minspecmjd, format='mjd').datetime source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'discoverdate', make_date_string(fldt.year, fldt.month, fldt.day), 'D,' + minspecsource) def get_best_redshift(name): bestsig = -1 bestkind = 10 for z in events[name]['redshift']: kind = prefkinds.index(z['kind'] if 'kind' in z else '') sig = get_sig_digits(z['value']) if sig > bestsig and kind <= bestkind: bestz = z['value'] bestkind = kind bestsig = sig return (bestz, bestkind, bestsig) def jd_to_mjd(jd): return jd - Decimal(2400000.5) def utf8(x): return str(x, 'utf-8') def convert_aq_output(row): return OrderedDict([(x, str(row[x]) if is_number(row[x]) else row[x]) for x in row.colnames]) def set_preferred_names(): if not len(events): load_stubs() for name in list(sorted(list(events.keys()))): if name not in events: continue newname = '' aliases = get_aliases(name) if len(aliases) <= 1: continue if (name.startswith('SN') and ((is_number(name[2:6]) and not is_number(name[6:])) or (is_number(name[2:5]) and not is_number(name[5:])))): continue for alias in aliases: if (alias[:2] == 'SN' and ((is_number(alias[2:6]) and not is_number(alias[6:])) or (is_number(alias[2:5]) and not is_number(alias[5:])))): newname = alias break if not newname and 'discoverer' in events[name]: discoverer = ','.join([x['value'].upper() for x in events[name]['discoverer']]) if 'ASAS' in discoverer: for alias in aliases: if 'ASASSN' in alias.upper(): newname = alias break if not newname and 'OGLE' in discoverer: for alias in aliases: if 'OGLE' in alias.upper(): newname = alias break if not newname and 'CRTS' in discoverer: for alias in aliases: if True in [x in alias.upper() for x in ['CSS', 'MLS', 'SSS', 'SNHUNT']]: newname = alias break if not newname and 'PS1' in discoverer: for alias in aliases: if 'PS1' in alias.upper(): newname = alias break if not newname and 'PTF' in discoverer: for alias in aliases: if 'PTF' in alias.upper(): newname = alias break if not newname and 'GAIA' in discoverer: for alias in aliases: if 'GAIA' in alias.upper(): newname = alias break if not newname: for alias in aliases: # Always prefer another alias over PSN if name.startswith('PSN'): newname = alias break if newname and name != newname: # Make sure new name doesn't already exist if load_event_from_file(newname): continue if load_event_from_file(name, delete = True): tprint('Changing event name (' + name + ') to preferred name (' + newname + ').') events[newname] = events[name] events[newname]['name'] = newname del(events[name]) journal_events() # Merge and remove duplicate events def merge_duplicates(): if not len(events): load_stubs() currenttask = 'Merging duplicate events' keys = list(sorted(list(events.keys()))) for n1, name1 in enumerate(tq(keys[:], currenttask)): if name1 not in events: continue allnames1 = get_aliases(name1) + (['AT' + name1[2:]] if (name1.startswith('SN') and is_number(name1[2:6])) else []) for name2 in keys[n1+1:]: if name2 not in events or name1 == name2: continue allnames2 = get_aliases(name2) + (['AT' + name2[2:]] if (name2.startswith('SN') and is_number(name2[2:6])) else []) if any(i in allnames1 for i in allnames2): tprint('Found single event with multiple entries (' + name1 + ' and ' + name2 + '), merging.') load1 = load_event_from_file(name1, delete = True) load2 = load_event_from_file(name2, delete = True) if load1 and load2: priority1 = 0 priority2 = 0 for an in allnames1: if len(an) >= 2 and an.startswith(('SN', 'AT')): priority1 = priority1 + 1 for an in allnames2: if len(an) >= 2 and an.startswith(('SN', 'AT')): priority2 = priority2 + 1 if priority1 > priority2: copy_to_event(name2, name1) keys.append(name1) del(events[name2]) else: copy_to_event(name1, name2) keys.append(name2) del(events[name1]) else: print ('Duplicate already deleted') journal_events() def derive_and_sanitize(): biberrordict = { "2012Sci..337..942D":"2012Sci...337..942D", "2012MNRAS.420.1135":"2012MNRAS.420.1135S", "2014MNRAS.438,368":"2014MNRAS.438..368T", "2006ApJ...636...400Q":"2006ApJ...636..400Q", "0609268":"2007AJ....133...58K", "2004MNRAS.tmp..131P":"2004MNRAS.352..457P", "2013MNRAS.tmp.1499F":"2013MNRAS.433.1312F", "1991MNRAS.247P.410B":"1991A&A...247..410B", "2011Sci.333..856S":"2011Sci...333..856S" } # Calculate some columns based on imported data, sanitize some fields for name in events: aliases = get_aliases(name, includename = False) if name not in aliases: if 'sources' in events[name]: add_quantity(name, 'alias', name, '1') else: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'alias', name, source) if (name.startswith('SN') and is_number(name[2:6]) and 'discoverdate' in events[name] and int(events[name]['discoverdate'][0]['value'].split('/')[0]) >= 2016 and not any(['AT' in x for x in aliases])): source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'alias', 'AT' + name[2:], source) events[name]['alias'] = list(sorted(events[name]['alias'], key=lambda key: alias_priority(name, key))) aliases = get_aliases(name) set_first_max_light(name) if 'claimedtype' in events[name]: events[name]['claimedtype'] = list(sorted(events[name]['claimedtype'], key=lambda key: ct_priority(name, key))) if 'discoverdate' not in events[name]: prefixes = ['MLS', 'SSS', 'CSS'] for alias in aliases: for prefix in prefixes: if alias.startswith(prefix) and is_number(alias.replace(prefix, '')[:2]): discoverdate = '/'.join(['20' + alias.replace(prefix, '')[:2], alias.replace(prefix, '')[2:4], alias.replace(prefix, '')[4:6]]) if args.verbose: tprint ('Added discoverdate from name: ' + discoverdate) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'discoverdate', discoverdate, source) break if 'discoverdate' in events[name]: break if 'discoverdate' not in events[name]: prefixes = ['ASASSN-', 'PS1-', 'PS1', 'PS', 'iPTF', 'PTF', 'SCP-'] for alias in aliases: for prefix in prefixes: if alias.startswith(prefix) and is_number(alias.replace(prefix, '')[:2]): discoverdate = '20' + alias.replace(prefix, '')[:2] if args.verbose: tprint ('Added discoverdate from name: ' + discoverdate) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'discoverdate', discoverdate, source) break if 'discoverdate' in events[name]: break if 'discoverdate' not in events[name]: prefixes = ['SNF'] for alias in aliases: for prefix in prefixes: if alias.startswith(prefix) and is_number(alias.replace(prefix, '')[:4]): discoverdate = '/'.join([alias.replace(prefix, '')[:4], alias.replace(prefix, '')[4:6], alias.replace(prefix, '')[6:8]]) if args.verbose: tprint ('Added discoverdate from name: ' + discoverdate) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'discoverdate', discoverdate, source) break if 'discoverdate' in events[name]: break if 'discoverdate' not in events[name]: prefixes = ['AT', 'SN'] for alias in aliases: for prefix in prefixes: if alias.startswith(prefix) and is_number(alias.replace(prefix, '')[:4]): discoverdate = alias.replace(prefix, '')[:4] if args.verbose: tprint ('Added discoverdate from name: ' + discoverdate) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'discoverdate', discoverdate, source) break if 'discoverdate' in events[name]: break if 'ra' not in events[name] or 'dec' not in events[name]: prefixes = ['PSN J', 'MASJ', 'CSS', 'SSS', 'MASTER OT J'] for alias in aliases: for prefix in prefixes: if alias.startswith(prefix) and is_number(alias.replace(prefix, '')[:6]): noprefix = alias.split(':')[-1].replace(prefix, '').replace('.', '') decsign = '+' if '+' in noprefix else '-' noprefix = noprefix.replace('+','|').replace('-','|') nops = noprefix.split('|') if len(nops) < 2: continue rastr = nops[0] decstr = nops[1] ra = ':'.join([rastr[:2], rastr[2:4], rastr[4:6]]) + ('.' + rastr[6:] if len(rastr) > 6 else '') dec = decsign + ':'.join([decstr[:2], decstr[2:4], decstr[4:6]]) + ('.' + decstr[6:] if len(decstr) > 6 else '') if args.verbose: tprint ('Added ra/dec from name: ' + ra + ' ' + dec) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'ra', ra, source) add_quantity(name, 'dec', dec, source) break if 'ra' in events[name]: break if ('ra' in events[name] and 'dec' in events[name] and (not 'host' in events[name] or not any([x['value'] == 'Milky Way' for x in events[name]['host']]))): if name not in extinctionsdict: try: result = IrsaDust.get_query_table(events[name]['ra'][0]['value'] + " " + events[name]['dec'][0]['value'], section = 'ebv') except: warnings.warn("Coordinate lookup for " + name + " failed in IRSA.") else: ebv = result['ext SandF mean'][0] ebverr = result['ext SandF std'][0] extinctionsdict[name] = [ebv, ebverr] if name in extinctionsdict: source = add_source(name, bibcode = '2011ApJ...737..103S') add_quantity(name, 'ebv', str(extinctionsdict[name][0]), source, error = str(extinctionsdict[name][1])) if 'claimedtype' in events[name]: events[name]['claimedtype'][:] = [ct for ct in events[name]['claimedtype'] if (ct['value'] != '?' and ct['value'] != '-')] if 'claimedtype' not in events[name] and name.startswith('AT'): source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'claimedtype', 'Candidate', source) if 'redshift' not in events[name] and 'velocity' in events[name]: # Find the "best" velocity to use for this bestsig = 0 for hv in events[name]['velocity']: sig = get_sig_digits(hv['value']) if sig > bestsig: besthv = hv['value'] bestsig = sig if bestsig > 0 and is_number(besthv): voc = float(besthv)*1.e5/clight source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'redshift', pretty_num(sqrt((1. + voc)/(1. - voc)) - 1., sig = bestsig), source, kind = 'heliocentric') if 'redshift' not in events[name] and has_task('nedd') and 'host' in events[name]: reference = "NED-D" refurl = "http://ned.ipac.caltech.edu/Library/Distances/" for host in events[name]['host']: if host['value'] in nedddict: secondarysource = add_source(name, refname = reference, url = refurl, secondary = True) meddist = statistics.median(nedddict[host['value']]) redshift = pretty_num(z_at_value(cosmo.comoving_distance, float(meddist) * un.Mpc), sig = get_sig_digits(str(meddist))) add_quantity(name, 'redshift', redshift, secondarysource, kind = 'host') if 'maxabsmag' not in events[name] and 'maxappmag' in events[name] and 'lumdist' in events[name]: # Find the "best" distance to use for this bestsig = 0 for ld in events[name]['lumdist']: sig = get_sig_digits(ld['value']) if sig > bestsig: bestld = ld['value'] bestsig = sig if bestsig > 0 and is_number(bestld) and float(bestld) > 0.: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'maxabsmag', pretty_num(float(events[name]['maxappmag'][0]['value']) - 5.0*(log10(float(bestld)*1.0e6) - 1.0), sig = bestsig), source) if 'redshift' in events[name]: # Find the "best" redshift to use for this (bestz, bestkind, bestsig) = get_best_redshift(name) if bestsig > 0: bestz = float(bestz) if 'velocity' not in events[name]: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'velocity', pretty_num(clight/km*((bestz + 1.)**2. - 1.)/ ((bestz + 1.)**2. + 1.), sig = bestsig), source, kind = prefkinds[bestkind]) if bestz > 0.: if 'lumdist' not in events[name]: dl = cosmo.luminosity_distance(bestz) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'lumdist', pretty_num(dl.value, sig = bestsig), source, kind = prefkinds[bestkind]) if 'maxabsmag' not in events[name] and 'maxappmag' in events[name]: source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'maxabsmag', pretty_num(float(events[name]['maxappmag'][0]['value']) - 5.0*(log10(dl.to('pc').value) - 1.0), sig = bestsig), source) if 'comovingdist' not in events[name]: dl = cosmo.comoving_distance(bestz) source = add_source(name, bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) add_quantity(name, 'comovingdist', pretty_num(dl.value, sig = bestsig), source) if 'photometry' in events[name]: events[name]['photometry'].sort(key=lambda x: ((float(x['time']) if isinstance(x['time'], str) else min([float(y) for y in x['time']])) if 'time' in x else 0.0, x['band'] if 'band' in x else '', float(x['magnitude']) if 'magnitude' in x else '')) if 'spectra' in events[name] and list(filter(None, ['time' in x for x in events[name]['spectra']])): events[name]['spectra'].sort(key=lambda x: (float(x['time']) if 'time' in x else 0.0)) if 'sources' in events[name]: for source in events[name]['sources']: if 'bibcode' in source: #First sanitize the bibcode if len(source['bibcode']) != 19: source['bibcode'] = urllib.parse.unquote(unescape(source['bibcode'])).replace('A.A.', 'A&A') if source['bibcode'] in biberrordict: source['bibcode'] = biberrordict[source['bibcode']] if source['bibcode'] not in bibauthordict: bibcode = source['bibcode'] adsquery = ('http://adsabs.harvard.edu/cgi-bin/nph-abs_connect?db_key=ALL&version=1&bibcode=' + urllib.parse.quote(bibcode) + '&data_type=Custom&format=%253m%20%25(y)') response = urllib.request.urlopen(adsquery) html = response.read().decode('utf-8') hsplit = html.split("\n") if len(hsplit) > 5: bibcodeauthor = hsplit[5] else: bibcodeauthor = '' if not bibcodeauthor: warnings.warn("Bibcode didn't return authors, not converting this bibcode.") bibauthordict[bibcode] = unescape(bibcodeauthor).strip() for source in events[name]['sources']: if 'bibcode' in source and source['bibcode'] in bibauthordict and bibauthordict[source['bibcode']]: source['reference'] = bibauthordict[source['bibcode']] if 'name' not in source and source['bibcode']: source['name'] = source['bibcode'] if 'redshift' in events[name]: events[name]['redshift'] = list(sorted(events[name]['redshift'], key=lambda key: frame_priority(key))) if 'velocity' in events[name]: events[name]['velocity'] = list(sorted(events[name]['velocity'], key=lambda key: frame_priority(key))) if 'claimedtype' in events[name]: events[name]['claimedtype'] = list(sorted(events[name]['claimedtype'], key=lambda key: ct_priority(name, key))) events[name] = OrderedDict(sorted(events[name].items(), key=lambda key: event_attr_priority(key[0]))) def delete_old_event_files(): # Delete all old event JSON files files = repo_file_list() for f in files: os.remove(f) def write_all_events(empty = False, gz = False, bury = False): # Write it all out! for name in events: if 'stub' in events[name]: if not empty: continue else: del(events[name]['stub']) if args.verbose and not args.travis: tprint('Writing ' + name) filename = get_event_filename(name) outdir = '../' if 'discoverdate' in events[name]: for r, year in enumerate(repoyears): if int(events[name]['discoverdate'][0]['value'].split('/')[0]) <= year: outdir += repofolders[r] break else: outdir += str(repofolders[0]) # Delete non-SN events here without IAU designations (those with only banned types) if bury: buryevent = False nonsneprefixes = ('PNVJ', 'PNV J', 'OGLE-2013-NOVA') if name.startswith(nonsneprefixes): tprint('Burying ' + name + ', non-SNe prefix.') continue if 'claimedtype' in events[name] and not (name.startswith('SN') and is_number(name[2:6])): for ct in events[name]['claimedtype']: if ct['value'].upper() not in nonsnetypes and ct['value'].upper() != 'CANDIDATE': buryevent = False break if ct['value'].upper() in nonsnetypes: buryevent = True if buryevent: tprint('Burying ' + name + ' (' + ct['value'] + ').') outdir = '../sne-boneyard' jsonstring = json.dumps({name:events[name]}, indent='\t', separators=(',', ':'), ensure_ascii=False) path = outdir + '/' + filename + '.json' with codecs.open(path, 'w', encoding='utf8') as f: f.write(jsonstring) if gz: if os.path.getsize(path) > 90000000: if not args.travis: tprint('Compressing ' + name) with open(path, 'rb') as f_in, gzip.open(path + '.gz', 'wb') as f_out: shutil.copyfileobj(f_in, f_out) os.remove(path) os.system('cd ' + outdir + '; git rm ' + filename + '.json; git add -f ' + filename + '.json.gz; cd ' + '../scripts') def null_field(obj, field): return obj[field] if field in obj else '' def copy_to_event(fromname, destname): tprint('Copying ' + fromname + ' to event ' + destname) newsourcealiases = {} keys = list(sorted(events[fromname].keys(), key=lambda key: event_attr_priority(key))) if 'sources' in events[fromname]: for source in events[fromname]['sources']: newsourcealiases[source['alias']] = (add_source(destname, bibcode = source['bibcode'] if 'bibcode' in source else '', refname = source['name'] if 'name' in source else '', reference = source['reference'] if 'reference' in source else '', url = source['url'] if 'url' in source else '')) for key in keys: if key not in ['name', 'sources']: for item in events[fromname][key]: isd = False sources = [] if 'source' not in item: ValueError("Item has no source!") for sid in item['source'].split(','): if sid == 'D': sources.append('D') elif sid in newsourcealiases: sources.append(newsourcealiases[sid]) else: ValueError("Couldn't find source alias!") sources = uniq_cdl(sources) if key == 'photometry': add_photometry(destname, u_time = null_field(item, "u_time"), time = null_field(item, "time"), e_time = null_field(item, "e_time"), telescope = null_field(item, "telescope"), instrument = null_field(item, "instrument"), band = null_field(item, "band"), magnitude = null_field(item, "magnitude"), e_magnitude = null_field(item, "e_magnitude"), source = sources, upperlimit = null_field(item, "upperlimit"), system = null_field(item, "system"), observatory = null_field(item, "observatory"), observer = null_field(item, "observer"), host = null_field(item, "host"), survey = null_field(item, "survey")) elif key == 'spectra': add_spectrum(destname, null_field(item, "waveunit"), null_field(item, "fluxunit"), data = null_field(item, "data"), u_time = null_field(item, "u_time"), time = null_field(item, "time"), instrument = null_field(item, "instrument"), deredshifted = null_field(item, "deredshifted"), dereddened = null_field(item, "dereddened"), errorunit = null_field(item, "errorunit"), source = sources, snr = null_field(item, "snr"), telescope = null_field(item, "telescope"), observer = null_field(item, "observer"), reducer = null_field(item, "reducer"), filename = null_field(item, "filename"), observatory = null_field(item, "observatory")) elif key == 'errors': add_quantity(destname, key, item['value'], sources, kind = null_field(item, "kind"), extra = null_field(item, "extra")) else: add_quantity(destname, key, item['value'], sources, error = null_field(item, "error"), unit = null_field(item, "unit"), kind = null_field(item, "kind")) def load_event_from_file(name = '', location = '', clean = False, delete = True, append = False): if not name and not location: raise ValueError('Either event name or location must be specified to load event') path = '' namepath = '' if location: path = location if name: indir = '../' for rep in repofolders: filename = get_event_filename(name) newpath = indir + rep + '/' + filename + '.json' if os.path.isfile(newpath): namepath = newpath if not path and not namepath: return False else: newevent = '' newevent2 = '' if path or namepath: if name in events: del events[name] if path and namepath: with open(path, 'r') as f, open(namepath, 'r') as nf: newevent = json.loads(f.read(), object_pairs_hook=OrderedDict) newevent2 = json.loads(nf.read(), object_pairs_hook=OrderedDict) elif path: with open(path, 'r') as f: newevent = json.loads(f.read(), object_pairs_hook=OrderedDict) elif namepath: with open(namepath, 'r') as f: newevent = json.loads(f.read(), object_pairs_hook=OrderedDict) if newevent: if clean: newevent = clean_event(newevent) name = next(reversed(newevent)) if append: indir = '../' for rep in repofolders: filename = get_event_filename(name) newpath = indir + rep + '/' + filename + '.json' if os.path.isfile(newpath): namepath = newpath if namepath: with open(namepath, 'r') as f: newevent2 = json.loads(f.read(), object_pairs_hook=OrderedDict) namename = next(reversed(newevent2)) if newevent2: # Needs to be fixed newevent = OrderedDict([['temp',newevent[name]]]) copy_to_event('temp', namename) else: events.update(newevent) if args.verbose and not args.travis: tprint('Loaded ' + name) if 'writeevents' in tasks and delete and namepath: os.remove(namepath) return name def clean_event(dirtyevent): bibcodes = [] name = next(reversed(dirtyevent)) # This is very hacky and is only necessary because we don't have a proper 'Event' object yet. events['temp'] = dirtyevent[name] if 'name' not in events['temp']: events['temp']['name'] = name if 'sources' in events['temp']: # Rebuild the sources newsources = [] oldsources = events['temp']['sources'] del(events['temp']['sources']) for s, source in enumerate(oldsources): if 'bibcode' in source: bibcodes.append(source['bibcode']) add_source('temp', bibcode = source['bibcode']) else: add_source('temp', refname = source['name'], url = source['url']) # Clean some legacy fields if 'aliases' in events['temp'] and isinstance(events['temp']['aliases'], list): source = add_source('temp', bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) for alias in events['temp']['aliases']: add_quantity('temp', 'alias', alias, source) del(events['temp']['aliases']) if ('distinctfrom' in events['temp'] and isinstance(events['temp']['distinctfrom'], list) and isinstance(events['temp']['distinctfrom'][0], str)): distinctfroms = [x for x in events['temp']['distinctfrom']] del(events['temp']['distinctfrom']) source = add_source('temp', bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) for df in distinctfroms: add_quantity('temp', 'distinctfrom', df, source) if ('errors' in events['temp'] and isinstance(events['temp']['errors'], list) and 'sourcekind' in events['temp']['errors'][0]): source = add_source('temp', bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) for err in events['temp']['errors']: add_quantity('temp', 'error', err['quantity'], source, kind = err['sourcekind'], extra = err['id']) del(events['temp']['errors']) if not bibcodes: add_source('temp', bibcode = oscbibcode, refname = oscname, url = oscurl, secondary = True) bibcodes = [oscbibcode] for key in list(events['temp'].keys()): if key in ['name', 'sources']: pass elif key == 'photometry': for p, photo in enumerate(events['temp']['photometry']): if photo['u_time'] == 'JD': events['temp']['photometry'][p]['u_time'] = 'MJD' events['temp']['photometry'][p]['time'] = str(jd_to_mjd(Decimal(photo['time']))) if bibcodes and 'source' not in photo: source = add_source('temp', bibcode = bibcodes[0]) events['temp']['photometry'][p]['source'] = source else: for qi, quantity in enumerate(events['temp'][key]): if bibcodes and 'source' not in quantity: source = add_source('temp', bibcode = bibcodes[0]) events['temp'][key][qi]['source'] = source cleanevent = events['temp'] del (events['temp']) return OrderedDict([[name,cleanevent]]) def has_task(task): return task in tasks and (not args.update or tasks[task]['update']) def archived_task(task): if 'archived' in tasks[task] and args.archived: return True if ('archived' in tasks[task] and tasks[task]['archived'] and task not in args.refreshlist.split(',') and not args.fullrefresh): return True return False def do_task(checktask, task, quiet = False): global currenttask dotask = has_task(task) and checktask == task if dotask and not quiet: currenttask = (tasks[task]['nicename'] if tasks[task]['nicename'] else task).replace('%pre', 'Updating' if args.update else 'Loading') return dotask def journal_events(clear = True): if 'writeevents' in tasks: write_all_events() if clear: clear_events() def clear_events(): global events events = OrderedDict((k, OrderedDict([['name', events[k]['name']]] + ([['alias', events[k]['alias']]] if 'alias' in events[k] else []) + [['stub', True]])) for k in events) def load_stubs(): global currenttask currenttask = 'Loading event stubs' files = repo_file_list() #try: # namepath = '../names.min.json' # with open(namepath, 'r') as f: # names = json.loads(f.read(), object_pairs_hook=OrderedDict) # for fi in tq(files): # name = os.path.basename(os.path.splitext(fi)[0]) # if name not in names: # name = name.replace("_", "/") # events[name] = OrderedDict(([['name', name], ['alias', [OrderedDict(([['value', x]])) for x in names[name]]], ['stub', True]])) #except: # events = OrderedDict() for fi in tq(files, currenttask): fname = fi if '.gz' in fi: fname = fi.replace('.gz', '') with gzip.open(fi, 'rb') as f_in, open(fname, 'wb') as f_out: shutil.copyfileobj(f_in, f_out) os.remove(fi) name = os.path.basename(os.path.splitext(fname)[0]).replace('.json', '') name = add_event(name, delete = False, loadifempty = False) events[name] = OrderedDict(([['name', events[name]['name']]] + ([['alias', events[name]['alias']]] if 'alias' in events[name] else []) + [['stub', True]])) path = '../atels.json' if os.path.isfile(path): with open(path, 'r') as f: atelsdict = json.loads(f.read(), object_pairs_hook=OrderedDict) else: atelsdict = OrderedDict() path = '../cbets.json' if os.path.isfile(path): with open(path, 'r') as f: cbetsdict = json.loads(f.read(), object_pairs_hook=OrderedDict) else: cbetsdict = OrderedDict() path = '../iaucs.json' if os.path.isfile(path): with open(path, 'r') as f: iaucsdict = json.loads(f.read(), object_pairs_hook=OrderedDict) else: iaucsdict = OrderedDict() for task in tasks: if do_task(task, 'deleteoldevents'): currenttask = 'Deleting old events' delete_old_event_files() # Import data provided directly to OSC if do_task(task, 'internal'): for datafile in tq(sorted(glob("../sne-internal/*.json"), key=lambda s: s.lower()), currenttask): if args.update: if not load_event_from_file(location = datafile, clean = True, delete = False, append = True): raise IOError('Failed to find specified file.') else: if not load_event_from_file(location = datafile, clean = True, delete = False): raise IOError('Failed to find specified file.') journal_events() if do_task(task, 'radio'): for datafile in tq(sorted(glob("../sne-external-radio/*.txt"), key=lambda s: s.lower()), currenttask): name = add_event(os.path.basename(datafile).split('.')[0]) radiosourcedict = OrderedDict() with open(datafile, 'r') as f: for li, line in enumerate([x.strip() for x in f.read().splitlines()]): if line.startswith('(') and li <= len(radiosourcedict): radiosourcedict[line.split()[0]] = add_source(name, bibcode = line.split()[-1]) elif li in [x + len(radiosourcedict) for x in range(3)]: continue else: cols = list(filter(None, line.split())) source = radiosourcedict[cols[6]] add_photometry(name, time = cols[0], frequency = cols[2], u_frequency = 'GHz', fluxdensity = cols[3], e_fluxdensity = cols[4], u_fluxdensity = 'µJy', instrument = cols[5], source = source) add_quantity(name, 'alias', name, source) journal_events() if do_task(task, 'xray'): for datafile in tq(sorted(glob("../sne-external-xray/*.txt"), key=lambda s: s.lower()), currenttask): name = add_event(os.path.basename(datafile).split('.')[0]) with open(datafile, 'r') as f: for li, line in enumerate(f.read().splitlines()): if li == 0: source = add_source(name, bibcode = line.split()[-1]) elif li in [1,2,3]: continue else: cols = list(filter(None, line.split())) add_photometry(name, time = cols[:2], energy = cols[2:4], u_energy = 'keV', counts = cols[4], flux = cols[6], unabsorbedflux = cols[8], u_flux = 'ergs/s/cm^2', photonindex = cols[15], instrument = cols[17], nhmw = cols[11], upperlimit = (float(cols[5]) < 0), source = source) add_quantity(name, 'alias', name, source) journal_events() #if do_task(task, 'simbad'): # Simbad.list_votable_fields() # customSimbad = Simbad() # customSimbad.add_votable_fields('otype', 'id(opt)') # result = customSimbad.query_object('SN 20[0-9][0-9]*', wildcard=True) # for r, row in enumerate(result): # if row['OTYPE'].decode() != "SN": # continue # name = row["MAIN_ID"].decode() # aliases = Simbad.query_objectids(name) # print(aliases) # if name[:3] == 'SN ': # name = 'SN' + name[3:] # if name[:2] == 'SN' and is_number(name[2:]): # name = name + 'A' # name = add_event(name) # journal_events() # Import primary data sources from Vizier if do_task(task, 'vizier'): Vizier.ROW_LIMIT = -1 # 2012ApJS..200...12H result = Vizier.get_catalogs("J/ApJS/200/12/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) oldname = '' for row in tq(table, currenttask): name = row['SN'] if is_number(name[:4]): name = 'SN' + name name = add_event(name) source = add_source(name, bibcode = "2012ApJS..200...12H") add_quantity(name, 'alias', name, source) if '[' not in row['Gal']: add_quantity(name, 'host', row['Gal'].replace('_', ' '), source) add_quantity(name, 'redshift', str(row['z']), source, kind = 'heliocentric') add_quantity(name, 'redshift', str(row['zCMB']), source, kind = 'cmb') add_quantity(name, 'ebv', str(row['E_B-V_']), source, error = str(row['e_E_B-V_']) if row['e_E_B-V_'] else '') add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) # 2012ApJ...746...85S result = Vizier.get_catalogs("J/ApJ/746/85/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) oldname = '' for row in tq(table, currenttask): name = row['Name'].replace('SCP', 'SCP-') name = add_event(name) source = add_source(name, bibcode = "2012ApJ...746...85S") add_quantity(name, 'alias', name, source) if row['f_Name']: add_quantity(name, 'claimedtype', 'Ia', source) if row['z']: add_quantity(name, 'redshift', str(row['z']), source, kind = 'spectroscopic') else: add_quantity(name, 'redshift', str(row['zCl']), source, kind = 'cluster') add_quantity(name, 'ebv', str(row['E_B-V_']), source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) result = Vizier.get_catalogs("J/ApJ/746/85/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) oldname = '' for row in tq(table, currenttask): name = row['Name'].replace('SCP', 'SCP-') flux = Decimal(float(row['Flux'])) if flux <= 0.0: continue err = Decimal(float(row['e_Flux'])) zp = Decimal(float(row['Zero'])) sig = get_sig_digits(str(row['Flux']))+1 magnitude = pretty_num(zp-Decimal(2.5)*(flux.log10()), sig = sig) e_magnitude = pretty_num(Decimal(2.5)*(Decimal(1.0) + err/flux).log10(), sig = sig) if float(e_magnitude) > 5.0: continue name = add_event(name) source = add_source(name, bibcode = "2012ApJ...746...85S") add_quantity(name, 'alias', name, source) add_photometry(name, time = str(row['MJD']), band = row['Filter'], instrument = row['Inst'], magnitude = magnitude, e_magnitude = e_magnitude, source = source) # 2004ApJ...602..571B result = Vizier.get_catalogs("J/ApJ/602/571/table8") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) oldname = '' for row in tq(table, currenttask): name = 'SN'+row['SN'] flux = Decimal(float(row['Flux'])) if flux <= 0.0: continue err = Decimal(float(row['e_Flux'])) sig = get_sig_digits(str(row['Flux']))+1 magnitude = pretty_num(Decimal(25.0)-Decimal(2.5)*(flux.log10()), sig = sig) e_magnitude = pretty_num(Decimal(2.5)*(Decimal(1.0) + err/flux).log10(), sig = sig) if float(e_magnitude) > 5.0: continue name = add_event(name) source = add_source(name, bibcode = "2004ApJ...602..571B") add_quantity(name, 'alias', name, source) band = row['Filt'] system = '' telescope = '' if band in ['R', 'I']: system = 'Cousins' if band == 'Z': telescope = 'Subaru' add_photometry(name, time = str(row['MJD']), band = band, system = system, telescope = telescope, magnitude = magnitude, e_magnitude = e_magnitude, source = source) # 2014MNRAS.444.3258M result = Vizier.get_catalogs("J/MNRAS/444/3258/SNe") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) oldname = '' for row in tq(table, currenttask): name = row['SN'] if name == oldname: continue oldname = name name = add_event(name) source = add_source(name, bibcode = '2014MNRAS.444.3258M') add_quantity(name, 'alias', name, source) add_quantity(name, 'redshift', str(row['z']), source, kind = 'heliocentric', error = str(row['e_z'])) add_quantity(name, 'ra', str(row['_RA']), source, unit = 'floatdegrees') add_quantity(name, 'dec', str(row['_DE']), source, unit = 'floatdegrees') journal_events() # 2014MNRAS.438.1391P result = Vizier.get_catalogs("J/MNRAS/438/1391/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = row['SN'] name = add_event(name) source = add_source(name, bibcode = '2014MNRAS.438.1391P') add_quantity(name, 'alias', name, source) add_quantity(name, 'redshift', str(row['zh']), source, kind = 'heliocentric') add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) journal_events() # 2012ApJ...749...18B result = Vizier.get_catalogs("J/ApJ/749/18/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = row['Name'].replace(' ','') name = add_event(name) source = add_source(name, bibcode = '2012ApJ...749...18B') add_quantity(name, 'alias', name, source) mjd = str(astrotime(2450000.+row['JD'], format='jd').mjd) band = row['Filt'] magnitude = str(row['mag']) e_magnitude = str(row['e_mag']) e_magnitude = '' if e_magnitude == '--' else e_magnitude upperlimit = True if row['l_mag'] == '>' else False add_photometry(name, time = mjd, band = band, magnitude = magnitude, e_magnitude = e_magnitude, instrument = 'UVOT', source = source, upperlimit = upperlimit, telescope = 'Swift', system = 'Swift') journal_events() # 2010A&A...523A...7G result = Vizier.get_catalogs("J/A+A/523/A7/table9") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = 'SNLS-' + row['SNLS'] name = add_event(name) source = add_source(name, bibcode = '2010A&A...523A...7G') add_quantity(name, 'alias', name, source) astrot = astrotime(2450000.+row['Date1'], format='jd').datetime add_quantity(name, 'discoverdate', make_date_string(astrot.year, astrot.month, astrot.day), source) add_quantity(name, 'ebv', str(row['E_B-V_']), source) add_quantity(name, 'redshift', str(row['z']), source, kind = 'heliocentric') add_quantity(name, 'claimedtype', (row['Type'].replace('*', '?').replace('SN','') .replace('(pec)',' P').replace('Ia? P?', 'Ia P?')), source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) journal_events() # 2004A&A...415..863G result = Vizier.get_catalogs("J/A+A/415/863/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = 'SN' + row['SN'] name = add_event(name) source = add_source(name, bibcode = '2004A&A...415..863G') add_quantity(name, 'alias', name, source) datesplit = row['Date'].split('-') add_quantity(name, 'discoverdate', make_date_string(datesplit[0], datesplit[1].lstrip('0'), datesplit[2].lstrip('0')), source) add_quantity(name, 'host', 'Abell ' + str(row['Abell']), source) add_quantity(name, 'claimedtype', row['Type'], source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) if row['zSN']: add_quantity(name, 'redshift', str(row['zSN']), source, kind = 'spectroscopic') else: add_quantity(name, 'redshift', str(row['zCl']), source, kind = 'cluster') journal_events() # 2008AJ....136.2306H result = Vizier.get_catalogs("J/AJ/136/2306/sources") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = 'SDSS-II ' + str(row['SNID']) name = add_event(name) source = add_source(name, bibcode = '2008AJ....136.2306H') add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', row['SpType'].replace('SN.', '').strip(':'), source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) # 2010ApJ...708..661D result = Vizier.get_catalogs("J/ApJ/708/661/sn") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = row['SN'] if not name: name = 'SDSS-II ' + str(row['SDSS-II']) else: name = 'SN' + name name = add_event(name) source = add_source(name, bibcode = '2010ApJ...708..661D') add_quantity(name, 'alias', name, source) add_quantity(name, 'alias', 'SDSS-II ' + str(row['SDSS-II']), source) add_quantity(name, 'claimedtype', 'II P', source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) result = Vizier.get_catalogs("J/ApJ/708/661/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): if row['f_SN'] == 'a': name = 'SDSS-II ' + str(row['SN']) else: name = 'SN' + row['SN'] name = add_event(name) source = add_source(name, bibcode = '2010ApJ...708..661D') add_quantity(name, 'alias', name, source) add_quantity(name, 'redshift', str(row['z']), source, error = str(row['e_z'])) journal_events() # 2014ApJ...795...44R result = Vizier.get_catalogs("J/ApJ/795/44/ps1_snIa") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = row['SN'] name = add_event(name) source = add_source(name, bibcode = '2014ApJ...795...44R') add_quantity(name, 'alias', name, source) astrot = astrotime(row['tdisc'], format='mjd').datetime add_quantity(name, 'discoverdate', make_date_string(astrot.year, astrot.month, astrot.day), source) add_quantity(name, 'redshift', str(row['z']), source, error = str(row['e_z']), kind = 'heliocentric') add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) add_quantity(name, 'claimedtype', 'Ia', source) result = Vizier.get_catalogs("J/ApJ/795/44/table6") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): name = row['SN'] name = add_event(name) source = add_source(name, bibcode = '2014ApJ...795...44R') add_quantity(name, 'alias', name, source) if row['mag'] != '--': add_photometry(name, time = str(row['MJD']), band = row['Filt'], magnitude = str(row['mag']), e_magnitude = str(row['e_mag']), source = source, system = 'AB', telescope = 'PS1', instrument = 'PS1') journal_events() # 1990A&AS...82..145C result = Vizier.get_catalogs("II/189/mag") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) with open('../sne-external/II_189_refs.csv') as f: tsvin = csv.reader(f, delimiter='\t', skipinitialspace=True) ii189bibdict = {} ii189refdict = {} for r, row in enumerate(tsvin): if row[0] != '0': ii189bibdict[r+1] = row[1] else: ii189refdict[r+1] = row[2] for row in tq(table, currenttask): if row['band'][0] == '(': continue name = 'SN' + row['SN'] name = add_event(name) source = '' secsource = add_source(name, bibcode = '1990A&AS...82..145C', secondary = True) mjd = str(jd_to_mjd(Decimal(row['JD']))) mag = str(row['m']) band = row['band'].strip("'") if row['r_m'] in ii189bibdict: source = add_source(name, bibcode = ii189bibdict[row['r_m']]) else: source = add_source(name, refname = ii189refdict[row['r_m']]) add_quantity(name, 'alias', name, source) add_photometry(name, time = mjd, band = band, magnitude = mag, source = uniq_cdl([source,secsource])) journal_events() # 2014yCat.7272....0G result = Vizier.get_catalogs("VII/272/snrs") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = '' if row["Names"]: names = row["Names"].split(',') for nam in names: if nam.strip()[:2] == 'SN': name = nam.strip() if is_number(name[2:]): name = name + 'A' if not name: for nam in names: if nam.strip('()') == nam: name = nam.strip() break if not name: name = row["SNR"].strip() name = add_event(name) source = (add_source(name, bibcode = '2014BASI...42...47G') + ',' + add_source(name, refname = 'Galactic SNRs', url = 'https://www.mrao.cam.ac.uk/surveys/snrs/snrs.data.html')) add_quantity(name, 'alias', name, source) add_quantity(name, "alias", row["SNR"].strip(), source) add_quantity(name, "alias", 'MWSNR '+row["SNR"].strip('G '), source) if row["Names"]: names = row["Names"].split(',') for nam in names: add_quantity(name, "alias", nam.replace('Vela (XYZ)', 'Vela').strip('()').strip(), source) if nam.strip()[:2] == 'SN': add_quantity(name, 'discoverdate', nam.strip()[2:], source) add_quantity(name, 'host', 'Milky Way', source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) journal_events() # 2014MNRAS.442..844F result = Vizier.get_catalogs("J/MNRAS/442/844/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = 'SN' + row['SN'] name = add_event(name) source = add_source(name, bibcode = '2014MNRAS.442..844F') add_quantity(name, 'alias', name, source) add_quantity(name, 'redshift', str(row['zhost']), source, kind = 'host') add_quantity(name, 'ebv', str(row['E_B-V_']), source) journal_events() result = Vizier.get_catalogs("J/MNRAS/442/844/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = 'SN' + str(row['SN']) name = add_event(name) source = add_source(name, bibcode = "2014MNRAS.442..844F") add_quantity(name, 'alias', name, source) for band in ['B', 'V', 'R', 'I']: bandtag = band + 'mag' if bandtag in row and is_number(row[bandtag]) and not isnan(float(row[bandtag])): add_photometry(name, time = row['MJD'], band = band, magnitude = row[bandtag], e_magnitude = row['e_' + bandtag], source = source, telescope = 'KAIT', instrument = 'KAIT') journal_events() # 2012MNRAS.425.1789S result = Vizier.get_catalogs("J/MNRAS/425/1789/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = ''.join(row['SimbadName'].split(' ')) name = add_event(name) source = add_source(name, bibcode = '2012MNRAS.425.1789S') add_quantity(name, 'alias', name, source) add_quantity(name, 'alias', 'SN' + row['SN'], source) add_quantity(name, 'host', row['Gal'], source) if is_number(row['cz']): add_quantity(name, 'redshift', str(round_sig(float(row['cz'])*km/clight, sig = get_sig_digits(str(row['cz'])))), source, kind = 'heliocentric') add_quantity(name, 'ebv', str(row['E_B-V_']), source) journal_events() # 2015ApJS..219...13W result = Vizier.get_catalogs("J/ApJS/219/13/table3") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = u'LSQ' + str(row['LSQ']) name = add_event(name) source = add_source(name, bibcode = "2015ApJS..219...13W") add_quantity(name, 'alias', name, source) add_quantity(name, 'ra', row['RAJ2000'], source) add_quantity(name, 'dec', row['DEJ2000'], source) add_quantity(name, 'redshift', row['z'], source, error = row['e_z'], kind = 'heliocentric') add_quantity(name, 'ebv', row['E_B-V_'], source) add_quantity(name, 'claimedtype', 'Ia', source) result = Vizier.get_catalogs("J/ApJS/219/13/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = 'LSQ' + row['LSQ'] name = add_event(name) source = add_source(name, bibcode = "2015ApJS..219...13W") add_quantity(name, 'alias', name, source) add_photometry(name, time = str(jd_to_mjd(Decimal(row['JD']))), instrument = 'QUEST', telescope = 'ESO Schmidt', observatory = 'La Silla', band = row['Filt'], magnitude = row['mag'], e_magnitude = row['e_mag'], system = "Swope", source = source) journal_events() # 2012Natur.491..228C result = Vizier.get_catalogs("J/other/Nat/491.228/tablef1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) name = 'SN2213-1745' name = add_event(name) source = add_source(name, bibcode = "2012Natur.491..228C") add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', 'SLSN-R', source) for row in tq(table, currenttask): row = convert_aq_output(row) for band in ['g', 'r', 'i']: bandtag = band + '_mag' if bandtag in row and is_number(row[bandtag]) and not isnan(float(row[bandtag])): add_photometry(name, time = row["MJD" + band + "_"], band = band + "'", magnitude = row[bandtag], e_magnitude = row["e_" + bandtag], source = source) result = Vizier.get_catalogs("J/other/Nat/491.228/tablef2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) name = 'SN1000+0216' name = add_event(name) source = add_source(name, bibcode = "2012Natur.491..228C") add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', 'SLSN-II?', source) for row in tq(table, currenttask): row = convert_aq_output(row) for band in ['g', 'r', 'i']: bandtag = band + '_mag' if bandtag in row and is_number(row[bandtag]) and not isnan(float(row[bandtag])): add_photometry(name, time = row["MJD" + band + "_"], band = band + "'", magnitude = row[bandtag], e_magnitude = row["e_" + bandtag], source = source) journal_events() # 2011Natur.474..484Q result = Vizier.get_catalogs("J/other/Nat/474.484/tables1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2011Natur.474..484Q") add_quantity(name, 'alias', name, source) add_photometry(name, time = row['MJD'], band = row['Filt'], telescope = row['Tel'], magnitude = row['mag'], e_magnitude = row['e_mag'], source = source) journal_events() # 2011ApJ...736..159G result = Vizier.get_catalogs("J/ApJ/736/159/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) name = 'PTF10vdl' name = add_event(name) source = add_source(name, bibcode = "2011ApJ...736..159G") add_quantity(name, 'alias', name, source) for row in tq(table, currenttask): row = convert_aq_output(row) add_photometry(name, time = str(jd_to_mjd(Decimal(row['JD']))), band = row['Filt'], telescope = row['Tel'], magnitude = row['mag'], e_magnitude = row['e_mag'] if is_number(row['e_mag']) else '', upperlimit = (not is_number(row['e_mag'])), source = source) journal_events() # 2012ApJ...760L..33B result = Vizier.get_catalogs("J/ApJ/760/L33/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) name = 'PTF12gzk' name = add_event(name) source = add_source(name, bibcode = "2012ApJ...760L..33B") add_quantity(name, 'alias', name, source) for row in tq(table, currenttask): row = convert_aq_output(row) # Fixing a typo in VizieR table if str(row['JD']) == '2455151.456': row['JD'] = '2456151.456' add_photometry(name, time = str(jd_to_mjd(Decimal(row['JD']))), band = row['Filt'], telescope = row['Inst'], magnitude = row['mag'], e_magnitude = row['e_mag'], source = source) journal_events() # 2013ApJ...769...39S result = Vizier.get_catalogs("J/ApJ/769/39/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) name = 'PS1-12sk' name = add_event(name) source = add_source(name, bibcode = "2013ApJ...769...39S") add_quantity(name, 'alias', name, source) for row in tq(table, currenttask): row = convert_aq_output(row) instrument = '' telescope = '' if row['Inst'] == 'RATCam': instrument = row['Inst'] else: telescope = row['Inst'] add_photometry(name, time = row['MJD'], band = row['Filt'], telescope = telescope, instrument = instrument, magnitude = row['mag'], e_magnitude = row['e_mag'] if not row['l_mag'] else '', upperlimit = (row['l_mag'] == '>'), source = source) journal_events() # 2009MNRAS.394.2266P # Note: Instrument info available via links in VizieR, can't auto-parse just yet. name = 'SN2005cs' name = add_event(name) source = add_source(name, bibcode = "2009MNRAS.394.2266P") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/MNRAS/394/2266/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) for band in ['U', 'B', 'V', 'R', 'I']: bandtag = band + 'mag' if bandtag in row and is_number(row[bandtag]) and not isnan(float(row[bandtag])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), band = band, magnitude = row[bandtag], e_magnitude = (row["e_" + bandtag] if row['l_' + bandtag] != '>' else ''), source = source, upperlimit = (row['l_' + bandtag] == '>')) if "zmag" in row and is_number(row["zmag"]) and not isnan(float(row["zmag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), band = "z", magnitude = row["zmag"], e_magnitude = row["e_zmag"], source = source) result = Vizier.get_catalogs("J/MNRAS/394/2266/table3") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) for band in ['B', 'V', 'R']: bandtag = band + 'mag' if bandtag in row and is_number(row[bandtag]) and not isnan(float(row[bandtag])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), band = band, magnitude = row[bandtag], e_magnitude = (row["e_" + bandtag] if row['l_' + bandtag] != '>' else ''), source = source, upperlimit = (row['l_' + bandtag] == '>')) result = Vizier.get_catalogs("J/MNRAS/394/2266/table4") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) for band in ['J', 'H', 'K']: bandtag = band + 'mag' if bandtag in row and is_number(row[bandtag]) and not isnan(float(row[bandtag])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), band = band, magnitude = row[bandtag], e_magnitude = row["e_" + bandtag], source = source) journal_events() # 2013AJ....145...99A result = Vizier.get_catalogs("J/AJ/145/99/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) name = 'SN2003ie' name = add_event(name) source = add_source(name, bibcode = "2013AJ....145...99A") add_quantity(name, 'alias', name, source) for row in tq(table, currenttask): row = convert_aq_output(row) if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = row["MJD"], band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"] if not row["l_Bmag"] else '', upperlimit = (row['l_Bmag'] == '>'), source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = row["MJD"], band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"] if is_number(row["e_Vmag"]) else '', upperlimit = (not is_number(row["e_Vmag"])), source = source) if "Rmag" in row and is_number(row["Rmag"]) and not isnan(float(row["Rmag"])): add_photometry(name, time = row["MJD"], band = "R", magnitude = row["Rmag"], e_magnitude = row["e_Rmag"] if not row["l_Rmag"] else '', upperlimit = (row['l_Rmag'] == '>'), source = source) if "Imag" in row and is_number(row["Imag"]) and not isnan(float(row["Imag"])): add_photometry(name, time = row["MJD"], band = "I", magnitude = row["Imag"], e_magnitude = row["e_Imag"], source = source) journal_events() # 2011ApJ...729..143C name = 'SN2008am' name = add_event(name) source = add_source(name, bibcode = "2011ApJ...729..143C") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/ApJ/729/143/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) add_photometry(name, time = row['MJD'], band = 'ROTSE', telescope = 'ROTSE', magnitude = row['mag'], e_magnitude = row['e_mag'] if not row['l_mag'] else '', upperlimit = (row['l_mag'] == '<'), source = source) result = Vizier.get_catalogs("J/ApJ/729/143/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) if "Jmag" in row and is_number(row["Jmag"]) and not isnan(float(row["Jmag"])): add_photometry(name, time = row["MJD"], telescope = "PAIRITEL", band = "J", magnitude = row["Jmag"], e_magnitude = row["e_Jmag"], source = source) if "Hmag" in row and is_number(row["Hmag"]) and not isnan(float(row["Hmag"])): add_photometry(name, time = row["MJD"], telescope = "PAIRITEL", band = "H", magnitude = row["Hmag"], e_magnitude = row["e_Hmag"], source = source) if "Ksmag" in row and is_number(row["Ksmag"]) and not isnan(float(row["Ksmag"])): add_photometry(name, time = row["MJD"], telescope = "PAIRITEL", band = "Ks", magnitude = row["Ksmag"], e_magnitude = row["e_Ksmag"], source = source) result = Vizier.get_catalogs("J/ApJ/729/143/table4") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) add_photometry(name, time = row['MJD'], band = row['Filt'], telescope = 'P60', magnitude = row['mag'], e_magnitude = row['e_mag'], source = source) result = Vizier.get_catalogs("J/ApJ/729/143/table5") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) add_photometry(name, time = row['MJD'], band = row['Filt'], instrument = 'UVOT', telescope = 'Swift', magnitude = row['mag'], e_magnitude = row['e_mag'], source = source) journal_events() # 2011ApJ...728...14P name = 'SN2009bb' name = add_event(name) source = add_source(name, bibcode = "2011ApJ...728...14P") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/ApJ/728/14/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"], source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"], source = source) if "Rmag" in row and is_number(row["Rmag"]) and not isnan(float(row["Rmag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "R", magnitude = row["Rmag"], e_magnitude = row["e_Rmag"], source = source) if "Imag" in row and is_number(row["Imag"]) and not isnan(float(row["Imag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "I", magnitude = row["Imag"], e_magnitude = row["e_Imag"], source = source) result = Vizier.get_catalogs("J/ApJ/728/14/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) if "u_mag" in row and is_number(row["u_mag"]) and not isnan(float(row["u_mag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "u'", magnitude = row["u_mag"], e_magnitude = row["e_u_mag"], source = source) if "g_mag" in row and is_number(row["g_mag"]) and not isnan(float(row["g_mag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "g'", magnitude = row["g_mag"], e_magnitude = row["e_g_mag"], source = source) if "r_mag" in row and is_number(row["r_mag"]) and not isnan(float(row["r_mag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "r'", magnitude = row["r_mag"], e_magnitude = row["e_r_mag"], source = source) if "i_mag" in row and is_number(row["i_mag"]) and not isnan(float(row["i_mag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "i'", magnitude = row["i_mag"], e_magnitude = row["e_i_mag"], source = source) if "z_mag" in row and is_number(row["z_mag"]) and not isnan(float(row["z_mag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), telescope = row['Tel'], band = "z'", magnitude = row["z_mag"], e_magnitude = row["e_z_mag"], source = source) result = Vizier.get_catalogs("J/ApJ/728/14/table3") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) if "Ymag" in row and is_number(row["Ymag"]) and not isnan(float(row["Ymag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), instrument = row['Inst'], band = "Y", magnitude = row["Ymag"], e_magnitude = row["e_Ymag"], source = source) if "Jmag" in row and is_number(row["Jmag"]) and not isnan(float(row["Jmag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), instrument = row['Inst'], band = "J", magnitude = row["Jmag"], e_magnitude = row["e_Jmag"], source = source) if "Hmag" in row and is_number(row["Hmag"]) and not isnan(float(row["Hmag"])): add_photometry(name, time = str(jd_to_mjd(Decimal(row["JD"]))), instrument = row['Inst'], band = "H", magnitude = row["Hmag"], e_magnitude = row["e_Hmag"], source = source) journal_events() # 2011PAZh...37..837T name = 'SN2009nr' name = add_event(name) source = add_source(name, bibcode = "2011PAZh...37..837T") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/PAZh/37/837/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = str(jd_to_mjd(Decimal(row["JD"]) + 2455000)) if "Umag" in row and is_number(row["Umag"]) and not isnan(float(row["Umag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "U", magnitude = row["Umag"], e_magnitude = row["e_Umag"], source = source) if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"], source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"], source = source) if "Rmag" in row and is_number(row["Rmag"]) and not isnan(float(row["Rmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "R", magnitude = row["Rmag"], e_magnitude = row["e_Rmag"], source = source) if "Imag" in row and is_number(row["Imag"]) and not isnan(float(row["Imag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "I", magnitude = row["Imag"], e_magnitude = row["e_Imag"], source = source) journal_events() # 2013MNRAS.433.1871B name = 'SN2012aw' name = add_event(name) source = add_source(name, bibcode = "2013MNRAS.433.1871B") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/MNRAS/433/1871/table3a") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = str(jd_to_mjd(Decimal(row["JD"]) + 2456000)) if "Umag" in row and is_number(row["Umag"]) and not isnan(float(row["Umag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "U", magnitude = row["Umag"], e_magnitude = row["e_Umag"], source = source) if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"], source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"], source = source) if "Rcmag" in row and is_number(row["Rcmag"]) and not isnan(float(row["Rcmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "Rc", magnitude = row["Rcmag"], e_magnitude = row["e_Rcmag"], source = source) if "Icmag" in row and is_number(row["Icmag"]) and not isnan(float(row["Icmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "Ic", magnitude = row["Icmag"], e_magnitude = row["e_Icmag"], source = source) result = Vizier.get_catalogs("J/MNRAS/433/1871/table3b") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = str(jd_to_mjd(Decimal(row["JD"]) + 2456000)) if "gmag" in row and is_number(row["gmag"]) and not isnan(float(row["gmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "g", magnitude = row["gmag"], e_magnitude = row["e_gmag"], source = source) if "rmag" in row and is_number(row["rmag"]) and not isnan(float(row["rmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "r", magnitude = row["rmag"], e_magnitude = row["e_rmag"], source = source) if "imag" in row and is_number(row["imag"]) and not isnan(float(row["imag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "i", magnitude = row["imag"], e_magnitude = row["e_imag"], source = source) if "zmag" in row and is_number(row["zmag"]) and not isnan(float(row["zmag"])): add_photometry(name, time = mjd, telescope = row['Tel'], band = "z", magnitude = row["zmag"], e_magnitude = row["e_zmag"], source = source) journal_events() # 2014AJ....148....1Z name = 'SN2012fr' name = add_event(name) source = add_source(name, bibcode = "2014AJ....148....1Z") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/AJ/148/1/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = row['MJD'] if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = mjd, telescope = "LJT", instrument = "YFOSC", band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"], source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = mjd, telescope = "LJT", instrument = "YFOSC", band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"], source = source) if "Rmag" in row and is_number(row["Rmag"]) and not isnan(float(row["Rmag"])): add_photometry(name, time = mjd, telescope = "LJT", instrument = "YFOSC", band = "R", magnitude = row["Rmag"], e_magnitude = row["e_Rmag"], source = source) if "Imag" in row and is_number(row["Imag"]) and not isnan(float(row["Imag"])): add_photometry(name, time = mjd, telescope = "LJT", instrument = "YFOSC", band = "I", magnitude = row["Imag"], e_magnitude = row["e_Imag"], source = source) result = Vizier.get_catalogs("J/AJ/148/1/table3") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = row['MJD'] if "Umag" in row and is_number(row["Umag"]) and not isnan(float(row["Umag"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = "U", magnitude = row["Umag"], e_magnitude = row["e_Umag"], source = source) if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"], source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"], source = source) if "UVW1" in row and is_number(row["UVW1"]) and not isnan(float(row["UVW1"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = "W1", magnitude = row["UVW1"], e_magnitude = row["e_UVW1"], source = source) if "UVW2" in row and is_number(row["UVW2"]) and not isnan(float(row["UVW2"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = "W2", magnitude = row["UVW2"], e_magnitude = row["e_UVW2"], source = source) if "UVM2" in row and is_number(row["UVM2"]) and not isnan(float(row["UVM2"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = "M2", magnitude = row["UVM2"], e_magnitude = row["e_UVM2"], source = source) result = Vizier.get_catalogs("J/AJ/148/1/table5") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = row['MJD'] if "Bmag" in row and is_number(row["Bmag"]) and not isnan(float(row["Bmag"])): add_photometry(name, time = mjd, telescope = "LJT", band = "B", magnitude = row["Bmag"], e_magnitude = row["e_Bmag"], source = source) if "Vmag" in row and is_number(row["Vmag"]) and not isnan(float(row["Vmag"])): add_photometry(name, time = mjd, telescope = "LJT", band = "V", magnitude = row["Vmag"], e_magnitude = row["e_Vmag"], source = source) if "Rmag" in row and is_number(row["Rmag"]) and not isnan(float(row["Rmag"])): add_photometry(name, time = mjd, telescope = "LJT", band = "R", magnitude = row["Rmag"], e_magnitude = row["e_Rmag"], source = source) if "Imag" in row and is_number(row["Imag"]) and not isnan(float(row["Imag"])): add_photometry(name, time = mjd, telescope = "LJT", band = "I", magnitude = row["Imag"], e_magnitude = row["e_Imag"], source = source) journal_events() # 2015ApJ...805...74B name = 'SN2014J' name = add_event(name) source = add_source(name, bibcode = "2014AJ....148....1Z") add_quantity(name, 'alias', name, source) result = Vizier.get_catalogs("J/ApJ/805/74/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) mjd = row['MJD'] if "mag" in row and is_number(row["mag"]) and not isnan(float(row["mag"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = row["Filt"], magnitude = row["mag"], e_magnitude = row["e_mag"], source = source) elif "maglim" in row and is_number(row["maglim"]) and not isnan(float(row["maglim"])): add_photometry(name, time = mjd, telescope = "Swift", instrument = "UVOT", band = row["Filt"], magnitude = row["maglim"], upperlimit = True, source = source) journal_events() # 2011ApJ...741...97D result = Vizier.get_catalogs("J/ApJ/741/97/table2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['SN']) name = add_event(name) source = add_source(name, bibcode = "2011ApJ...741...97D") add_quantity(name, 'alias', name, source) add_photometry(name, time = str(jd_to_mjd(Decimal(row['JD']))), band = row['Filt'], magnitude = row['mag'], e_magnitude = row['e_mag'] if is_number(row['e_mag']) else '', upperlimit = (not is_number(row['e_mag'])), source = source) journal_events() # 2015MNRAS.448.1206M # Note: Photometry from two SN can also be added from this source. result = Vizier.get_catalogs("J/MNRAS/448/1206/table3") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2015MNRAS.448.1206M") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + name[4:6], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'redshift', row['zsp'], source, kind = 'spectroscopic') add_quantity(name, 'maxappmag', row['rP1mag'], source, error = row['e_rP1mag']) add_quantity(name, 'maxband', 'r', source) add_quantity(name, 'claimedtype', 'Ia', source) result = Vizier.get_catalogs("J/MNRAS/448/1206/table4") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2015MNRAS.448.1206M") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + name[4:6], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'redshift', row['zph'], source, error = row['e_zph'], kind = 'photometric') add_quantity(name, 'maxappmag', row['rP1mag'], source, error = row['e_rP1mag']) add_quantity(name, 'maxband', 'r', source) add_quantity(name, 'claimedtype', 'Ia?', source) result = Vizier.get_catalogs("J/MNRAS/448/1206/table5") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2015MNRAS.448.1206M") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + name[4:6], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'redshift', row['zsp'], source, kind = 'spectroscopic') add_quantity(name, 'maxappmag', row['rP1mag'], source, error = row['e_rP1mag']) add_quantity(name, 'maxband', 'r', source) add_quantity(name, 'claimedtype', row['Type'], source) result = Vizier.get_catalogs("J/MNRAS/448/1206/table6") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2015MNRAS.448.1206M") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + name[4:6], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'maxappmag', row['rP1mag'], source, error = row['e_rP1mag']) add_quantity(name, 'maxband', 'r', source) add_quantity(name, 'claimedtype', row['Type'], source) result = Vizier.get_catalogs("J/MNRAS/448/1206/tablea2") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2015MNRAS.448.1206M") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + name[4:6], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'maxappmag', row['rP1mag'], source, error = row['e_rP1mag']) add_quantity(name, 'maxband', 'r', source) add_quantity(name, 'claimedtype', row['Typesoft']+'?', source) add_quantity(name, 'claimedtype', row['Typepsnid']+'?', source) result = Vizier.get_catalogs("J/MNRAS/448/1206/tablea3") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = str(row['Name']) name = add_event(name) source = add_source(name, bibcode = "2015MNRAS.448.1206M") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + name[4:6], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'maxappmag', row['rP1mag'], source, error = row['e_rP1mag']) add_quantity(name, 'maxband', 'r', source) add_quantity(name, 'claimedtype', 'Candidate', source) journal_events() # 2012AJ....143..126B result = Vizier.get_catalogs("J/AJ/143/126/table4") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): if not row['Wcl'] or row['Wcl'] == 'N': continue row = convert_aq_output(row) name = str(row['SN']).replace(' ', '') name = add_event(name) source = add_source(name, bibcode = "2012AJ....143..126B") add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', 'Ia-' + row['Wcl'], source) journal_events() # 2015ApJS..220....9F for viztab in ['1', '2']: result = Vizier.get_catalogs("J/ApJS/220/9/table" + viztab) table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = add_event(row['SN']) source = add_source(name, bibcode = "2015ApJS..220....9F") add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', row['Type'], source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') if '?' not in row['Host']: add_quantity(name, 'host', row['Host'].replace('_', ' '), source) kind = '' if 'Host' in row['n_z']: kind = 'host' elif 'Spectrum' in row['n_z']: kind = 'spectroscopic' add_quantity(name, 'redshift', row['z'], source, error = row['e_z'], kind = kind) result = Vizier.get_catalogs("J/ApJS/220/9/table8") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = add_event(row['SN']) source = add_source(name, bibcode = "2015ApJS..220....9F") add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', row['Type'], source) add_photometry(name, time = row['MJD'], band = row['Band'], magnitude = row['mag'], e_magnitude = row["e_mag"], telescope = row["Tel"], source = source) journal_events() result = Vizier.get_catalogs("J/ApJ/673/999/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) for row in tq(table, currenttask): row = convert_aq_output(row) name = add_event('SN'+row['SN']) source = add_source(name, bibcode = "2008ApJ...673..999P") add_quantity(name, 'alias', name, source) add_quantity(name, 'ra', row['RAJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'dec', row['DEJ2000'], source, unit = 'floatdegrees') add_quantity(name, 'redshift', row['z'], source, kind = 'host') add_quantity(name, 'hostra', row['RAGdeg'], source, unit = 'floatdegrees') add_quantity(name, 'hostdec', row['DEGdeg'], source, unit = 'floatdegrees') add_quantity(name, 'claimedtype', row['Type'].strip(':'), source) journal_events() if do_task(task, 'donations'): # Nicholl 04-01-16 donation with open("../sne-external/Nicholl-04-01-16/bibcodes.json", 'r') as f: bcs = json.loads(f.read()) for datafile in sorted(glob("../sne-external/Nicholl-04-01-16/*.txt"), key=lambda s: s.lower()): name = os.path.basename(datafile).split('_')[0] name = add_event(name) bibcode = '' for bc in bcs: if name in bcs[bc]: bibcode = bc if not bibcode: raise(ValueError('Bibcode not found!')) source = add_source(name, bibcode = bibcode) add_quantity(name, 'alias', name, source) with open(datafile,'r') as f: tsvin = csv.reader(f, delimiter='\t', skipinitialspace=True) for r, rrow in enumerate(tsvin): row = list(filter(None, rrow)) if not row: continue if row[0][0] == '#' and row[0] != '#MJD': continue if row[0] == '#MJD': bands = [x for x in row[1:] if x and 'err' not in x] continue mjd = row[0] if not is_number(mjd): continue for v, val in enumerate(row[1::2]): upperlimit = '' if '>' in val: upperlimit = True mag = val.strip('>') if not is_number(mag) or isnan(float(mag)) or float(mag) > 90.0: continue err = '' if is_number(row[2*v+2]) and not isnan(float(row[2*v+2])): err = row[2*v+2] add_photometry(name, time = mjd, band = bands[v], magnitude = mag, e_magnitude = err, upperlimit = upperlimit, source = source) journal_events() # Maggi 04-11-16 donation (MC SNRs) with open('../sne-external/Maggi-04-11-16/LMCSNRs_OpenSNe.csv') as f: tsvin = csv.reader(f, delimiter=',') for row in tsvin: name = 'MCSNR ' + row[0] name = add_event(name) source = add_source(name, bibcode = '2016A&A...585A.162M') add_quantity(name, 'alias', name, source) if row[1] != 'noname': add_quantity(name, "alias", row[1], source) add_quantity(name, 'ra', row[2], source) add_quantity(name, 'dec', row[3], source) add_quantity(name, 'host', 'LMC', source) if row[4] == '1': add_quantity(name, 'claimedtype', 'Ia', source) elif row[4] == '2': add_quantity(name, 'claimedtype', 'CC', source) with open('../sne-external/Maggi-04-11-16/SMCSNRs_OpenSNe.csv') as f: tsvin = csv.reader(f, delimiter=',') for row in tsvin: name = 'MCSNR ' + row[0] name = add_event(name) source = add_source(name, refname = 'Pierre Maggi') add_quantity(name, 'alias', name, source) add_quantity(name, "alias", row[1], source) add_quantity(name, "alias", row[2], source) add_quantity(name, 'ra', row[3], source) add_quantity(name, 'dec', row[4], source) add_quantity(name, 'host', 'SMC', source) journal_events() # Galbany 04-18-16 donation folders = next(os.walk('../sne-external/galbany-04-18-16/'))[1] bibcode = '2016AJ....151...33G' for folder in folders: infofiles = glob("../sne-external/galbany-04-18-16/" + folder + "/*.info") photfiles = glob("../sne-external/galbany-04-18-16/" + folder + "/*.out*") zhel = '' zcmb = '' zerr = '' for path in infofiles: with open(path, 'r') as f: lines = f.read().splitlines() for line in lines: splitline = line.split(':') field = splitline[0].strip().lower() value = splitline[1].strip() if field == 'name': name = value[:6].upper() + (value[6].upper() if len(value) == 7 else value[6:]) name = add_event(name) source = add_source(name, bibcode = bibcode) add_quantity(name, 'alias', name, source) elif field == 'type': claimedtype = value.replace('SN', '') add_quantity(name, 'claimedtype', claimedtype, source) elif field == 'zhel': zhel = value elif field == 'redshift_error': zerr = value elif field == 'zcmb': zcmb = value elif field == 'ra': add_quantity(name, 'ra', value, source, unit = 'floatdegrees') elif field == 'dec': add_quantity(name, 'dec', value, source, unit = 'floatdegrees') elif field == 'host': add_quantity(name, 'host', value.replace('- ', '-').replace('G ', 'G'), source) elif field == 'e(b-v)_mw': add_quantity(name, 'ebv', value, source) add_quantity(name, 'redshift', zhel, source, error = zerr, kind = 'heliocentric') add_quantity(name, 'redshift', zcmb, source, error = zerr, kind = 'cmb') for path in photfiles: with open(path, 'r') as f: band = '' lines = f.read().splitlines() for li, line in enumerate(lines): if li in [0, 2, 3]: continue if li == 1: band = line.split(':')[-1].strip() else: cols = list(filter(None, line.split())) if not cols: continue add_photometry(name, time = cols[0], magnitude = cols[1], e_magnitude = cols[2], band = band, system = cols[3], telescope = cols[4], source = source) journal_events() # Brown 05-14-16 files = glob("../sne-external/brown-05-14-16/*.dat") for fi in tq(files, currenttask): name = os.path.basename(fi).split('_')[0] name = add_event(name) source = add_source(name, refname = 'Swift Supernovae', bibcode = '2014Ap&SS.354...89B', url = 'http://people.physics.tamu.edu/pbrown/SwiftSN/swift_sn.html') add_quantity(name, 'alias', name, source) with open(fi, 'r') as f: lines = f.read().splitlines() for line in lines: if not line or line[0] == '#': continue cols = list(filter(None, line.split())) band = cols[0] mjd = cols[1] # Skip lower limit entries for now if cols[2] == 'NULL' and cols[6] == 'NULL': continue isupp = cols[2] == 'NULL' and cols[6] != 'NULL' mag = cols[2] if not isupp else cols[4] e_mag = cols[3] if not isupp else '' upp = '' if not isupp else True add_photometry(name, time = mjd, magnitude = mag, e_magnitude = e_mag, upperlimit = upp, band = band, source = source, telescope = 'Swift', instrument = 'UVOT', system = 'Vega') journal_events() # Nicholl 05-03-16 files = glob("../sne-external/nicholl-05-03-16/*.txt") name = add_event('SN2015bn') source = add_source(name, bibcode = '2016arXiv160304748N') add_quantity(name, 'alias', name, source) add_quantity(name, 'alias', 'PS15ae', source) for fi in tq(files, currenttask): telescope = os.path.basename(fi).split('_')[1] with open(fi, 'r') as f: lines = f.read().splitlines() for li, line in enumerate(lines): if not line or (line[0] == '#' and li != 0): continue cols = list(filter(None, line.split())) if not cols: continue if li == 0: bands = cols[1:] continue mjd = cols[0] for ci, col in enumerate(cols[1::2]): if not is_number(col): continue emag = cols[2*ci+2] upp = '' if not is_number(emag): emag = '' upp = True add_photometry(name, time = mjd, magnitude = col, e_magnitude = emag, upperlimit = upp, band = bands[ci], source = source, telescope = telescope, instrument = 'UVOT' if telescope == 'Swift' else '') journal_events() if do_task(task, 'pessto-dr1'): with open("../sne-external/PESSTO_MPHOT.csv", 'r') as f: tsvin = csv.reader(f, delimiter=',') for ri, row in enumerate(tsvin): if ri == 0: bands = [x.split('_')[0] for x in row[3::2]] systems = [x.split('_')[1].capitalize().replace('Ab', 'AB') for x in row[3::2]] continue name = row[1] name = add_event(name) source = add_source(name, bibcode = "2015A&A...579A..40S") add_quantity(name, 'alias', name, source) for hi, ci in enumerate(range(3,len(row)-1,2)): if not row[ci]: continue add_photometry(name, time = row[2], magnitude = row[ci], e_magnitude = row[ci+1], band = bands[hi], system = systems[hi], telescope = 'Swift' if systems[hi] == 'Swift' else '', source = source) journal_events() if do_task(task, 'scp'): with open("../sne-external/SCP09.csv", 'r') as f: tsvin = csv.reader(f, delimiter=',') for ri, row in enumerate(tq(tsvin, currenttask)): if ri == 0: continue name = row[0].replace('SCP', 'SCP-') name = add_event(name) source = add_source(name, refname = 'Supernova Cosmology Project', url = 'http://supernova.lbl.gov/2009ClusterSurvey/') add_quantity(name, 'alias', name, source) if row[1]: add_quantity(name, 'alias', row[1], source) if row[2]: add_quantity(name, 'redshift', row[2], source, kind = 'spectroscopic' if row[3] == 'sn' else 'host') if row[4]: add_quantity(name, 'redshift', row[2], source, kind = 'cluster') if row[6]: claimedtype = row[6].replace('SN ', '') kind = ('spectroscopic/light curve' if 'a' in row[7] and 'c' in row[7] else 'spectroscopic' if 'a' in row[7] else 'light curve' if 'c' in row[7] else '') if claimedtype != '?': add_quantity(name, 'claimedtype', claimedtype, source, kind = kind) journal_events() if do_task(task, 'ascii'): # 2006ApJ...645..841N with open("../sne-external/2006ApJ...645..841N-table3.csv", 'r') as f: tsvin = csv.reader(f, delimiter=',') for ri, row in enumerate(tq(tsvin, currenttask)): name = 'SNLS-' + row[0] name = add_event(name) source = add_source(name, bibcode = '2006ApJ...645..841N') add_quantity(name, 'alias', name, source) add_quantity(name, 'redshift', row[1], source, kind = 'spectroscopic') astrot = astrotime(float(row[4]) + 2450000., format = 'jd').datetime add_quantity(name, 'discoverdate', make_date_string(astrot.year, astrot.month, astrot.day), source) journal_events() # Anderson 2014 for datafile in tq(sorted(glob("../sne-external/SNII_anderson2014/*.dat"), key=lambda s: s.lower()), currenttask): basename = os.path.basename(datafile) if not is_number(basename[:2]): continue if basename == '0210_V.dat': name = 'SN0210' else: name = ('SN20' if int(basename[:2]) < 50 else 'SN19') + basename.split('_')[0] name = add_event(name) source = add_source(name, bibcode = '2014ApJ...786...67A') add_quantity(name, 'alias', name, source) if name in ['SN1999ca','SN2003dq','SN2008aw']: system = 'Swope' else: system = 'Landolt' with open(datafile,'r') as f: tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True) for row in tsvin: if not row[0]: continue add_photometry(name, time = str(jd_to_mjd(Decimal(row[0]))), band = 'V', magnitude = row[1], e_magnitude = row[2], system = system, source = source) journal_events() # stromlo stromlobands = ['B','V','R','I','VM','RM'] with open('../sne-external/J_A+A_415_863-1/photometry.csv', 'r') as f: tsvin = csv.reader(f, delimiter=',') for row in tq(tsvin, currenttask): name = row[0] name = add_event(name) source = add_source(name, bibcode = "2004A&A...415..863G") add_quantity(name, 'alias', name, source) mjd = str(jd_to_mjd(Decimal(row[1]))) for ri, ci in enumerate(range(2,len(row),3)): if not row[ci]: continue band = stromlobands[ri] upperlimit = True if (not row[ci+1] and row[ci+2]) else False e_upper_magnitude = str(abs(Decimal(row[ci+1]))) if row[ci+1] else '' e_lower_magnitude = str(abs(Decimal(row[ci+2]))) if row[ci+2] else '' add_photometry(name, time = mjd, band = band, magnitude = row[ci], e_upper_magnitude = e_upper_magnitude, e_lower_magnitude = e_lower_magnitude, upperlimit = upperlimit, telescope = 'MSSSO 1.3m' if band in ['VM', 'RM'] else 'CTIO', instrument = 'MaCHO' if band in ['VM', 'RM'] else '', source = source) journal_events() # 2015MNRAS.449..451W with open("../sne-external/2015MNRAS.449..451W.dat", 'r') as f: data = csv.reader(f, delimiter='\t', quotechar='"', skipinitialspace = True) for r, row in enumerate(tq(data, currenttask)): if r == 0: continue namesplit = row[0].split('/') name = namesplit[-1] if name.startswith('SN'): name = name.replace(' ', '') name = add_event(name) source = add_source(name, bibcode = '2015MNRAS.449..451W') add_quantity(name, 'alias', name, source) if len(namesplit) > 1: add_quantity(name, 'alias', namesplit[0], source) add_quantity(name, 'claimedtype', row[1], source) add_photometry(name, time = row[2], band = row[4], magnitude = row[3], source = source) journal_events() # 2016MNRAS.459.1039T with open("../sne-external/2016MNRAS.459.1039T.tsv", 'r') as f: data = csv.reader(f, delimiter='\t', quotechar='"', skipinitialspace = True) name = add_event('LSQ13zm') source = add_source(name, bibcode = '2016MNRAS.459.1039T') add_quantity(name, 'alias', name, source) for r, row in enumerate(tq(data, currenttask)): if row[0][0] == '#': bands = [x.replace('(err)', '') for x in row[3:-1]] continue mjd = row[1] mags = [re.sub(r'\([^)]*\)', '', x) for x in row[3:-1]] upps = [True if '>' in x else '' for x in mags] mags = [x.replace('>', '') for x in mags] errs = [x[x.find("(")+1:x.find(")")] if "(" in x else '' for x in row[3:-1]] for mi, mag in enumerate(mags): if not is_number(mag): continue add_photometry(name, time = mjd, band = bands[mi], magnitude = mag, e_magnitude = errs[mi], instrument = row[-1], upperlimit = upps[mi], source = source) journal_events() # 2015ApJ...804...28G with open("../sne-external/2015ApJ...804...28G.tsv", 'r') as f: data = csv.reader(f, delimiter='\t', quotechar='"', skipinitialspace = True) name = add_event('PS1-13arp') source = add_source(name, bibcode = '2015ApJ...804...28G') add_quantity(name, 'alias', name, source) for r, row in enumerate(tq(data, currenttask)): if r == 0: continue mjd = row[1] mag = row[3] upp = True if '<' in mag else '' mag = mag.replace('<', '') err = row[4] if is_number(row[4]) else '' ins = row[5] add_photometry(name, time = mjd, band = row[0], magnitude = mag, e_magnitude = err, instrument = ins, upperlimit = upp, source = source) journal_events() # 2016ApJ...819...35A with open("../sne-external/2016ApJ...819...35A.tsv", 'r') as f: data = csv.reader(f, delimiter='\t', quotechar='"', skipinitialspace = True) for r, row in enumerate(tq(data, currenttask)): if row[0][0] == '#': continue name = add_event(row[0]) source = add_source(name, bibcode = '2016ApJ...819...35A') add_quantity(name, 'alias', name, source) add_quantity(name, 'ra', row[1], source) add_quantity(name, 'dec', row[2], source) add_quantity(name, 'redshift', row[3], source) add_quantity(name, 'discoverdate', datetime.strptime(row[4], '%Y %b %d').isoformat().split('T')[0].replace('-', '/'), source) journal_events() # 2014ApJ...784..105W with open("../sne-external/2014ApJ...784..105W.tsv", 'r') as f: data = csv.reader(f, delimiter='\t', quotechar='"', skipinitialspace = True) for r, row in enumerate(tq(data, currenttask)): if row[0][0] == '#': continue name = add_event(row[0]) source = add_source(name, bibcode = '2014ApJ...784..105W') add_quantity(name, 'alias', name, source) mjd = row[1] band = row[2] mag = row[3] err = row[4] add_photometry(name, time = mjd, band = row[2], magnitude = mag, e_magnitude = err, instrument = 'WHIRC', telescope = 'WIYN 3.5 m', observatory = 'NOAO', system = 'WHIRC', source = source) journal_events() # 2012MNRAS.425.1007B with open("../sne-external/2012MNRAS.425.1007B.tsv", 'r') as f: data = csv.reader(f, delimiter='\t', quotechar='"', skipinitialspace = True) for r, row in enumerate(tq(data, currenttask)): if row[0][0] == '#': bands = row[2:] continue name = add_event(row[0]) source = add_source(name, bibcode = '2012MNRAS.425.1007B') add_quantity(name, 'alias', name, source) mjd = row[1] mags = [x.split('±')[0].strip() for x in row[2:]] errs = [x.split('±')[1].strip() if '±' in x else '' for x in row[2:]] if row[0] == 'PTF09dlc': ins = 'HAWK-I' tel = 'VLT 8.1m' obs = 'ESO' else: ins = 'NIRI' tel = 'Gemini North 8.2m' obs = 'Gemini' for mi, mag in enumerate(mags): if not is_number(mag): continue add_photometry(name, time = mjd, band = bands[mi], magnitude = mag, e_magnitude = errs[mi], instrument = ins, telescope = tel, observatory = obs, system = 'Natural', source = source) journal_events() # CCCP if do_task(task, 'cccp'): cccpbands = ['B', 'V', 'R', 'I'] for datafile in sorted(glob("../sne-external/CCCP/apj407397*.txt"), key=lambda s: s.lower()): with open(datafile,'r') as f: tsvin = csv.reader(f, delimiter='\t', skipinitialspace=True) for r, row in enumerate(tsvin): if r == 0: continue elif r == 1: name = 'SN' + row[0].split('SN ')[-1] name = add_event(name) source = add_source(name, bibcode = '2012ApJ...744...10K') add_quantity(name, 'alias', name, source) elif r >= 5: mjd = str(Decimal(row[0]) + 53000) for b, band in enumerate(cccpbands): if row[2*b + 1]: if not row[2*b + 2]: upplim = True add_photometry(name, time = mjd, band = band, magnitude = row[2*b + 1].strip('>'), e_magnitude = row[2*b + 2], upperlimit = (not row[2*b + 2]), source = source) if archived_task('cccp'): with open('../sne-external/CCCP/sc_cccp.html', 'r') as f: html = f.read() else: session = requests.Session() response = session.get("https://webhome.weizmann.ac.il/home/iair/sc_cccp.html") html = response.text with open('../sne-external/CCCP/sc_cccp.html', 'w') as f: f.write(html) soup = BeautifulSoup(html, "html5lib") links = soup.body.findAll("a") for link in tq(links, currenttask): if 'sc_sn' in link['href']: name = add_event(link.text.replace(' ', '')) source = add_source(name, refname = 'CCCP', url = 'https://webhome.weizmann.ac.il/home/iair/sc_cccp.html') add_quantity(name, 'alias', name, source) if archived_task('cccp'): with open('../sne-external/CCCP/' + link['href'].split('/')[-1], 'r') as f: html2 = f.read() else: response2 = session.get("https://webhome.weizmann.ac.il/home/iair/" + link['href']) html2 = response2.text with open('../sne-external/CCCP/' + link['href'].split('/')[-1], 'w') as f: f.write(html2) soup2 = BeautifulSoup(html2, "html5lib") links2 = soup2.body.findAll("a") for link2 in links2: if ".txt" in link2['href'] and '_' in link2['href']: band = link2['href'].split('_')[1].split('.')[0].upper() if archived_task('cccp'): fname = '../sne-external/CCCP/' + link2['href'].split('/')[-1] if not os.path.isfile(fname): continue with open(fname, 'r') as f: html3 = f.read() else: response3 = session.get("https://webhome.weizmann.ac.il/home/iair/cccp/" + link2['href']) if response3.status_code == 404: continue html3 = response3.text with open('../sne-external/CCCP/' + link2['href'].split('/')[-1], 'w') as f: f.write(html3) table = [[str(Decimal(y.strip())).rstrip('0') for y in x.split(",")] for x in list(filter(None, html3.split("\n")))] for row in table: add_photometry(name, time = str(Decimal(row[0]) + 53000), band = band, magnitude = row[1], e_magnitude = row[2], source = source) journal_events() # Suspect catalog if do_task(task, 'suspect'): with open('../sne-external/suspectreferences.csv','r') as f: tsvin = csv.reader(f, delimiter=',', skipinitialspace=True) suspectrefdict = {} for row in tsvin: suspectrefdict[row[0]] = row[1] for datafile in tq(sorted(glob("../sne-external/SUSPECT/*.html"), key=lambda s: s.lower()), currenttask): basename = os.path.basename(datafile) basesplit = basename.split('-') name = basesplit[1] name = add_event(name) if name.startswith('SN') and is_number(name[2:]): name = name + 'A' band = basesplit[3].split('.')[0] ei = int(basesplit[2]) bandlink = 'file://' + os.path.abspath(datafile) bandresp = urllib.request.urlopen(bandlink) bandsoup = BeautifulSoup(bandresp, "html5lib") bandtable = bandsoup.find('table') names = bandsoup.body.findAll(text=re.compile("Name")) reference = '' for link in bandsoup.body.findAll('a'): if 'adsabs' in link['href']: reference = str(link).replace('"', "'") bibcode = unescape(suspectrefdict[reference]) source = add_source(name, bibcode = bibcode) secondaryreference = "SUSPECT" secondaryrefurl = "https://www.nhn.ou.edu/~suspect/" secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, secondary = True) add_quantity(name, 'alias', name, secondarysource) if ei == 1: year = re.findall(r'\d+', name)[0] add_quantity(name, 'discoverdate', year, secondarysource) add_quantity(name, 'host', names[1].split(':')[1].strip(), secondarysource) redshifts = bandsoup.body.findAll(text=re.compile("Redshift")) if redshifts: add_quantity(name, 'redshift', redshifts[0].split(':')[1].strip(), secondarysource, kind = 'heliocentric') hvels = bandsoup.body.findAll(text=re.compile("Heliocentric Velocity")) #if hvels: # add_quantity(name, 'velocity', hvels[0].split(':')[1].strip().split(' ')[0], # secondarysource, kind = 'heliocentric') types = bandsoup.body.findAll(text=re.compile("Type")) add_quantity(name, 'claimedtype', types[0].split(':')[1].strip().split(' ')[0], secondarysource) for r, row in enumerate(bandtable.findAll('tr')): if r == 0: continue col = row.findAll('td') mjd = str(jd_to_mjd(Decimal(col[0].contents[0]))) mag = col[3].contents[0] if mag.isspace(): mag = '' else: mag = str(mag) e_magnitude = col[4].contents[0] if e_magnitude.isspace(): e_magnitude = '' else: e_magnitude = str(e_magnitude) add_photometry(name, time = mjd, band = band, magnitude = mag, e_magnitude = e_magnitude, source = secondarysource + ',' + source) journal_events() # CfA data if do_task(task, 'cfa'): for fname in tq(sorted(glob("../sne-external/cfa-input/*.dat"), key=lambda s: s.lower()), currenttask): f = open(fname,'r') tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True) csv_data = [] for r, row in enumerate(tsvin): new = [] for item in row: new.extend(item.split("\t")) csv_data.append(new) for r, row in enumerate(csv_data): for c, col in enumerate(row): csv_data[r][c] = col.strip() csv_data[r] = [_f for _f in csv_data[r] if _f] eventname = os.path.basename(os.path.splitext(fname)[0]) eventparts = eventname.split('_') name = snname(eventparts[0]) name = add_event(name) secondaryname = 'CfA Supernova Archive' secondaryurl = 'https://www.cfa.harvard.edu/supernova/SNarchive.html' secondarysource = add_source(name, refname = secondaryname, url = secondaryurl, secondary = True, acknowledgment = cfaack) add_quantity(name, 'alias', name, secondarysource) year = re.findall(r'\d+', name)[0] add_quantity(name, 'discoverdate', year, secondarysource) eventbands = list(eventparts[1]) tu = 'MJD' jdoffset = Decimal(0.) for rc, row in enumerate(csv_data): if len(row) > 0 and row[0][0] == "#": if len(row[0]) > 2 and row[0][:3] == "#JD": tu = 'JD' rowparts = row[0].split('-') jdoffset = Decimal(rowparts[1]) elif len(row[0]) > 6 and row[0][:7] == "#Julian": tu = 'JD' jdoffset = Decimal(0.) elif len(row) > 1 and row[1].lower() == "photometry": for ci, col in enumerate(row[2:]): if col[0] == "(": refstr = ' '.join(row[2+ci:]) refstr = refstr.replace('(','').replace(')','') bibcode = unescape(refstr) source = add_source(name, bibcode = bibcode) elif len(row) > 1 and row[1] == "HJD": tu = "HJD" continue elif len(row) > 0: mjd = row[0] for v, val in enumerate(row): if v == 0: if tu == 'JD': mjd = str(jd_to_mjd(Decimal(val) + jdoffset)) tuout = 'MJD' elif tu == 'HJD': mjd = str(jd_to_mjd(Decimal(val))) tuout = 'MJD' else: mjd = val tuout = tu elif v % 2 != 0: if float(row[v]) < 90.0: add_photometry(name, u_time = tuout, time = mjd, band = eventbands[(v-1)//2], magnitude = row[v], e_magnitude = row[v+1], source = secondarysource + ',' + source) f.close() # Hicken 2012 f = open("../sne-external/hicken-2012-standard.dat", 'r') tsvin = csv.reader(f, delimiter='|', skipinitialspace=True) for r, row in enumerate(tq(tsvin, currenttask)): if r <= 47: continue if row[0][:2] != 'sn': name = 'SN' + row[0].strip() else: name = row[0].strip() name = add_event(name) source = add_source(name, bibcode = '2012ApJS..200...12H') add_quantity(name, 'alias', name, source) add_quantity(name, 'claimedtype', 'Ia', source) add_photometry(name, u_time = 'MJD', time = row[2].strip(), band = row[1].strip(), magnitude = row[6].strip(), e_magnitude = row[7].strip(), source = source) # Bianco 2014 tsvin = open("../sne-external/bianco-2014-standard.dat", 'r') tsvin = csv.reader(tsvin, delimiter=' ', skipinitialspace=True) for row in tq(tsvin, currenttask): name = 'SN' + row[0] name = add_event(name) source = add_source(name, bibcode = '2014ApJS..213...19B') add_quantity(name, 'alias', name, source) add_photometry(name, u_time = 'MJD', time = row[2], band = row[1], magnitude = row[3], e_magnitude = row[4], telescope = row[5], system = "Standard", source = source) f.close() journal_events() # New UCB import if do_task(task, 'ucb'): secondaryreference = "UCB Filippenko Group's Supernova Database (SNDB)" secondaryrefurl = "http://heracles.astro.berkeley.edu/sndb/info" secondaryrefbib = "2012MNRAS.425.1789S" jsontxt = load_cached_url("http://heracles.astro.berkeley.edu/sndb/download?id=allpubphot", '../sne-external-spectra/UCB/allpub.json') if not jsontxt: continue photom = json.loads(jsontxt) photom = sorted(photom, key = lambda k: k['ObjName']) for phot in tq(photom, currenttask = currenttask): name = phot["ObjName"] name = add_event(name) secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, bibcode = secondaryrefbib, secondary = True) add_quantity(name, 'alias', name, secondarysource) sources = [secondarysource] if phot["Reference"]: sources += [add_source(name, bibcode = phot["Reference"])] sources = uniq_cdl(sources) if phot["Type"] and phot["Type"].strip() != "NoMatch": for ct in phot["Type"].strip().split(','): add_quantity(name, 'claimedtype', ct.replace('-norm', '').strip(), sources) if phot["DiscDate"]: add_quantity(name, 'discoverdate', phot["DiscDate"].replace('-', '/'), sources) if phot["HostName"]: add_quantity(name, 'host', urllib.parse.unquote(phot["HostName"]).replace('*', ''), sources) filename = phot["Filename"] if phot["Filename"] else '' if not filename: raise(ValueError('Filename not found for SNDB phot!')) if not phot["PhotID"]: raise(ValueError('ID not found for SNDB phot!')) filepath = '../sne-external/SNDB/' + filename if archived_task('ucb') and os.path.isfile(filepath): with open(filepath, 'r') as f: phottxt = f.read() else: session = requests.Session() response = session.get("http://heracles.astro.berkeley.edu/sndb/download?id=dp:" + str(phot["PhotID"])) phottxt = response.text with open(filepath, 'w') as f: f.write(phottxt) tsvin = csv.reader(phottxt.splitlines(), delimiter=' ', skipinitialspace=True) for r, row in enumerate(tsvin): if len(row) > 0 and row[0] == "#": continue mjd = row[0] magnitude = row[1] if magnitude and float(magnitude) > 99.0: continue e_magnitude = row[2] band = row[4] telescope = row[5] add_photometry(name, time = mjd, telescope = telescope, band = band, magnitude = magnitude, e_magnitude = e_magnitude, source = sources) journal_events() # Import SDSS if do_task(task, 'sdss'): with open('../sne-external/SDSS/2010ApJ...708..661D.txt', 'r') as f: bibcodes2010 = f.read().split("\n") sdssbands = ['u', 'g', 'r', 'i', 'z'] for fname in tq(sorted(glob("../sne-external/SDSS/*.sum"), key=lambda s: s.lower()), currenttask): f = open(fname,'r') tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True) basename = os.path.basename(fname) if basename in bibcodes2010: bibcode = '2010ApJ...708..661D' else: bibcode = '2008AJ....136.2306H' for r, row in enumerate(tsvin): if r == 0: if row[5] == "RA:": name = "SDSS-II " + row[3] else: name = "SN" + row[5] name = add_event(name) source = add_source(name, bibcode = bibcode) add_quantity(name, 'alias', name, source) add_quantity(name, 'alias', "SDSS-II " + row[3], source) if row[5] != "RA:": year = re.findall(r'\d+', name)[0] add_quantity(name, 'discoverdate', year, source) add_quantity(name, 'ra', row[-4], source, unit = 'floatdegrees') add_quantity(name, 'dec', row[-2], source, unit = 'floatdegrees') if r == 1: error = row[4] if float(row[4]) >= 0.0 else '' add_quantity(name, 'redshift', row[2], source, error = error, kind = 'heliocentric') if r >= 19: # Skip bad measurements if int(row[0]) > 1024: continue mjd = row[1] band = sdssbands[int(row[2])] magnitude = row[3] e_magnitude = row[4] telescope = "SDSS" add_photometry(name, time = mjd, telescope = telescope, band = band, magnitude = magnitude, e_magnitude = e_magnitude, source = source, system = "SDSS") f.close() journal_events() #Import GAIA if do_task(task, 'gaia'): fname = '../sne-external/GAIA/alerts.csv' csvtxt = load_cached_url('http://gsaweb.ast.cam.ac.uk/alerts/alerts.csv', fname) if not csvtxt: continue tsvin = csv.reader(csvtxt.splitlines(), delimiter=',', skipinitialspace=True) reference = "Gaia Photometric Science Alerts" refurl = "http://gsaweb.ast.cam.ac.uk/alerts/alertsindex" for ri, row in enumerate(tq(tsvin, currenttask)): if ri == 0 or not row: continue name = add_event(row[0]) source = add_source(name, refname = reference, url = refurl) add_quantity(name, 'alias', name, source) year = '20' + re.findall(r'\d+', row[0])[0] add_quantity(name, 'discoverdate', year, source) add_quantity(name, 'ra', row[2], source, unit = 'floatdegrees') add_quantity(name, 'dec', row[3], source, unit = 'floatdegrees') if row[7] and row[7] != 'unknown': add_quantity(name, 'claimedtype', row[7].replace('SNe', '').replace('SN', '').strip(), source) elif (True in [x in row[9].upper() for x in ['SN CANDIATE', 'CANDIDATE SN', 'HOSTLESS SN']]): add_quantity(name, 'claimedtype', 'Candidate', source) if 'aka' in row[9].replace('gakaxy','galaxy').lower() and 'AKARI' not in row[9]: commentsplit = (row[9].replace('_', ' ').replace('MLS ', 'MLS').replace('CSS ', 'CSS'). replace('SN iPTF', 'iPTF').replace('SN ', 'SN').replace('AT ', 'AT').split()) for csi, cs in enumerate(commentsplit): if 'aka' in cs.lower() and csi < len(commentsplit) - 1: alias = commentsplit[csi+1].strip('(),:.').replace('PSNJ', 'PSN J') if alias[:6] == 'ASASSN' and alias[6] != '-': alias = 'ASASSN-' + alias[6:] add_quantity(name, 'alias', alias, source) break fname = '../sne-external/GAIA/' + row[0] + '.csv' if not args.fullrefresh and archived_task('gaia') and os.path.isfile(fname): with open(fname, 'r') as f: csvtxt = f.read() else: response = urllib.request.urlopen("http://gsaweb.ast.cam.ac.uk/alerts/alert/" + row[0] + "/lightcurve.csv") with open(fname, 'w') as f: csvtxt = response.read().decode('utf-8') f.write(csvtxt) tsvin2 = csv.reader(csvtxt.splitlines()) for ri2, row2 in enumerate(tsvin2): if ri2 <= 1 or not row2: continue mjd = str(jd_to_mjd(Decimal(row2[1].strip()))) magnitude = row2[2].strip() if magnitude == 'null': continue e_magnitude = 0. telescope = 'GAIA' band = 'G' add_photometry(name, time = mjd, telescope = telescope, band = band, magnitude = magnitude, e_magnitude = e_magnitude, source = source) if args.update: journal_events() journal_events() # Import CSP # VizieR catalogs exist for this: J/AJ/139/519, J/AJ/142/156. Should replace eventually. if do_task(task, 'csp'): cspbands = ['u', 'B', 'V', 'g', 'r', 'i', 'Y', 'J', 'H', 'K'] for fname in tq(sorted(glob("../sne-external/CSP/*.dat"), key=lambda s: s.lower()), currenttask): f = open(fname,'r') tsvin = csv.reader(f, delimiter='\t', skipinitialspace=True) eventname = os.path.basename(os.path.splitext(fname)[0]) eventparts = eventname.split('opt+') name = snname(eventparts[0]) name = add_event(name) reference = "Carnegie Supernova Project" refbib = "2010AJ....139..519C" refurl = "http://csp.obs.carnegiescience.edu/data" source = add_source(name, bibcode = refbib, refname = reference, url = refurl) add_quantity(name, 'alias', name, source) year = re.findall(r'\d+', name)[0] add_quantity(name, 'discoverdate', year, source) for r, row in enumerate(tsvin): if len(row) > 0 and row[0][0] == "#": if r == 2: add_quantity(name, 'redshift', row[0].split(' ')[-1], source, kind = 'cmb') add_quantity(name, 'ra', row[1].split(' ')[-1], source) add_quantity(name, 'dec', row[2].split(' ')[-1], source) continue for v, val in enumerate(row): if v == 0: mjd = val elif v % 2 != 0: if float(row[v]) < 90.0: add_photometry(name, time = mjd, observatory = 'LCO', band = cspbands[(v-1)//2], system = 'CSP', magnitude = row[v], e_magnitude = row[v+1], source = source) f.close() journal_events() # Import ITEP if do_task(task, 'itep'): itepbadsources = ['2004ApJ...602..571B'] needsbib = [] with open("../sne-external/itep-refs.txt",'r') as f: refrep = f.read().splitlines() refrepf = dict(list(zip(refrep[1::2], refrep[::2]))) f = open("../sne-external/itep-lc-cat-28dec2015.txt",'r') tsvin = csv.reader(f, delimiter='|', skipinitialspace=True) curname = '' for r, row in enumerate(tq(tsvin, currenttask)): if r <= 1 or len(row) < 7: continue name = 'SN' + row[0].strip() mjd = str(jd_to_mjd(Decimal(row[1].strip()))) band = row[2].strip() magnitude = row[3].strip() e_magnitude = row[4].strip() reference = row[6].strip().strip(',') if curname != name: curname = name name = add_event(name) secondaryreference = "Sternberg Astronomical Institute Supernova Light Curve Catalogue" secondaryrefurl = "http://dau.itep.ru/sn/node/72" secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, secondary = True) add_quantity(name, 'alias', name, secondarysource) year = re.findall(r'\d+', name)[0] add_quantity(name, 'discoverdate', year, secondarysource) if reference in refrepf: bibcode = unescape(refrepf[reference]) source = add_source(name, bibcode = bibcode) else: needsbib.append(reference) source = add_source(name, refname = reference) if reference else '' if bibcode not in itepbadsources: add_photometry(name, time = mjd, band = band, magnitude = magnitude, e_magnitude = e_magnitude, source = secondarysource + ',' + source) f.close() # Write out references that could use a bibcode needsbib = list(OrderedDict.fromkeys(needsbib)) with open('../itep-needsbib.txt', 'w') as f: f.writelines(["%s\n" % i for i in needsbib]) journal_events() # Now import the Asiago catalog if do_task(task, 'asiago'): #response = urllib.request.urlopen('http://graspa.oapd.inaf.it/cgi-bin/sncat.php') path = os.path.abspath('../sne-external/asiago-cat.php') response = urllib.request.urlopen('file://' + path) html = response.read().decode('utf-8') html = html.replace("\r", "") soup = BeautifulSoup(html, "html5lib") table = soup.find("table") records = [] for r, row in enumerate(table.findAll('tr')): if r == 0: continue col = row.findAll('td') records.append([utf8(x.renderContents()) for x in col]) for record in tq(records, currenttask): if len(record) > 1 and record[1] != '': name = snname("SN" + record[1]).strip('?') name = add_event(name) reference = 'Asiago Supernova Catalogue' refurl = 'http://graspa.oapd.inaf.it/cgi-bin/sncat.php' refbib = '1989A&AS...81..421B' source = add_source(name, refname = reference, url = refurl, bibcode = refbib, secondary = True) add_quantity(name, 'alias', name, source) year = re.findall(r'\d+', name)[0] add_quantity(name, 'discoverdate', year, source) hostname = record[2] hostra = record[3] hostdec = record[4] ra = record[5].strip(':') dec = record[6].strip(':') redvel = record[11].strip(':') discoverer = record[19] datestring = year monthday = record[18] if "*" in monthday: datekey = 'discover' else: datekey = 'max' if monthday.strip() != '': monthstr = ''.join(re.findall("[a-zA-Z]+", monthday)) monthstr = str(list(calendar.month_abbr).index(monthstr)) datestring = datestring + '/' + monthstr dayarr = re.findall(r'\d+', monthday) if dayarr: daystr = dayarr[0] datestring = datestring + '/' + daystr add_quantity(name, datekey + 'date', datestring, source) velocity = '' redshift = '' if redvel != '': if round(float(redvel)) == float(redvel): velocity = int(redvel) else: redshift = float(redvel) redshift = str(redshift) velocity = str(velocity) claimedtype = record[17].replace(':', '').replace('*', '').strip() if (hostname != ''): add_quantity(name, 'host', hostname, source) if (claimedtype != ''): add_quantity(name, 'claimedtype', claimedtype, source) if (redshift != ''): add_quantity(name, 'redshift', redshift, source, kind = 'host') if (velocity != ''): add_quantity(name, 'velocity', velocity, source, kind = 'host') if (hostra != ''): add_quantity(name, 'hostra', hostra, source, unit = 'nospace') if (hostdec != ''): add_quantity(name, 'hostdec', hostdec, source, unit = 'nospace') if (ra != ''): add_quantity(name, 'ra', ra, source, unit = 'nospace') if (dec != ''): add_quantity(name, 'dec', dec, source, unit = 'nospace') if (discoverer != ''): add_quantity(name, 'discoverer', discoverer, source) journal_events() if do_task(task, 'lennarz'): Vizier.ROW_LIMIT = -1 result = Vizier.get_catalogs("J/A+A/538/A120/usc") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) bibcode = "2012A&A...538A.120L" for row in tq(table, currenttask): row = convert_aq_output(row) name = 'SN' + row['SN'] name = add_event(name) source = add_source(name, bibcode = bibcode) add_quantity(name, 'alias', name, source) if row['RAJ2000']: add_quantity(name, 'ra', row['RAJ2000'], source) if row['DEJ2000']: add_quantity(name, 'dec', row['DEJ2000'], source) if row['RAG']: add_quantity(name, 'hostra', row['RAG'], source) if row['DEG']: add_quantity(name, 'hostdec', row['DEG'], source) if row['Gal']: add_quantity(name, 'host', row['Gal'], source) if row['Type']: claimedtypes = row['Type'].split('|') for claimedtype in claimedtypes: add_quantity(name, 'claimedtype', claimedtype.strip(' -'), source) if row['z']: if name not in ['SN1985D', 'SN2004cq']: add_quantity(name, 'redshift', row['z'], source, kind = 'host') if row['Dist']: if row['e_Dist']: add_quantity(name, 'lumdist', row['Dist'], source, error = row['e_Dist'], kind = 'host') else: add_quantity(name, 'lumdist', row['Dist'], source, kind = 'host') if row['Ddate']: datestring = row['Ddate'].replace('-', '/') add_quantity(name, 'discoverdate', datestring, source) if 'photometry' not in events[name]: if 'Dmag' in row and is_number(row['Dmag']) and not isnan(float(row['Dmag'])): datesplit = row['Ddate'].strip().split('-') if len(datesplit) == 3: datestr = row['Ddate'].strip() elif len(datesplit) == 2: datestr = row['Ddate'].strip() + '-01' elif len(datesplit) == 1: datestr = row['Ddate'].strip() + '-01-01' mjd = str(astrotime(datestr).mjd) add_photometry(name, time = mjd, band = row['Dband'], magnitude = row['Dmag'], source = source) if row['Mdate']: datestring = row['Mdate'].replace('-', '/') add_quantity(name, 'maxdate', datestring, source) if 'photometry' not in events[name]: if 'MMag' in row and is_number(row['MMag']) and not isnan(float(row['MMag'])): datesplit = row['Mdate'].strip().split('-') if len(datesplit) == 3: datestr = row['Mdate'].strip() elif len(datesplit) == 2: datestr = row['Mdate'].strip() + '-01' elif len(datesplit) == 1: datestr = row['Mdate'].strip() + '-01-01' mjd = str(astrotime(datestr).mjd) add_photometry(name, time = mjd, band = row['Mband'], magnitude = row['Mmag'], source = source) f.close() journal_events() if do_task(task, 'fermi'): with open("../sne-external/1SC_catalog_v01.asc", 'r') as f: tsvin = csv.reader(f, delimiter=',') for ri, row in enumerate(tq(tsvin, currenttask)): if row[0].startswith('#'): if len(row) > 1 and 'UPPER_LIMITS' in row[1]: break continue if 'Classified' not in row[1]: continue name = row[0].replace('SNR', 'G') name = add_event(name) source = add_source(name, bibcode = '2016ApJS..224....8A') add_quantity(name, 'alias', name, source) add_quantity(name, 'alias', row[0].replace('SNR', 'MWSNR'), source) add_quantity(name, 'ra', row[2], source, unit = 'floatdegrees') add_quantity(name, 'dec', row[3], source, unit = 'floatdegrees') journal_events() if do_task(task, 'tns'): session = requests.Session() csvtxt = load_cached_url("https://wis-tns.weizmann.ac.il/search?&num_page=1&format=html&sort=desc&order=id&format=csv&page=0", "../sne-external/TNS/index.csv") if not csvtxt: continue maxid = csvtxt.splitlines()[1].split(",")[0].strip('"') maxpages = ceil(int(maxid)/1000.) for page in tq(range(maxpages), currenttask): fname = '../sne-external/TNS/page-' + str(page).zfill(2) + '.csv' if archived_task('tns') and os.path.isfile(fname) and page < 7: with open(fname, 'r') as f: csvtxt = f.read() else: with open(fname, 'w') as f: session = requests.Session() response = session.get("https://wis-tns.weizmann.ac.il/search?&num_page=1000&format=html&edit[type]=&edit[objname]=&edit[id]=&sort=asc&order=id&display[redshift]=1&display[hostname]=1&display[host_redshift]=1&display[source_group_name]=1&display[programs_name]=1&display[internal_name]=1&display[isTNS_AT]=1&display[public]=1&display[end_pop_period]=0&display[spectra_count]=1&display[discoverymag]=1&display[discmagfilter]=1&display[discoverydate]=1&display[discoverer]=1&display[sources]=1&display[bibcode]=1&format=csv&page=" + str(page)) csvtxt = response.text f.write(csvtxt) tsvin = csv.reader(csvtxt.splitlines(), delimiter=',') for ri, row in enumerate(tq(tsvin, currenttask, leave = False)): if ri == 0: continue if row[4] and 'SN' not in row[4]: continue name = row[1].replace(' ', '') name = add_event(name) source = add_source(name, refname = 'Transient Name Server', url = 'https://wis-tns.weizmann.ac.il') add_quantity(name, 'alias', name, source) if row[2] and row[2] != '00:00:00.00': add_quantity(name, 'ra', row[2], source) if row[3] and row[3] != '+00:00:00.00': add_quantity(name, 'dec', row[3], source) if row[4]: add_quantity(name, 'claimedtype', row[4].replace('SN', '').strip(), source) if row[5]: add_quantity(name, 'redshift', row[5], source, kind = 'spectroscopic') if row[6]: add_quantity(name, 'host', row[6], source) if row[7]: add_quantity(name, 'redshift', row[7], source, kind = 'host') if row[8]: add_quantity(name, 'discoverer', row[8], source) # Currently, all events listing all possible observers. TNS bug? #if row[9]: # observers = row[9].split(',') # for observer in observers: # add_quantity(name, 'observer', observer.strip(), source) if row[10]: add_quantity(name, 'alias', row[10], source) if row[8] and row[14] and row[15] and row[16]: survey = row[8] magnitude = row[14] band = row[15].split('-')[0] mjd = astrotime(row[16]).mjd add_photometry(name, time = mjd, magnitude = magnitude, band = band, survey = survey, source = source) if row[16]: date = row[16].split()[0].replace('-', '/') if date != '0000/00/00': date = date.replace('/00', '') time = row[16].split()[1] if time != '00:00:00': ts = time.split(':') date += pretty_num(timedelta(hours = int(ts[0]), minutes = int(ts[1]), seconds = int(ts[2])).total_seconds()/(24*60*60), sig=6).lstrip('0') add_quantity(name, 'discoverdate', date, source) if args.update: journal_events() journal_events() if do_task(task, 'rochester'): rochesterpaths = ['http://www.rochesterastronomy.org/snimages/snredshiftall.html', 'http://www.rochesterastronomy.org/sn2016/snredshift.html'] rochesterupdate = [False, True] for p, path in enumerate(tq(rochesterpaths, currenttask)): if args.update and not rochesterupdate[p]: continue filepath = '../sne-external/rochester/' + os.path.basename(path) html = load_cached_url(path, filepath) if not html: continue soup = BeautifulSoup(html, "html5lib") rows = soup.findAll('tr') secondaryreference = "Latest Supernovae" secondaryrefurl = "http://www.rochesterastronomy.org/snimages/snredshiftall.html" for r, row in enumerate(tq(rows, currenttask)): if r == 0: continue cols = row.findAll('td') if not len(cols): continue name = '' if cols[14].contents: aka = str(cols[14].contents[0]).strip() if is_number(aka.strip('?')): aka = 'SN' + aka.strip('?') + 'A' name = add_event(aka) elif len(aka) >= 4 and is_number(aka[:4]): aka = 'SN' + aka name = add_event(aka) ra = str(cols[3].contents[0]).strip() dec = str(cols[4].contents[0]).strip() sn = re.sub('<[^<]+?>', '', str(cols[0].contents[0])).strip() if is_number(sn.strip('?')): sn = 'SN' + sn.strip('?') + 'A' elif len(sn) >= 4 and is_number(sn[:4]): sn = 'SN' + sn if not name: if not sn: continue if sn[:8] == 'MASTER J': sn = sn.replace('MASTER J', 'MASTER OT J').replace('SNHunt', 'SNhunt') if 'POSSIBLE' in sn.upper() and ra and dec: sn = 'PSN J' + ra.replace(':', '').replace('.', '') + dec.replace(':', '').replace('.', '') name = add_event(sn) reference = cols[12].findAll('a')[0].contents[0].strip() refurl = cols[12].findAll('a')[0]['href'].strip() source = add_source(name, refname = reference, url = refurl) secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, secondary = True) sources = uniq_cdl(list(filter(None, [source, secondarysource]))) add_quantity(name, 'alias', name, sources) add_quantity(name, 'alias', sn, sources) if cols[14].contents: if aka == 'SNR G1.9+0.3': aka = 'G001.9+00.3' if aka[:4] == 'PS1 ': aka = 'PS1-' + aka[4:] if aka[:8] == 'MASTER J': aka = aka.replace('MASTER J', 'MASTER OT J').replace('SNHunt', 'SNhunt') if 'POSSIBLE' in aka.upper() and ra and dec: aka = 'PSN J' + ra.replace(':', '').replace('.', '') + dec.replace(':', '').replace('.', '') add_quantity(name, 'alias', aka, sources) if str(cols[1].contents[0]).strip() != 'unk': add_quantity(name, 'claimedtype', str(cols[1].contents[0]).strip(' :,'), sources) if str(cols[2].contents[0]).strip() != 'anonymous': add_quantity(name, 'host', str(cols[2].contents[0]).strip(), sources) add_quantity(name, 'ra', ra, sources) add_quantity(name, 'dec', dec, sources) if str(cols[6].contents[0]).strip() not in ['2440587', '2440587.292']: astrot = astrotime(float(str(cols[6].contents[0]).strip()), format='jd').datetime add_quantity(name, 'discoverdate', make_date_string(astrot.year, astrot.month, astrot.day), sources) if str(cols[7].contents[0]).strip() not in ['2440587', '2440587.292']: astrot = astrotime(float(str(cols[7].contents[0]).strip()), format='jd') if (float(str(cols[8].contents[0]).strip()) <= 90.0 and not any('GRB' in x for x in get_aliases(name))): add_photometry(name, time = str(astrot.mjd), magnitude = str(cols[8].contents[0]).strip(), source = sources) if cols[11].contents[0] != 'n/a': add_quantity(name, 'redshift', str(cols[11].contents[0]).strip(), sources) add_quantity(name, 'discoverer', str(cols[13].contents[0]).strip(), sources) if args.update: journal_events() if not args.update: vsnetfiles = ["latestsne.dat"] for vsnetfile in vsnetfiles: f = open("../sne-external/" + vsnetfile,'r',encoding='latin1') tsvin = csv.reader(f, delimiter=' ', skipinitialspace=True) for r, row in enumerate(tsvin): if not row or row[0][:4] in ['http', 'www.'] or len(row) < 3: continue name = row[0].strip() if name[:4].isdigit(): name = 'SN' + name if name.startswith('PSNJ'): name = 'PSN J' + name[4:] if name.startswith('MASTEROTJ'): name = name.replace('MASTEROTJ', 'MASTER OT J') name = add_event(name) secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, secondary = True) add_quantity(name, 'alias', name, secondarysource) if not is_number(row[1]): continue year = row[1][:4] month = row[1][4:6] day = row[1][6:] if '.' not in day: day = day[:2] + '.' + day[2:] mjd = astrotime(year + '-' + month + '-' + str(floor(float(day))).zfill(2)).mjd + float(day) - floor(float(day)) magnitude = row[2].rstrip(ascii_letters) if not is_number(magnitude): continue if magnitude.isdigit(): if int(magnitude) > 100: magnitude = magnitude[:2] + '.' + magnitude[2:] if float(str(cols[8].contents[0]).strip()) >= 90.0: continue if len(row) >= 4: if is_number(row[3]): e_magnitude = row[3] refind = 4 else: e_magnitude = '' refind = 3 if refind >= len(row): sources = secondarysource else: reference = ' '.join(row[refind:]) source = add_source(name, refname = reference) add_quantity(name, 'alias', name, secondarysource) sources = uniq_cdl([source,secondarysource]) else: sources = secondarysource band = row[2].lstrip('1234567890.') add_photometry(name, time = mjd, band = band, magnitude = magnitude, e_magnitude = e_magnitude, source = sources) f.close() journal_events() if do_task(task, 'ogle'): basenames = ['transients', 'transients/2014b', 'transients/2014', 'transients/2013', 'transients/2012'] oglenames = [] ogleupdate = [True, False, False, False, False] for b, bn in enumerate(tq(basenames, currenttask)): if args.update and not ogleupdate[b]: continue filepath = '../sne-external/OGLE-' + bn.replace('/', '-') + '-transients.html' htmltxt = load_cached_url('http://ogle.astrouw.edu.pl/ogle4/' + bn + '/transients.html', filepath) if not htmltxt: continue soup = BeautifulSoup(htmltxt, "html5lib") links = soup.findAll('a') breaks = soup.findAll('br') datalinks = [] datafnames = [] for a in links: if a.has_attr('href'): if '.dat' in a['href']: datalinks.append('http://ogle.astrouw.edu.pl/ogle4/' + bn + '/' + a['href']) datafnames.append(bn.replace('/', '-') + '-' + a['href'].replace('/', '-')) ec = -1 reference = 'OGLE-IV Transient Detection System' refurl = 'http://ogle.astrouw.edu.pl/ogle4/transients/transients.html' for br in tq(breaks, currenttask): sibling = br.nextSibling if 'Ra,Dec=' in sibling: line = sibling.replace("\n", '').split('Ra,Dec=') name = line[0].strip() ec += 1 if 'NOVA' in name or 'dupl' in name: continue if name in oglenames: continue oglenames.append(name) name = add_event(name) mySibling = sibling.nextSibling atelref = '' claimedtype = '' while 'Ra,Dec=' not in mySibling: if isinstance(mySibling, NavigableString): if 'Phot.class=' in str(mySibling): claimedtype = re.sub(r'\([^)]*\)', '', str(mySibling).split('=')[-1]).replace('SN','').strip() if isinstance(mySibling, Tag): atela = mySibling if atela and atela.has_attr('href') and 'astronomerstelegram' in atela['href']: atelref = atela.contents[0].strip() atelurl = atela['href'] mySibling = mySibling.nextSibling if mySibling is None: break nextSibling = sibling.nextSibling if isinstance(nextSibling, Tag) and nextSibling.has_attr('alt') and nextSibling.contents[0].strip() != 'NED': radec = nextSibling.contents[0].strip().split() else: radec = line[-1].split() ra = radec[0] dec = radec[1] fname = '../sne-external/OGLE/' + datafnames[ec] if not args.fullrefresh and archived_task('ogle') and os.path.isfile(fname): with open(fname, 'r') as f: csvtxt = f.read() else: response = urllib.request.urlopen(datalinks[ec]) with open(fname, 'w') as f: csvtxt = response.read().decode('utf-8') f.write(csvtxt) lcdat = csvtxt.splitlines() sources = [add_source(name, refname = reference, url = refurl)] add_quantity(name, 'alias', name, sources[0]) if atelref and atelref != 'ATel#----': sources.append(add_source(name, refname = atelref, url = atelurl)) sources = uniq_cdl(sources) if name.startswith('OGLE'): if name[4] == '-': if is_number(name[5:9]): add_quantity(name, 'discoverdate', name[5:9], sources) else: if is_number(name[4:6]): add_quantity(name, 'discoverdate', '20' + name[4:6], sources) # RA and Dec from OGLE pages currently not reliable #add_quantity(name, 'ra', ra, sources) #add_quantity(name, 'dec', dec, sources) if claimedtype and claimedtype != '-': add_quantity(name, 'claimedtype', claimedtype, sources) elif 'SN' not in name and 'claimedtype' not in events[name]: add_quantity(name, 'claimedtype', 'Candidate', sources) for row in lcdat: row = row.split() mjd = str(jd_to_mjd(Decimal(row[0]))) magnitude = row[1] if float(magnitude) > 90.0: continue e_magnitude = row[2] upperlimit = False if e_magnitude == '-1' or float(e_magnitude) > 10.0: e_magnitude = '' upperlimit = True add_photometry(name, time = mjd, band = 'I', magnitude = magnitude, e_magnitude = e_magnitude, system = 'Vega', source = sources, upperlimit = upperlimit) if args.update: journal_events() journal_events() if do_task(task, 'snls'): with open("../sne-external/SNLS-ugriz.dat", 'r') as f: data = csv.reader(f, delimiter=' ', quotechar='"', skipinitialspace = True) for row in data: flux = row[3] err = row[4] # Being extra strict here with the flux constraint, see note below. if float(flux) < 3.0*float(err): continue name = 'SNLS-' + row[0] name = add_event(name) source = add_source(name, bibcode = '2010A&A...523A...7G') add_quantity(name, 'alias', name, source) band = row[1] mjd = row[2] sig = get_sig_digits(flux.split('E')[0])+1 # Conversion comes from SNLS-Readme # NOTE: Datafiles available for download suggest different zeropoints than 30, need to inquire. magnitude = pretty_num(30.0-2.5*log10(float(flux)), sig = sig) e_magnitude = pretty_num(2.5*log10(1.0 + float(err)/float(flux)), sig = sig) #e_magnitude = pretty_num(2.5*(log10(float(flux) + float(err)) - log10(float(flux))), sig = sig) add_photometry(name, time = mjd, band = band, magnitude = magnitude, e_magnitude = e_magnitude, counts = flux, e_counts = err, source = source) journal_events() if do_task(task, 'psthreepi'): fname = '../sne-external/3pi/page00.html' html = load_cached_url("http://psweb.mp.qub.ac.uk/ps1threepi/psdb/public/?page=1&sort=followup_flag_date", fname, write = False) if not html: continue bs = BeautifulSoup(html, "html5lib") div = bs.find('div', {"class":"pagination"}) offline = False if not div: offline = True else: links = div.findAll('a') if not links: offline = True if offline: if args.update: continue warnings.warn("Pan-STARRS 3pi offline, using local files only.") with open(fname, 'r') as f: html = f.read() bs = BeautifulSoup(html, "html5lib") div = bs.find('div', {"class":"pagination"}) links = div.findAll('a') else: with open(fname, 'w') as f: f.write(html) numpages = int(links[-2].contents[0]) oldnumpages = len(glob('../sne-external/3pi/page*')) for page in tq(range(1,numpages), currenttask): fname = '../sne-external/3pi/page' + str(page).zfill(2) + '.html' if not args.fullrefresh and archived_task('psthreepi') and os.path.isfile(fname) and page < oldnumpages: with open(fname, 'r') as f: html = f.read() elif not offline: response = urllib.request.urlopen("http://psweb.mp.qub.ac.uk/ps1threepi/psdb/public/?page=" + str(page) + "&sort=followup_flag_date") with open(fname, 'w') as f: html = response.read().decode('utf-8') f.write(html) else: continue bs = BeautifulSoup(html, "html5lib") trs = bs.findAll('tr') for tr in tq(trs, currenttask): tds = tr.findAll('td') if not tds: continue refs = [] aliases = [] ttype = '' ctype = '' for tdi, td in enumerate(tds): if tdi == 0: psname = td.contents[0] pslink = psname['href'] psname = psname.text elif tdi == 1: ra = td.contents[0] elif tdi == 2: dec = td.contents[0] elif tdi == 3: ttype = td.contents[0] if ttype != 'sn' and ttype != 'orphan': break elif tdi == 5: if not td.contents: continue ctype = td.contents[0] if ctype == 'Observed': ctype = '' elif tdi == 16: if td.contents: crossrefs = td.findAll('a') for cref in crossrefs: if 'atel' in cref.contents[0].lower(): refs.append([cref.contents[0], cref['href']]) elif is_number(cref.contents[0][:4]): continue else: aliases.append(cref.contents[0]) if ttype != 'sn' and ttype != 'orphan': continue name = '' for alias in aliases: if alias[:2] == 'SN': name = alias if not name: name = psname name = add_event(name) sources = [add_source(name, refname = 'Pan-STARRS 3Pi', url = 'http://psweb.mp.qub.ac.uk/ps1threepi/psdb/')] add_quantity(name, 'alias', name, sources[0]) for ref in refs: sources.append(add_source(name, refname = ref[0], url = ref[1])) source = uniq_cdl(sources) for alias in aliases: newalias = alias if alias[:3] in ['CSS', 'SSS', 'MLS']: newalias = alias.replace('-', ':', 1) newalias = newalias.replace('PSNJ', 'PSN J') add_quantity(name, 'alias', newalias, source) add_quantity(name, 'ra', ra, source) add_quantity(name, 'dec', dec, source) add_quantity(name, 'claimedtype', ctype, source) fname2 = '../sne-external/3pi/candidate-' + pslink.rstrip('/').split('/')[-1] + '.html' if archived_task('psthreepi') and os.path.isfile(fname2): with open(fname2, 'r') as f: html2 = f.read() elif not offline: pslink = 'http://psweb.mp.qub.ac.uk/ps1threepi/psdb/public/' + pslink with open(fname2, 'w') as f: response2 = urllib.request.urlopen(pslink) html2 = response2.read().decode('utf-8') f.write(html2) else: continue bs2 = BeautifulSoup(html2, "html5lib") scripts = bs2.findAll('script') nslines = [] nslabels = [] for script in scripts: if 'jslcdata.push' not in script.text: continue slines = script.text.splitlines() for line in slines: if 'jslcdata.push' in line: nslines.append(json.loads(line.strip().replace('jslcdata.push(','').replace(');',''))) if 'jslabels.push' in line and 'blanks' not in line and 'non det' not in line: nslabels.append(json.loads(line.strip().replace('jslabels.push(','').replace(');',''))['label']) for li, line in enumerate(nslines[:len(nslabels)]): if not line: continue for obs in line: add_photometry(name, time = str(obs[0]), band = nslabels[li], magnitude = str(obs[1]), e_magnitude = str(obs[2]), source = source, telescope = 'Pan-STARRS1') for li, line in enumerate(nslines[2*len(nslabels):]): if not line: continue for obs in line: add_photometry(name, time = str(obs[0]), band = nslabels[li], magnitude = str(obs[1]), upperlimit = True, source = source, telescope = 'Pan-STARRS1') assoctab = bs2.find('table', {"class":"generictable"}) hostname = '' redshift = '' if assoctab: trs = assoctab.findAll('tr') headertds = [x.contents[0] for x in trs[1].findAll('td')] tds = trs[1].findAll('td') for tdi, td in enumerate(tds): if tdi == 1: hostname = td.contents[0].strip() elif tdi == 4: if 'z' in headertds: redshift = td.contents[0].strip() # Skip galaxies with just SDSS id if is_number(hostname): continue add_quantity(name, 'host', hostname, source) if redshift: add_quantity(name, 'redshift', redshift, source, kind = 'host') if args.update: journal_events() journal_events() if do_task(task, 'psmds'): with open('../sne-external/MDS/apj506838t1_mrt.txt') as f: for ri, row in enumerate(tq(f.read().splitlines(), currenttask)): if ri < 35: continue cols = [x.strip() for x in row.split(',')] name = add_event(cols[0]) source = add_source(name, bibcode = '2015ApJ...799..208S') add_quantity(name, 'alias', name, source) add_quantity(name, 'ra', cols[2], source) add_quantity(name, 'dec', cols[3], source) astrot = astrotime(float(cols[4]), format='mjd').datetime add_quantity(name, 'discoverdate', make_date_string(astrot.year, astrot.month, astrot.day), source) add_quantity(name, 'redshift', cols[5], source, kind = 'spectroscopic') add_quantity(name, 'claimedtype', 'II P', source) journal_events() if do_task(task, 'crts'): crtsnameerrors = ['2011ax'] folders = ["catalina", "MLS", "SSS"] for fold in tq(folders, currenttask): html = load_cached_url("http://nesssi.cacr.caltech.edu/" + fold + "/AllSN.html", '../sne-external/CRTS/' + fold + '.html') if not html: continue bs = BeautifulSoup(html, "html5lib") trs = bs.findAll('tr') for tr in tq(trs, currenttask): tds = tr.findAll('td') if not tds: continue refs = [] aliases = [] ttype = '' ctype = '' for tdi, td in enumerate(tds): if tdi == 0: crtsname = td.contents[0].text.strip() elif tdi == 1: ra = td.contents[0] elif tdi == 2: dec = td.contents[0] elif tdi == 11: lclink = td.find('a')['onclick'] lclink = lclink.split("'")[1] elif tdi == 13: aliases = re.sub('[()]', '', re.sub('<[^<]+?>', '', td.contents[-1].strip())) aliases = [x.strip('; ') for x in list(filter(None, aliases.split(' ')))] name = '' hostmag = '' hostupper = False validaliases = [] for ai, alias in enumerate(aliases): if alias in ['SN', 'SDSS']: continue if alias in crtsnameerrors: continue if alias == 'mag': if ai < len(aliases) - 1: ind = ai+1 if aliases[ai+1] in ['SDSS']: ind = ai+2 elif aliases[ai+1] in ['gal', 'obj', 'object', 'source']: ind = ai-1 if '>' in aliases[ind]: hostupper = True hostmag = aliases[ind].strip('>~').replace(',', '.') continue if is_number(alias[:4]) and alias[:2] == '20' and len(alias) > 4: name = 'SN' + alias lalias = alias.lower() if (('asassn' in alias and len(alias) > 6) or ('ptf' in alias and len(alias) > 3) or ('ps1' in alias and len(alias) > 3) or 'snhunt' in alias or ('mls' in alias and len(alias) > 3) or 'gaia' in alias or ('lsq' in alias and len(alias) > 3)): alias = alias.replace('SNHunt', 'SNhunt') validaliases.append(alias) if not name: name = crtsname name = add_event(name) source = add_source(name, refname = 'Catalina Sky Survey', bibcode = '2009ApJ...696..870D', url = 'http://nesssi.cacr.caltech.edu/catalina/AllSN.html') add_quantity(name, 'alias', name, source) for alias in validaliases: add_quantity(name, 'alias', alias, source) add_quantity(name, 'ra', ra, source, unit = 'floatdegrees') add_quantity(name, 'dec', dec, source, unit = 'floatdegrees') if hostmag: # 1.0 magnitude error based on Drake 2009 assertion that SN are only considered real if they are 2 mags brighter than host. add_photometry(name, band = 'C', magnitude = hostmag, e_magnitude = 1.0, source = source, host = True, telescope = 'Catalina Schmidt', upperlimit = hostupper) fname2 = '../sne-external/' + fold + '/' + lclink.split('.')[-2].rstrip('p').split('/')[-1] + '.html' if not args.fullrefresh and archived_task('crts') and os.path.isfile(fname2): with open(fname2, 'r') as f: html2 = f.read() else: with open(fname2, 'w') as f: response2 = urllib.request.urlopen(lclink) html2 = response2.read().decode('utf-8') f.write(html2) lines = html2.splitlines() for line in lines: if 'javascript:showx' in line: mjdstr = re.search("showx\('(.*?)'\)", line).group(1).split('(')[0].strip() if not is_number(mjdstr): continue mjd = str(Decimal(mjdstr) + Decimal(53249.0)) else: continue if 'javascript:showy' in line: mag = re.search("showy\('(.*?)'\)", line).group(1) if 'javascript:showz' in line: err = re.search("showz\('(.*?)'\)", line).group(1) add_photometry(name, time = mjd, band = 'C', magnitude = mag, source = source, includeshost = True, telescope = 'Catalina Schmidt', e_magnitude = err if float(err) > 0.0 else '', upperlimit = (float(err) == 0.0)) if args.update: journal_events() journal_events() if do_task(task, 'snhunt'): html = load_cached_url('http://nesssi.cacr.caltech.edu/catalina/current.html', '../sne-external/SNhunt/current.html') if not html: continue text = html.splitlines() findtable = False for ri, row in enumerate(text): if 'Supernova Discoveries' in row: findtable = True if findtable and '<table' in row: tstart = ri+1 if findtable and '</table>' in row: tend = ri-1 tablestr = '<html><body><table>' for row in text[tstart:tend]: if row[:3] == 'tr>': tablestr = tablestr + '<tr>' + row[3:] else: tablestr = tablestr + row tablestr = tablestr + '</table></body></html>' bs = BeautifulSoup(tablestr, 'html5lib') trs = bs.find('table').findAll('tr') for tr in tq(trs, currenttask): cols = [str(x.text) for x in tr.findAll('td')] if not cols: continue name = re.sub('<[^<]+?>', '', cols[4]).strip().replace(' ', '').replace('SNHunt', 'SNhunt') name = add_event(name) source = add_source(name, refname = 'Supernova Hunt', url = 'http://nesssi.cacr.caltech.edu/catalina/current.html') add_quantity(name, 'alias', name, source) host = re.sub('<[^<]+?>', '', cols[1]).strip().replace('_', ' ') add_quantity(name, 'host', host, source) add_quantity(name, 'ra', cols[2], source, unit = 'floatdegrees') add_quantity(name, 'dec', cols[3], source, unit = 'floatdegrees') dd = cols[0] discoverdate = dd[:4] + '/' + dd[4:6] + '/' + dd[6:8] add_quantity(name, 'discoverdate', discoverdate, source) discoverers = cols[5].split('/') for discoverer in discoverers: add_quantity(name, 'discoverer', 'CRTS', source) add_quantity(name, 'discoverer', discoverer, source) if args.update: journal_events() journal_events() if do_task(task, 'nedd'): f = open("../sne-external/NED25.12.1-D-10.4.0-20151123.csv", 'r') data = csv.reader(f, delimiter=',', quotechar='"') reference = "NED-D" refurl = "http://ned.ipac.caltech.edu/Library/Distances/" nedddict = OrderedDict() oldhostname = '' for r, row in enumerate(data): if r <= 12: continue hostname = row[3] if args.update and oldhostname != hostname: journal_events() distmod = row[4] moderr = row[5] dist = row[6] bibcode = unescape(row[8]) name = '' if hostname.startswith('SN '): if is_number(hostname[3:7]): name = 'SN' + hostname[3:] else: name = hostname[3:] elif hostname.startswith('SNLS '): name = 'SNLS-' + hostname[5:].split()[0] else: cleanhost = hostname.replace('MESSIER 0', 'M').replace('MESSIER ', 'M').strip() if True in [x in cleanhost for x in ['UGC', 'PGC', 'IC']]: cleanhost = ' '.join([x.lstrip('0') for x in cleanhost.split()]) if 'ESO' in cleanhost: cleanhost = cleanhost.replace(' ', '').replace('ESO', 'ESO ') nedddict.setdefault(cleanhost,[]).append(Decimal(dist)) if name: name = add_event(name) secondarysource = add_source(name, refname = reference, url = refurl, secondary = True) add_quantity(name, 'alias', name, secondarysource) if bibcode: source = add_source(name, bibcode = bibcode) sources = uniq_cdl([source, secondarysource]) else: sources = secondarysource add_quantity(name, 'comovingdist', dist, sources) oldhostname = hostname journal_events() # Import CPCS if do_task(task, 'cpcs'): jsontxt = load_cached_url("http://gsaweb.ast.cam.ac.uk/followup/list_of_alerts?format=json&num=100000&published=1&observed_only=1&hashtag=JG_530ad9462a0b8785bfb385614bf178c6", "../sne-external/CPCS/index.json") if not jsontxt: continue alertindex = json.loads(jsontxt, object_pairs_hook=OrderedDict) ids = [x["id"] for x in alertindex] for i, ai in enumerate(tq(ids, currenttask)): name = alertindex[i]['ivorn'].split('/')[-1].strip() # Skip a few weird entries if name == 'ASASSNli': continue # Just use a whitelist for now since naming seems inconsistent if True in [x in name.upper() for x in ['GAIA', 'OGLE', 'ASASSN', 'MASTER', 'OTJ', 'PS1', 'IPTF']]: name = name.replace('Verif', '').replace('_', ' ') if 'ASASSN' in name and name[6] != '-': name = 'ASASSN-' + name[6:] if 'MASTEROTJ' in name: name = name.replace('MASTEROTJ', 'MASTER OT J') if 'OTJ' in name: name = name.replace('OTJ', 'MASTER OT J') if name.upper().startswith('IPTF'): name = 'iPTF' + name[4:] # Only add events that are classified as SN. if event_exists(name): continue name = add_event(name) else: continue secondarysource = add_source(name, refname = 'Cambridge Photometric Calibration Server', url = 'http://gsaweb.ast.cam.ac.uk/followup/', secondary = True) add_quantity(name, 'alias', name, secondarysource) add_quantity(name, 'ra', str(alertindex[i]['ra']), secondarysource, unit = 'floatdegrees') add_quantity(name, 'dec', str(alertindex[i]['dec']), secondarysource, unit = 'floatdegrees') alerturl = "http://gsaweb.ast.cam.ac.uk/followup/get_alert_lc_data?alert_id=" + str(ai) source = add_source(name, refname = 'CPCS Alert ' + str(ai), url = alerturl) fname = '../sne-external/CPCS/alert-' + str(ai).zfill(2) + '.json' if archived_task('cpcs') and os.path.isfile(fname): with open(fname, 'r') as f: jsonstr = f.read() else: session = requests.Session() response = session.get(alerturl + "&hashtag=JG_530ad9462a0b8785bfb385614bf178c6") with open(fname, 'w') as f: jsonstr = response.text f.write(jsonstr) try: cpcsalert = json.loads(jsonstr) except: continue mjds = [round_sig(x, sig=9) for x in cpcsalert['mjd']] mags = [round_sig(x, sig=6) for x in cpcsalert['mag']] errs = [round_sig(x, sig=6) if (is_number(x) and float(x) > 0.0) else '' for x in cpcsalert['magerr']] bnds = cpcsalert['filter'] obs = cpcsalert['observatory'] for mi, mjd in enumerate(mjds): add_photometry(name, time = mjd, magnitude = mags[mi], e_magnitude = errs[mi], band = bnds[mi], observatory = obs[mi], source = uniq_cdl([source,secondarysource])) if args.update: journal_events() journal_events() if do_task(task, 'ptf'): #response = urllib.request.urlopen("http://wiserep.weizmann.ac.il/objects/list") #bs = BeautifulSoup(response, "html5lib") #select = bs.find('select', {"name":"objid"}) #options = select.findAll('option') #for option in options: # print(option.text) # name = option.text # if ((name.startswith('PTF') and is_number(name[3:5])) or # name.startswith('PTFS') or name.startswith('iPTF')): # name = add_event(name) if archived_task('ptf'): with open('../sne-external/PTF/update.html', 'r') as f: html = f.read() else: session = requests.Session() response = session.get("http://wiserep.weizmann.ac.il/spectra/update") html = response.text with open('../sne-external/PTF/update.html', 'w') as f: f.write(html) bs = BeautifulSoup(html, "html5lib") select = bs.find('select', {"name":"objid"}) options = select.findAll('option') for option in options: name = option.text if ((name.startswith('PTF') and is_number(name[3:5])) or name.startswith('PTFS') or name.startswith('iPTF')): if '(' in name: alias = name.split('(')[0].strip(' ') name = name.split('(')[-1].strip(') ').replace('sn', 'SN') name = add_event(name) source = add_source(name, bibcode = '2012PASP..124..668Y') add_quantity(name, 'alias', alias, source) else: name = add_event(name) with open('../sne-external/PTF/old-ptf-events.csv') as f: for suffix in f.read().splitlines(): name = add_event('PTF' + suffix) with open('../sne-external/PTF/perly-2016.csv') as f: for row in f.read().splitlines(): cols = [x.strip() for x in row.split(',')] alias = '' if cols[8]: name = cols[8] alias = 'PTF' + cols[0] else: name = 'PTF' + cols[0] name = add_event(name) source = add_source(name, bibcode = '2016arXiv160408207P') add_quantity(name, 'alias', name, source) if alias: add_quantity(name, 'alias', alias, source) add_quantity(name, 'ra', cols[1], source) add_quantity(name, 'dec', cols[2], source) add_quantity(name, 'claimedtype', 'SLSN-' + cols[3], source) add_quantity(name, 'redshift', cols[4], source, kind = 'spectroscopic') maxdate = cols[6].replace('-', '/') add_quantity(name, 'maxdate', maxdate.lstrip('<'), source, upperlimit = maxdate.startswith('<')) add_quantity(name, 'ebv', cols[7], source, kind = 'spectroscopic') name = add_event('PTF' + suffix) journal_events() if do_task(task, 'des'): html = load_cached_url("https://portal.nersc.gov/des-sn/transients/", "../sne-external/DES/transients.html") if not html: continue bs = BeautifulSoup(html, "html5lib") trs = bs.find('tbody').findAll('tr') for tri, tr in enumerate(tq(trs, currenttask)): name = '' source = '' if tri == 0: continue tds = tr.findAll('td') for tdi, td in enumerate(tds): if tdi == 0: name = add_event(td.text.strip()) if tdi == 1: (ra, dec) = [x.strip() for x in td.text.split('\xa0')] if tdi == 6: atellink = td.find('a') if atellink: atellink = atellink['href'] else: atellink = '' sources = [add_source(name, url = 'https://portal.nersc.gov/des-sn/', refname = 'DES Bright Transients', acknowledgment = 'http://www.noao.edu/noao/library/NOAO_Publications_Acknowledgments.html#DESdatause')] if atellink: sources.append(add_source(name, refname = 'ATel ' + atellink.split('=')[-1], url = atellink)) sources += [add_source(name, bibcode = '2012ApJ...753..152B'), add_source(name, bibcode = '2015AJ....150..150F'), add_source(name, bibcode = '2015AJ....150...82G'), add_source(name, bibcode = '2015AJ....150..172K')] sources = ','.join(sources) add_quantity(name, 'alias', name, sources) add_quantity(name, 'ra', ra, sources) add_quantity(name, 'dec', dec, sources) html2 = load_cached_url("https://portal.nersc.gov/des-sn/transients/" + name, "../sne-external/DES/" + name + ".html") if not html2: continue lines = html2.splitlines() for line in lines: if 'var data = ' in line: jsontxt = json.loads(line.split('=')[-1].rstrip(';')) for i, band in enumerate(jsontxt['band']): add_photometry(name, time = jsontxt['mjd'][i], magnitude = jsontxt['mag'][i], e_magnitude = jsontxt['mag_error'][i], band = band, observatory = 'CTIO', telescope = 'Blanco 4m', instrument = 'DECam', upperlimit = True if float(jsontxt['snr'][i]) <= 3.0 else '', source = sources) journal_events() if do_task(task, 'asassn'): html = load_cached_url("http://www.astronomy.ohio-state.edu/~assassin/sn_list.html", "../sne-external/ASASSN/sn_list.html") if not html: continue bs = BeautifulSoup(html, "html5lib") trs = bs.find('table').findAll('tr') for tri, tr in enumerate(tq(trs, currenttask)): name = '' source = '' ra = '' dec = '' redshift = '' hostoff = '' claimedtype = '' host = '' atellink = '' typelink = '' if tri == 0: continue tds = tr.findAll('td') for tdi, td in enumerate(tds): if tdi == 1: name = add_event(td.text.strip()) atellink = td.find('a') if atellink: atellink = atellink['href'] else: atellink = '' if tdi == 2: discdate = td.text.replace('-', '/') if tdi == 3: ra = td.text if tdi == 4: dec = td.text if tdi == 5: redshift = td.text if tdi == 8: hostoff = td.text if tdi == 9: claimedtype = td.text typelink = td.find('a') if typelink: typelink = typelink['href'] else: typelink = '' if tdi == 12: host = td.text sources = [add_source(name, url = 'http://www.astronomy.ohio-state.edu/~assassin/sn_list.html', refname = 'ASAS-SN Supernovae')] typesources = sources[:] if atellink: sources.append(add_source(name, refname = 'ATel ' + atellink.split('=')[-1], url = atellink)) if typelink: typesources.append(add_source(name, refname = 'ATel ' + typelink.split('=')[-1], url = typelink)) sources = ','.join(sources) typesources = ','.join(typesources) add_quantity(name, 'alias', name, sources) add_quantity(name, 'discoverdate', discdate, sources) add_quantity(name, 'ra', ra, sources, unit = 'floatdegrees') add_quantity(name, 'dec', dec, sources, unit = 'floatdegrees') add_quantity(name, 'redshift', redshift, sources) add_quantity(name, 'hostoffset', hostoff, sources, unit = 'arcseconds') for ct in claimedtype.split('/'): if ct != 'Unk': add_quantity(name, 'claimedtype', ct, typesources) if host != 'Uncatalogued': add_quantity(name, 'host', host, sources) journal_events() if do_task(task, 'asiagospectra'): html = load_cached_url("http://sngroup.oapd.inaf.it./cgi-bin/output_class.cgi?sn=1990", "../sne-external-spectra/Asiago/spectra.html") if not html: continue bs = BeautifulSoup(html, "html5lib") trs = bs.findAll('tr') for tr in tq(trs, currenttask): tds = tr.findAll('td') name = '' host = '' fitsurl = '' source = '' reference = '' for tdi, td in enumerate(tds): if tdi == 0: butt = td.find('button') if not butt: break alias = butt.text.strip() alias = alias.replace('PSNJ', 'PSN J').replace('GAIA', 'Gaia') elif tdi == 1: name = td.text.strip().replace('PSNJ', 'PSN J').replace('GAIA', 'Gaia') if name.startswith('SN '): name = 'SN' + name[3:] if not name: name = alias if is_number(name[:4]): name = 'SN' + name name = add_event(name) reference = 'Asiago Supernova Catalogue' refurl = 'http://graspa.oapd.inaf.it/cgi-bin/sncat.php' secondarysource = add_source(name, refname = reference, url = refurl, secondary = True) add_quantity(name, 'alias', name, secondarysource) if alias != name: add_quantity(name, 'alias', alias, secondarysource) elif tdi == 2: host = td.text.strip() if host == 'anonymous': host = '' elif tdi == 3: discoverer = td.text.strip() elif tdi == 5: ra = td.text.strip() elif tdi == 6: dec = td.text.strip() elif tdi == 7: claimedtype = td.text.strip() elif tdi == 8: redshift = td.text.strip() elif tdi == 9: epochstr = td.text.strip() if epochstr: mjd = (astrotime(epochstr[:4] + '-' + epochstr[4:6] + '-' + str(floor(float(epochstr[6:]))).zfill(2)).mjd + float(epochstr[6:]) - floor(float(epochstr[6:]))) else: mjd = '' elif tdi == 10: refs = td.findAll('a') source = '' reference = '' refurl = '' for ref in refs: if ref.text != 'REF': reference = ref.text refurl = ref['href'] if reference: source = add_source(name, refname = reference, url = refurl) add_quantity(name, 'alias', name, secondarysource) sources = uniq_cdl(list(filter(None, [source, secondarysource]))) elif tdi == 12: fitslink = td.find('a') if fitslink: fitsurl = fitslink['href'] if name: add_quantity(name, 'claimedtype', claimedtype, sources) add_quantity(name, 'ra', ra, sources) add_quantity(name, 'dec', dec, sources) add_quantity(name, 'redshift', redshift, sources) add_quantity(name, 'discoverer', discoverer, sources) add_quantity(name, 'host', host, sources) #if fitsurl: # response = urllib.request.urlopen("http://sngroup.oapd.inaf.it./" + fitsurl) # compressed = io.BytesIO(response.read()) # decompressed = gzip.GzipFile(fileobj=compressed) # hdulist = fits.open(decompressed) # scidata = hdulist[0].data # print(hdulist[0].header) # print(scidata[3]) # sys.exit() journal_events() if do_task(task, 'wiserepspectra'): secondaryreference = 'WISeREP' secondaryrefurl = 'http://wiserep.weizmann.ac.il/' secondarybibcode = '2012PASP..124..668Y' wiserepcnt = 0 # These are known to be in error on the WISeREP page, either fix or ignore them. wiserepbibcorrectdict = {'2000AJ....120..367G]':'2000AJ....120..367G', 'Harutyunyan+et+al.+2008':'2008A&A...488..383H', '0609268':'2007AJ....133...58K', '2006ApJ...636...400Q':'2006ApJ...636..400Q', '2011ApJ...741...76':'2011ApJ...741...76C', '2016PASP...128...961':'2016PASP..128...961', '2002AJ....1124..417H':'2002AJ....1124.417H', '2013ApJ…774…58D':'2013ApJ...774...58D', '2011Sci.333..856S':'2011Sci...333..856S', '2014MNRAS.438,368':'2014MNRAS.438..368T', '2012MNRAS.420.1135':'2012MNRAS.420.1135S', '2012Sci..337..942D':'2012Sci...337..942D', 'stt1839':''} oldname = '' for folder in tq(sorted(next(os.walk("../sne-external-WISEREP"))[1], key=lambda s: s.lower()), currenttask): files = glob("../sne-external-WISEREP/" + folder + '/*') for fname in tq(files, currenttask): if '.html' in fname: lfiles = deepcopy(files) with open(fname, 'r') as f: path = os.path.abspath(fname) response = urllib.request.urlopen('file://' + path) bs = BeautifulSoup(response, "html5lib") trs = bs.findAll('tr', {'valign': 'top'}) for tri, tr in enumerate(trs): if "Click to show/update object" in str(tr.contents): claimedtype = '' instrument = '' epoch = '' observer = '' reducer = '' specfile = '' produceoutput = True specpath = '' tds = tr.findAll('td') for tdi, td in enumerate(tds): if td.contents: if tdi == 3: name = re.sub('<[^<]+?>', '', str(td.contents[0])).strip() elif tdi == 5: claimedtype = re.sub('<[^<]+?>', '', str(td.contents[0])).strip() if claimedtype == 'SN': claimedtype = '' continue if claimedtype[:3] == 'SN ': claimedtype = claimedtype[3:].strip() claimedtype = claimedtype.replace('-like', '').strip() elif tdi == 9: instrument = re.sub('<[^<]+?>', '', str(td.contents[0])).strip() elif tdi == 11: epoch = re.sub('<[^<]+?>', '', str(td.contents[0])).strip() elif tdi == 13: observer = re.sub('<[^<]+?>', '', str(td.contents[0])).strip() if observer == 'Unknown' or observer == 'Other': observer = '' elif tdi == 17: reducer = re.sub('<[^<]+?>', '', str(td.contents[0])).strip() if reducer == 'Unknown' or reducer == 'Other': reducer = '' elif tdi == 25: speclinks = td.findAll('a') try: for link in speclinks: if 'Ascii' in link['href']: specfile = link.contents[0].strip() tfiles = deepcopy(lfiles) for fi, fname in enumerate(lfiles): if specfile in fname: specpath = fname del(tfiles[fi]) lfiles = deepcopy(tfiles) raise(StopIteration) except StopIteration: pass if not specpath: warnings.warn('Spectrum file not found, "' + specfile + '"') else: continue if "Spec Type:</span>" in str(tr.contents) and produceoutput: produceoutput = False trstr = str(tr) result = re.search('redshift=(.*?)&amp;', trstr) redshift = '' if result: redshift = result.group(1) if not is_number(redshift) or float(redshift) > 100.: redshift = '' result = re.search('publish=(.*?)&amp;', trstr) bibcode = '' if result: bibcode = unescape(urllib.parse.unquote(urllib.parse.unquote(result.group(1))).split('/')[-1]) if not bibcode: biblink = tr.find('a', {'title': 'Link to NASA ADS'}) if biblink: bibcode = biblink.contents[0] if name.startswith('sn'): name = 'SN' + name[2:] if name.startswith(('CSS', 'SSS', 'MLS')) and ':' not in name: name = name.replace('-', ':', 1) if name.startswith('MASTERJ'): name = name.replace('MASTERJ', 'MASTER OT J') if name.startswith('PSNJ'): name = name.replace('PSNJ', 'PSN J') name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) #print(name + " " + claimedtype + " " + epoch + " " + observer + " " + reducer + " " + specfile + " " + bibcode + " " + redshift) secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, bibcode = secondarybibcode, secondary = True) add_quantity(name, 'alias', name, secondarysource) if bibcode: newbibcode = bibcode if bibcode in wiserepbibcorrectdict: newbibcode = wiserepbibcorrectdict[bibcode] if newbibcode: source = add_source(name, bibcode = unescape(newbibcode)) else: source = add_source(name, refname = unescape(bibcode)) sources = uniq_cdl([source, secondarysource]) else: sources = secondarysource if claimedtype not in ['Other']: add_quantity(name, 'claimedtype', claimedtype, secondarysource) add_quantity(name, 'redshift', redshift, secondarysource) if not specpath: continue with open(specpath,'r') as f: data = [x.split() for x in f] skipspec = False newdata = [] oldval = '' for row in data: if row and '#' not in row[0]: if len(row) >= 2 and is_number(row[0]) and is_number(row[1]) and row[1] != oldval: newdata.append(row) oldval = row[1] if skipspec or not newdata: warnings.warn('Skipped adding spectrum file ' + specfile) continue data = [list(i) for i in zip(*newdata)] wavelengths = data[0] fluxes = data[1] errors = '' if len(data) == 3: errors = data[1] time = str(astrotime(epoch).mjd) if max([float(x) for x in fluxes]) < 1.0e-5: fluxunit = 'erg/s/cm^2/Angstrom' else: fluxunit = 'Uncalibrated' add_spectrum(name = name, waveunit = 'Angstrom', fluxunit = fluxunit, errors = errors, errorunit = fluxunit, wavelengths = wavelengths, fluxes = fluxes, u_time = 'MJD', time = time, instrument = instrument, source = sources, observer = observer, reducer = reducer, filename = specfile) wiserepcnt = wiserepcnt + 1 if args.travis and wiserepcnt % travislimit == 0: break tprint('Unadded files: ' + str(len(lfiles) - 1) + "/" + str(len(files)-1)) tprint('WISeREP spectrum count: ' + str(wiserepcnt)) journal_events() if do_task(task, 'cfaspectra'): # Ia spectra oldname = '' for name in tq(sorted(next(os.walk("../sne-external-spectra/CfA_SNIa"))[1], key=lambda s: s.lower()), currenttask): fullpath = "../sne-external-spectra/CfA_SNIa/" + name origname = name if name.startswith('sn') and is_number(name[2:6]): name = 'SN' + name[2:] if name.startswith('snf') and is_number(name[3:7]): name = 'SNF' + name[3:] name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) reference = 'CfA Supernova Archive' refurl = 'https://www.cfa.harvard.edu/supernova/SNarchive.html' source = add_source(name, refname = reference, url = refurl, secondary = True, acknowledgment = cfaack) add_quantity(name, 'alias', name, source) for fi, fname in enumerate(sorted(glob(fullpath + '/*'), key=lambda s: s.lower())): filename = os.path.basename(fname) fileparts = filename.split('-') if origname.startswith("sn") and is_number(origname[2:6]): year = fileparts[1][:4] month = fileparts[1][4:6] day = fileparts[1][6:] instrument = fileparts[2].split('.')[0] else: year = fileparts[2][:4] month = fileparts[2][4:6] day = fileparts[2][6:] instrument = fileparts[3].split('.')[0] time = str(astrotime(year + '-' + month + '-' + str(floor(float(day))).zfill(2)).mjd + float(day) - floor(float(day))) f = open(fname,'r') data = csv.reader(f, delimiter=' ', skipinitialspace=True) data = [list(i) for i in zip(*data)] wavelengths = data[0] fluxes = data[1] errors = data[2] sources = uniq_cdl([source, add_source(name, bibcode = '2012AJ....143..126B'), add_source(name, bibcode = '2008AJ....135.1598M')]) add_spectrum(name = name, waveunit = 'Angstrom', fluxunit = 'erg/s/cm^2/Angstrom', filename = filename, wavelengths = wavelengths, fluxes = fluxes, u_time = 'MJD' if time else '', time = time, instrument = instrument, errorunit = "ergs/s/cm^2/Angstrom", errors = errors, source = sources, dereddened = False, deredshifted = False) if args.travis and fi >= travislimit: break journal_events() # Ibc spectra oldname = '' for name in tq(sorted(next(os.walk("../sne-external-spectra/CfA_SNIbc"))[1], key=lambda s: s.lower()), currenttask): fullpath = "../sne-external-spectra/CfA_SNIbc/" + name if name.startswith('sn') and is_number(name[2:6]): name = 'SN' + name[2:] name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) reference = 'CfA Supernova Archive' refurl = 'https://www.cfa.harvard.edu/supernova/SNarchive.html' source = add_source(name, refname = reference, url = refurl, secondary = True, acknowledgment = cfaack) add_quantity(name, 'alias', name, source) for fi, fname in enumerate(sorted(glob(fullpath + '/*'), key=lambda s: s.lower())): filename = os.path.basename(fname) fileparts = filename.split('-') instrument = '' year = fileparts[1][:4] month = fileparts[1][4:6] day = fileparts[1][6:].split('.')[0] if len(fileparts) > 2: instrument = fileparts[-1].split('.')[0] time = str(astrotime(year + '-' + month + '-' + str(floor(float(day))).zfill(2)).mjd + float(day) - floor(float(day))) f = open(fname,'r') data = csv.reader(f, delimiter=' ', skipinitialspace=True) data = [list(i) for i in zip(*data)] wavelengths = data[0] fluxes = data[1] sources = uniq_cdl([source, add_source(name, bibcode = '2014AJ....147...99M')]) add_spectrum(name = name, waveunit = 'Angstrom', fluxunit = 'erg/s/cm^2/Angstrom', wavelengths = wavelengths, filename = filename, fluxes = fluxes, u_time = 'MJD' if time else '', time = time, instrument = instrument, source = sources, dereddened = False, deredshifted = False) if args.travis and fi >= travislimit: break journal_events() # Other spectra oldname = '' for name in tq(sorted(next(os.walk("../sne-external-spectra/CfA_Extra"))[1], key=lambda s: s.lower()), currenttask): fullpath = "../sne-external-spectra/CfA_Extra/" + name if name.startswith('sn') and is_number(name[2:6]): name = 'SN' + name[2:] name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) reference = 'CfA Supernova Archive' refurl = 'https://www.cfa.harvard.edu/supernova/SNarchive.html' source = add_source(name, refname = reference, url = refurl, secondary = True, acknowledgment = cfaack) add_quantity(name, 'alias', name, source) for fi, fname in enumerate(sorted(glob(fullpath + '/*'), key=lambda s: s.lower())): if not os.path.isfile(fname): continue filename = os.path.basename(fname) if (not filename.startswith('sn') or not filename.endswith('flm') or any(x in filename for x in ['-interp', '-z', '-dered', '-obj', '-gal'])): continue fileparts = filename.split('.')[0].split('-') instrument = '' time = '' if len(fileparts) > 1: year = fileparts[1][:4] month = fileparts[1][4:6] day = fileparts[1][6:] if is_number(year) and is_number(month) and is_number(day): if len(fileparts) > 2: instrument = fileparts[-1] time = str(astrotime(year + '-' + month + '-' + str(floor(float(day))).zfill(2)).mjd + float(day) - floor(float(day))) f = open(fname,'r') data = csv.reader(f, delimiter=' ', skipinitialspace=True) data = [list(i) for i in zip(*data)] wavelengths = data[0] fluxes = [str(Decimal(x)*Decimal(1.0e-15)) for x in data[1]] add_spectrum(name = name, waveunit = 'Angstrom', fluxunit = 'erg/s/cm^2/Angstrom', wavelengths = wavelengths, filename = filename, fluxes = fluxes, u_time = 'MJD' if time else '', time = time, instrument = instrument, source = source, dereddened = False, deredshifted = False) if args.travis and fi >= travislimit: break journal_events() if do_task(task, 'snlsspectra'): result = Vizier.get_catalogs("J/A+A/507/85/table1") table = result[list(result.keys())[0]] table.convert_bytestring_to_unicode(python3_only=True) datedict = {} for row in table: datedict['SNLS-' + row['SN']] = str(astrotime(row['Date']).mjd) oldname = '' for fi, fname in enumerate(tq(sorted(glob('../sne-external-spectra/SNLS/*'), key=lambda s: s.lower()), currenttask = currenttask)): filename = os.path.basename(fname) fileparts = filename.split('_') name = 'SNLS-' + fileparts[1] name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) source = add_source(name, bibcode = "2009A&A...507...85B") add_quantity(name, 'alias', name, source) add_quantity(name, 'discoverdate', '20' + fileparts[1][:2], source) f = open(fname,'r') data = csv.reader(f, delimiter=' ', skipinitialspace=True) specdata = [] for r, row in enumerate(data): if row[0] == '@TELESCOPE': telescope = row[1].strip() elif row[0] == '@REDSHIFT': add_quantity(name, 'redshift', row[1].strip(), source) if r < 14: continue specdata.append(list(filter(None, [x.strip(' \t') for x in row]))) specdata = [list(i) for i in zip(*specdata)] wavelengths = specdata[1] fluxes = [pretty_num(float(x)*1.e-16, sig = get_sig_digits(x)) for x in specdata[2]] errors = [pretty_num(float(x)*1.e-16, sig = get_sig_digits(x)) for x in specdata[3]] add_spectrum(name = name, waveunit = 'Angstrom', fluxunit = 'erg/s/cm^2/Angstrom', wavelengths = wavelengths, fluxes = fluxes, u_time = 'MJD' if name in datedict else '', time = datedict[name] if name in datedict else '', telescope = telescope, source = source, filename = filename) if args.travis and fi >= travislimit: break journal_events() if do_task(task, 'cspspectra'): oldname = '' for fi, fname in enumerate(tq(sorted(glob('../sne-external-spectra/CSP/*'), key=lambda s: s.lower()), currenttask = currenttask)): filename = os.path.basename(fname) sfile = filename.split('.') if sfile[1] == 'txt': continue sfile = sfile[0] fileparts = sfile.split('_') name = 'SN20' + fileparts[0][2:] name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) telescope = fileparts[-2] instrument = fileparts[-1] source = add_source(name, bibcode = "2013ApJ...773...53F") add_quantity(name, 'alias', name, source) f = open(fname,'r') data = csv.reader(f, delimiter=' ', skipinitialspace=True) specdata = [] for r, row in enumerate(data): if row[0] == '#JDate_of_observation:': jd = row[1].strip() time = str(jd_to_mjd(Decimal(jd))) elif row[0] == '#Redshift:': add_quantity(name, 'redshift', row[1].strip(), source) if r < 7: continue specdata.append(list(filter(None, [x.strip(' ') for x in row]))) specdata = [list(i) for i in zip(*specdata)] wavelengths = specdata[0] fluxes = specdata[1] add_spectrum(name = name, u_time = 'MJD', time = time, waveunit = 'Angstrom', fluxunit = 'erg/s/cm^2/Angstrom', wavelengths = wavelengths, fluxes = fluxes, telescope = telescope, instrument = instrument, source = source, deredshifted = True, filename = filename) if args.travis and fi >= travislimit: break journal_events() if do_task(task, 'ucbspectra'): secondaryreference = "UCB Filippenko Group's Supernova Database (SNDB)" secondaryrefurl = "http://heracles.astro.berkeley.edu/sndb/info" secondaryrefbib = "2012MNRAS.425.1789S" ucbspectracnt = 0 jsontxt = load_cached_url("http://heracles.astro.berkeley.edu/sndb/download?id=allpubspec", '../sne-external-spectra/UCB/allpub.json') if not jsontxt: continue spectra = json.loads(jsontxt) spectra = sorted(spectra, key = lambda k: k['ObjName']) oldname = '' for spectrum in tq(spectra, currenttask = currenttask): name = spectrum["ObjName"] if oldname and name != oldname: journal_events() oldname = name name = add_event(name) secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, bibcode = secondaryrefbib, secondary = True) add_quantity(name, 'alias', name, secondarysource) sources = [secondarysource] if spectrum["Reference"]: sources += [add_source(name, bibcode = spectrum["Reference"])] sources = uniq_cdl(sources) if spectrum["Type"] and spectrum["Type"].strip() != "NoMatch": for ct in spectrum["Type"].strip().split(','): add_quantity(name, 'claimedtype', ct.replace('-norm', '').strip(), sources) if spectrum["DiscDate"]: add_quantity(name, 'discoverdate', spectrum["DiscDate"].replace('-', '/'), sources) if spectrum["HostName"]: add_quantity(name, 'host', urllib.parse.unquote(spectrum["HostName"]).replace('*', ''), sources) if spectrum["UT_Date"]: epoch = str(spectrum["UT_Date"]) year = epoch[:4] month = epoch[4:6] day = epoch[6:] sig = get_sig_digits(day) + 5 mjd = pretty_num(astrotime(year + '-' + month + '-' + str(floor(float(day))).zfill(2)).mjd + float(day) - floor(float(day)), sig = sig) filename = spectrum["Filename"] if spectrum["Filename"] else '' instrument = spectrum["Instrument"] if spectrum["Instrument"] else '' reducer = spectrum["Reducer"] if spectrum["Reducer"] else '' observer = spectrum["Observer"] if spectrum["Observer"] else '' snr = str(spectrum["SNR"]) if spectrum["SNR"] else '' if not filename: raise(ValueError('Filename not found for SNDB spectrum!')) if not spectrum["SpecID"]: raise(ValueError('ID not found for SNDB spectrum!')) filepath = '../sne-external-spectra/UCB/' + filename if archived_task('ucbspectra') and os.path.isfile(filepath): with open(filepath, 'r') as f: spectxt = f.read() else: session = requests.Session() response = session.get("http://heracles.astro.berkeley.edu/sndb/download?id=ds:" + str(spectrum["SpecID"])) spectxt = response.text with open(filepath, 'w') as f: f.write(spectxt) specdata = list(csv.reader(spectxt.splitlines(), delimiter=' ', skipinitialspace=True)) startrow = 0 for row in specdata: if row[0][0] == '#': startrow += 1 else: break specdata = specdata[startrow:] haserrors = len(specdata[0]) == 3 and specdata[0][2] and specdata[0][2] != 'NaN' specdata = [list(i) for i in zip(*specdata)] wavelengths = specdata[0] fluxes = specdata[1] errors = '' if haserrors: errors = specdata[2] if not list(filter(None, errors)): errors = '' add_spectrum(name = name, u_time = 'MJD', time = mjd, waveunit = 'Angstrom', fluxunit = 'Uncalibrated', wavelengths = wavelengths, filename = filename, fluxes = fluxes, errors = errors, errorunit = 'Uncalibrated', instrument = instrument, source = sources, snr = snr, observer = observer, reducer = reducer, deredshifted = ('-noz' in filename)) ucbspectracnt = ucbspectracnt + 1 if args.travis and ucbspectracnt >= travislimit: break journal_events() if do_task(task, 'suspectspectra'): with open('../sne-external-spectra/Suspect/sources.json', 'r') as f: sourcedict = json.loads(f.read()) with open('../sne-external-spectra/Suspect/filename-changes.txt', 'r') as f: rows = f.readlines() changedict = {} for row in rows: if not row.strip() or row[0] == "#": continue items = row.strip().split(' ') changedict[items[1]] = items[0] suspectcnt = 0 folders = next(os.walk('../sne-external-spectra/Suspect'))[1] for folder in tq(folders, currenttask): eventfolders = next(os.walk('../sne-external-spectra/Suspect/'+folder))[1] oldname = '' for eventfolder in tq(eventfolders, currenttask): name = eventfolder if is_number(name[:4]): name = 'SN' + name name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) secondaryreference = "SUSPECT" secondaryrefurl = "https://www.nhn.ou.edu/~suspect/" secondarybibcode = "2001AAS...199.8408R" secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, bibcode = secondarybibcode, secondary = True) add_quantity(name, 'alias', name, secondarysource) eventspectra = next(os.walk('../sne-external-spectra/Suspect/'+folder+'/'+eventfolder))[2] for spectrum in eventspectra: sources = [secondarysource] bibcode = '' if spectrum in changedict: specalias = changedict[spectrum] else: specalias = spectrum if specalias in sourcedict: bibcode = sourcedict[specalias] elif name in sourcedict: bibcode = sourcedict[name] if bibcode: source = add_source(name, bibcode = unescape(bibcode)) sources += source sources = uniq_cdl(sources) date = spectrum.split('_')[1] year = date[:4] month = date[4:6] day = date[6:] sig = get_sig_digits(day) + 5 time = pretty_num(astrotime(year + '-' + month + '-' + str(floor(float(day))).zfill(2)).mjd + float(day) - floor(float(day)), sig = sig) with open('../sne-external-spectra/Suspect/'+folder+'/'+eventfolder+'/'+spectrum) as f: specdata = list(csv.reader(f, delimiter=' ', skipinitialspace=True)) specdata = list(filter(None, specdata)) newspec = [] oldval = '' for row in specdata: if row[1] == oldval: continue newspec.append(row) oldval = row[1] specdata = newspec haserrors = len(specdata[0]) == 3 and specdata[0][2] and specdata[0][2] != 'NaN' specdata = [list(i) for i in zip(*specdata)] wavelengths = specdata[0] fluxes = specdata[1] errors = '' if haserrors: errors = specdata[2] add_spectrum(name = name, u_time = 'MJD', time = time, waveunit = 'Angstrom', fluxunit = 'Uncalibrated', wavelengths = wavelengths, fluxes = fluxes, errors = errors, errorunit = 'Uncalibrated', source = sources, filename = spectrum) suspectcnt = suspectcnt + 1 if args.travis and suspectcnt % travislimit == 0: break journal_events() if do_task(task, 'snfspectra'): eventfolders = next(os.walk('../sne-external-spectra/SNFactory'))[1] bibcodes = {'SN2005gj':'2006ApJ...650..510A', 'SN2006D':'2007ApJ...654L..53T', 'SN2007if':'2010ApJ...713.1073S', 'SN2011fe':'2013A&A...554A..27P'} oldname = '' snfcnt = 0 for eventfolder in eventfolders: name = eventfolder name = get_preferred_name(name) if oldname and name != oldname: journal_events() oldname = name name = add_event(name) secondaryreference = "Nearby Supernova Factory" secondaryrefurl = "http://snfactory.lbl.gov/" secondarybibcode = "2002SPIE.4836...61A" secondarysource = add_source(name, refname = secondaryreference, url = secondaryrefurl, bibcode = secondarybibcode, secondary = True) add_quantity(name, 'alias', name, secondarysource) bibcode = bibcodes[name] source = add_source(name, bibcode = bibcode) sources = uniq_cdl([source,secondarysource]) eventspectra = glob('../sne-external-spectra/SNFactory/'+eventfolder+'/*.dat') for spectrum in eventspectra: filename = os.path.basename(spectrum) with open(spectrum) as f: specdata = list(csv.reader(f, delimiter=' ', skipinitialspace=True)) specdata = list(filter(None, specdata)) newspec = [] time = '' telescope = '' instrument = '' observer = '' observatory = '' if 'Keck_20060202_R' in spectrum: time = '53768.23469' elif 'Spectrum05_276' in spectrum: time = pretty_num(astrotime('2005-10-03').mjd, sig = 5) elif 'Spectrum05_329' in spectrum: time = pretty_num(astrotime('2005-11-25').mjd, sig = 5) elif 'Spectrum05_336' in spectrum: time = pretty_num(astrotime('2005-12-02').mjd, sig = 5) for row in specdata: if row[0][0] == '#': joinrow = (' '.join(row)).split('=') if len(joinrow) < 2: continue field = joinrow[0].strip('# ') value = joinrow[1].split('/')[0].strip("' ") if not time: if field == 'JD': time = str(jd_to_mjd(Decimal(value))) elif field == 'MJD': time = value elif field == 'MJD-OBS': time = value if field == 'OBSERVER': observer = value.capitalize() if field == 'OBSERVAT': observatory = value.capitalize() if field == 'TELESCOP': telescope = value.capitalize() if field == 'INSTRUME': instrument = value.capitalize() else: newspec.append(row) if not time: raise(ValueError('Time missing from spectrum.')) specdata = newspec haserrors = len(specdata[0]) == 3 and specdata[0][2] and specdata[0][2] != 'NaN' specdata = [list(i) for i in zip(*specdata)] wavelengths = specdata[0] fluxes = specdata[1] errors = '' if haserrors: errors = specdata[2] add_spectrum(name = name, u_time = 'MJD', time = time, waveunit = 'Angstrom', fluxunit = 'erg/s/cm^2/Angstrom', wavelengths = wavelengths, fluxes = fluxes, errors = errors, observer = observer, observatory = observatory, telescope = telescope, instrument = instrument, errorunit = ('Variance' if name == 'SN2011fe' else 'erg/s/cm^2/Angstrom'), source = sources, filename = filename) snfcnt = snfcnt + 1 if args.travis and snfcnt % travislimit == 0: break journal_events() if do_task(task, 'superfitspectra'): sfdirs = glob('../sne-external-spectra/superfit/*') for sfdir in tq(sfdirs, currenttask = currenttask): sffiles = sorted(glob(sfdir + "/*.dat")) lastname = '' oldname = '' for sffile in tq(sffiles, currenttask = currenttask): basename = os.path.basename(sffile) name = basename.split('.')[0] if name.startswith('sn'): name = 'SN' + name[2:] if len(name) == 7: name = name[:6] + name[6].upper() elif name.startswith('ptf'): name = 'PTF' + name[3:] if 'theory' in name: continue if event_exists(name): prefname = get_preferred_name(name) if 'spectra' in events[prefname] and lastname != prefname: continue if oldname and name != oldname: journal_events() oldname = name name = add_event(name) epoch = basename.split('.')[1] (mldt, mlmag, mlband, mlsource) = get_max_light(name) if mldt: epoff = Decimal(0.0) if epoch == 'max' else (Decimal(epoch[1:]) if epoch[0] == 'p' else -Decimal(epoch[1:])) else: epoff = '' source = add_source(name, refname = 'Superfit', url = 'http://www.dahowell.com/superfit.html', secondary = True) add_quantity(name, 'alias', name, source) with open(sffile) as f: rows = f.read().splitlines() specdata = [] for row in rows: if row.strip(): specdata.append(list(filter(None,re.split('\t+|\s+', row, maxsplit=0)))) specdata = [[x.replace('D','E') for x in list(i)] for i in zip(*specdata)] wavelengths = specdata[0] fluxes = specdata[1] mlmjd = str(Decimal(astrotime('-'.join([str(mldt.year), str(mldt.month), str(mldt.day)])).mjd) + epoff) if (epoff != '') else '' add_spectrum(name, u_time = 'MJD' if mlmjd else '', time = mlmjd, waveunit = 'Angstrom', fluxunit = 'Uncalibrated', wavelengths = wavelengths, fluxes = fluxes, source = source) lastname = name journal_events() if do_task(task, 'mergeduplicates'): if args.update and not len(events): tprint('No sources changed, event files unchanged in update.') sys.exit(1) merge_duplicates() if do_task(task, 'setprefnames'): set_preferred_names() files = repo_file_list() path = '../bibauthors.json' if os.path.isfile(path): with open(path, 'r') as f: bibauthordict = json.loads(f.read(), object_pairs_hook=OrderedDict) else: bibauthordict = OrderedDict() path = '../extinctions.json' if os.path.isfile(path): with open(path, 'r') as f: extinctionsdict = json.loads(f.read(), object_pairs_hook=OrderedDict) else: extinctionsdict = OrderedDict() for fi in tq(files, 'Sanitizing and deriving quantities for events'): events = OrderedDict() name = os.path.basename(os.path.splitext(fi)[0]).replace('.json', '') name = add_event(name, loadifempty = False) derive_and_sanitize() if has_task('writeevents'): write_all_events(empty = True, gz = True, bury = True) jsonstring = json.dumps(bibauthordict, indent='\t', separators=(',', ':'), ensure_ascii=False) with codecs.open('../bibauthors.json', 'w', encoding='utf8') as f: f.write(jsonstring) jsonstring = json.dumps(extinctionsdict, indent='\t', separators=(',', ':'), ensure_ascii=False) with codecs.open('../extinctions.json', 'w', encoding='utf8') as f: f.write(jsonstring) print("Memory used (MBs on Mac, GBs on Linux): " + "{:,}".format(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/1024./1024.)) sys.exit(0)

mit

dparks1134/STAMP

stamp/plugins/samples/plots/SeqHistogram.py

1

9822

#======================================================================= # Author: Donovan Parks # # Sequence histogram plot. # # Copyright 2011 Donovan Parks # # This file is part of STAMP. # # STAMP is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # STAMP is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with STAMP. If not, see <http://www.gnu.org/licenses/>. #======================================================================= import sys import math from PyQt4 import QtCore, QtGui from stamp.plugins.samples.AbstractSamplePlotPlugin import AbstractSamplePlotPlugin, TestWindow, ConfigureDialog from stamp.plugins.samples.plots.configGUI.seqHistogramUI import Ui_SeqHistogramDialog class SeqHistogram(AbstractSamplePlotPlugin): ''' Sequence histogram plot. ''' def __init__(self, preferences, parent=None): AbstractSamplePlotPlugin.__init__(self, preferences, parent) self.preferences = preferences self.name = 'Sequence histogram' self.type = 'Exploratory' self.settings = preferences['Settings'] self.figWidth = self.settings.value(self.name + '/width', 7.0).toDouble()[0] self.figHeight = self.settings.value(self.name + '/height', 7.0).toDouble()[0] self.bCustomBinWidth = self.settings.value(self.name + '/custom bin width', False).toBool() self.binWidth = self.settings.value(self.name + '/bin width', 100.0).toDouble()[0] self.yAxisLogScale = self.settings.value(self.name + '/log scale', False).toBool() self.bCustomXaxis = self.settings.value(self.name + '/custom x-axis extents', False).toBool() self.xLimitLeft = self.settings.value(self.name + '/min value', 0.0).toDouble()[0] self.xLimitRight = self.settings.value(self.name + '/max value', 1.0).toDouble()[0] self.legendPos = self.settings.value(self.name + '/legend position', 0).toInt()[0] def mirrorProperties(self, plotToCopy): self.name = plotToCopy.name self.figWidth = plotToCopy.figWidth self.figHeight = plotToCopy.figHeight self.bCustomBinWidth = plotToCopy.bCustomBinWidth self.binWidth = plotToCopy.binWidth self.yAxisLogScale = plotToCopy.yAxisLogScale self.bCustomXaxis = plotToCopy.bCustomXaxis self.xLimitLeft = plotToCopy.xLimitLeft self.xLimitRight = plotToCopy.xLimitRight self.legendPos = plotToCopy.legendPos def plot(self, profile, statsResults): if len(profile.profileDict) <= 0: self.emptyAxis() return # *** Colour of plot elements axesColour = str(self.preferences['Axes colour'].name()) profile1Colour = str(self.preferences['Sample 1 colour'].name()) profile2Colour = str(self.preferences['Sample 2 colour'].name()) # *** Get sequence counts seqs1 = profile.getSequenceCounts(0) seqs2 = profile.getSequenceCounts(1) # *** Set x-axis limit self.xMin = min(min(seqs1),min(seqs2)) if self.xLimitLeft == None: self.xLimitLeft = self.xMin self.xMax = max(max(seqs1),max(seqs2)) if self.xLimitRight == None: self.xLimitRight = self.xMax # Set bin width if not self.bCustomBinWidth: self.binWidth = (self.xMax - self.xMin) / 40 # *** Set size of figure self.fig.clear() self.fig.set_size_inches(self.figWidth, self.figHeight) heightBottomLabels = 0.4 # inches widthSideLabel = 0.5 # inches padding = 0.2 # inches axesHist = self.fig.add_axes([widthSideLabel/self.figWidth,heightBottomLabels/self.figHeight,\ 1.0-(widthSideLabel+padding)/self.figWidth,\ 1.0-(heightBottomLabels+padding)/self.figHeight]) # *** Histogram plot bins = [0] binEnd = self.binWidth while binEnd <= self.xMax: bins.append(binEnd) binEnd += self.binWidth bins.append(binEnd) n, b, patches = axesHist.hist([seqs1, seqs2], bins=bins, log=self.yAxisLogScale) for patch in patches[0]: patch.set_facecolor(profile1Colour) for patch in patches[1]: patch.set_facecolor(profile2Colour) if self.bCustomXaxis: axesHist.set_xlim(self.xLimitLeft, self.xLimitRight) axesHist.set_xlabel('Sequences') axesHist.set_ylabel('Number of features') # *** Prettify plot if self.legendPos != -1: legend = axesHist.legend([patches[0][0], patches[1][0]], (profile.sampleNames[0], profile.sampleNames[1]), loc=self.legendPos) legend.get_frame().set_linewidth(0) for a in axesHist.yaxis.majorTicks: a.tick1On=True a.tick2On=False for a in axesHist.xaxis.majorTicks: a.tick1On=True a.tick2On=False for line in axesHist.yaxis.get_ticklines(): line.set_color(axesColour) for line in axesHist.xaxis.get_ticklines(): line.set_color(axesColour) for loc, spine in axesHist.spines.iteritems(): if loc in ['right','top']: spine.set_color('none') else: spine.set_color(axesColour) self.updateGeometry() self.draw() def configure(self, profile, statsResults): self.profile = profile self.configDlg = ConfigureDialog(Ui_SeqHistogramDialog) self.connect(self.configDlg.ui.chkCustomBinWidth, QtCore.SIGNAL('toggled(bool)'), self.changeCustomBinWidth) self.connect(self.configDlg.ui.chkCustomXaxis, QtCore.SIGNAL('toggled(bool)'), self.changeCustomXaxis) self.connect(self.configDlg.ui.btnXmin, QtCore.SIGNAL('clicked()'), self.setXaxisMin) self.connect(self.configDlg.ui.btnXmax, QtCore.SIGNAL('clicked()'), self.setXaxisMax) self.configDlg.ui.spinFigWidth.setValue(self.figWidth) self.configDlg.ui.spinFigHeight.setValue(self.figHeight) self.configDlg.ui.chkCustomBinWidth.setChecked(self.bCustomBinWidth) self.configDlg.ui.spinBinWidth.setValue(self.binWidth) self.configDlg.ui.chkLogScale.setChecked(self.yAxisLogScale) self.configDlg.ui.chkCustomXaxis.setChecked(self.bCustomXaxis) self.configDlg.ui.spinXmin.setValue(self.xLimitLeft) self.configDlg.ui.spinXmax.setValue(self.xLimitRight) self.changeCustomBinWidth() self.changeCustomXaxis() # legend position if self.legendPos == 0: self.configDlg.ui.radioLegendPosBest.setDown(True) elif self.legendPos == 1: self.configDlg.ui.radioLegendPosUpperRight.setChecked(True) elif self.legendPos == 7: self.configDlg.ui.radioLegendPosCentreRight.setChecked(True) elif self.legendPos == 4: self.configDlg.ui.radioLegendPosLowerRight.setChecked(True) elif self.legendPos == 2: self.configDlg.ui.radioLegendPosUpperLeft.setChecked(True) elif self.legendPos == 6: self.configDlg.ui.radioLegendPosCentreLeft.setChecked(True) elif self.legendPos == 3: self.configDlg.ui.radioLegendPosLowerLeft.setChecked(True) else: self.configDlg.ui.radioLegendPosNone.setChecked(True) if self.configDlg.exec_() == QtGui.QDialog.Accepted: self.figWidth = self.configDlg.ui.spinFigWidth.value() self.figHeight = self.configDlg.ui.spinFigHeight.value() self.bCustomBinWidth = self.configDlg.ui.chkCustomBinWidth.isChecked() self.binWidth = self.configDlg.ui.spinBinWidth.value() self.yAxisLogScale = self.configDlg.ui.chkLogScale.isChecked() self.bCustomXaxis = self.configDlg.ui.chkCustomXaxis.isChecked() self.xLimitLeft = self.configDlg.ui.spinXmin.value() self.xLimitRight = self.configDlg.ui.spinXmax.value() # legend position if self.configDlg.ui.radioLegendPosBest.isChecked() == True: self.legendPos = 0 elif self.configDlg.ui.radioLegendPosUpperRight.isChecked() == True: self.legendPos = 1 elif self.configDlg.ui.radioLegendPosCentreRight.isChecked() == True: self.legendPos = 7 elif self.configDlg.ui.radioLegendPosLowerRight.isChecked() == True: self.legendPos = 4 elif self.configDlg.ui.radioLegendPosUpperLeft.isChecked() == True: self.legendPos = 2 elif self.configDlg.ui.radioLegendPosCentreLeft.isChecked() == True: self.legendPos = 6 elif self.configDlg.ui.radioLegendPosLowerLeft.isChecked() == True: self.legendPos = 3 else: self.legendPos = -1 self.settings.setValue(self.name + '/width', self.figWidth) self.settings.setValue(self.name + '/height', self.figHeight) self.settings.setValue(self.name + '/custom bin width', self.bCustomBinWidth) self.settings.setValue(self.name + '/bin width', self.binWidth) self.settings.setValue(self.name + '/log scale', self.yAxisLogScale) self.settings.setValue(self.name + '/custom x-axis extents', self.bCustomXaxis) self.settings.setValue(self.name + '/min value', self.xLimitLeft) self.settings.setValue(self.name + '/max value', self.xLimitRight) self.settings.setValue(self.name + '/legend position', self.legendPos) self.plot(profile, statsResults) def changeCustomBinWidth(self): self.configDlg.ui.spinBinWidth.setEnabled(self.configDlg.ui.chkCustomBinWidth.isChecked()) def changeCustomXaxis(self): self.configDlg.ui.spinXmin.setEnabled(self.configDlg.ui.chkCustomXaxis.isChecked()) self.configDlg.ui.spinXmax.setEnabled(self.configDlg.ui.chkCustomXaxis.isChecked()) def setXaxisMin(self): seqs1 = self.profile.getSequenceCounts(0) seqs2 = self.profile.getSequenceCounts(1) self.configDlg.ui.spinXmin.setValue(min(min(seqs1), min(seqs2))) def setXaxisMax(self): seqs1 = self.profile.getSequenceCounts(0) seqs2 = self.profile.getSequenceCounts(1) self.configDlg.ui.spinXmax.setValue(max(max(seqs1), max(seqs2))) if __name__ == "__main__": app = QtGui.QApplication(sys.argv) testWindow = TestWindow(SeqHistogram) testWindow.show() sys.exit(app.exec_())

gpl-3.0

jtladner/Scripts

BEAST_prep/beast_nexus_prep_v2.0.py

1

4797

#!/usr/bin/env python from __future__ import division import optparse, os #This script uses an aligned fasta file and a tab deliminted file containing CDS coordinates to create a nexus input for BEAST #In version 2.0, added a flag to throw if you only want coding sequence to be included in the nexus file def main(): usage = '%prog [options]' p = optparse.OptionParser() p.add_option('-f', '--fasta', help='Aligned fasta. [None]') p.add_option('-c', '--coords', help='Tab delimited file with coordinates of CDS. Should have at least 3 tab delimited columns. The first is not used, will probably have some sort of CDS name. The next two have start and stop base positions.[None]') p.add_option('-o', '--out', help='Name for output nexus file. [None]') p.add_option('--onlyCDS', default=False, action="store_true", help='Use this flag if you only want coding regions to be included in the output nexus file. [None]') opts, args = p.parse_args() make_beast_nexus(opts) #----------------------End of main() def make_beast_nexus(opts): fout=open(opts.out, 'w') #Read in seqs names, seqs = read_fasta_lists(opts.fasta) #Get coding coordinates coding_coords=get_coords(opts.coords) #Make concatenated coding seqs coding_seqs=['']*len(seqs) for start, end in coding_coords: for i in range(len(seqs)): coding_seqs[i]+=seqs[i][start-1:end] if opts.onlyCDS: fout.write("#NEXUS\n[File created using beast_nexus_prep.py using %s and %s]\n\nBEGIN TAXA;\n" % (opts.fasta, opts.coords)) fout.write("DIMENSIONS NTAX=%d;\n\nTAXLABELS\n%s\n;\n\nEND;\n" % (len(names), '\n'.join(names))) fout.write("BEGIN CHARACTERS;\nDIMENSIONS NCHAR=%d;\nFORMAT DATATYPE=DNA MISSING=N GAP=-;\nMATRIX\n\n%s\n;\n\nEND;\n\n" % (len(coding_seqs[0]), '\n'.join(['%s %s' % (names[x], coding_seqs[x]) for x in range(len(names))]))) fout.write("BEGIN ASSUMPTIONS;\n\tcharset coding = 1-%d;\nend;\n" % (len(coding_seqs[0]))) else: #Get non-coding coordinates noncoding_coords=extrap_noncoding(coding_coords, len(seqs[0])) #Make concatenated noncoding seqs noncoding_seqs=['']*len(seqs) for start, end in noncoding_coords: for i in range(len(seqs)): noncoding_seqs[i]+=seqs[i][start-1:end] concat_seqs=[coding_seqs[i]+noncoding_seqs[i] for i in range(len(seqs))] coding_start=1 coding_end=len(coding_seqs[0]) noncoding_start=coding_end+1 noncoding_end=len(concat_seqs[0]) fout.write("#NEXUS\n[File created using beast_nexus_prep.py using %s and %s]\n\nBEGIN TAXA;\n" % (opts.fasta, opts.coords)) fout.write("DIMENSIONS NTAX=%d;\n\nTAXLABELS\n%s\n;\n\nEND;\n" % (len(names), '\n'.join(names))) fout.write("BEGIN CHARACTERS;\nDIMENSIONS NCHAR=%d;\nFORMAT DATATYPE=DNA MISSING=N GAP=-;\nMATRIX\n\n%s\n;\n\nEND;\n\n" % (len(concat_seqs[0]), '\n'.join(['%s %s' % (names[x], concat_seqs[x]) for x in range(len(names))]))) fout.write("BEGIN ASSUMPTIONS;\n\tcharset coding = %d-%d;\n\tcharset noncoding = %d-%d;\nend;\n" % (coding_start, coding_end, noncoding_start, noncoding_end )) fout.close() def extrap_noncoding(coding_coords, seq_len): non_coords=[] #To handle noncoding at the very beginning of the sequence if coding_coords[0][0] != 1: non_coords.append((1,coding_coords[0][0]-1)) #To handle noncoding regions in between coding seqs coding_sorted=sorted(coding_coords[:]) for i in range(len(coding_sorted[:-1])): if coding_sorted[i+1][0]-coding_sorted[i][1]>0: non_coords.append((coding_sorted[i][1]+1,coding_sorted[i+1][0]-1)) #To handle non-coding at the very end of the sequence if coding_coords[-1][1] != seq_len: non_coords.append((coding_coords[-1][1]+1, seq_len)) print non_coords return non_coords def get_coords(c_file): fin=open(c_file, 'r') coords=[] for line in fin: cols=line.strip().split('\t') coords.append((int(cols[1]), int(cols[2]))) return coords # Extracts data from a fasta sequence file. Returns two lists, the first holds the names of the seqs (excluding the '>' symbol), and the second holds the sequences def read_fasta_lists(file): fin = open(file, 'r') count=0 names=[] seqs=[] seq='' for line in fin: line=line.strip() if line and line[0] == '>': #indicates the name of the sequence count+=1 names.append(line[1:]) if count>1: seqs.append(seq) seq='' else: seq +=line seqs.append(seq) return names, seqs ###------------------------------------->>>> if __name__ == "__main__": main()

gpl-3.0

jhuapl-boss/intern

examples/cutout_timeseries_ex.py

1

1548

from intern.remote.boss import BossRemote from intern.resource.boss.resource import * import numpy as np from requests import HTTPError rmt = BossRemote('neurodata.cfg') xmax = 8 ymax = 4 zmax = 5 tmax = 10 COLL_NAME = 'gray' EXP_NAME = 'timeseries_test' CHAN_NAME = 'Ch1' COORD_FRAME = COLL_NAME + '_' + EXP_NAME coord = CoordinateFrameResource( COORD_FRAME, '', 0, xmax, 0, ymax, 0, zmax) try: coord_actual = rmt.get_project(coord) except HTTPError: coord_actual = rmt.create_project(coord) # Create or get experiment chan_setup = ExperimentResource( EXP_NAME, COLL_NAME, coord_frame=COORD_FRAME, num_time_samples=tmax, time_step=1) try: chan_actual = rmt.get_project(chan_setup) except HTTPError: chan_actual = rmt.create_project(chan_setup) # Create or get a channel to write to chan_setup = ChannelResource( CHAN_NAME, COLL_NAME, EXP_NAME, 'image', '', datatype='uint16') try: chan_actual = rmt.get_project(chan_setup) except HTTPError: chan_actual = rmt.create_project(chan_setup) x_rng = [0, xmax] y_rng = [0, ymax] z_rng = [0, zmax] t_rng = [0, tmax] print('Data model setup.') data = np.random.randint(1, 3000, (tmax, zmax, ymax, xmax)) data = data.astype(np.uint16) # Upload the cutout to the channel. rmt.create_cutout(chan_actual, 0, x_rng, y_rng, z_rng, data, time_range=t_rng) cutout_data = rmt.get_cutout( chan_actual, 0, x_rng, y_rng, z_rng, time_range=t_rng) np.testing.assert_array_equal(data, cutout_data) print(np.shape(cutout_data)) # (10, 5, 4, 8)

apache-2.0

Xicnet/radioflow-scheduler

project/icecast_stats/views.py

1

4776

import os.path import datetime import pytz from django.conf import settings from django.db.models import F from datetime import timedelta from django.shortcuts import render from django.contrib.auth.decorators import login_required from django.utils.decorators import method_decorator from django.contrib.auth.models import User from django.shortcuts import render_to_response, redirect, get_object_or_404 from django.template import RequestContext from rest_framework import generics from rest_framework import serializers from timeslot.models import Program, Day, Config from icecast_stats.models import IcecastLog, ProgramStat from realtime_stats import StatsCollector @login_required def index(request): logs = IcecastLog.objects.all()[:50] return render_to_response( 'icecast_stats/dashboard.html', { 'logs': logs, 'weekly_programs': Program.get_weekly(request), }, context_instance=RequestContext(request) ) @login_required def programacion(request): return redirect('/program/') @login_required def realtime(request): print settings.ICECAST_URL stats = StatsCollector( settings.ICECAST_URL, settings.ICECAST_USER, settings.ICECAST_PASS, settings.ICECAST_REALM, settings.ICECAST_MOUNT ) stats_data = stats.run() return render_to_response( 'icecast_stats/realtime.html', { 'listeners': stats_data, }, context_instance=RequestContext(request) ) @login_required def chat(request): return render_to_response( 'icecast_stats/chat.html', { 'weekly_programs': Program.get_weekly(request), }, context_instance=RequestContext(request) ) # Serializers define the API representation. class IcecastLogSerializer(serializers.ModelSerializer): class Meta: model = IcecastLog class IcecastLogViewSet( generics.ListAPIView): #@method_decorator(login_required) def dispatch(self, *args, **kwargs): return super(IcecastLogViewSet, self).dispatch(*args, **kwargs) serializer_class = IcecastLogSerializer def get_queryset(self): """ This view should return a list of all the purchases for the user as determined by the mount portion of the URL. """ mount = self.request.query_params.get('mount', None) start = "%s 00:00:00" % self.request.query_params.get('start', None) end = "%s 00:00:00" % self.request.query_params.get('end', None) #end = datetime.date("%s 00:00:00" % self.request.query_params.get('end', None), tzinfo=pytz.UTC) limit = self.request.query_params.get('limit', None) if self.request.user.is_superuser: #logs = IcecastLog.objects.all() logs = IcecastLog.objects.filter(mount=mount) else: #mount = os.path.basename(User.objects.get(username=self.request.user.username).config.streamurl) logs = IcecastLog.objects.filter(mount=mount) if mount: logs = logs.filter(mount=mount) if start and end: logs = logs.filter(datetime_start__gte=start, datetime_end__lte=end, datetime_end__gt=F('datetime_start') + timedelta(seconds=5) ) return logs[:limit] class ProgramStatSerializer(serializers.ModelSerializer): class Meta: model = ProgramStat class ProgramStatViewSet( generics.ListAPIView): #@method_decorator(login_required) def dispatch(self, *args, **kwargs): return super(ProgramStatViewSet, self).dispatch(*args, **kwargs) serializer_class = ProgramStatSerializer def get_queryset(self): """ This view should return a list of all the purchases for the user as determined by the mount portion of the URL. """ mount = self.request.query_params.get('mount', None) start = "%s 00:00:00" % self.request.query_params.get('start', None) end = "%s 00:00:00" % self.request.query_params.get('end', None) limit = self.request.query_params.get('limit', None) if self.request.user.is_superuser: #program_stat = ProgramStat.objects.all() program_stat = ProgramStat.objects.filter(log_entry__mount=mount) else: program_stat = ProgramStat.objects.filter(log_entry__mount=mount) if mount: program_stat = program_stat.filter(log_entry__mount=mount) if start and end: program_stat = program_stat.filter(log_entry__datetime_start__gte=start, log_entry__datetime_end__lte=end) return program_stat[:limit]

agpl-3.0

jsharkey13/isaac-selenium-testing

isaactest/tests/back_to_board.py

1

2871

import time from ..utils.log import log, INFO, ERROR, PASS from ..utils.isaac import get_hexagon_properties from ..utils.i_selenium import assert_tab, image_div from ..tests import TestWithDependency from selenium.common.exceptions import NoSuchElementException __all__ = ["back_to_board"] ##### # Test : Back to Board Button ##### @TestWithDependency("BACK_TO_BOARD") def back_to_board(driver, ISAAC_WEB, WAIT_DUR, **kwargs): """Test whether the back to board button works. - 'driver' should be a Selenium WebDriver. - 'ISAAC_WEB' is the string URL of the Isaac website to be tested. - 'WAIT_DUR' is the time in seconds to wait for JavaScript to run/load. """ assert_tab(driver, ISAAC_WEB) driver.get(ISAAC_WEB) log(INFO, "Got: %s" % ISAAC_WEB) time.sleep(WAIT_DUR) try: questions_tab = driver.find_element_by_xpath("//a[@ui-sref='gameBoards({filter: true})']") questions_tab.click() time.sleep(WAIT_DUR) except NoSuchElementException: log(ERROR, "Can't find 'Questions' tab link; can't continue!") return False try: url = str(driver.current_url).replace("?filter=true", "").replace("?filter", "") # Ignore whether the filter state is set! log(INFO, "Currently on '%s', attempt to access 5 hexagons." % url) for i in range(5): hexagons = driver.find_elements_by_xpath("//a[@class='ru-hex-home-content']") # This has to be inside the loop hexagon = get_hexagon_properties(hexagons[i]) # so that we don't get stale elements. log(INFO, "Got hexagon %s." % (i + 1)) if hexagon["type"] == "Question": hexagons[i].click() log(INFO, "Hexagon is a question; clicked on it.") time.sleep(WAIT_DUR) back_to_board_button = driver.find_element_by_xpath("//a[@ng-click='backToBoard()']") back_to_board_button.click() log(INFO, "Clicked back to board button.") time.sleep(WAIT_DUR) new_url = str(driver.current_url).replace("?filter=true", "").replace("?filter", "") assert new_url == url, "Expected to end on '%s', actually ended on '%s'!" % (url, new_url) log(PASS, "Back to board button worked as expected.") return True except NoSuchElementException: image_div(driver, "ERROR_back_to_board") log(ERROR, "Couldn't find 'Back to Board' button; see 'ERROR_back_to_board.png'! Can't continue!") return False except AssertionError, e: image_div(driver, "ERROR_back_to_board") log(ERROR, "Back to board button failed! %s" % e.message) return False except IndexError: log(ERROR, "Not enough hexagons to click; can't continue!") return False

mit

ndp-systemes/odoo-addons

stock_specific_inventory/__openerp__.py

1

1636

# -*- coding: utf8 -*- # # Copyright (C) 2015 NDP Systèmes (<http://www.ndp-systemes.fr>). # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # { 'name': 'Stock Specific Inventory', 'version': '0.1', 'author': 'NDP Systèmes', 'maintainer': 'NDP Systèmes', 'category': 'Warehouse', 'depends': ['stock'], 'description': """ Stock Specific Inventory ========================== This module adds the possibility to make inventories on a product selection. It also improves the view of last inventories per product. Products can be selected directly from this view and a new inventory on these products be made. """, 'website': 'http://www.ndp-systemes.fr', 'data': [ 'security/ir.model.access.csv', 'views/stock_specific_product_for_inventory.xml' ], 'demo': [ 'test_stock_specific_inventory_demo.xml' ], 'test': [], 'installable': True, 'auto_install': False, 'license': 'AGPL-3', 'application': False, }

agpl-3.0

PaddoInWonderland/PaddoCogs

schmeckles/schmeckles.py

1

2347

import re class Schmeckles: def __init__(self, bot): self.bot = bot self.p = re.compile('([^\n\.\,\r\d-]{0,30})(-?[\d|,]{0,300}\.{0,1}\d{1,300} schmeckle[\w]{0,80})([^\n\.\,\r\d-]{0,30})', re.IGNORECASE) async def schmeckle2usd(self, schmeckle): """1 Schmeckle = $148 USD https://www.reddit.com/r/IAmA/comments/202owt/we_are_dan_harmon_and_justin_roiland_creators_of/cfzfv79""" return schmeckle * 148.0 async def schmeckle2eur(self, schmeckle): return schmeckle * 139.25 # latest USDEUR value async def schmeckle2yen(self, schmeckle): return schmeckle * 139.25 # latest USDYEN value async def schmeckle2rub(self, schmeckle): return schmeckle * 139.25 # latest USDRUB value async def searchForSchmeckles(self, content): if any([x in content.lower() for x in ['?', 'how much', 'what is', 'how many', 'euro', 'usd', 'dollars', 'dollar', 'euros']]): return self.p.search(content) return None async def getSchmeckles(self, content): get_schmeckles = await self.searchForSchmeckles(content) if get_schmeckles: match = get_schmeckles.groups() euro = any([x in match[-1].lower() for x in ['eur', 'euro', 'euros']]) dollar = any([x in match[-1].lower() for x in ['usd', 'dollar', 'dollars']]) if euro and not dollar: value = await self.schmeckle2eur(float(match[1].split()[0])), 'EUR', match[1].split()[0] elif dollar and not euro: value = await self.schmeckle2usd(float(match[1].split()[0])), 'USD', match[1].split()[0] elif not dollar and not euro: value = await self.schmeckle2usd(float(match[1].split()[0])), 'USD', match[1].split()[0] return value return None async def _on_message(self, message): content = message.content author = message.author channel = message.channel if author.id != self.bot.user.id: schmeckles = await self.getSchmeckles(content) if schmeckles: await self.bot.send_message(channel, '{0[2]} SHM is about {0[0]:.2f} {0[1]}'.format(schmeckles)) def setup(bot): cog = Schmeckles(bot) bot.add_listener(cog._on_message, "on_message") bot.add_cog(cog)

gpl-3.0

gabstopper/smc-python

smc/core/general.py

1

15630

""" General configuration areas for an engine. This correlates to service level settings such as DNSRelay, SNMP, etc. """ import collections from smc.base.model import Element from smc.base.util import element_resolver from smc.elements.profiles import DNSRelayProfile from smc.base.structs import NestedDict from smc.policy.interface import InterfacePolicy from smc.api.exceptions import LoadPolicyFailed class SNMP(object): """ SNMP configuration details for applying SNMP on an engine. SNMP requires at minimum an assigned SNMPAgent configuration which defines the SNMP specific settings (version, community string, etc). You can also define specific interfaces to enable SNMP on. By default, if no addresses are specified, SNMP will be defined on all interfaces. .. seealso:: :class:`smc.elements.profiles.SNMPAgent` """ def __init__(self, engine): self.engine = engine @property def agent(self): """ The SNMP agent profile used for this engine. :rtype: SNMPAgent """ return self.engine.from_href( getattr(self.engine, 'snmp_agent_ref', None)) @property def status(self): return bool(getattr(self.engine, 'snmp_agent_ref', False)) def disable(self): """ Disable SNMP on this engine. You must call `update` on the engine for this to take effect. :return: None """ self.engine.data.update( snmp_agent_ref=None, snmp_location='', snmp_interface=[]) def enable(self, snmp_agent, snmp_location=None, snmp_interface=None): """ Enable SNMP on the engine. Specify a list of interfaces by ID to enable only on those interfaces. Only interfaces that have NDI's are supported. :param str,Element snmp_agent: the SNMP agent reference for this engine :param str snmp_location: the SNMP location identifier for the engine :param list snmp_interface: list of interface IDs to enable SNMP :raises ElementNotFound: unable to resolve snmp_agent :raises InterfaceNotFound: specified interface by ID not found """ agent = element_resolver(snmp_agent) snmp_interface = [] if not snmp_interface else snmp_interface interfaces = self._iface_dict(snmp_interface) self.engine.data.update( snmp_agent_ref=agent, snmp_location=snmp_location if snmp_location else '', snmp_interface=interfaces) def _iface_dict(self, snmp_interface): return [values for interface in snmp_interface for values in self.engine.interface.get(interface).ndi_interfaces] @property def _nicids(self): return [str(nic.get('nicid')) for nic in getattr(self.engine, 'snmp_interface', [])] def update_configuration(self, **kwargs): """ Update the SNMP configuration using any kwargs supported in the `enable` constructor. Return whether a change was made. You must call update on the engine to commit any changes. :param dict kwargs: keyword arguments supported by enable constructor :rtype: bool """ updated = False if 'snmp_agent' in kwargs: kwargs.update(snmp_agent_ref=kwargs.pop('snmp_agent')) snmp_interface = kwargs.pop('snmp_interface', None) for name, value in kwargs.items(): _value = element_resolver(value) if getattr(self.engine, name, None) != _value: self.engine.data[name] = _value updated = True if snmp_interface is not None: _snmp_interface = getattr(self.engine, 'snmp_interface', []) if not len(snmp_interface) and len(_snmp_interface): self.engine.data.update(snmp_interface=[]) updated = True elif len(snmp_interface): if set(self._nicids) ^ set(map(str, snmp_interface)): self.engine.data.update( snmp_interface=self._iface_dict(snmp_interface)) updated = True return updated @property def location(self): """ Return the SNMP location string :rtype: str """ return getattr(self.engine, 'snmp_location', None) @property def interface(self): """ Return a list of physical interfaces that the SNMP agent is bound to. :rtype: list(PhysicalInterface) """ nics = set([nic.get('nicid') for nic in \ getattr(self.engine, 'snmp_interface', [])]) return [self.engine.interface.get(nic) for nic in nics] def __repr__(self): return '{0}(enabled={1})'.format( self.__class__.__name__, self.status) class DNSRelay(object): """ DNS Relay allows the engine to provide DNS caching or specific host, IP and domain replies to clients. It can also be used to sinkhole specific DNS requests. .. seealso:: :class:`smc.elements.profiles.DNSRelayProfile` """ def __init__(self, engine): self.engine = engine @property def status(self): """ Status of DNS Relay on this engine. :rtype: bool """ return getattr(self.engine, 'dns_relay_profile_ref', False) def enable(self, interface_id, dns_relay_profile=None): """ Enable the DNS Relay service on this engine. :param int interface_id: interface id to enable relay :param str,DNSRelayProfile dns_relay_profile: DNSRelayProfile element or str href :raises EngineCommandFailed: interface not found :raises ElementNotFound: profile not found :return: None """ if not dns_relay_profile: # Use default href = DNSRelayProfile('Cache Only').href else: href = element_resolver(dns_relay_profile) intf = self.engine.interface.get(interface_id) self.engine.data.update(dns_relay_profile_ref=href) self.engine.data.update(dns_relay_interface=intf.ndi_interfaces) def disable(self): """ Disable DNS Relay on this engine :return: None """ self.engine.data.update(dns_relay_interface=[]) self.engine.data.pop('dns_relay_profile_ref', None) def __repr__(self): return '{0}(enabled={1})'.format( self.__class__.__name__, self.status) class DefaultNAT(object): """ Default NAT on the engine is used to automatically create NAT configurations based on internal routing. This simplifies the need to create specific NAT rules, primarily for outbound traffic. .. note:: You must call engine.update() to commit any changes. """ def __init__(self, engine): self.engine = engine @property def status(self): """ Status of default nat on the engine. :rtype: bool """ return self.engine.data['default_nat'] def enable(self): """ Enable default NAT on this engine """ self.engine.data['default_nat'] = True def disable(self): """ Disable default NAT on this engine """ self.engine.data['default_nat'] = False def __repr__(self): return '{0}(enabled={1})'.format( self.__class__.__name__, self.status) class RankedDNSAddress(object): """ A RankedDNSAddress represents a list of DNS entries used as a ranked list to provide an ordered way to perform DNS queries. DNS entries can be added as raw IP addresses, or as elements of type :class:`smc.elements.network.Host` or :class:`smc.elements.servers.DNSServer` (or combination of both). This is an iterable class yielding namedtuples of type :class:`.DNSEntry`. Normal access is done through an engine reference:: >>> list(engine.dns) [DNSEntry(rank=0,value=8.8.8.8,ne_ref=None), DNSEntry(rank=1,value=None,ne_ref=DNSServer(name=mydnsserver))] >>> engine.dns.append(['8.8.8.8', '9.9.9.9']) >>> engine.dns.prepend(['1.1.1.1']) >>> engine.dns.remove(['8.8.8.8', DNSServer('mydnsserver')]) .. note:: You must call engine.update() to commit any changes. """ def __init__(self, entries): self.entries = entries def __iter__(self): for entry in self.entries: yield DNSEntry(**entry) def __len__(self): return len(self.entries) def __contains__(self, entry): for e in self: try: if e.ne_ref == entry.href: return True except AttributeError: if e.value == entry: return True return False def _rank_dns(self, entry, prepend=False): if prepend and len(self) or not len(self): start_rank = 0 else: start_rank = self.entries[-1].get('rank')+1 additions = [] for e in entry: if e not in self and e not in additions: additions.append(e) if not additions: return if prepend: # Rerank for e in self.entries: e.update((k, v+1) for k, v in e.items() if k == 'rank') for num, addr in enumerate(additions, int(start_rank)): try: self.entries.append({'rank': float(num), 'ne_ref': addr.href}) except AttributeError: self.entries.append({'rank': float(num), 'value': addr}) def add(self, values): return self.append(values) def append(self, values): """ Add DNS entries to the engine at the end of the existing list (if any). A DNS entry can be either a raw IP Address, or an element of type :class:`smc.elements.network.Host` or :class:`smc.elements.servers.DNSServer`. :param list values: list of IP addresses, Host and/or DNSServer elements. :return: None .. note:: If the DNS entry added already exists, it will not be added. It's not a valid configuration to enter the same DNS IP multiple times. This is also true if the element is assigned the same address as a raw IP address already defined. """ self._rank_dns(values) def prepend(self, values): """ Prepend DNS entries to the engine at the beginning of the existing list (if any). A DNS entry can be either a raw IP Address, or an element of type :class:`smc.elements.network.Host` or :class:`smc.elements.servers.DNSServer`. :param list values: list of IP addresses, Host and/or DNSServer elements. :return: None """ self._rank_dns(values, prepend=True) def remove(self, values): """ Remove DNS entries from this ranked DNS list. A DNS entry can be either a raw IP Address, or an element of type :class:`smc.elements.network.Host` or :class:`smc.elements.servers.DNSServer`. :param list values: list of IP addresses, Host and/or DNSServer elements. :return: None """ removables = [] for value in values: if value in self: removables.append(value) if removables: self.entries[:] = [entry._asdict() for entry in self if entry.value not in removables and not entry.element in removables] # Rerank to maintain order for i, entry in enumerate(self.entries): entry.update(rank='{}'.format(i)) class DNSEntry(collections.namedtuple('DNSEntry', 'value rank ne_ref')): """ DNSEntry represents a single DNS entry within an engine DNSAddress list. :ivar str value: IP address value of this entry (None if type Element is used) :ivar int rank: order rank for the entry :ivar str ne_ref: network element href of entry. Use element property to resolve to type Element. :ivar Element element: If the DNS entry is an element type, this property will returned a resolved version of the ne_ref field. """ __slots__ = () def __new__(cls, rank, value=None, ne_ref=None): # @ReservedAssignment return super(DNSEntry, cls).__new__(cls, value, rank, ne_ref) @property def element(self): return Element.from_href(self.ne_ref) def __repr__(self): return 'DNSEntry(rank={0},value={1},ne_ref={2})'\ .format(self.rank, self.value, self.element) class Layer2Settings(NestedDict): """ Layer 2 Settings are only applicable on Layer 3 Firewall engines that want to run specific interfaces in layer 2 mode. This requires that a Layer 2 Interface Policy is applied to the engine. You can also set connection tracking and bypass on overload settings for these interfaces as well. Set policy for the engine:: engine.l2fw_settings.enable(InterfacePolicy('mylayer2')) :ivar bool bypass_overload_traffic: whether to bypass traffic on overload :ivar str tracking_mode: connection tracking mode .. note:: You must call engine.update() to commit any changes. .. warning:: This feature requires SMC and engine version >= 6.3 """ def __init__(self, engine): l2 = engine.data['l2fw_settings'] super(Layer2Settings, self).__init__(data=l2) def connection_tracking(self, mode): """ Set the connection tracking mode for these layer 2 settings. :param str mode: normal, strict, loose :return: None """ if mode in ('normal', 'strict', 'loose'): self.update(tracking_mode=mode) def bypass_on_overload(self, value): """ Set the l2fw settings to bypass on overload. :param bool value: boolean to indicate bypass setting :return: None """ self.update(bypass_overload_traffic=value) def disable(self): """ Disable the layer 2 interface policy """ self.pop('l2_interface_policy_ref', None) def enable(self, policy): """ Set a layer 2 interface policy. :param str,Element policy: an InterfacePolicy or str href :raises LoadPolicyFailed: Invalid policy specified :raises ElementNotFound: InterfacePolicy not found :return: None """ if hasattr(policy, 'href'): if not isinstance(policy, InterfacePolicy): raise LoadPolicyFailed('Invalid policy type specified. The policy' 'type must be InterfacePolicy') self.update(l2_interface_policy_ref=element_resolver(policy)) @property def policy(self): """ Return the InterfacePolicy for this layer 3 firewall. :rtype: InterfacePolicy """ return InterfacePolicy.from_href(self.get('l2_interface_policy_ref')) def __repr__(self): return '{0}(policy={1})'.format( self.__class__.__name__, self.policy)

apache-2.0

joshua-cogliati-inl/raven

framework/Optimizers/GradientBasedOptimizer.py

1

52237

# Copyright 2017 Battelle Energy Alliance, LLC # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """ This module contains the Gradient Based Optimization strategy Created on June 16, 2016 @author: chenj """ #for future compatibility with Python 3-------------------------------------------------------------- from __future__ import division, print_function, unicode_literals, absolute_import #End compatibility block for Python 3---------------------------------------------------------------- #External Modules------------------------------------------------------------------------------------ import sys import os import copy import abc import numpy as np from numpy import linalg as LA from sklearn.neighbors import NearestNeighbors #External Modules End-------------------------------------------------------------------------------- #Internal Modules------------------------------------------------------------------------------------ from .Optimizer import Optimizer from Assembler import Assembler from utils import utils,cached_ndarray,mathUtils #Internal Modules End-------------------------------------------------------------------------------- class GradientBasedOptimizer(Optimizer): """ This is the base class for gradient based optimizer. The following methods need to be overridden by all derived class self.localLocalInputAndChecks(self, xmlNode,paraminput) self.localLocalInitialize(self, solutionExport) self.localLocalGenerateInput(self,model,oldInput) self.localEvaluateGradient(self, optVarsValues, gradient = None) """ ########################## # Initialization Methods # ########################## def __init__(self): """ Default Constructor that will initialize member variables with reasonable defaults or empty lists/dictionaries where applicable. @ In, None @ Out, None """ Optimizer.__init__(self) self.ableToHandelFailedRuns = True # is this optimizer able to handle failed runs? self.constraintHandlingPara = {} # Dict containing parameters for parameters related to constraints handling self.gradientNormTolerance = 1.e-3 # tolerance on the L2 norm of the gradient self.gradDict = {} # Dict containing information for gradient related operations self.gradDict['numIterForAve' ] = 1 # Number of iterations for gradient estimation averaging, denoising number. self.gradDict['pertNeeded' ] = 1 # Number of perturbation needed to evaluate gradient (globally, considering denoising) for example, pertNeeded = dimension * 1(if not central differenc) * denoise in Finite Difference self.paramDict['pertSingleGrad'] = 1 # Number of perturbation needed to evaluate a single gradient denoised points needed to evaluate gradient, eg, 1 for SPSA, dim for FD w/o central diff, 2*dim for central diff self.gradDict['pertPoints' ] = {} # Dict containing normalized inputs sent to model for gradient evaluation self.readyVarsUpdate = {} # Bool variable indicating the finish of gradient evaluation and the ready to update decision variables self.counter['perturbation' ] = {} # Counter for the perturbation performed. self.counter['gradientHistory' ] = {} # In this dict we store the gradient value (versor) for current and previous iterations {'trajectoryID':[{},{}]} self.counter['gradNormHistory' ] = {} # In this dict we store the gradient norm for current and previous iterations {'trajectoryID':[float,float]} self.counter['varsUpdate' ] = {} self.counter['solutionUpdate' ] = {} self.counter['lastStepSize' ] = {} # counter to track the last step size taken, by trajectory # line search parameters used in dcsrch function inside minpack2 from Scipy self.counter['iSave'] = {} # integer work array of dimension 2 for line search in scipy minpack2 # isave(1): whether a minimizer has been bracketed in an interval with endpoints # isave(2): whether a lower function value has been obtained self.counter['dSave'] = {} # double precision work array of dimension 13 for line search, this array store the previous line search results as: # dsave(1): derivative of the problem at previous step # dsave(2) nonnegative tolerance for the sufficient decrease condition on gradient calculation # dsave(3) derivative at the best step on variables # dsave(4) derivative at best residuals; # dsave(5) value of the problem at step # dsave(6) value of the problem at best step # dsave(7) value of the problem at second best step # dsave(8) best step obtained so far, endpoint of the interval that contains the minimizer. # dsave(9) second endpoint of the interval that contains the minimizer. # dsave(10) minimum step in line search # dsave(11) maximum step in line search # dsave(12) range of the step # dsave(13) range to decide if a bisection step is needed self.counter['task'] = {} # bite string for the task in line search, initial entry task must be set to 'START', at the end of each line search exit with convergence, a warning or an error # Conjugate gradient parameters self.counter['gtol'] = {} # specifies a nonnegative tolerance for the curvature condition in conjugate gradient calculation self.counter['xk'] = {} # ndarray, best optimal point as an array for conjugate gradient calculation self.counter['gfk'] = {} # ndarray, gradient value as an array for current point in searching the strong wolfe condition in conjugate calculation self.counter['pk'] = {} # ndarray, search direction in searching the strong wolfe condition in conjugate calculation self.counter['newFVal'] = {} # float, function value for a new optimal point self.counter['oldFVal'] = {} # float, function value for last optimal point self.counter['oldOldFVal'] = {} # float, function value for penultimate optimal point self.counter['oldGradK'] = {} # ndarray, gradient value as an array for current best optimal point self.counter['gNorm'] = {} # float, norm of the current gradient self.counter['deltaK'] = {} # float, inner product of the current gradient for calculation of the Polak–Ribière stepsize self.counter['derPhi0'] = {} # float, objective function derivative at each begining of the line search self.counter['alpha'] = {} # float, stepsize for conjugate gradient method in current dirrection self.resampleSwitch = True # bool, resample switch self.resample = {} # bool, whether next point is a resample opt point if True, then the next submit point is a resample opt point with new perturbed gradient point self.convergeTraj = {} self.convergenceProgress = {} # tracks the convergence progress, by trajectory self.trajectoriesKilled = {} # by traj, store traj killed, so that there's no mutual destruction self.recommendToGain = {} # recommended action to take in next step, by trajectory self.gainGrowthFactor = 2. # max step growth factor self.gainShrinkFactor = 2. # max step shrinking factor self.optPointIndices = [] # in this list we store the indices that correspond to the opt point self.perturbationIndices = [] # in this list we store the indices that correspond to the perturbation. self.useCentralDiff = False # whether to use central differencing self.useGradHist = False # whether to use Gradient history # REWORK 2018-10 for simultaneous point-and-gradient evaluations self.realizations = {} # by trajectory, stores the results obtained from the jobs running, see setupNewStorage for structure # register metadata self.addMetaKeys(['trajID','varsUpdate','prefix']) def localInputAndChecks(self, xmlNode, paramInput): """ Method to read the portion of the xml input that belongs to all gradient based optimizer only and initialize some stuff based on the inputs got @ In, xmlNode, xml.etree.ElementTree.Element, Xml element node @ In, paramInput, InputData.ParameterInput, the parsed parameters @ Out, None """ for child in paramInput.subparts: if child.getName() == "initialization": for grandchild in child.subparts: tag = grandchild.getName() if tag == "resample": self.resampleSwitch = grandchild.value if child.getName() == "convergence": for grandchild in child.subparts: tag = grandchild.getName() if tag == "gradientThreshold": self.gradientNormTolerance = grandchild.value elif tag == "gainGrowthFactor": self.gainGrowthFactor = grandchild.value self.raiseADebug('Gain growth factor is set at',self.gainGrowthFactor) elif tag == "gainShrinkFactor": self.gainShrinkFactor = grandchild.value self.raiseADebug('Gain shrink factor is set at',self.gainShrinkFactor) elif tag == "centralDifference": self.useCentralDiff = grandchild.value elif tag == "useGradientHistory": self.useGradHist = grandchild.value self.gradDict['numIterForAve'] = int(self.paramDict.get('numGradAvgIterations', 1)) def localInitialize(self,solutionExport): """ Method to initialize settings that belongs to all gradient based optimizer @ In, solutionExport, DataObject, a PointSet to hold the solution @ Out, None """ for traj in self.optTraj: self.gradDict['pertPoints'][traj] = {} self.counter['perturbation'][traj] = 0 self.counter['varsUpdate'][traj] = 0 self.counter['solutionUpdate'][traj] = 0 self.counter['gradientHistory'][traj] = [{},{}] self.counter['lastStepSize'][traj] = [{},{}] self.counter['gradNormHistory'][traj] = [0.0,0.0] self.counter['persistence'][traj] = 0 self.counter['iSave'][traj] = np.zeros((2,), np.intc) self.counter['dSave'][traj] = np.zeros((13,), float) self.counter['task'][traj] = b'START' self.counter['gtol'][traj] = 1e-08 self.counter['xk'][traj] = None self.counter['gfk'][traj] = None self.counter['pk'][traj] = None self.counter['newFVal'][traj] = None self.counter['oldFVal'][traj] = None self.counter['oldOldFVal'][traj] = None self.counter['oldGradK'][traj] = None self.counter['gNorm'][traj] = None self.counter['deltaK'][traj] = None self.counter['derPhi0'][traj] = None self.counter['alpha'][traj] = None self.resample[traj] = False self.optVarsHist[traj] = {} self.readyVarsUpdate[traj] = False self.convergeTraj[traj] = False self.status[traj] = {'process':'submitting new opt points', 'reason':'just started'} self.counter['recentOptHist'][traj] = [{},{}] self.trajectoriesKilled[traj] = [] # end job runnable equal to number of trajectory self._endJobRunnable = len(self.optTraj) # initialize index lists ## opt point evaluations are indices 0 through number of re-evaluation points self.optPointIndices = list(range(0,self.gradDict['numIterForAve']+1)) ## perturbation evaluations are indices starting at the end of optPoint and going through all the rest self.perturbationIndices = list(range(self.gradDict['numIterForAve'],self.gradDict['numIterForAve']*(self.paramDict['pertSingleGrad']+1))) #specializing the self.localLocalInitialize() self.localLocalInitialize(solutionExport=solutionExport) @abc.abstractmethod def localLocalInitialize(self, solutionExport): """ Method to initialize local settings. @ In, solutionExport, DataObject, a PointSet to hold the solution @ Out, None """ pass ############### # Run Methods # ############### def evaluateGradient(self, traj): """ Method to evaluate gradient based on perturbed points and model evaluations. @ In, traj, int, the trajectory id @ Out, gradient, dict, dictionary containing gradient estimation. gradient should have the form {varName: gradEstimation} """ # let the local do the main gradient evaluation gradient = self.localEvaluateGradient(traj) # we intend for gradient to give direction only, so get the versor ## NOTE this assumes gradient vectors are 0 or 1 dimensional, not 2 or more! (vectors or scalars, not matrices) gradientNorm = self.calculateMultivectorMagnitude(gradient.values()) # store this norm, infinite or not self.counter['gradNormHistory'][traj][0] = gradientNorm #fix inf if gradientNorm == np.inf: # if there are infinites, then only infinites should remain, and they are +-1 for v,var in enumerate(gradient.keys()): # first, set all non-infinites to 0, since they can't compete with infinites gradient[var][-np.inf < gradient[var] < np.inf] = 0.0 # set +- infinites to +- 1 (arbitrary) since they're all equally important gradient[var][gradient[var] == -np.inf] = -1.0 gradient[var][gradient[var] == np.inf] = 1.0 # set up the new grad norm gradientNorm = self.calculateMultivectorMagnitude(gradient.values()) # normalize gradient (if norm is zero, skip this) if gradientNorm != 0.0: for var in gradient.keys(): gradient[var] = gradient[var]/gradientNorm # if float coming in, make it a float going out if len(gradient[var])==1: gradient[var] = float(gradient[var]) # store gradient try: self.counter['gradientHistory'][traj][1] = self.counter['gradientHistory'][traj][0] self.counter['lastStepSize'][traj][1] = self.counter['lastStepSize'][traj][0] except IndexError: pass # don't have a history on the first pass self.counter['gradientHistory'][traj][0] = gradient return gradient def finalizeSampler(self, failedRuns): """ Method called at the end of the Step when no more samples will be taken. Closes out optimizer. @ In, failedRuns, list, list of JobHandler.ExternalRunner objects @ Out, None """ Optimizer.handleFailedRuns(self, failedRuns) # get the most optimal point among the trajectories bestValue = None bestTraj = None for traj in self.counter['recentOptHist'].keys(): value = self.counter['recentOptHist'][traj][0][self.objVar] self.raiseADebug('For trajectory "{}" the best value was'.format(traj+1),value) if bestTraj is None: bestTraj = traj bestValue = value continue if self.checkIfBetter(value,bestValue): bestTraj = traj bestValue = value # now have the best trajectory, so write solution export bestPoint = self.denormalizeData(self.counter['recentOptHist'][bestTraj][0]) self.raiseADebug('The best overall trajectory ending was for trajectory "{}".'.format(bestTraj+1)) self.raiseADebug(' The optimal location is at:') for v in self.getOptVars(): self.raiseADebug(' {} = {}'.format(v,bestPoint[v])) self.raiseADebug(' The objective value there: {}'.format(bestValue)) self.raiseADebug('====================') self.raiseADebug('| END OPTIMIZATION |') self.raiseADebug('====================') # _always_ re-add the last point to the solution export, but use a new varsUpdate value overwrite = {'varsUpdate': self.counter['varsUpdate'][traj]} self.writeToSolutionExport(bestTraj, self.normalizeData(bestPoint), True, overwrite=overwrite) def localEvaluateGradient(self, optVarsValues, gradient = None): """ Local method to evaluate gradient. @ In, optVarsValues, dict, dictionary containing perturbed points. optVarsValues should have the form {pertIndex: {varName: [varValue1 varValue2]}} Therefore, each optVarsValues[pertIndex] should return a dict of variable values that is sufficient for gradient evaluation for at least one variable (depending on specific optimization algorithm) @ In, gradient, dict, optional, dictionary containing gradient estimation by the caller. gradient should have the form {varName: gradEstimation} @ Out, gradient, dict, dictionary containing gradient estimation. gradient should have the form {varName: gradEstimation} """ return gradient def localFinalizeActualSampling(self,jobObject,model,myInput): """ Overwrite only if you need something special at the end of each run.... This function is used by optimizers that need to collect information from the just ended run @ In, jobObject, instance, an instance of a Runner @ In, model, Model, instance of a RAVEN model @ In, myInput, list, the generating input @ Out, None """ # collect finished jobs prefix = jobObject.getMetadata()['prefix'] traj, step, identifier = [int(x) for x in prefix.split('_')] # FIXME This isn't generic for any prefixing system self.raiseADebug('Collected sample "{}"'.format(prefix)) failed = jobObject.getReturnCode() != 0 if failed: self.raiseADebug(' ... sample "{}" FAILED. Cutting step and re-queueing.'.format(prefix)) # since run failed, cut the step and requeue ## cancel any further runs at this point self.cancelJobs([self._createEvaluationIdentifier(traj, self.counter['varsUpdate'][traj], i) for i in range(1, self.perturbationIndices[-1]+1)]) self.recommendToGain[traj] = 'cut' grad = self.counter['gradientHistory'][traj][0] new = self._newOptPointAdd(grad, traj) if new is not None: self._createPerturbationPoints(traj, new) else: self.raiseADebug('After failing a point, trajectory {} is not adding new points!'.format(traj)) self._setupNewStorage(traj) else: # update self.realizations dictionary for the right trajectory # category: is this point an "opt" or a "grad" evaluations? # number is which variable is being perturbed, ie which dimension 0 indexed category, number, _, cdId = self._identifierToLabel(identifier) # done is whether the realization finished # index: where is it in the dataObject # find index of sample in the target evaluation data object done, index = self._checkModelFinish(str(traj), str(step), str(identifier)) # sanity check if not done: self.raiseAnError(RuntimeError,'Trying to collect "{}" but identifies as not done!'.format(prefix)) # store index for future use # number is the varID number = number + (cdId * len(self.fullOptVars)) self.realizations[traj]['collect'][category][number].append(index) # check if any further action needed because we have all the points we need for opt or grad if len(self.realizations[traj]['collect'][category][number]) == self.realizations[traj]['need']: # get the output space (input space included as well) outputs = self._averageCollectedOutputs(self.realizations[traj]['collect'][category][number]) # store denoised results self.realizations[traj]['denoised'][category][number] = outputs # if we just finished "opt", check some acceptance and convergence checking if category == 'opt': converged = self._finalizeOptimalCandidate(traj,outputs) else: converged = False # if both opts and grads are now done, then we can do an evaluation ## note that by now we've ALREADY accepted the point; if it was rejected, it would have been reset by now. optDone = bool(len(self.realizations[traj]['denoised']['opt'][0])) gradDone = all( len(self.realizations[traj]['denoised']['grad'][i]) for i in range(self.paramDict['pertSingleGrad'])) if not converged and optDone and gradDone: optCandidate = self.normalizeData(self.realizations[traj]['denoised']['opt'][0]) # update solution export ## only write here if we want to write on EVERY optimizer iteration (each new optimal point) if self.writeSolnExportOn == 'every': self.writeToSolutionExport(traj, optCandidate, self.realizations[traj]['accepted']) # whether we wrote to solution export or not, update the counter self.counter['solutionUpdate'][traj] += 1 self.counter['varsUpdate'][traj] += 1 ## since accepted, update history try: self.counter['recentOptHist'][traj][1] = copy.deepcopy(self.counter['recentOptHist'][traj][0]) except KeyError: # this means we don't have an entry for this trajectory yet, so don't copy anything pass # store realization of most recent developments self.counter['recentOptHist'][traj][0] = optCandidate # find the new gradient for this trajectory at the new opt point grad = self.evaluateGradient(traj) # get a new candidate new = self._newOptPointAdd(grad, traj) if new is not None: # add new gradient points self._createPerturbationPoints(traj, new) # reset storage self._setupNewStorage(traj) def localGenerateInput(self,model,oldInput): """ Method to generate input for model to run @ In, model, model instance, it is the instance of a RAVEN model @ In, oldInput, list, a list of the original needed inputs for the model (e.g. list of files, etc. etc) @ Out, None """ self.readyVarsUpdate = {traj:False for traj in self.optTrajLive} def localStillReady(self,ready, convergence = False): #,lastOutput=None """ Determines if optimizer is ready to provide another input. If not, and if jobHandler is finished, this will end sampling. @ In, ready, bool, variable indicating whether the caller is prepared for another input. @ In, convergence, bool, optional, variable indicating whether the convergence criteria has been met. @ Out, ready, bool, boolean variable indicating whether the caller is prepared for another input. """ #let this be handled at the local subclass level for now return ready ################### # Utility Methods # ################### def _averageCollectedOutputs(self,collection): """ Averages the results of several realizations that are denoising evaluations of a single point @ In, collection, list, list of indices of evaluations for a single point @ Out, outputs, dict, dictionary of average values """ # make a place to store distinct evaluation values outputs = dict((var,np.zeros(self.gradDict['numIterForAve'],dtype=object)) for var in self.solutionExport.getVars('output') if var in self.mdlEvalHist.getVars('output')) for i, index in enumerate(collection): vals = self.mdlEvalHist.realization(index=index) # store the inputs for later on first iteration if i == 0: inputs = dict((var,vals[var]) for var in self.getOptVars()) for var in outputs.keys(): # store values; cover vector variables as well as scalars, as well as vectors that should be scalars if hasattr(vals[var],'__len__') and len(vals[var]) == 1: outputs[var][i] = float(vals[var]) else: outputs[var][i] = vals[var] # average the collected outputs for the opt point for var,vals in outputs.items(): outputs[var] = vals.mean() outputs.update(inputs) return outputs def calculateMultivectorMagnitude(self,values): """ Calculates the magnitude of vector "values", where values might be a combination of scalars and vectors (but not matrices [yet]). Calculates the magnitude as if "values" were flattened into a 1d array. @ In, values, list, values for which the magnitude will be calculated @ Out, mag, float, magnitude """ # use np.linalg.norm (Frobenius norm) to calculate magnitude ## pre-normalise vectors, this is mathematically equivalent to flattening the vector first ## NOTE this assumes gradient vectors are 0 or 1 dimensional, not 2 or more! (vectors or scalars, not matrices) # TODO this could be sped up if we could avoid calling np.atleast_1d twice, but net slower if we loop first preMag = [np.linalg.norm(val) if len(np.atleast_1d(val))>1 else np.atleast_1d(val)[0] for val in values] ## then get the magnitude of the result, and return it return np.linalg.norm(preMag) def checkConvergence(self): """ Method to check whether the convergence criteria has been met. @ In, None @ Out, convergence, list, list of bool variable indicating whether the convergence criteria has been met for each trajectory. """ convergence = True for traj in self.optTraj: if not self.convergeTraj[traj]: convergence = False break return convergence def _checkModelFinish(self, traj, updateKey, evalID): """ Determines if the Model has finished running an input and returned the output @ In, traj, int, traj on which the input is being checked @ In, updateKey, int, the id of variable update on which the input is being checked @ In, evalID, int or string, indicating the id of the perturbation (int) or its a variable update (string 'v') @ Out, _checkModelFinish, tuple(bool, int), (1,realization dictionary), (indicating whether the Model has finished the evaluation over input identified by traj+updateKey+evalID, the index of the location of the input in dataobject) """ if len(self.mdlEvalHist) == 0: return (False,-1) lookFor = '{}_{}_{}'.format(traj,updateKey,evalID) index,match = self.mdlEvalHist.realization(matchDict = {'prefix':lookFor}) # if no match, return False if match is None: return False,-1 # otherwise, return index of match return True, index def _createEvaluationIdentifier(self,trajID,iterID,evalType): """ Create evaluation identifier @ In, trajID, integer, trajectory identifier @ In, iterID, integer, iteration number (identifier) @ In, evalType, integer or string, evaluation type (v for variable update; otherwise id for gradient evaluation) @ Out, identifier, string, the evaluation identifier """ identifier = str(trajID) + '_' + str(iterID) + '_' + str(evalType) return identifier def _finalizeOptimalCandidate(self,traj,outputs): """ Once all the data for an opt point has been collected: - determine convergence - determine redundancy - determine acceptability - queue new points (if rejected) @ In, traj, int, the trajectory we are currently considering @ In, outputs, dict, denoised new optimal point @ Out, converged, bool, if True then indicates convergence has been reached """ # check convergence and check if new point is accepted (better than old point) if self.resample[traj]: accepted = True else: accepted = self._updateConvergenceVector(traj, self.counter['solutionUpdate'][traj], outputs) # if converged, we can wrap up this trajectory if self.convergeTraj[traj]: # end any excess gradient evaluation jobs self.cancelJobs([self._createEvaluationIdentifier(traj,self.counter['varsUpdate'][traj],i) for i in self.perturbationIndices]) return True #converged # if not accepted, we need to scrap this run and set up a new one if accepted: # store acceptance for later if self.resample[traj]: self.realizations[traj]['accepted'] = 'resample' self.raiseADebug('This is a resample point') else: self.realizations[traj]['accepted'] = 'accepted' self.resample[traj] = False else: self.resample[traj] = self.checkResampleOption(traj) # cancel all gradient evaluations for the rejected candidate immediately self.cancelJobs([self._createEvaluationIdentifier(traj,self.counter['varsUpdate'][traj],i) for i in self.perturbationIndices]) # update solution export optCandidate = self.normalizeData(self.realizations[traj]['denoised']['opt'][0]) ## only write here if we want to write on EVERY optimizer iteration (each new optimal point) if self.writeSolnExportOn == 'every': self.writeToSolutionExport(traj, optCandidate, self.realizations[traj]['accepted']) # whether we wrote to solution export or not, update the counter self.counter['solutionUpdate'][traj] += 1 self.counter['varsUpdate'][traj] += 1 # new point setup ## keep the old grad point grad = self.counter['gradientHistory'][traj][0] new = self._newOptPointAdd(grad, traj,resample = self.resample[traj]) if new is not None: self._createPerturbationPoints(traj, new, resample = self.resample[traj]) self._setupNewStorage(traj) return False #not converged def fractionalStepChangeFromGradHistory(self,traj): """ Uses the dot product between two successive gradients to determine a fractional multiplier for the step size. For instance, if the dot product is 1.0, we're consistently moving in a straight line, so increase step size. If the dot product is -1.0, we've gone forward and then backward again, so cut the step size down before moving again. If the dot product is 0.0, we're moving orthogonally, so don't change step size just yet. @ In, traj, int, the trajectory for whom we are creating a fractional step size @ Out, frac, float, the fraction by which to multiply the existing step size """ # if we have a recommendation from elsewhere, take that first if traj in self.recommendToGain.keys(): recommend = self.recommendToGain.pop(traj) if recommend == 'cut': frac = 1./self.gainShrinkFactor elif recommend == 'grow': frac = self.gainGrowthFactor else: self.raiseAnError(RuntimeError,'unrecognized gain recommendation:',recommend) self.raiseADebug('Based on recommendation "{}", step size multiplier is: {}'.format(recommend,frac)) return frac # otherwise, no recommendation for this trajectory, so move on #if we don't have two evaluated gradients, just return 1.0 grad1 = self.counter['gradientHistory'][traj][1] if len(grad1) == 0: # aka if grad1 is empty dict return 1.0 #otherwise, do the dot product between the last two gradients grad0 = self.counter['gradientHistory'][traj][0] # scalar product ## NOTE assumes scalar or vector, not matrix, values prod = np.sum( [np.sum(grad0[key]*grad1[key]) for key in grad0.keys()] ) #rescale from [-1, 1] to [1/g, g] if prod > 0: frac = self.gainGrowthFactor**prod else: frac = self.gainShrinkFactor**prod self.raiseADebug('Based on gradient history, step size multiplier is:',frac) return frac def _getJobsByID(self,traj): """ Overwrite only if you need something special at the end of each run.... This function is used by optimizers that need to collect information from the just ended run @ In, traj, int, ID of the trajectory for whom we collect jobs @ Out, solutionExportUpdatedFlag, bool, True if the solutionExport needs updating @ Out, solutionIndeces, list(int), location of updates within the full targetEvaluation data object """ solutionUpdateList = [] solutionIndeces = [] # get all the opt point results (these are the multiple evaluations of the opt point) for i in range(self.gradDict['numIterForAve']): identifier = i solutionExportUpdatedFlag, index = self._checkModelFinish(traj, self.counter['solutionUpdate'][traj], str(identifier)) solutionUpdateList.append(solutionExportUpdatedFlag) solutionIndeces.append(index) solutionExportUpdatedFlag = all(solutionUpdateList) return solutionExportUpdatedFlag,solutionIndeces def getQueuedPoint(self,traj,denorm=True): """ Pops the first point off the submission queue (or errors if empty). By default denormalized the point before returning. @ In, traj, int, the trajectory from whose queue we should obtain an entry @ In, denorm, bool, optional, if True the input data will be denormalized before returning @ Out, prefix, #_#_# @ Out, point, dict, {var:val} """ try: entry = self.submissionQueue[traj].popleft() except IndexError: self.raiseAnError(RuntimeError,'Tried to get a point from submission queue of trajectory "{}" but it is empty!'.format(traj)) prefix = entry['prefix'] point = entry['inputs'] if denorm: point = self.denormalizeData(point) return prefix,point def _identifierToLabel(self,identifier): """ Maps identifiers (eg. prefix = trajectory_step_identifier) to labels (eg. ("grad",2) or ("opt",0)) @ In, identifier, int, number of evaluation within trajectory and step @ Out, label, tuple, first entry is "grad" or "opt", second is which grad it belongs to (opt is always 0) """ if identifier in self.perturbationIndices: category = 'grad' if self.paramDict['pertSingleGrad'] == 1: # no need to calculate the pertPerVar if pertSingleGrad is 1 pertPerVar = 1 else: pertPerVar = self.paramDict['pertSingleGrad'] // (1+self.useCentralDiff) varId = (identifier - self.gradDict['numIterForAve']) % pertPerVar denoId = (identifier - self.gradDict['numIterForAve'])// self.paramDict['pertSingleGrad'] # for cdId 0 is the first cdID 1 is the second side of central Diff if len(self.fullOptVars) == 1: #expect 0 or 1 for cdID, but % len(self.fullOptVars) will always be 0 if len(self.fullOptVars)=1 cdId = (identifier - self.gradDict['numIterForAve']) % self.paramDict['pertSingleGrad'] else: cdId = ((identifier - self.gradDict['numIterForAve'])// pertPerVar) % len(self.fullOptVars) if not self.useCentralDiff: cdId = 0 else: category = 'opt' varId = 0 denoId = identifier cdId = 0 return category, varId, denoId, cdId def localCheckConstraint(self, optVars, satisfaction = True): """ Local method to check whether a set of decision variables satisfy the constraint or not @ In, optVars, dict, dictionary containing the value of decision variables to be checked, in form of {varName: varValue} @ In, satisfaction, bool, optional, variable indicating how the caller determines the constraint satisfaction at the point optVars @ Out, satisfaction, bool, variable indicating the satisfaction of constraints at the point optVars """ return satisfaction def proposeNewPoint(self,traj,point): """ See base class. Used to set next recommended point to use for algorithm, overriding the gradient descent. @ In, traj, int, trajectory who gets proposed point @ In, point, dict, input space as dictionary {var:val} @ Out, None """ Optimizer.proposeNewPoint(self,traj,point) self.counter['varsUpdate'][traj] += 1 #usually done when evaluating gradient, but we're bypassing that self.queueUpOptPointRuns(traj,self.recommendedOptPoint[traj]) def queueUpOptPointRuns(self,traj,point): """ Establishes a queue of runs, all on the point currently stored in "point", to satisfy stochastic denoising. @ In, traj, int, the trajectory who needs the queue @ In, point, dict, input space as {var:val} NORMALIZED @ Out, None """ # TODO sanity check, this could be removed for efficiency later for i in range(self.gradDict['numIterForAve']): #entries into the queue are as {'inputs':{var:val}, 'prefix':runid} where runid is <traj>_<varUpdate>_<evalNumber> as 0_0_2 nPoint = {'inputs':copy.deepcopy(point)} #deepcopy to prevent simultaneous alteration nPoint['prefix'] = self._createEvaluationIdentifier(traj,self.counter['varsUpdate'][traj],i) # from 0 to self.gradDict['numIterForAve'] are opt point evals # this submission queue only have the denoise number of opt point self.submissionQueue[traj].append(nPoint) def _removeRedundantTraj(self, trajToRemove, currentInput): """ Local method to remove multiple trajectory @ In, trajToRemove, int, identifier of the trajector to remove @ In, currentInput, dict, the last variable on trajectory traj @ Out, removed, bool, if True then trajectory was halted """ # TODO replace this with a kdtree search removeFlag = False def getRemoved(trajThatSurvived, fullList=None): """ Collect list of all the trajectories removed by this one, or removed by trajectories removed by this one, and etc @ In, trajThatSurvived, int, surviving trajectory that has potentially removed others @ In, fullList, list, optional, if included is the partial list to add to @ Out, fullList, list, list of all traj removed (explicitly or implicitly) by this one """ if fullList is None: fullList = [] removed = self.trajectoriesKilled[trajThatSurvived] fullList += removed for rm in removed: fullList = getRemoved(rm, fullList) return fullList #end function definition notEligibleToRemove = [trajToRemove] + getRemoved(trajToRemove) # determine if "trajToRemove" should be terminated because it is following "traj" for traj in self.optTraj: #don't consider removal if comparing against itself, # or a trajectory removed by this one, or a trajectory removed by a trajectory removed by this one (recursive) # -> this prevents mutual destruction cases if traj not in notEligibleToRemove: #FIXME this can be quite an expensive operation, looping through each other trajectory for updateKey in self.optVarsHist[traj].keys(): inp = self.optVarsHist[traj][updateKey] #FIXME deepcopy needed? Used to be present, but removed for now. if len(inp) < 1: #empty continue dist = self.calculateMultivectorMagnitude( [inp[var] - currentInput[var] for var in self.getOptVars()] ) if dist < self.thresholdTrajRemoval: self.raiseADebug('Halting trajectory "{}" because it is following trajectory "{}"'.format(trajToRemove,traj)) # cancel existing jobs for trajectory self.cancelJobs([self._createEvaluationIdentifier(traj, self.counter['varsUpdate'][traj]-1, i) for i in self.perturbationIndices]) self.trajectoriesKilled[traj].append(trajToRemove) #TODO the trajectory to remove should be chosen more carefully someday, for example, the one that has the smallest steps or lower loss value currently removeFlag = True break if removeFlag: break if removeFlag: for trajInd, tr in enumerate(self.optTrajLive): if tr == trajToRemove: self.optTrajLive.pop(trajInd) self.status[trajToRemove] = {'process':'following traj '+str(traj),'reason':'removed as redundant'} break return True else: return False def _setupNewStorage(self,traj,keepOpt=False): """ Assures correct structure for receiving results from sample evaluations @ In, traj, int, trajectory of interest @ In, keepOpt, bool, optional, if True then don't reset the denoised opt @ Out, None """ # store denoised opt if requested if keepOpt: den = self.realizations[traj]['denoised']['opt'] denoises = self.gradDict['numIterForAve'] self.realizations[traj] = {'collect' : {'opt' : [ [] ], 'grad': [ [] for _ in range(self.paramDict['pertSingleGrad']) ] }, 'denoised': {'opt' : [ [] ], 'grad': [ [] for _ in range(self.paramDict['pertSingleGrad']) ] }, 'need' : denoises, 'accepted': 'rejected', } # reset opt if requested if keepOpt: self.realizations[traj]['denoised']['opt'] = den self.realizations[traj]['accepted'] = True def _updateConvergenceVector(self, traj, varsUpdate, currentPoint, conj=False): """ Local method to update convergence vector. @ In, traj, int, identifier of the trajector to update @ In, varsUpdate, int, current variables update iteration number @ In, currentPoint, float, candidate point for optimization path @ In, conj, bool, optional, identify whether using conjugate gradient to check convergence, if true then do not clear the persistance @ Out, accepted, True if point was rejected otherwise False """ # first, check if we're at varsUpdate 0 (first entry); if so, we are at our first point if varsUpdate == 0: # we don't have enough points to decide to accept or reject the new point, so accept it as the initial point self.raiseADebug('Accepting first point, since we have no rejection criteria.') return True ## first, determine if we want to keep the new point # obtain the loss values for comparison currentLossVal = currentPoint[self.objVar] oldPoint = self.counter['recentOptHist'][traj][0] oldLossVal = oldPoint[self.objVar] # see if new point is better than old point newerIsBetter = self.checkIfBetter(currentLossVal,oldLossVal) # if this was a recommended preconditioning point, we should not be converged. pointFromRecommendation = self.status[traj]['reason'] == 'received recommended point' # if improved, keep it and move forward; otherwise, reject it and recommend cutting step size if newerIsBetter: self.status[traj]['reason'] = 'found new opt point' self.raiseADebug('Accepting potential opt point for improved loss value. Diff: {}, New: {}, Old: {}'.format(abs(currentLossVal-oldLossVal),currentLossVal,oldLossVal)) else: self.status[traj]['reason'] = 'rejecting bad opt point' self.raiseADebug('Rejecting potential opt point for worse loss value. old: "{}", new: "{}"'.format(oldLossVal,currentLossVal)) # cut the next step size to hopefully stay in the valley instead of climb up the other side self.recommendToGain[traj] = 'cut' ## determine convergence if pointFromRecommendation: self.raiseAMessage('Setting convergence for Trajectory "{}" to "False" because of preconditioning.'.format(traj)) converged = False else: self.raiseAMessage('Checking convergence for Trajectory "{}":'.format(traj)) self.convergenceProgress[traj] = {} # tracks progress for grad norm, abs, rel tolerances converged = False # updated for each individual criterion using "or" (pass one, pass all) #printing utility printString = ' {:<21}: {:<5}' printVals = printString + ' (check: {:>+9.2e} < {:>+9.2e}, diff: {:>9.2e})' # TODO rewrite this action as a lambda? def printProgress(name,boolCheck,test,gold): """ Consolidates a commonly-used print statement to prevent errors and improve readability. @ In, name, str, printed name of convergence check @ In, boolCheck, bool, boolean convergence results for this check @ In, test, float, value of check at current opt point @ In, gold, float, convergence threshold value @ Out, None """ self.raiseAMessage(printVals.format(name,str(boolCheck),test,gold,abs(test-gold))) # "min step size" and "gradient norm" are both always valid checks, whether rejecting or accepting new point ## min step size check try: lastStep = self.counter['lastStepSize'][traj][0] minStepSizeCheck = lastStep <= self.minStepSize except KeyError: #we reset the step size, so we don't have a value anymore lastStep = np.nan minStepSizeCheck = False printProgress('Min step size',minStepSizeCheck,lastStep,self.minStepSize) converged = converged or minStepSizeCheck # if accepting new point, then "same coordinate" and "abs" and "rel" checks are also valid reasons to converge if newerIsBetter: #absolute tolerance absLossDiff = abs(mathUtils.diffWithInfinites(currentLossVal,oldLossVal)) self.convergenceProgress[traj]['abs'] = absLossDiff absTolCheck = absLossDiff <= self.absConvergenceTol printProgress('Absolute Loss Diff',absTolCheck,absLossDiff,self.absConvergenceTol) converged = converged or absTolCheck #relative tolerance relLossDiff = mathUtils.relativeDiff(currentLossVal,oldLossVal) self.convergenceProgress[traj]['rel'] = relLossDiff relTolCheck = relLossDiff <= self.relConvergenceTol printProgress('Relative Loss Diff',relTolCheck,relLossDiff,self.relConvergenceTol) converged = converged or relTolCheck #same coordinate check sameCoordinateCheck = True for var in self.getOptVars(): # don't check constants, of course they're the same if var in self.constants: continue old = oldPoint[var] current = currentPoint[var] # differentiate vectors and scalars for checking if hasattr(old,'__len__'): if any(old != current): sameCoordinateCheck = False break else: if old != current: sameCoordinateCheck = False break self.raiseAMessage(printString.format('Same coordinate check',str(sameCoordinateCheck))) converged = converged or sameCoordinateCheck if converged: # update number of successful convergences self.counter['persistence'][traj] += 1 # check if we've met persistence requirement; if not, keep going if self.counter['persistence'][traj] >= self.convergencePersistence: self.raiseAMessage(' ... Trajectory "{}" converged {} times consecutively!'.format(traj,self.counter['persistence'][traj])) self.convergeTraj[traj] = True self.removeConvergedTrajectory(traj) else: self.raiseAMessage(' ... converged Traj "{}" {} times, required persistence is {}.'.format(traj,self.counter['persistence'][traj],self.convergencePersistence)) else: if not conj: self.counter['persistence'][traj] = 0 self.raiseAMessage(' ... continuing trajectory "{}".'.format(traj)) return newerIsBetter def writeToSolutionExport(self,traj, recent, accepted, overwrite=None): """ Standardizes how the solution export is written to. Uses data from "recentOptHist" and other counters to fill in values. @ In, traj, int, the trajectory for which an entry is being written @ In, recent, dict, the new optimal point (NORMALIZED) that needs to get written to the solution export @ In, accepted, string, whether the most recent point was accepted or rejected as a bad move @ In, overwrite, dict, optional, values to overwrite if requested as {key:val} @ Out, None """ if overwrite is None: overwrite = {} # create realization to add to data object rlz = {} badValue = -1.0 #value to use if we don't have a value # TODO make this accessible to user? for var in self.solutionExport.getVars(): # if this variable has indices, add them to the realization indexes = self.solutionExport.getDimensions(var)[var] if len(indexes): # use the prefix to find the right realization ## NOTE there will be a problem with unsynchronized histories! varUpdate = self.counter['solutionUpdate'][traj] # negative values wouldn't make sense varUpdate = max(0,varUpdate-1) prefix = self._createEvaluationIdentifier(traj, varUpdate, 0) _,match = self.mdlEvalHist.realization(matchDict = {'prefix':prefix}) for index in indexes: rlz[index] = match[index] # CASE: what variable is asked for: # inputs, objVar, other outputs if var in overwrite: new = overwrite[var] elif var in recent.keys(): new = self.denormalizeData(recent)[var] elif var in self.constants: new = self.constants[var] # custom counters: varsUpdate, trajID, stepSize elif var == 'varsUpdate': new = self.counter['solutionUpdate'][traj] elif var == 'trajID': new = traj+1 # +1 is for historical reasons, when histories were indexed on 1 instead of 0 elif var == 'stepSize': try: new = self.counter['lastStepSize'][traj][0] except KeyError: new = badValue elif var == 'accepted': new = accepted elif var.startswith( 'convergenceAbs'): try: new = self.convergenceProgress[traj].get('abs',badValue) except KeyError: new = badValue elif var.startswith( 'convergenceRel'): try: new = self.convergenceProgress[traj].get('rel',badValue) except KeyError: new = badValue else: self.raiseAnError(IOError,'Unrecognized output request:',var) # format for realization rlz[var] = np.atleast_1d(new) self.solutionExport.addRealization(rlz) def checkResampleOption(self,traj): """ Turn on self.resample[traj] while checking self.resampleSwitch. This method is equivalent to self.resample[traj] = self.resampleSwitch while needed @ In, traj, int, the trajectory for which an entry is being written @ Out, self.resampleSwitch, bool, True if resample switch is on """ return self.resampleSwitch

apache-2.0

marcwagner/alarmclock

testset.py

1

6477

import time, datetime import unittest import alarm format = "%a %d-%b-%Y %H:%M" current_time = datetime.datetime(2015,4,4,16,4,0) #april 4 2015 16:04 default = {'name' : 'default', 'time' : datetime.time(12,0,0), 'days' : ('MO','TU','WE','TH','FR','SA','SU'), 'date' : None, 'path' : './', 'date' : None, 'active' : True} alarms_list = ({'name' : 'current', 'time' : datetime.time(16,4,0)}, # the current time {'name' : 'alarm1', 'time' : datetime.time(11,0,0)}, # every day at 11 am {'name' : 'alarm2', 'time' : datetime.time(9,0,0), 'days' : ('MO','TU')},#monday and tuesday an 9 am {'name' : 'alarm3', 'time' : datetime.time(22,0,0), 'days' : ('WE','TU','SA')}, # tuesday, wednesday, sunday at 10 pm {'name' : 'christmas','time' : datetime.time(21,0,0), 'date' : datetime.date(2015,12,24)}, # 9pm on christmas eve {'name' : 'past', 'time' : datetime.time(12,0,0), 'date' : datetime.date(1999,12,31)}, # noon on dec 31 1999 --> in the past {'name' : 'path', 'time' : datetime.time(12,0,0), 'path' : '/media/music/1Kindermuziek/K3/K3-Eyo(2011)MP3 Nlt-release/'}, {'name' : 'n_active','time' : datetime.time(12,0,0), 'active' : False}, default) alarm_times = {'current': datetime.datetime(2015,4,4,16,4,0), 'alarm1': datetime.datetime(2015,4,5,11,0,0), 'alarm2': datetime.datetime(2015,4,6,9,0,0), 'alarm3': datetime.datetime(2015,4,4,22,0,0), 'christmas': datetime.datetime(2015,12,24,21,0,0), 'past': None, 'path': datetime.datetime(2015,4,5,12,0,0), 'n_active':None, 'default': datetime.datetime(2015,4,5,12,0,0)} root_playlist = ['engeltjes.mp3'] path_playlist = ['01 Eyo.mp3', '02 Hallo K3.mp3', '03 Willem - Alexander.mp3', '04 Smoorverliefd.mp3', '05 K3 - Airlines.mp3', '06 Beroemd.mp3', '07 Meiden Van De Brandweer.mp3', '08 Verstoppertje.mp3', '09 Telepathie.mp3', '10 Dubbeldekkertrein.mp3', '11 Bel Me Ringeling.mp3', '12 Cowboys En Indianen.mp3'] class testcases_alarm(unittest.TestCase): '''test all cases of working alarms''' def are_all_the_vars_present(self, alarm, default, **a): self.assertEqual(a.get('name'), alarm.name) self.assertEqual(a.get('time'), alarm.time) self.assertEqual(a.get('date', default['date']), alarm.date) self.assertEqual(a.get('days', default['days']), alarm.days) self.assertEqual(a.get('path', default['path']), alarm.path) self.assertEqual(a.get('active', default['active']), alarm.active) def test_create_alarm(self): '''create a basic alarm''' for a in alarms_list: al = alarm.alarm(**a) self.are_all_the_vars_present(al, default, **a) def test_edit_alarm_correct(self): '''update an alarm with the parameters of another alarm''' if len(alarms_list) < 2: # need at least 2 alarms for this test return for i in range(len(alarms_list)-1): a1 = alarms_list[i] a2 = alarms_list[i+1] al = alarm.alarm(**a1) copy_of_default = default.copy() self.are_all_the_vars_present(al, copy_of_default, **a1) al.update_alarm(**a2) copy_of_default.update(a1) self.are_all_the_vars_present(al, copy_of_default, **a2) def test_is_the_next_alarm_correct(self): '''test next_alarm''' for a in alarms_list: myalarm = alarm.alarm(**a) nexttime = alarm_times[myalarm.name] self.assertEqual(myalarm.next_alarm(current_time), nexttime) def test_add_alarm_correct_alarms(self): '''create a set of alarms''' alarms = alarm.alarmset() for a in alarms_list: alarms.add(alarm.alarm(**a)) al = alarms[-1] self.are_all_the_vars_present(al, default, **a) self.assertEqual(alarms.exists(a['name']), True) def test_remove_alarm(self): '''remove an alarm from a set''' alarms = alarm.alarmset() for a in alarms_list: name = a['name'] alarms.add(alarm.alarm(**a)) self.assertEqual(alarms.exists(name), True) alarms.remove(alarms[name]) self.assertEqual(alarms.exists(name), False) def test_the_next_alarm_in_set(self): '''alarmset next_alarm''' alarms = alarm.alarmset() for a in alarms_list: alarms.add(alarm.alarm(**a)) self.assertEqual(alarms.next_alarm(current_time).next_alarm(current_time), current_time) def test_generate_playlist(self): '''based on the path, generate a list of files''' alarm1 = alarm.alarm(**alarms_list[1]) path = alarm.alarm(**alarms_list[6]) self.assertEqual(alarm1.generate_playlist(), root_playlist) self.assertEqual(path.generate_playlist(), path_playlist) def test_play_a_song(self): '''play a song form file''' alarm1 = alarm.alarm(**alarms_list[1]) self.assertEqual(alarm1.playing, False) self.assertEqual(alarm1.blocking, False) self.assertEqual(alarm1.player_active(), False) alarm1.play(root_playlist[0]) time.sleep(0.2) self.assertEqual(alarm1.playing, True) self.assertEqual(alarm1.blocking, False) self.assertEqual(alarm1.player_active(), True) alarm1.stop() def test_save_and_load_alarms(self): alarms_1 = alarm.alarmset() alarms_2 = alarm.alarmset() for a in alarms_list: alarms_1.add(alarm.alarm(**a)) alarms_1.save_alarms('test_config.file') alarms_2.load_alarms('test_config.file') for a_1, a_2 in zip (alarms_1, alarms_2): self.assertEqual(a_1.name, a_2.name) self.assertEqual(a_1.time, a_2.time) self.assertEqual(a_1.date, a_2.date) self.assertEqual(a_1.days, a_2.days) self.assertEqual(a_1.path, a_2.path) self.assertEqual(a_1.active, a_2.active) def test_player_active(self): pass def test_stop(self): pass if __name__ == '__main__': unittest.main()

mit

timsavage/extopen

setup.py

1

1140

from setuptools import setup, find_packages setup( name = 'extopen', version = '0.1.1', description = "Cross platform helper for opening a file with the default external application.", long_description = open('README.rst').read(), url='https://github.com/timsavage/extopen', author = 'Tim Savage', author_email = '[email protected]', license = 'BSD', platforms = 'Posix; MacOS X; Windows', classifiers = [ 'Development Status :: 4 - Beta', 'Intended Audience :: Developers', 'License :: OSI Approved :: BSD License', 'Topic :: Software Development :: Libraries :: Python Modules', 'Programming Language :: Python', 'Programming Language :: Python :: 2', 'Programming Language :: Python :: 2.7', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: Implementation :: CPython', 'Programming Language :: Python :: Implementation :: PyPy', ], zip_safe = True, py_modules = ['extopen'] )

bsd-3-clause

reinaldomaslim/Singaboat_RobotX2016

robotx_vision/nodes/color_sequence.py

1

20932

#! /usr/bin/python """ detect color sequence ren ye 2016-10-21 reference: http://stackoverflow.com/questions/14476683/identifying-color-sequence-in-opencv algorithm: # image preparation 1. subwindowing to light buoy by laser and camera 2. convert to hsv 3. check hue for the blob # detection 1. wait until first detection is made 2. wait until no detection is found for 2 seconds 3. record color 4. if color is different from previous frame, add to sequence 5. if no detection, to step 2 6. if sequence is length 3, report and end """ #!/usr/bin/env python """ camshift_color.py - Version 1.1 2013-12-20 Modification of the ROS OpenCV Camshift example using cv_bridge and publishing the ROI coordinates to the /roi topic. """ import time import rospy import cv2 from cv2 import cv as cv from robotx_vision.ros2opencv2 import ROS2OpenCV2 from std_msgs.msg import String, Float64MultiArray, MultiArrayDimension from nav_msgs.msg import Odometry from geometry_msgs.msg import Vector3 from sensor_msgs.msg import Image, RegionOfInterest import numpy as np from sklearn.cluster import KMeans class ColorSequence(ROS2OpenCV2): # taken from robotx_vision.find_shapes.Color_Detection x0, y0 = 0, 0 hist_list = list() MAX_LEN = 7 * 5 counter = 0 roi_x_offset, roi_y_offset, roi_width, roi_height = [0, 0, 0, 0] def __init__(self, node_name, debug=False): ROS2OpenCV2.__init__(self, node_name, debug) self.sequence_pub = rospy.Publisher("color_sequence", Vector3, queue_size=10) # self.odom_received = False # rospy.Subscriber("odometry/filtered/global", Odometry, self.odom_callback, queue_size=50) # while not self.odom_received: # pass # print "waiting for roi" rospy.wait_for_message("led_sequence_roi", RegionOfInterest) rospy.Subscriber("led_sequence_roi", RegionOfInterest, self.roi_callback, queue_size=50) # print "roi received" self.node_name = node_name # The minimum saturation of the tracked color in HSV space, # as well as the min and max value (the V in HSV) and a # threshold on the backprojection probability image. self.smin = rospy.get_param("~smin", 85) self.vmin = rospy.get_param("~vmin", 50) self.vmax = rospy.get_param("~vmax", 254) self.threshold = rospy.get_param("~threshold", 50) # all done in ros2opencv2.py: # self.depth_sub, self.depth_callback, self.depth_image # self.depth_image can be used globally # self.depth_sub = rospy.Subscriber("input_depth_image", Image, self.depth_callback, queue_size=1) # Create a number of windows for displaying the histogram, # parameters controls, and backprojection image if self.debug: cv.NamedWindow("Histogram", cv.CV_WINDOW_NORMAL) cv.MoveWindow("Histogram", 300, 50) cv.NamedWindow("Parameters", 0) cv.MoveWindow("Parameters", 700, 50) cv.NamedWindow("Backproject", 0) cv.MoveWindow("Backproject", 700, 325) # cv.NamedWindow("Tracked_obj", 0) # cv.MoveWindow("Tracked_obj", 700, 900) # Create the slider controls for saturation, value and threshold cv.CreateTrackbar("Saturation", "Parameters", self.smin, 255, self.set_smin) cv.CreateTrackbar("Min Value", "Parameters", self.vmin, 255, self.set_vmin) cv.CreateTrackbar("Max Value", "Parameters", self.vmax, 255, self.set_vmax) cv.CreateTrackbar("Threshold", "Parameters", self.threshold, 255, self.set_threshold) # Initialize a number of variables self.hist = None self.track_window = None self.show_backproj = False # These are the callbacks for the slider controls def set_smin(self, pos): self.smin = pos def set_vmin(self, pos): self.vmin = pos def set_vmax(self, pos): self.vmax = pos def set_threshold(self, pos): self.threshold = pos # def color_masking(self, frame): # hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV) # mask = cv2.inRange(hsv, self.lower_orange, self.upper_orange) + \ # cv2.inRange(hsv, self.lower_yellow, self.upper_yellow) # return mask # def depth_masking(self): # self.depth_array = np.array(self.depth_image, dtype=np.float32) # # self.depth_image # depth_mask = np.zeros((self.frame_height, self.frame_width)) # for x in range(self.frame_height): # for y in range(self.frame_width): # try: # # Get a depth value in meters # z = self.depth_array[y, x] # # Check for NaN values returned by the camera driver # if isnan(z): # continue # except: # # It seems to work best if we convert exceptions to big value # z = 255 # if z < self.depth_threshold: # depth_mask[y, x] = 255 # white # else: # depth_mask[y, x] = 0 # return depth_mask def find_max_contour(self, mask): # find contours contours, hierarchy = cv2.findContours(mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE) # for multiple contours, find the maximum area=list() approx=list() for i, cnt in enumerate(contours): approx.append(cv2.approxPolyDP(cnt, 0.01 * cv2.arcLength(cnt, True), True)) area.append(cv2.contourArea(cnt)) # overwrite selection box by automatic color matching return cv2.boundingRect(approx[np.argmax(area)]) def find_contours(self, mask): # find contours mask = self.morphological(mask) contours, hierarchy = cv2.findContours(mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE) # for multiple contours, find the maximum area=list() approx=list() for i, cnt in enumerate(contours): approx.append(cv2.approxPolyDP(cnt, 0.01 * cv2.arcLength(cnt, True), True)) area.append(cv2.contourArea(cnt)) # overwrite selection box by automatic color matching self.area_ratio = np.sum(area) / (self.frame_width * self.frame_height) if np.max(area) / np.sum(area) > 0.95: # print "one blob" self.number_blob = 1 else: # print "more than one blobs" self.number_blob = 2 if len(area) > 1: # more than one blob, find the ratio of the 1st and 2nd largest area_rev_sorted = np.sort(area)[::-1] self.area_ratio = area_rev_sorted[0] / area_rev_sorted[1] else: # only one blob found self.area_ratio = 0 # print self.area_ratio def morphological(self, mask): """ tune the mask """ # morphological openning (remove small objects from the foreground) kernel = np.ones((5, 5), np.uint8) mask = cv2.morphologyEx(mask, cv2.MORPH_OPEN, kernel) # # morphological closing (fill small objects from the foreground) kernel = np.ones((10, 10), np.uint8) mask = cv2.morphologyEx(mask, cv2.MORPH_CLOSE, kernel) return mask # The main processing function computes the histogram and backprojection def process_image(self, cv_image): try: # First blur the image frame = cv2.blur(cv_image, (5, 5)) # Convert from RGB to HSV space hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV) # Create a mask using the current saturation and value parameters mask = cv2.inRange(hsv, np.array((0., self.smin, self.vmin)), np.array((180., 255., self.vmax))) # not select any region, do automatic color rectangle if self.selection is None: # obtain the color mask # edge_roi = self.edge_masking() # print "edge mask", edge_mask # create bounding box from the maximum mask self.selection = [self.roi_x_offset, self.roi_y_offset, self.roi_width, self.roi_height] # in x y w h # print "selection", self.selection self.detect_box = self.selection self.track_box = None # If the user is making a selection with the mouse, # calculate a new histogram to track if self.selection is not None: x0, y0, w, h = self.selection x1 = x0 + w y1 = y0 + h self.track_window = (x0, y0, x1, y1) hsv_roi = hsv[y0:y1, x0:x1] mask_roi = mask[y0:y1, x0:x1] self.hist = cv2.calcHist( [hsv_roi], [0], mask_roi, [16], [0, 180] ) cv2.normalize(self.hist, self.hist, 0, 255, cv2.NORM_MINMAX) self.hist = self.hist.reshape(-1) self.hist_prob = np.argmax(self.hist) # print self.hist_prob self.show_hist() if self.detect_box is not None: self.selection = None # If we have a histogram, track it with CamShift # if self.hist is not None: # # Compute the backprojection from the histogram # backproject = cv2.calcBackProject([hsv], [0], self.hist, [0, 180], 1) # # Mask the backprojection with the mask created earlier # backproject &= mask # # Threshold the backprojection # ret, backproject = cv2.threshold(backproject, self.threshold, 255, cv.CV_THRESH_TOZERO) # # self.find_contours(backproject) # # Detect blobs. # # keypoints = self.blob_detector.detect(backproject) # # print keypoints # x, y, w, h = self.track_window # if self.track_window is None or w <= 0 or h <=0: # self.track_window = 0, 0, self.frame_width - 1, self.frame_height - 1 # # Set the criteria for the CamShift algorithm # term_crit = ( cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT, 10, 1 ) # # Run the CamShift algorithm # self.track_box, self.track_window = cv2.CamShift(backproject, self.track_window, term_crit) # x0, y0, x1, y1 = self.track_window # # print self.track_window # # Display the resulting backprojection # cv2.imshow("Backproject", backproject) except: pass return cv_image def show_hist(self): bin_count = self.hist.shape[0] bin_w = 24 img = np.zeros((256, bin_count*bin_w, 3), np.uint8) # print np.argmax(self.hist) self.hist_prob = np.argmax(self.hist) for i in xrange(bin_count): h = int(self.hist[i]) cv2.rectangle(img, (i*bin_w+2, 255), ((i+1)*bin_w-2, 255-h), (int(180.0*i/bin_count), 255, 255), -1) img = cv2.cvtColor(img, cv2.COLOR_HSV2BGR) if self.debug: cv2.imshow('Histogram', img) def hue_histogram_as_image(self, hist): """ Returns a nice representation of a hue histogram """ histimg_hsv = cv.CreateImage((320, 200), 8, 3) mybins = cv.CloneMatND(hist.bins) cv.Log(mybins, mybins) (_, hi, _, _) = cv.MinMaxLoc(mybins) cv.ConvertScale(mybins, mybins, 255. / hi) w,h = cv.GetSize(histimg_hsv) hdims = cv.GetDims(mybins)[0] for x in range(w): xh = (180 * x) / (w - 1) # hue sweeps from 0-180 across the image val = int(mybins[int(hdims * x / w)] * h / 255) cv2.rectangle(histimg_hsv, (x, 0), (x, h-val), (xh,255,64), -1) cv2.rectangle(histimg_hsv, (x, h-val), (x, h), (xh,255,255), -1) histimg = cv2.cvtColor(histimg_hsv, cv.CV_HSV2BGR) return histimg def odom_callback(self, msg): """ call back to subscribe, get odometry data: pose and orientation of the current boat, suffix 0 is for origin """ self.x0 = msg.pose.pose.position.x self.y0 = msg.pose.pose.position.y self.odom_received = True def image_callback(self, data): # Store the image header in a global variable self.image_header = data.header # Time this loop to get cycles per second start = time.time() # Convert the ROS image to OpenCV format using a cv_bridge helper function frame = self.convert_image(data) # Some webcams invert the image if self.flip_image: frame = cv2.flip(frame, 0) # Store the frame width and height in a pair of global variables if self.frame_width is None: self.frame_size = (frame.shape[1], frame.shape[0]) self.frame_width, self.frame_height = self.frame_size # Create the marker image we will use for display purposes if self.marker_image is None: self.marker_image = np.zeros_like(frame) # Copy the current frame to the global image in case we need it elsewhere self.frame = frame.copy() # Reset the marker image if we're not displaying the history if not self.keep_marker_history: self.marker_image = np.zeros_like(self.marker_image) # Process the image to detect and track objects or features processed_image = self.process_image(frame) # If the result is a greyscale image, convert to 3-channel for display purposes """ #if processed_image.channels == 1: #cv.CvtColor(processed_image, self.processed_image, cv.CV_GRAY2BGR) #else: # Make a global copy self.processed_image = processed_image.copy() # Display the user-selection rectangle or point self.display_selection() # Night mode: only display the markers if self.night_mode: self.processed_image = np.zeros_like(self.processed_image) # Merge the processed image and the marker image self.display_image = cv2.bitwise_or(self.processed_image, self.marker_image) # If we have a track box, then display it. The track box can be either a regular # cvRect (x,y,w,h) or a rotated Rect (center, size, angle). if self.show_boxes: if self.track_box is not None and self.is_rect_nonzero(self.track_box): if len(self.track_box) == 4: x,y,w,h = self.track_box size = (w, h) center = (x + w / 2, y + h / 2) angle = 0 self.track_box = (center, size, angle) else: (center, size, angle) = self.track_box # For face tracking, an upright rectangle looks best if self.face_tracking: pt1 = (int(center[0] - size[0] / 2), int(center[1] - size[1] / 2)) pt2 = (int(center[0] + size[0] / 2), int(center[1] + size[1] / 2)) cv2.rectangle(self.display_image, pt1, pt2, cv.RGB(50, 255, 50), self.feature_size, 8, 0) else: # Otherwise, display a rotated rectangle vertices = np.int0(cv2.cv.BoxPoints(self.track_box)) cv2.drawContours(self.display_image, [vertices], 0, cv.RGB(50, 255, 50), self.feature_size) # If we don't yet have a track box, display the detect box if present elif self.detect_box is not None and self.is_rect_nonzero(self.detect_box): (pt1_x, pt1_y, w, h) = self.detect_box if self.show_boxes: cv2.rectangle(self.display_image, (pt1_x, pt1_y), (pt1_x + w, pt1_y + h), cv.RGB(50, 255, 50), self.feature_size, 8, 0) # Publish the ROI self.publish_roi() self.publish_sequence() # Compute the time for this loop and estimate CPS as a running average end = time.time() duration = end - start fps = int(1.0 / duration) self.cps_values.append(fps) if len(self.cps_values) > self.cps_n_values: self.cps_values.pop(0) self.cps = int(sum(self.cps_values) / len(self.cps_values)) # Display CPS and image resolution if asked to if self.show_text: font_face = cv2.FONT_HERSHEY_SIMPLEX font_scale = 0.5 """ Print cycles per second (CPS) and resolution (RES) at top of the image """ if self.frame_size[0] >= 640: vstart = 25 voffset = int(50 + self.frame_size[1] / 120.) elif self.frame_size[0] == 320: vstart = 15 voffset = int(35 + self.frame_size[1] / 120.) else: vstart = 10 voffset = int(20 + self.frame_size[1] / 120.) cv2.putText(self.display_image, "CPS: " + str(self.cps), (10, vstart), font_face, font_scale, cv.RGB(255, 255, 0)) cv2.putText(self.display_image, "RES: " + str(self.frame_size[0]) + "X" + str(self.frame_size[1]), (10, voffset), font_face, font_scale, cv.RGB(255, 255, 0)) if self.debug: # Update the image display cv2.imshow(self.node_name, self.display_image) # Process any keyboard commands self.keystroke = cv2.waitKey(5) if self.keystroke is not None and self.keystroke != -1: try: cc = chr(self.keystroke & 255).lower() if cc == 'n': self.night_mode = not self.night_mode elif cc == 'f': self.show_features = not self.show_features elif cc == 'b': self.show_boxes = not self.show_boxes elif cc == 't': self.show_text = not self.show_text elif cc == 'q': # The has press the q key, so exit rospy.signal_shutdown("User hit q key to quit.") except: pass def publish_sequence(self): # Watch out for negative offsets # pass # append all data to hist_list if len(self.hist_list) > self.MAX_LEN: self.hist_list.pop(0) try: self.hist_list.append([self.counter, self.hist_prob]) except: pass # print self.hist_list self.counter += 1 # find distinct hist_prob try: kmeans = KMeans(n_clusters=3) kmeans.fit(np.array(self.hist_list)) color_sequence = kmeans.cluster_centers_ order = np.argsort(color_sequence[:,0])[::-1] ordered_sequence = color_sequence[order,1] # print "ordered seq", ordered_sequence color_seq = ["", "", ""] c = 0 for i in ordered_sequence: print i if i< 1 or i > 14: color_seq[c] = "red" elif 7 < i < 12: color_seq[c] = "blue" elif 1 < i < 4: color_seq[c] = "yellow" elif 3 < i < 7: color_seq[c] = "green" c += 1 print "color_seq", color_seq a = Vector3() a.x = ordered_sequence[0] a.y = ordered_sequence[1] a.z = ordered_sequence[2] self.sequence_pub.publish(a) rospy.set_param("/gui/color1", color_seq[0]) rospy.set_param("/gui/color2", color_seq[1]) rospy.set_param("/gui/color3", color_seq[2]) except: print "sequence publish failed" def roi_callback(self, msg): # print msg.x_offset self.roi_x_offset = msg.x_offset self.roi_y_offset = msg.y_offset self.roi_width = msg.width self.roi_height = msg.height # try: # sequence = Vector3() # sequence.data.x = self.x0 # sequence.data.y = self.y0 # sequence.data.z = self.hist_prob # print sequence.data # self.sequence_pub.publish(sequence) # except: # rospy.loginfo("Publishing sequence failed") if __name__ == '__main__': try: node_name = "color_sequence" ColorSequence(node_name, debug=True) try: rospy.init_node(node_name) except: pass rospy.spin() except KeyboardInterrupt: print "Shutting down vision node." cv.DestroyAllWindows()

gpl-3.0

albertobeta/UberSimpleWebsockets

send.py

1

1219

import tornado.httpserver import tornado.websocket import tornado.ioloop from tornado.ioloop import PeriodicCallback import tornado.web from random import randint #Random generator #Config port = 9000 #Websocket Port timeInterval= 2000 #Milliseconds class WSHandler(tornado.websocket.WebSocketHandler): #check_origin fixes an error 403 with Tornado #http://stackoverflow.com/questions/24851207/tornado-403-get-warning-when-opening-websocket def check_origin(self, origin): return True def open(self): #Send message periodic via socket upon a time interval self.callback = PeriodicCallback(self.send_values, timeInterval) self.callback.start() def send_values(self): #Generates random values to send via websocket self.write_message(str(randint(1,10)) + ';' + str(randint(1,10)) + ';' + str(randint(1,10)) + ';' + str(randint(1,10))) def on_message(self, message): pass def on_close(self): self.callback.stop() application = tornado.web.Application([ (r'/', WSHandler), ]) if __name__ == "__main__": http_server = tornado.httpserver.HTTPServer(application) http_server.listen(port) tornado.ioloop.IOLoop.instance().start()

mit

vojtechtrefny/anaconda

pyanaconda/anaconda.py

1

8728

# anaconda: The Red Hat Linux Installation program # # Copyright (C) 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007 # Red Hat, Inc. All rights reserved. # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. # # Author(s): Brent Fox <[email protected]> # Mike Fulbright <[email protected]> # Jakub Jelinek <[email protected]> # Jeremy Katz <[email protected]> # Chris Lumens <[email protected]> # Paul Nasrat <[email protected]> # Erik Troan <[email protected]> # Matt Wilson <[email protected]> # import os import sys import stat from glob import glob from tempfile import mkstemp import threading from pyanaconda.bootloader import get_bootloader from pyanaconda import constants from pyanaconda import iutil from pyanaconda import addons import logging log = logging.getLogger("anaconda") stdoutLog = logging.getLogger("anaconda.stdout") class Anaconda(object): def __init__(self): from pyanaconda import desktop self._bootloader = None self.canReIPL = False self.desktop = desktop.Desktop() self.dir = None self.displayMode = None self.id = None self._instClass = None self._intf = None self.isHeadless = False self.ksdata = None self.mediaDevice = None self.methodstr = None self.opts = None self._payload = None self.proxy = None self.proxyUsername = None self.proxyPassword = None self.reIPLMessage = None self.rescue_mount = True self.rootParts = None self.stage2 = None self._storage = None self.updateSrc = None self.mehConfig = None # *sigh* we still need to be able to write this out self.xdriver = None # Data for inhibiting the screensaver self.dbus_session_connection = None self.dbus_inhibit_id = None # This is used to synchronize Gtk.main calls between the graphical # interface and error dialogs. Whoever gets to their initialization code # first will lock gui_initializing self.gui_initialized = threading.Lock() @property def bootloader(self): if not self._bootloader: self._bootloader = get_bootloader() return self._bootloader @property def instClass(self): if not self._instClass: from pyanaconda.installclass import DefaultInstall self._instClass = DefaultInstall() return self._instClass def _getInterface(self): return self._intf def _setInterface(self, v): # "lambda cannot contain assignment" self._intf = v def _delInterface(self): del self._intf intf = property(_getInterface, _setInterface, _delInterface) @property def payload(self): # Try to find the packaging payload class. First try the install # class. If it doesn't give us one, fall back to the default. if not self._payload: klass = self.instClass.getBackend() if not klass: from pyanaconda.flags import flags if self.ksdata.ostreesetup.seen: from pyanaconda.packaging.rpmostreepayload import RPMOSTreePayload klass = RPMOSTreePayload elif flags.livecdInstall: from pyanaconda.packaging.livepayload import LiveImagePayload klass = LiveImagePayload elif self.ksdata.method.method == "liveimg": from pyanaconda.packaging.livepayload import LiveImageKSPayload klass = LiveImageKSPayload else: from pyanaconda.packaging.dnfpayload import DNFPayload klass = DNFPayload self._payload = klass(self.ksdata) return self._payload @property def protected(self): specs = [] if os.path.exists("/run/initramfs/livedev") and \ stat.S_ISBLK(os.stat("/run/initramfs/livedev")[stat.ST_MODE]): specs.append(os.readlink("/run/initramfs/livedev")) if self.methodstr and self.methodstr.startswith("hd:"): specs.append(self.methodstr[3:].split(":", 3)[0]) if self.stage2 and self.stage2.startswith("hd:"): specs.append(self.stage2[3:].split(":", 3)[0]) # zRAM swap devices need to be protected for zram_dev in glob("/dev/zram*"): specs.append(zram_dev) return specs @property def storage(self): if not self._storage: import blivet self._storage = blivet.Blivet(ksdata=self.ksdata) if self.instClass.defaultFS: self._storage.setDefaultFSType(self.instClass.defaultFS) return self._storage def dumpState(self): from meh import ExceptionInfo from meh.dump import ReverseExceptionDump from inspect import stack as _stack from traceback import format_stack # Skip the frames for dumpState and the signal handler. stack = _stack()[2:] stack.reverse() exn = ReverseExceptionDump(ExceptionInfo(None, None, stack), self.mehConfig) # gather up info on the running threads threads = "\nThreads\n-------\n" for thread_id, frame in sys._current_frames().items(): threads += "\nThread %s\n" % (thread_id,) threads += "".join(format_stack(frame)) # dump to a unique file (fd, filename) = mkstemp(prefix="anaconda-tb-", dir="/tmp") dump_text = exn.traceback_and_object_dump(self) dump_text += threads dump_text = dump_text.encode("utf-8") iutil.eintr_retry_call(os.write, fd, dump_text) iutil.eintr_retry_call(os.close, fd) # append to a given file with open("/tmp/anaconda-tb-all.log", "a+") as f: f.write("--- traceback: %s ---\n" % filename) f.write(dump_text + "\n") def initInterface(self, addon_paths=None): if self._intf: raise RuntimeError("Second attempt to initialize the InstallInterface") if self.displayMode == 'g': from pyanaconda.ui.gui import GraphicalUserInterface # Run the GUI in non-fullscreen mode, so live installs can still # use the window manager self._intf = GraphicalUserInterface(self.storage, self.payload, self.instClass, gui_lock=self.gui_initialized, fullscreen=False) # needs to be refreshed now we know if gui or tui will take place addon_paths = addons.collect_addon_paths(constants.ADDON_PATHS, ui_subdir="gui") elif self.displayMode in ['t', 'c']: # text and command line are the same from pyanaconda.ui.tui import TextUserInterface self._intf = TextUserInterface(self.storage, self.payload, self.instClass) # needs to be refreshed now we know if gui or tui will take place addon_paths = addons.collect_addon_paths(constants.ADDON_PATHS, ui_subdir="tui") else: raise RuntimeError("Unsupported displayMode: %s" % self.displayMode) if addon_paths: self._intf.update_paths(addon_paths) def writeXdriver(self, root=None): # this should go away at some point, but until it does, we # need to keep it around. if self.xdriver is None: return if root is None: root = iutil.getSysroot() if not os.path.isdir("%s/etc/X11" %(root,)): os.makedirs("%s/etc/X11" %(root,), mode=0o755) f = open("%s/etc/X11/xorg.conf" %(root,), 'w') f.write('Section "Device"\n\tIdentifier "Videocard0"\n\tDriver "%s"\nEndSection\n' % self.xdriver) f.close()

gpl-2.0

swisscom/cleanerversion

versions_tests/tests/test_utils.py

1

4249

from unittest import skipUnless from django.db import IntegrityError from django.db import connection from django.test import TestCase, TransactionTestCase from versions.util.postgresql import get_uuid_like_indexes_on_table from versions_tests.models import ChainStore, Color @skipUnless(connection.vendor == 'postgresql', "Postgresql-specific test") class PostgresqlVersionUniqueTests(TransactionTestCase): def setUp(self): self.red = Color.objects.create(name='red') self.green = Color.objects.create(name='green') self.black = Color.objects.create(name='black') self.yellow = Color.objects.create(name='yellow') # - only one store with the same name and subchain_id can exist in a # single city # - no two stores can share the same door_frame_color and door_color store = { 'subchain_id': 1, 'city': 'Santa Barbara', 'name': 'Barbara style', 'opening_hours': '9-9 everyday', 'door_frame_color': self.red, 'door_color': self.black, } self.sb1 = ChainStore.objects.create(**store) def test_version_unique(self): # It should not be possible to create another store with the same name, # city, and subchain_id with self.assertRaises(IntegrityError): sb2 = ChainStore.objects.create( subchain_id=self.sb1.subchain_id, city=self.sb1.city, name=self.sb1.name, door_frame_color=self.sb1.door_frame_color, door_color=self.green ) # It should not be possible to create another store with the same door # and door_frame color with self.assertRaises(IntegrityError): sb3 = ChainStore.objects.create( subchain_id=self.sb1.subchain_id, city=self.sb1.city, name="Bearded Bob's style", door_frame_color=self.sb1.door_frame_color, door_color=self.sb1.door_color ) # It should be possible to create objects as long as they follow the # unique constraints, though: sb4 = ChainStore.objects.create( subchain_id=self.sb1.subchain_id, city=self.sb1.city, name="Bearded Bob's style", door_frame_color=self.sb1.door_frame_color, door_color=self.green ) sb5 = ChainStore.objects.create( subchain_id=sb4.subchain_id + 1, city=sb4.city, name=sb4.name, door_frame_color=sb4.door_frame_color, door_color=self.yellow ) # If a version is soft-deleted, it should be possible to create a new # object with the # value of that old version sb4.delete() sb6 = ChainStore.objects.create( subchain_id=sb4.subchain_id, city=sb4.city, name=sb4.name, door_frame_color=sb4.door_frame_color, door_color=sb4.door_color ) def test_identity_unique(self): c = Color.objects.create(name='sky blue') c.identity = self.green.identity # It should not be possible to have two "current" objects with the # same identity: with self.assertRaises(IntegrityError): c.save() @skipUnless(connection.vendor == 'postgresql', "Postgresql-specific test") class PostgresqlUuidLikeIndexesTest(TestCase): def test_no_like_indexes_on_uuid_columns(self): # Django creates like indexes on char columns. In Django 1.7.x and # below, there is no support for native uuid columns, so # CleanerVersion uses a CharField to store the uuid values. For # postgresql, Django creates special indexes for char fields so that # like searches (e.g. WHERE foo like '%bar') are fast. # Those indexes are not going to be used in our case, and extra # indexes will slow down updates and inserts. So, they should have # been removed by the post_migrate handler in # versions_tests.apps.VersionsTestsConfig.ready. self.assertEqual(0, len(get_uuid_like_indexes_on_table(ChainStore)))

apache-2.0

globocom/database-as-a-service

dbaas/workflow/steps/tests/test_dns_step.py

1

1957

from random import randint from mock import patch from workflow.steps.util.dns import ChangeTTL, ChangeTTLTo5Minutes, ChangeTTLTo3Hours from . import TestBaseStep class FakeDNSProvider(object): dns_ttl = {} @classmethod def update_database_dns_ttl(cls, infra, seconds): cls.dns_ttl[infra] = seconds class DNSStepTests(TestBaseStep): def setUp(self): super(DNSStepTests, self).setUp() FakeDNSProvider.dns_ttl = {} @patch( 'dbaas_dnsapi.provider.DNSAPIProvider.update_database_dns_ttl', new=FakeDNSProvider.update_database_dns_ttl ) def test_change_ttl_five_minutes(self): self.assertEqual(FakeDNSProvider.dns_ttl, {}) ChangeTTLTo5Minutes(self.instance).do() self.assertEqual(len(FakeDNSProvider.dns_ttl), 1) self.assertIn(self.infra, FakeDNSProvider.dns_ttl) ttl_seconds = FakeDNSProvider.dns_ttl[self.infra] self.assertEqual(ttl_seconds, 300) @patch( 'dbaas_dnsapi.provider.DNSAPIProvider.update_database_dns_ttl', new=FakeDNSProvider.update_database_dns_ttl ) def test_change_ttl_3_hours(self): self.assertEqual(FakeDNSProvider.dns_ttl, {}) ChangeTTLTo3Hours(self.instance).do() self.assertEqual(len(FakeDNSProvider.dns_ttl), 1) self.assertIn(self.infra, FakeDNSProvider.dns_ttl) ttl_seconds = FakeDNSProvider.dns_ttl[self.infra] self.assertEqual(ttl_seconds, 10800) def test_minutes_to_seconds(self): change_ttl = ChangeTTLTo5Minutes(self.instance) change_ttl.minutes = randint(1, 10000) self.assertEqual(change_ttl.seconds, change_ttl.minutes*60) def test_unicode(self): change_ttl = ChangeTTLTo5Minutes(self.instance) change_ttl.minutes = randint(1, 10000) self.assertEqual( unicode(change_ttl), 'Changing DNS TLL to {} minutes...'.format(change_ttl.minutes) )

bsd-3-clause

pnpnpn/gimsan-py

gimsan_result.py

1

15480

#!/usr/bin/env python from __future__ import print_function from __future__ import unicode_literals from __future__ import division from __future__ import absolute_import import time_benchmark import os import sys import json import re import time import numpy as np import ConfigParser import subprocess from tornado import template from argparse_plus import ArgumentParserPlus from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.Alphabet import IUPAC from Bio.Motif import Motif from gibbslib.batch_experiment import * from gibbslib.simple_logging import * from gibbslib.gimsan_base import GimsanJob from gibbslib.gimsan_exception import * class FinderResult(): def __init__(self, finder_meta, nullset_size, statsig_dir, outdir, gimsan_home): self.logger = logging.getLogger(self.__class__.__name__) self.finder_id = finder_meta['finder_id'] self.finder_id_alt = self.finder_id.replace('_', '-') self.finder_outdir = finder_meta['finder_outdir'] #per-finder self.width = finder_meta['width'] self.nullset_size = nullset_size self.statsig_dir = statsig_dir self.outdir = outdir #per-template self.load_template_json() self.pval_r_path = os.path.join(gimsan_home, 'misc', "conf_pval_only.R") #results self.pvalue_comment = None self.kmer_lst = None self.kmer_filename = None self.logowidth = 5 self.weblogo_basename = None self.weblogo_revcompl_basename = None self.coldep_outfile = None self.coldep_num_pairs = None def construct_weblogo(self, weblogo_filename, weblogo_revcompl_filename): self.weblogo_basename = os.path.basename(weblogo_filename) self.weblogo_revcompl_basename = os.path.basename(weblogo_revcompl_filename) motif = Motif(alphabet=IUPAC.unambiguous_dna) for kmer in self.kmer_lst: motif.add_instance(Seq(kmer, motif.alphabet)) logowidth_normal = self.construct_weblogo_helper(weblogo_filename, motif) #reverse complement motif_revcompl = motif.reverse_complement() logowidth_revcompl = self.construct_weblogo_helper(weblogo_revcompl_filename, motif_revcompl) self.logowidth = max(self.logowidth, logowidth_normal, logowidth_revcompl) def construct_weblogo_helper(self, weblogo_filename, motif): logowidth = (20.0/45.0) * self.width + 2; motif.weblogo(weblogo_filename, logowidth=logowidth) #return logowidth * 50 #width to pixel conversion return logowidth def load_json(self, filename): json_dct = {} with open(filename, 'rb') as fh: json_dct = json.loads(fh.read()) if json_dct is None or "kmers" not in json_dct: raise InvalidMotifJsonFileError("File does not seem to be a valid json file for motif results: %s" % json_filename) return json_dct def get_pvalue_comment_from_rout(self): rout_filename = self.get_rout_filename() with open(rout_filename, 'rb') as fh: for ln in fh: ln = unicode(ln, 'utf-8') if 'MLE of the p-value' in ln: self.pvalue_comment = ln.strip() break if not self.pvalue_comment: raise ParsingMotifResultError('Cannot find P-value comment: %s' % rout_filename) def load_template_json(self): json_filename = os.path.join(self.finder_outdir, 'motif-00000.stdout') self.template_json = self.load_json(json_filename) def extract_and_write_kmers(self): self.kmer_lst = [l[1] for l in self.template_json['kmers'].values()] self.kmer_filename = os.path.join(self.statsig_dir, '%s.kmers' % self.finder_id) self.write_kmers_file(self.kmer_lst, self.kmer_filename) def write_kmers_file(self, curr_kmer_lst, curr_kmer_filename): self.logger.info('Writing kmers: %s' % curr_kmer_filename) with open(curr_kmer_filename, 'wb') as fh: for kmer in curr_kmer_lst: print('>FASTA header', file=fh) print(kmer, file=fh) def get_rscript_text(self, template_score, null_scores_path): params = { 'pval_r_path' : self.pval_r_path, 'null_scores_path' : null_scores_path, 'template_score' : template_score, } rscript_text = """ source("%(pval_r_path)s") library(MASS) sample<-scan("%(null_scores_path)s") getConfPvalLat(%(template_score)s, sample, conf=0.1, mins=7, maxs=200) """ % params return rscript_text def get_rout_filename(self): return os.path.join(self.statsig_dir, '%s.r_out' % self.finder_id) def extract_and_write_scores(self): score_lst = [None] * (self.nullset_size + 1) for i in range(self.nullset_size+1): if i == 0: json_filename = os.path.join(self.finder_outdir, 'motif-00000.stdout') else: json_filename = os.path.join(self.finder_outdir, 'null-%05d.stdout' % i ) json_dct = self.load_json(json_filename) score_lst[i] = json_dct['score_ranking_runs'] #write gm_width008.scores file nullscores_filename = os.path.join(self.statsig_dir, '%s.scores' % self.finder_id) self.logger.info('Writing null scores: %s' % nullscores_filename) with open(nullscores_filename, 'wb') as fh: print('\n' . join([str(s) for s in score_lst[1:]]), file=fh) #write R file rscript_text = self.get_rscript_text(score_lst[0], nullscores_filename) rscript_filename = os.path.join(self.statsig_dir, '%s.R' % self.finder_id) self.logger.info('Writing R script: %s' % rscript_filename) with open(rscript_filename, 'wb') as fh: print(rscript_text, file=fh) return rscript_filename class GimsanResultManager(GimsanJob): def __init__(self, name, template_file, outdir, config, conf_file, is_overwrite=False, dryrun=False, verbose=False): super(GimsanResultManager, self).__init__(outdir, config) self.logger = logging.getLogger(self.__class__.__name__) self.name = name self.template_file = template_file self.outdir = outdir self.conf_file = conf_file self.verbose = verbose self.dryrun = dryrun self.is_overwrite = is_overwrite self.css_outdir = os.path.join(self.outdir, 'css') self.js_outdir = os.path.join(self.outdir, 'js') self.statsig_dir = os.path.join(self.outdir, 'statsig') self.r_path = os.path.expanduser(self.config.get('result', 'r_path')) self.check_result_path() self.get_finders() #column-dependency self.column_dependency_exec = os.path.join(self.gimsan_home, 'column_dependency_app/column_dependency.out') if not os.path.isfile(self.column_dependency_exec): raise Exception('Column-Dependency executable missing: %s' % self.column_dependency_exec) def check_result_path(self): if not os.path.isdir(self.outdir): raise MissingDirError('Missing output directory: %s' % self.outdir) if not os.path.isdir(self.statsig_dir): os.mkdir(self.statsig_dir) elif not self.is_overwrite: raise AlreadyExistOutputDirError('Directory already exist: %s' % self.statsig_dir) if not os.path.isdir(self.css_outdir): os.mkdir(self.css_outdir) elif not self.is_overwrite: raise AlreadyExistOutputDirError('Directory already exist: %s' % self.css_outdir) if not os.path.isdir(self.js_outdir): os.mkdir(self.js_outdir) elif not self.is_overwrite: raise AlreadyExistOutputDirError('Directory already exist: %s' % self.js_outdir) def get_all_finder_meta(self): lst = [] for width in self.width_lst: lst.append(self.get_gibbsmarkov_meta(width)) return lst def generate_finder_result_list(self): finder_meta_lst = self.get_all_finder_meta() finder_res_lst = [] for finder_meta in finder_meta_lst: finder_res_lst.append(FinderResult(finder_meta, self.nullset_size, self.statsig_dir, self.outdir, self.gimsan_home)) rscript_jobs = [] for finder_res in finder_res_lst: rscript_filename = finder_res.extract_and_write_scores() cmd = "%s -f %s &>%s" % (self.r_path, rscript_filename, finder_res.get_rout_filename()) job = { 'cmd' : cmd, 'job_id' : rscript_filename, } rscript_jobs.append(job) #run R in parallel if self.dryrun: for job in rscript_jobs: self.logger.info(job['cmd']) else: import multiprocessing pool = multiprocessing.Pool(processes=self.num_proc) pool.map(subprocess_exec_func, rscript_jobs) #pvalue for finder_res in finder_res_lst: finder_res.get_pvalue_comment_from_rout() #weblogo img_dir = os.path.join(self.outdir, 'images') if not os.path.isdir(img_dir): os.mkdir(img_dir) for finder_res in finder_res_lst: finder_res.extract_and_write_kmers() weblogo_filename = os.path.join(img_dir, '%s.png' % finder_res.finder_id) weblogo_revcompl_filename = os.path.join(img_dir, '%s.revcompl.png' % finder_res.finder_id) finder_res.construct_weblogo(weblogo_filename, weblogo_revcompl_filename) #column dependency self.compute_column_dependency(finder_res_lst) return finder_res_lst def compute_column_dependency(self, finder_res_lst): coldep_dir = os.path.join(self.outdir, 'coldep') if not os.path.isdir(coldep_dir): os.mkdir(coldep_dir) if self.config.has_option('column_dependency', 'randseed'): randseed_param = '-s %d' % self.config.getint('column_dependency', 'randseed') else: randseed_param = '' job_lst = [] for finder_res in finder_res_lst: coldep_fileroot = '%s.coldep' % finder_res.finder_id stdout_fn = coldep_fileroot + ".txt" stderr_fn = coldep_fileroot + ".stderr" finder_res.coldep_outfile = os.path.join('coldep', stdout_fn) cmd = "%s -fsa %s %s 1>%s 2>%s" % ( self.column_dependency_exec, finder_res.kmer_filename, randseed_param, os.path.join(coldep_dir, stdout_fn), os.path.join(coldep_dir, stderr_fn)) job = { 'cmd' : cmd, 'job_id' : coldep_fileroot, } job_lst.append(job) #run R in parallel if self.dryrun: for job in job_lst: self.logger.info(job['cmd']) else: import multiprocessing pool = multiprocessing.Pool(processes=self.num_proc) pool.map(subprocess_exec_func, job_lst) for finder_res in finder_res_lst: full_path = os.path.join(self.outdir, finder_res.coldep_outfile) with open(full_path, 'rb') as fh: for ln in fh: m = re.search(r'for statistically significant pairs \((\d+) pairs\)', ln) if m: finder_res.coldep_num_pairs = int(m.group(1)) break if finder_res.coldep_num_pairs is None: raise Exception('Unable to find statistically significant pairs from %s' % full_path) if finder_res.coldep_num_pairs == 0: finder_res.coldep_btn_style = 'btn-default' else: finder_res.coldep_btn_style = 'btn-success' def generate_html(self): finder_res_lst = self.generate_finder_result_list() gm_finder0 = self.finder_lst[0] tp = None out_tp_file = os.path.join(self.gimsan_home, 'misc/output_template.html') with open(out_tp_file) as fh: tp = template.Template(fh.read()) if tp is None: raise MissingFileError('Unable to generate HTML from template: %s' % out_tp_file) output_html = tp.generate( experiment_name = self.name, config_filename = os.path.join('../meta', os.path.basename(self.conf_file)), fsa_filename = os.path.basename(self.template_file), nullset_size = self.nullset_size, per_seq_model_comment = gm_finder0.get_per_seq_model(), stop_crit_comment = gm_finder0.get_stop_crit(), rapid_conv = gm_finder0.get_rapid_conv(), double_strand_comment = 'yes' if gm_finder0.get_double_strand() else 'no', markov_order = gm_finder0.markov_order, genomic_file_comment = self.genome_filename if self.genome_filename else 'input FASTA file', finder_res_lst = finder_res_lst, ) output_html_file = os.path.join(self.outdir, 'output.html') self.logger.info('Writing HTML file to: %s' % output_html_file) with open(output_html_file, 'wb') as fh: print(output_html, file=fh) self.copy_html_assets() def copy_html_assets(self): lst = [ (os.path.join(self.gimsan_home, 'misc', 'css', "bootstrap.min.css"), self.css_outdir), (os.path.join(self.gimsan_home, 'misc', 'js', "bootstrap.min.js"), self.js_outdir), (os.path.join(self.gimsan_home, 'misc', 'js', "jquery-1.10.2.min.js"), self.js_outdir), ] for l in lst: os.system('cp -v %s %s' % (l[0], l[1])) def subprocess_exec_func(job): import logging logging.info('(%s): %s' % (job['job_id'], job['cmd'])) ret_code = subprocess.call(job['cmd'], shell=True) if __name__ == '__main__': benchmark = time_benchmark.Benchmark() #defaults description = """ Generate GIMSAN result """ epilog = """ Examples: %(prog)s --dir=testout -v """ argp = ArgumentParserPlus(description=description, epilog=epilog) argp.add_argument('--dir', required=True, help="main output directory used with gimsan_submit.py") argp.add_argument('--overwrite', action="store_true", help="") argp.add_argument('--dryrun', action="store_true", help="") argp.add_argument('-v', '--verbose', action='store_true') args = argp.parse_args() import logging if args.verbose: log_level = logging.DEBUG else: log_level = logging.INFO simple_stream_logging(log_level) args.dir = os.path.expanduser(args.dir) conf_file = BatchExperiment.get_conf_file(args.dir) batch_exp = BatchExperiment(conf_file, args.overwrite) for exp in batch_exp.experiments: gr_manager = GimsanResultManager( exp['name'], exp['fasta_file'], exp['outdir'], batch_exp.config, batch_exp.conf_file, is_overwrite = args.overwrite, dryrun = args.dryrun, verbose = args.verbose) gr_manager.generate_html() benchmark.print_time(sys.stderr)

mit

PolicyStat/docx2html

docx2html/core.py

1

48167

import cgi import logging import os import os.path import re from PIL import Image from lxml import etree from lxml.etree import XMLSyntaxError from collections import namedtuple, defaultdict from zipfile import ZipFile, BadZipfile from docx2html.exceptions import ( ConversionFailed, FileNotDocx, MalformedDocx, UnintendedTag, SyntaxNotSupported, ) DETECT_FONT_SIZE = False EMUS_PER_PIXEL = 9525 NSMAP = {} IMAGE_EXTENSIONS_TO_SKIP = ['emf', 'wmf', 'svg'] DEFAULT_LIST_NUMBERING_STYLE = 'decimal' logger = logging.getLogger(__name__) ### # Help functions ### def replace_ext(file_path, new_ext): """ >>> replace_ext('one/two/three.four.doc', '.html') 'one/two/three.four.html' >>> replace_ext('one/two/three.four.DOC', '.html') 'one/two/three.four.html' >>> replace_ext('one/two/three.four.DOC', 'html') 'one/two/three.four.html' """ if not new_ext.startswith(os.extsep): new_ext = os.extsep + new_ext index = file_path.rfind(os.extsep) return file_path[:index] + new_ext def ensure_tag(tags): # For some functions we can short-circuit and early exit if the tag is not # the right kind. def wrapped(f): def wrap(*args, **kwargs): passed_in_tag = args[0] if passed_in_tag is None: return None w_namespace = get_namespace(passed_in_tag, 'w') valid_tags = [ '%s%s' % (w_namespace, t) for t in tags ] if passed_in_tag.tag in valid_tags: return f(*args, **kwargs) return None return wrap return wrapped def get_namespace(el, namespace): if namespace not in NSMAP: NSMAP[namespace] = '{%s}' % el.nsmap[namespace] return NSMAP[namespace] def convert_image(target, image_size): _, extension = os.path.splitext(os.path.basename(target)) # If the image size has a zero in it early return if image_size and not all(image_size): return target # All the image types need to be converted to gif. invalid_extensions = ( '.bmp', '.dib', '.tiff', '.tif', ) # Open the image and get the format. try: image = Image.open(target) except IOError: return target image_format = image.format image_file_name = target # Make sure the size of the image and the size of the embedded image are # the same. if image_size is not None and image.size != image_size: # Resize if needed try: image = image.resize(image_size, Image.ANTIALIAS) except IOError: pass # If we have an invalid extension, change the format to gif. if extension.lower() in invalid_extensions: image_format = 'GIF' image_file_name = replace_ext(target, '.gif') # Resave the image (Post resizing) with the correct format try: image.save(image_file_name, image_format) except IOError: return target return image_file_name @ensure_tag(['p']) def get_font_size(p, styles_dict): w_namespace = get_namespace(p, 'w') r = p.find('%sr' % w_namespace) if r is None: return None rpr = r.find('%srPr' % w_namespace) if rpr is None: return None size = rpr.find('%ssz' % w_namespace) if size is None: # Need to get the font size off the styleId pPr = p.find('%spPr' % w_namespace) if pPr is None: return None pStyle = pPr.find('%spStyle' % w_namespace) if pStyle is None: return None pStyle = pStyle.get('%sval' % w_namespace) font_size = None style_value = styles_dict.get(pStyle, None) if style_value is None: return None if 'font_size' in style_value: font_size = styles_dict[pStyle]['font_size'] while font_size is None: old_pStyle = pStyle # If pStyle is not in the styles_dict then we have to break. if pStyle not in styles_dict: break # If based on is not in the styles_dict for pStyle then we have to # break. if 'based_on' not in styles_dict[pStyle]: break # Try to derive what the font size is based on what the current # style is based on. pStyle = styles_dict[pStyle]['based_on'] if old_pStyle == pStyle: break # If pStyle is not in styles_dict then break. if pStyle not in styles_dict: break # We have found a new font size font_size = styles_dict[pStyle]['font_size'] return font_size return size.get('%sval' % w_namespace) @ensure_tag(['p']) def is_natural_header(el, styles_dict): w_namespace = get_namespace(el, 'w') pPr = el.find('%spPr' % w_namespace) if pPr is None: return False pStyle = pPr.find('%spStyle' % w_namespace) if pStyle is None: return False style_id = pStyle.get('%sval' % w_namespace) if ( style_id in styles_dict and 'header' in styles_dict[style_id] and styles_dict[style_id]['header']): return styles_dict[style_id]['header'] @ensure_tag(['p']) def is_header(el, meta_data): if _is_top_level_upper_roman(el, meta_data): return 'h2' el_is_natural_header = is_natural_header(el, meta_data.styles_dict) if el_is_natural_header: return el_is_natural_header if _is_li(el): return False w_namespace = get_namespace(el, 'w') if el.tag == '%stbl' % w_namespace: return False # Check to see if this is a header because the font size is different than # the normal font size. # Since get_font_size is a method used before meta is created, just pass in # styles_dict. if DETECT_FONT_SIZE: font_size = get_font_size(el, meta_data.styles_dict) if font_size is not None: if meta_data.font_sizes_dict[font_size]: return meta_data.font_sizes_dict[font_size] # If a paragraph is longer than eight words it is likely not supposed to be # an h tag. num_words = len( etree.tostring( el, encoding=unicode, method='text', ).split(' ') ) if num_words > 8: return False # Check to see if the full line is bold. whole_line_bold, whole_line_italics = whole_line_styled(el) if whole_line_bold or whole_line_italics: return 'h2' return False @ensure_tag(['p']) def _is_top_level_upper_roman(el, meta_data): w_namespace = get_namespace(el, 'w') ilvl = get_ilvl(el, w_namespace) # If this list is not in the root document (indentation of 0), then it # cannot be a top level upper roman list. if ilvl != 0: return False numId = get_numId(el, w_namespace) list_type = meta_data.numbering_dict[numId].get(ilvl, False) return list_type == 'upperRoman' @ensure_tag(['p']) def _is_li(el): return len(el.xpath('.//w:numPr/w:ilvl', namespaces=el.nsmap)) != 0 @ensure_tag(['p']) def is_li(el, meta_data): """ The only real distinction between an ``li`` tag and a ``p`` tag is that an ``li`` tag has an attribute called numPr which holds the list id and ilvl (indentation level) """ if is_header(el, meta_data): return False return _is_li(el) def has_text(p): """ It is possible for a ``p`` tag in document.xml to not have any content. If this is the case we do not want that tag interfering with things like lists. Detect if this tag has any content. """ return '' != etree.tostring(p, encoding=unicode, method='text').strip() def is_last_li(li, meta_data, current_numId): """ Determine if ``li`` is the last list item for a given list """ if not is_li(li, meta_data): return False w_namespace = get_namespace(li, 'w') next_el = li while True: # If we run out of element this must be the last list item if next_el is None: return True next_el = next_el.getnext() # Ignore elements that are not a list item if not is_li(next_el, meta_data): continue new_numId = get_numId(next_el, w_namespace) if current_numId != new_numId: return True # If we have gotten here then we have found another list item in the # current list, so ``li`` is not the last li in the list. return False @ensure_tag(['p']) def get_single_list_nodes_data(li, meta_data): """ Find consecutive li tags that have content that have the same list id. """ yield li w_namespace = get_namespace(li, 'w') current_numId = get_numId(li, w_namespace) starting_ilvl = get_ilvl(li, w_namespace) el = li while True: el = el.getnext() if el is None: break # If the tag has no content ignore it. if not has_text(el): continue # Stop the lists if you come across a list item that should be a # heading. if _is_top_level_upper_roman(el, meta_data): break if ( is_li(el, meta_data) and (starting_ilvl > get_ilvl(el, w_namespace))): break new_numId = get_numId(el, w_namespace) if new_numId is None or new_numId == -1: # Not a p tag or a list item yield el continue # If the list id of the next tag is different that the previous that # means a new list being made (not nested) if current_numId != new_numId: # Not a subsequent list. break if is_last_li(el, meta_data, current_numId): yield el break yield el @ensure_tag(['p']) def get_ilvl(li, w_namespace): """ The ilvl on an li tag tells the li tag at what level of indentation this tag is at. This is used to determine if the li tag needs to be nested or not. """ ilvls = li.xpath('.//w:ilvl', namespaces=li.nsmap) if len(ilvls) == 0: return -1 return int(ilvls[0].get('%sval' % w_namespace)) @ensure_tag(['p']) def get_numId(li, w_namespace): """ The numId on an li tag maps to the numbering dictionary along side the ilvl to determine what the list should look like (unordered, digits, lower alpha, etc) """ numIds = li.xpath('.//w:numId', namespaces=li.nsmap) if len(numIds) == 0: return -1 return numIds[0].get('%sval' % w_namespace) def create_list(list_type): """ Based on the passed in list_type create a list objects (ol/ul). In the future this function will also deal with what the numbering of an ordered list should look like. """ list_types = { 'bullet': 'ul', } el = etree.Element(list_types.get(list_type, 'ol')) # These are the supported list style types and their conversion to css. list_type_conversions = { 'decimal': DEFAULT_LIST_NUMBERING_STYLE, 'decimalZero': 'decimal-leading-zero', 'upperRoman': 'upper-roman', 'lowerRoman': 'lower-roman', 'upperLetter': 'upper-alpha', 'lowerLetter': 'lower-alpha', 'ordinal': DEFAULT_LIST_NUMBERING_STYLE, 'cardinalText': DEFAULT_LIST_NUMBERING_STYLE, 'ordinalText': DEFAULT_LIST_NUMBERING_STYLE, } if list_type != 'bullet': el.set( 'data-list-type', list_type_conversions.get(list_type, DEFAULT_LIST_NUMBERING_STYLE), ) return el @ensure_tag(['tc']) def get_v_merge(tc): """ vMerge is what docx uses to denote that a table cell is part of a rowspan. The first cell to have a vMerge is the start of the rowspan, and the vMerge will be denoted with 'restart'. If it is anything other than restart then it is a continuation of another rowspan. """ if tc is None: return None v_merges = tc.xpath('.//w:vMerge', namespaces=tc.nsmap) if len(v_merges) != 1: return None v_merge = v_merges[0] return v_merge @ensure_tag(['tc']) def get_grid_span(tc): """ gridSpan is what docx uses to denote that a table cell has a colspan. This is much more simple than rowspans in that there is a one-to-one mapping from gridSpan to colspan. """ w_namespace = get_namespace(tc, 'w') grid_spans = tc.xpath('.//w:gridSpan', namespaces=tc.nsmap) if len(grid_spans) != 1: return 1 grid_span = grid_spans[0] return int(grid_span.get('%sval' % w_namespace)) @ensure_tag(['tr']) def get_td_at_index(tr, index): """ When calculating the rowspan for a given cell it is required to find all table cells 'below' the initial cell with a v_merge. This function will return the td element at the passed in index, taking into account colspans. """ current = 0 for td in tr.xpath('.//w:tc', namespaces=tr.nsmap): if index == current: return td current += get_grid_span(td) @ensure_tag(['tbl']) def get_rowspan_data(table): w_namespace = get_namespace(table, 'w') # We need to keep track of what table row we are on as well as which table # cell we are on. tr_index = 0 td_index = 0 # Get a list of all the table rows. tr_rows = list(table.xpath('.//w:tr', namespaces=table.nsmap)) # Loop through each table row. for tr in table.xpath('.//w:tr', namespaces=table.nsmap): # Loop through each table cell. for td in tr.xpath('.//w:tc', namespaces=tr.nsmap): # Check to see if this cell has a v_merge v_merge = get_v_merge(td) # If not increment the td_index and move on if v_merge is None: td_index += get_grid_span(td) continue # If it does have a v_merge we need to see if it is the ``root`` # table cell (the first in a row to have a rowspan) # If the value is restart then this is the table cell that needs # the rowspan. if v_merge.get('%sval' % w_namespace) == 'restart': row_span = 1 # Loop through each table row after the current one. for tr_el in tr_rows[tr_index + 1:]: # Get the table cell at the current td_index. td_el = get_td_at_index(tr_el, td_index) td_el_v_merge = get_v_merge(td_el) # If the td_ell does not have a v_merge then the rowspan is # done. if td_el_v_merge is None: break val = td_el_v_merge.get('%sval' % w_namespace) # If the v_merge is restart then there is another cell that # needs a rowspan, so the current cells rowspan is done. if val == 'restart': break # Increment the row_span row_span += 1 yield row_span # Increment the indexes. td_index += get_grid_span(td) tr_index += 1 # Reset the td_index when we finish each table row. td_index = 0 @ensure_tag(['b', 'i', 'u']) def style_is_false(style): """ For bold, italics and underline. Simply checking to see if the various tags are present will not suffice. If the tag is present and set to False then the style should not be present. """ if style is None: return False w_namespace = get_namespace(style, 'w') return style.get('%sval' % w_namespace) != 'false' @ensure_tag(['r']) def is_bold(r): """ The function will return True if the r tag passed in is considered bold. """ w_namespace = get_namespace(r, 'w') rpr = r.find('%srPr' % w_namespace) if rpr is None: return False bold = rpr.find('%sb' % w_namespace) return style_is_false(bold) @ensure_tag(['r']) def is_italics(r): """ The function will return True if the r tag passed in is considered italicized. """ w_namespace = get_namespace(r, 'w') rpr = r.find('%srPr' % w_namespace) if rpr is None: return False italics = rpr.find('%si' % w_namespace) return style_is_false(italics) @ensure_tag(['r']) def is_underlined(r): """ The function will return True if the r tag passed in is considered underlined. """ w_namespace = get_namespace(r, 'w') rpr = r.find('%srPr' % w_namespace) if rpr is None: return False underline = rpr.find('%su' % w_namespace) return style_is_false(underline) @ensure_tag(['p']) def is_title(p): """ Certain p tags are denoted as ``Title`` tags. This function will return True if the passed in p tag is considered a title. """ w_namespace = get_namespace(p, 'w') styles = p.xpath('.//w:pStyle', namespaces=p.nsmap) if len(styles) == 0: return False style = styles[0] return style.get('%sval' % w_namespace) == 'Title' @ensure_tag(['r']) def get_text_run_content_data(r): """ It turns out that r tags can contain both t tags and drawing tags. Since we need both, this function will return them in the order in which they are found. """ w_namespace = get_namespace(r, 'w') valid_elements = ( '%st' % w_namespace, '%sdrawing' % w_namespace, '%spict' % w_namespace, '%sbr' % w_namespace, ) for el in r: if el.tag in valid_elements: yield el @ensure_tag(['drawing', 'pict']) def get_image_id(drawing): r_namespace = get_namespace(drawing, 'r') for el in drawing.iter(): # For drawing image_id = el.get('%sembed' % r_namespace) if image_id is not None: return image_id # For pict if 'v' not in el.nsmap: continue v_namespace = get_namespace(drawing, 'v') if el.tag == '%simagedata' % v_namespace: image_id = el.get('%sid' % r_namespace) if image_id is not None: return image_id @ensure_tag(['p']) def whole_line_styled(p): """ Checks to see if the whole p tag will end up being bold or italics. Returns a tuple (boolean, boolean). The first boolean will be True if the whole line is bold, False otherwise. The second boolean will be True if the whole line is italics, False otherwise. """ r_tags = p.xpath('.//w:r', namespaces=p.nsmap) tags_are_bold = [ is_bold(r) or is_underlined(r) for r in r_tags ] tags_are_italics = [ is_italics(r) for r in r_tags ] return all(tags_are_bold), all(tags_are_italics) MetaData = namedtuple( 'MetaData', [ 'numbering_dict', 'relationship_dict', 'styles_dict', 'font_sizes_dict', 'image_handler', 'image_sizes', ], ) ### # Pre-processing ### def get_numbering_info(tree): """ There is a separate file called numbering.xml that stores how lists should look (unordered, digits, lower case letters, etc.). Parse that file and return a dictionary of what each combination should be based on list Id and level of indentation. """ if tree is None: return {} w_namespace = get_namespace(tree, 'w') num_ids = {} result = defaultdict(dict) # First find all the list types for list_type in tree.findall('%snum' % w_namespace): list_id = list_type.get('%snumId' % w_namespace) # Each list type is assigned an abstractNumber that defines how lists # should look. abstract_number = list_type.find('%sabstractNumId' % w_namespace) num_ids[abstract_number.get('%sval' % w_namespace)] = list_id # Loop through all the abstractNumbers for abstract_number in tree.findall('%sabstractNum' % w_namespace): abstract_num_id = abstract_number.get('%sabstractNumId' % w_namespace) # If we find an abstractNumber that is not being used in the document # then ignore it. if abstract_num_id not in num_ids: continue # Get the level of the abstract number. for lvl in abstract_number.findall('%slvl' % w_namespace): ilvl = int(lvl.get('%silvl' % w_namespace)) lvl_format = lvl.find('%snumFmt' % w_namespace) list_style = lvl_format.get('%sval' % w_namespace) # Based on the list type and the ilvl (indentation level) store the # needed style. result[num_ids[abstract_num_id]][ilvl] = list_style return result def get_style_dict(tree): """ Some things that are considered lists are actually supposed to be H tags (h1, h2, etc.) These can be denoted by their styleId """ # This is a partial document and actual h1 is the document title, which # will be displayed elsewhere. headers = { 'heading 1': 'h2', 'heading 2': 'h3', 'heading 3': 'h4', 'heading 4': 'h5', 'heading 5': 'h6', 'heading 6': 'h6', 'heading 7': 'h6', 'heading 8': 'h6', 'heading 9': 'h6', 'heading 10': 'h6', } if tree is None: return {} w_namespace = get_namespace(tree, 'w') result = {} for el in tree: style_id = el.get('%sstyleId' % w_namespace) el_result = { 'header': False, 'font_size': None, 'based_on': None, } # Get the header info name = el.find('%sname' % w_namespace) if name is None: continue value = name.get('%sval' % w_namespace).lower() if value in headers: el_result['header'] = headers[value] # Get the size info. rpr = el.find('%srPr' % w_namespace) if rpr is None: continue size = rpr.find('%ssz' % w_namespace) if size is None: el_result['font_size'] = None else: el_result['font_size'] = size.get('%sval' % w_namespace) # Get based on info. based_on = el.find('%sbasedOn' % w_namespace) if based_on is None: el_result['based_on'] = None else: el_result['based_on'] = based_on.get('%sval' % w_namespace) result[style_id] = el_result return result def get_image_sizes(tree): drawings = [] result = {} w_namespace = get_namespace(tree, 'w') for el in tree.iter(): if el.tag == '%sdrawing' % w_namespace: drawings.append(el) for d in drawings: for el in d.iter(): if 'a' not in el.nsmap: continue a_namespace = get_namespace(el, 'a') if el.tag == '%sxfrm' % a_namespace: ext = el.find('%sext' % a_namespace) cx = int(ext.get('cx')) / EMUS_PER_PIXEL cy = int(ext.get('cy')) / EMUS_PER_PIXEL result[get_image_id(d)] = (cx, cy) return result def get_relationship_info(tree, media, image_sizes): """ There is a separate file holds the targets to links as well as the targets for images. Return a dictionary based on the relationship id and the target. """ if tree is None: return {} result = {} # Loop through each relationship. for el in tree.iter(): el_id = el.get('Id') if el_id is None: continue # Store the target in the result dict. target = el.get('Target') if any( target.lower().endswith(ext) for ext in IMAGE_EXTENSIONS_TO_SKIP): continue if target in media: image_size = image_sizes.get(el_id) target = convert_image(media[target], image_size) # cgi will replace things like & < > with &amp; &lt; &gt; result[el_id] = cgi.escape(target) return result def get_font_sizes_dict(tree, styles_dict): font_sizes_dict = defaultdict(int) # Get all the fonts sizes and how often they are used in a dict. for p in tree.xpath('//w:p', namespaces=tree.nsmap): # If this p tag is a natural header, skip it if is_natural_header(p, styles_dict): continue if _is_li(p): continue font_size = get_font_size(p, styles_dict) if font_size is None: continue font_sizes_dict[font_size] += 1 # Find the most used font size. most_used_font_size = -1 highest_count = -1 for size, count in font_sizes_dict.items(): if count > highest_count: highest_count = count most_used_font_size = size # Consider the most used font size to be the 'default' font size. Any font # size that is different will be considered an h tag. result = {} for size in font_sizes_dict: if size is None: continue if int(size) > int(most_used_font_size): # Not an h tag result[size] = 'h2' else: result[size] = None return result def _get_document_data(f, image_handler=None): ''' ``f`` is a ``ZipFile`` that is open Extract out the document data, numbering data and the relationship data. ''' if image_handler is None: def image_handler(image_id, relationship_dict): return relationship_dict.get(image_id) document_xml = None numbering_xml = None relationship_xml = None styles_xml = None parser = etree.XMLParser(strip_cdata=False) path, _ = os.path.split(f.filename) media = {} image_sizes = {} # Loop through the files in the zip file. for item in f.infolist(): # This file holds all the content of the document. if item.filename == 'word/document.xml': xml = f.read(item.filename) document_xml = etree.fromstring(xml, parser) # This file tells document.xml how lists should look. elif item.filename == 'word/numbering.xml': xml = f.read(item.filename) numbering_xml = etree.fromstring(xml, parser) elif item.filename == 'word/styles.xml': xml = f.read(item.filename) styles_xml = etree.fromstring(xml, parser) # This file holds the targets for hyperlinks and images. elif item.filename == 'word/_rels/document.xml.rels': xml = f.read(item.filename) try: relationship_xml = etree.fromstring(xml, parser) except XMLSyntaxError: relationship_xml = etree.fromstring('<xml></xml>', parser) if item.filename.startswith('word/media/'): # Strip off the leading word/ media[item.filename[len('word/'):]] = f.extract( item.filename, path, ) # Close the file pointer. f.close() # Get dictionaries for the numbering and the relationships. numbering_dict = get_numbering_info(numbering_xml) image_sizes = get_image_sizes(document_xml) relationship_dict = get_relationship_info( relationship_xml, media, image_sizes ) styles_dict = get_style_dict(styles_xml) font_sizes_dict = defaultdict(int) if DETECT_FONT_SIZE: font_sizes_dict = get_font_sizes_dict(document_xml, styles_dict) meta_data = MetaData( numbering_dict=numbering_dict, relationship_dict=relationship_dict, styles_dict=styles_dict, font_sizes_dict=font_sizes_dict, image_handler=image_handler, image_sizes=image_sizes, ) return document_xml, meta_data ### # HTML Building functions ### def get_ordered_list_type(meta_data, numId, ilvl): """ Return the list type. If numId or ilvl not in the numbering dict then default to returning decimal. This function only cares about ordered lists, unordered lists get dealt with elsewhere. """ # Early return if numId or ilvl are not valid numbering_dict = meta_data.numbering_dict if numId not in numbering_dict: return DEFAULT_LIST_NUMBERING_STYLE if ilvl not in numbering_dict[numId]: return DEFAULT_LIST_NUMBERING_STYLE return meta_data.numbering_dict[numId][ilvl] def build_list(li_nodes, meta_data): """ Build the list structure and return the root list """ # Need to keep track of all incomplete nested lists. ol_dict = {} # Need to keep track of the current indentation level. current_ilvl = -1 # Need to keep track of the current list id. current_numId = -1 # Need to keep track of list that new li tags should be added too. current_ol = None # Store the first list created (the root list) for the return value. root_ol = None visited_nodes = [] list_contents = [] def _build_li(list_contents): data = '<br />'.join(t for t in list_contents if t is not None) return etree.XML('<li>%s</li>' % data) def _build_non_li_content(el, meta_data): w_namespace = get_namespace(el, 'w') if el.tag == '%stbl' % w_namespace: new_el, visited_nodes = build_table(el, meta_data) return etree.tostring(new_el), visited_nodes elif el.tag == '%sp' % w_namespace: return get_element_content(el, meta_data), [el] if has_text(el): raise UnintendedTag('Did not expect %s' % el.tag) def _merge_lists(ilvl, current_ilvl, ol_dict, current_ol): for i in reversed(range(ilvl, current_ilvl)): # Any list that is more indented that ilvl needs to # be merged to the list before it. if i not in ol_dict: continue if ol_dict[i] is not current_ol: if ol_dict[i] is current_ol: continue ol_dict[i][-1].append(current_ol) current_ol = ol_dict[i] # Clean up finished nested lists. for key in list(ol_dict): if key > ilvl: del ol_dict[key] return current_ol for li_node in li_nodes: w_namespace = get_namespace(li_node, 'w') if not is_li(li_node, meta_data): # Get the content and visited nodes new_el, el_visited_nodes = _build_non_li_content( li_node, meta_data, ) list_contents.append(new_el) visited_nodes.extend(el_visited_nodes) continue if list_contents: li_el = _build_li(list_contents) list_contents = [] current_ol.append(li_el) # Get the data needed to build the current list item list_contents.append(get_element_content( li_node, meta_data, )) ilvl = get_ilvl(li_node, w_namespace) numId = get_numId(li_node, w_namespace) list_type = get_ordered_list_type(meta_data, numId, ilvl) # If the ilvl is greater than the current_ilvl or the list id is # changing then we have the first li tag in a nested list. We need to # create a new list object and update all of our variables for keeping # track. if (ilvl > current_ilvl) or (numId != current_numId): # Only create a new list ol_dict[ilvl] = create_list(list_type) current_ol = ol_dict[ilvl] current_ilvl = ilvl current_numId = numId # Both cases above are not True then we need to close all lists greater # than ilvl and then remove them from the ol_dict else: # Merge any nested lists that need to be merged. current_ol = _merge_lists( ilvl=ilvl, current_ilvl=current_ilvl, ol_dict=ol_dict, current_ol=current_ol, ) # Set the root list after the first list is created. if root_ol is None: root_ol = current_ol # Set the current list. if ilvl in ol_dict: current_ol = ol_dict[ilvl] else: # In some instances the ilvl is not in the ol_dict, if that is the # case, create it here (not sure how this happens but it has # before.) Only do this if the current_ol is not the root_ol, # otherwise etree will crash. if current_ol is not root_ol: # Merge the current_ol into the root_ol. _merge_lists is not # equipped to handle this situation since the only way to get # into this block of code is to have mangled ilvls. root_ol[-1].append(current_ol) # Reset the current_ol current_ol = create_list(list_type) # Create the li element. visited_nodes.extend(list(li_node.iter())) # If a list item is the last thing in a document, then you will need to add # it here. Should probably figure out how to get the above logic to deal # with it. if list_contents: li_el = _build_li(list_contents) list_contents = [] current_ol.append(li_el) # Merge up any nested lists that have not been merged. current_ol = _merge_lists( ilvl=0, current_ilvl=current_ilvl, ol_dict=ol_dict, current_ol=current_ol, ) return root_ol, visited_nodes @ensure_tag(['tr']) def build_tr(tr, meta_data, row_spans): """ This will return a single tr element, with all tds already populated. """ # Create a blank tr element. tr_el = etree.Element('tr') w_namespace = get_namespace(tr, 'w') visited_nodes = [] for el in tr: if el in visited_nodes: continue visited_nodes.append(el) # Find the table cells. if el.tag == '%stc' % w_namespace: v_merge = get_v_merge(el) # If there is a v_merge and it is not restart then this cell can be # ignored. if ( v_merge is not None and v_merge.get('%sval' % w_namespace) != 'restart'): continue # Loop through each and build a list of all the content. texts = [] for td_content in el: # Since we are doing look-a-heads in this loop we need to check # again to see if we have already visited the node. if td_content in visited_nodes: continue # Check to see if it is a list or a regular paragraph. if is_li(td_content, meta_data): # If it is a list, create the list and update # visited_nodes. li_nodes = get_single_list_nodes_data( td_content, meta_data, ) list_el, list_visited_nodes = build_list( li_nodes, meta_data, ) visited_nodes.extend(list_visited_nodes) texts.append(etree.tostring(list_el)) elif td_content.tag == '%stbl' % w_namespace: table_el, table_visited_nodes = build_table( td_content, meta_data, ) visited_nodes.extend(table_visited_nodes) texts.append(etree.tostring(table_el)) elif td_content.tag == '%stcPr' % w_namespace: # Do nothing visited_nodes.append(td_content) continue else: text = get_element_content( td_content, meta_data, is_td=True, ) texts.append(text) data = '<br />'.join(t for t in texts if t is not None) td_el = etree.XML('<td>%s</td>' % data) # if there is a colspan then set it here. colspan = get_grid_span(el) if colspan > 1: td_el.set('colspan', '%d' % colspan) v_merge = get_v_merge(el) # If this td has a v_merge and it is restart then set the rowspan # here. if ( v_merge is not None and v_merge.get('%sval' % w_namespace) == 'restart'): rowspan = next(row_spans) td_el.set('rowspan', '%d' % rowspan) tr_el.append(td_el) return tr_el @ensure_tag(['tbl']) def build_table(table, meta_data): """ This returns a table object with all rows and cells correctly populated. """ # Create a blank table element. table_el = etree.Element('table') w_namespace = get_namespace(table, 'w') # Get the rowspan values for cells that have a rowspan. row_spans = get_rowspan_data(table) for el in table: if el.tag == '%str' % w_namespace: # Create the tr element. tr_el = build_tr( el, meta_data, row_spans, ) # And append it to the table. table_el.append(tr_el) visited_nodes = list(table.iter()) return table_el, visited_nodes @ensure_tag(['t']) def get_t_tag_content( t, parent, remove_bold, remove_italics, meta_data): """ Generate the string data that for this particular t tag. """ if t is None or t.text is None: return '' # Need to escape the text so that we do not accidentally put in text # that is not valid XML. # cgi will replace things like & < > with &amp; &lt; &gt; text = cgi.escape(t.text) # Wrap the text with any modifiers it might have (bold, italics or # underline) el_is_bold = not remove_bold and ( is_bold(parent) or is_underlined(parent) ) el_is_italics = not remove_italics and is_italics(parent) if el_is_bold: text = '<strong>%s</strong>' % text if el_is_italics: text = '<em>%s</em>' % text return text def _get_image_size_from_image(target): image = Image.open(target) return image.size def build_hyperlink(el, meta_data): # If we have a hyperlink we need to get relationship_id r_namespace = get_namespace(el, 'r') hyperlink_id = el.get('%sid' % r_namespace) # Once we have the hyperlink_id then we need to replace the # hyperlink tag with its child run tags. content = get_element_content( el, meta_data, remove_bold=True, remove_italics=True, ) if not content: return '' if hyperlink_id in meta_data.relationship_dict: href = meta_data.relationship_dict[hyperlink_id] # Do not do any styling on hyperlinks return '<a href="%s">%s</a>' % (href, content) return '' def build_image(el, meta_data): image_id = get_image_id(el) if image_id not in meta_data.relationship_dict: # This image does not have an image_id return '' src = meta_data.image_handler( image_id, meta_data.relationship_dict, ) if image_id in meta_data.image_sizes: width, height = meta_data.image_sizes[image_id] else: target = meta_data.relationship_dict[image_id] width, height = _get_image_size_from_image(target) # Make sure the width and height are not zero if all((width, height)): return '<img src="%s" height="%d" width="%d" />' % ( src, height, width, ) else: return '<img src="%s" />' % src return '' def get_text_run_content(el, meta_data, remove_bold, remove_italics): w_namespace = get_namespace(el, 'w') text_output = '' for child in get_text_run_content_data(el): if child.tag == '%st' % w_namespace: text_output += get_t_tag_content( child, el, remove_bold, remove_italics, meta_data, ) elif child.tag == '%sbr' % w_namespace: text_output += '<br />' elif child.tag in ( '%spict' % w_namespace, '%sdrawing' % w_namespace, ): text_output += build_image(child, meta_data) else: raise SyntaxNotSupported( '"%s" is not a supported content-containing ' 'text run child.' % child.tag ) return text_output @ensure_tag(['p', 'ins', 'smartTag', 'hyperlink']) def get_element_content( p, meta_data, is_td=False, remove_italics=False, remove_bold=False, ): """ P tags are made up of several runs (r tags) of text. This function takes a p tag and constructs the text that should be part of the p tag. image_handler should be a callable that returns the desired ``src`` attribute for a given image. """ # Only remove bold or italics if this tag is an h tag. # Td elements have the same look and feel as p/h elements. Right now we are # never putting h tags in td elements, as such if we are in a td we will # never be stripping bold/italics since that is only done on h tags if not is_td and is_header(p, meta_data): # Check to see if the whole line is bold or italics. remove_bold, remove_italics = whole_line_styled(p) p_text = '' w_namespace = get_namespace(p, 'w') if len(p) == 0: return '' # Only these tags contain text that we care about (eg. We don't care about # delete tags) content_tags = ( '%sr' % w_namespace, '%shyperlink' % w_namespace, '%sins' % w_namespace, '%ssmartTag' % w_namespace, ) elements_with_content = [] for child in p: if child is None: break if child.tag in content_tags: elements_with_content.append(child) # Gather the content from all of the children for el in elements_with_content: # Hyperlinks and insert tags need to be handled differently than # r and smart tags. if el.tag in ('%sins' % w_namespace, '%ssmartTag' % w_namespace): p_text += get_element_content( el, meta_data, remove_bold=remove_bold, remove_italics=remove_italics, ) elif el.tag == '%shyperlink' % w_namespace: p_text += build_hyperlink(el, meta_data) elif el.tag == '%sr' % w_namespace: p_text += get_text_run_content( el, meta_data, remove_bold=remove_bold, remove_italics=remove_italics, ) else: raise SyntaxNotSupported( 'Content element "%s" not handled.' % el.tag ) # This function does not return a p tag since other tag types need this as # well (td, li). return p_text def _strip_tag(tree, tag): """ Remove all tags that have the tag name ``tag`` """ for el in tree.iter(): if el.tag == tag: el.getparent().remove(el) def get_zip_file_handler(file_path): return ZipFile(file_path) def read_html_file(file_path): with open(file_path) as f: html = f.read() return html def convert(file_path, image_handler=None, fall_back=None, converter=None): """ ``file_path`` is a path to the file on the file system that you want to be converted to html. ``image_handler`` is a function that takes an image_id and a relationship_dict to generate the src attribute for images. (see readme for more details) ``fall_back`` is a function that takes a ``file_path``. This function will only be called if for whatever reason the conversion fails. ``converter`` is a function to convert a document that is not docx to docx (examples in docx2html.converters) Returns html extracted from ``file_path`` """ file_base, extension = os.path.splitext(os.path.basename(file_path)) if extension == '.html' or extension == '.htm': return read_html_file(file_path) # Create the converted file as a file in the same dir with the # same name only with a .docx extension docx_path = replace_ext(file_path, '.docx') if extension == '.docx': # If the file is already html, just leave it in place. docx_path = file_path else: if converter is None: raise FileNotDocx('The file passed in is not a docx.') converter(docx_path, file_path) if not os.path.isfile(docx_path): if fall_back is None: raise ConversionFailed('Conversion to docx failed.') else: return fall_back(file_path) try: # Docx files are actually just zip files. zf = get_zip_file_handler(docx_path) except BadZipfile: raise MalformedDocx('This file is not a docx') # Need to populate the xml based on word/document.xml tree, meta_data = _get_document_data(zf, image_handler) return create_html(tree, meta_data) def create_html(tree, meta_data): # Start the return value new_html = etree.Element('html') w_namespace = get_namespace(tree, 'w') visited_nodes = [] _strip_tag(tree, '%ssectPr' % w_namespace) for el in tree.iter(): # The way lists are handled could double visit certain elements; keep # track of which elements have been visited and skip any that have been # visited already. if el in visited_nodes: continue header_value = is_header(el, meta_data) if is_header(el, meta_data): p_text = get_element_content(el, meta_data) if p_text == '': continue new_html.append( etree.XML('<%s>%s</%s>' % ( header_value, p_text, header_value, )) ) elif el.tag == '%sp' % w_namespace: # Strip out titles. if is_title(el): continue if is_li(el, meta_data): # Parse out the needed info from the node. li_nodes = get_single_list_nodes_data(el, meta_data) new_el, list_visited_nodes = build_list( li_nodes, meta_data, ) visited_nodes.extend(list_visited_nodes) # Handle generic p tag here. else: p_text = get_element_content(el, meta_data) # If there is not text do not add an empty tag. if p_text == '': continue new_el = etree.XML('<p>%s</p>' % p_text) new_html.append(new_el) elif el.tag == '%stbl' % w_namespace: table_el, table_visited_nodes = build_table( el, meta_data, ) visited_nodes.extend(table_visited_nodes) new_html.append(table_el) continue # Keep track of visited_nodes visited_nodes.append(el) result = etree.tostring( new_html, method='html', with_tail=True, ) return _make_void_elements_self_close(result) def _make_void_elements_self_close(html): #XXX Hack not sure how to get etree to do this by default. void_tags = [ r'br', r'img', ] for tag in void_tags: regex = re.compile(r'<%s.*?>' % tag) matches = regex.findall(html) for match in matches: new_tag = match.strip('<>') new_tag = '<%s />' % new_tag html = re.sub(match, new_tag, html) return html

bsd-3-clause

Guymer/PyGuymer

simplify_poly.py

1

1717

# -*- coding: utf-8 -*- ############################################################################################## # This file is deprecated because Python 2.x is deprecated # # A Python 3.x version of this file can be found at: # # # # https://github.com/Guymer/PyGuymer3/blob/master/simplify_poly.py # ############################################################################################## def simplify_poly(poly1, simp = 0.1): """ This function accepts either a Polygon or a MultiPolygon and creates a Polygon or a MultiPolygon from the simplified (member) Polygon(s). """ # Import modules ... import shapely import shapely.geometry import shapely.validation # Create empty list ... poly2 = [] # Check what the argument is ... if isinstance(poly1, shapely.geometry.multipolygon.MultiPolygon): # Loop over Polygons and add simplified copys to the list ... for tmp1 in poly1.geoms: poly2.append(tmp1.simplify(simp)) elif isinstance(poly1, shapely.geometry.polygon.Polygon): # Add simplified copy to the list ... poly2.append(poly1.simplify(simp)) else: raise TypeError("\"poly1\" is an unexpected type") # Convert list to MultiPolygon ... poly2 = shapely.geometry.multipolygon.MultiPolygon(poly2) if not poly2.is_valid: raise Exception("\"poly2\" is not a valid [Multi]Polygon ({0:s})".format(shapely.validation.explain_validity(poly2))) # Return answer ... return poly2

apache-2.0

pymir3/pymir3

mir3/modules/supervised/linear/decomposer/beta_nmf.py

1

19321

import argparse import numpy import numpy.random import mir3.data.linear_decomposition as ld import mir3.data.metadata as md import mir3.data.spectrogram as spectrogram import mir3.module # TODO: maybe split this into 2 modules to compute activation and # basis+activation class BetaNMF(mir3.module.Module): def get_help(self): return """use beta nmf algorithm to compute the activations""" def build_arguments(self, parser): parser.add_argument('-b','--beta', type=float, default=2., help="""beta value to be used by the algorithm (default: %(default)s)""") parser.add_argument('-i','--max-iterations', type=int, default=100, help="""maximum number of iterations""") parser.add_argument('-d','--min-delta', type=float, default=0., help="""minimum difference between iterations to consider convergence""") parser.add_argument('-B','--basis', type=argparse.FileType('rb'), help="""basis file to be used""") parser.add_argument('-s','--size', nargs=3, metavar=('SIZE', 'INSTRUMENT', 'NOTE'), help="""size of the decomposition and instrument and note names to be used for the basis. 'INSTRUMENT' or 'NOTE' can be set to 'None' or 'null' to ignore that parameter""") parser.add_argument('piece', nargs='+', help="""piece spectrogram file""") parser.add_argument('outfile', type=argparse.FileType('wb'), help="""linear decomposition file""") def run(self, args): # Loads basis if present if args.basis is not None: b = ld.LinearDecomposition().load(args.basis) else: b = None if args.basis is not None and b.data.right != {}: print "Basis doesn't have empty right side. Ignoring it." # Size of the decomposition (used when finding a basis too) if args.size is None: args.size = [None, None, None] # Simulate 3 values for i in range(len(args.size)): if args.size[i] == 'None' or args.size[i] == 'null': args.size[i] = None # Gather input spectrograms s_list = [] s_meta = [] for filename in args.piece: with open(filename, 'rb') as handler: s_list.append(spectrogram.Spectrogram().load(handler)) s_meta.append(md.FileMetadata(handler)) # Converts arguments size = int(args.size[0]) if args.size[0] is not None else None instrument = args.size[1] if args.size[1] is not None else '' note = args.size[2] if args.size[2] is not None else '' # Decompose d = self.compute(s_list, size, instrument, note, b, args.beta, args.min_delta, args.max_iterations, False) # Associates an activation metadata with its given spectrogram's # metadata for k, data, metadata in d.right(): metadata.spectrogram_input = s_meta[k[-1]] # Checks if basis was provided if b is not None: # If provided, adds it as basis metadata for each activation meta = md.FileMetadata(args.basis) for k, data, metadata in d.right(): metadata.basis_input = meta else: # Otherwise, the basis was computed right now, so we set its # metadata with the list of all spectrograms' metadata d.metadata.left[(args.size[1], args.size[2])].spectrogram_input = \ s_meta d.save(args.outfile) def compute(self, spectrograms, size=None, instrument=None, note=None, basis=None, beta=2., min_delta=0., max_iterations=100, save_metadata=True): """Computes the activation matrix from a basis matrix and a spectrogram. Uses the beta divergence to compute the activations. If min_delta is zero, the code may run faster because no beta divergence is actually computed. Otherwise, the code stops computing if two iterations of the algorithm don't improve the result by more than min_delta. Only one of 'basis' and 'size' arguments may be set, as they specify different things. With 'size', the user extracts both a basis and an activation from the spectrogram, while with 'basis' only an activation is computed. Each activation computed has the same key as the corresponding basis plus the spectrogram's index in the list provided. If a basis is being created, it's name is a tuple of (instrument, note), even if they are None. Args: spectrograms: list of Spectrograms to be merged and used to compute the activations. size: Number of basis to extract from the spectrogram. Must be None if the 'basis' argument is defined. instrument: Name of the instrument. This is used only if size is set. If None, it's ignored. Default: None. note: Name of the note. This is used only if size is set. If None, it's ignored. Default: None. basis: LinearDecomposition object describing the basis to be used. Must be none if the 'size' argument is defined. beta: value for the beta used in divergence. Default: 2. min_delta: threshold for early stop. Default: 0. max_iterations: maximum number of iterations to use. Default: 100. save_metadata: flag indicating whether the metadata should be computed. Default: True. Returns: LinearDecomposition object with basis and activations for the spectrograms. Raises: ValueError: matrices have incompatible sizes. """ # Check arguments compatibility if size is None and basis is None: raise ValueError("One of 'size' or 'basis' must not be None.") if basis is not None and size is not None: raise ValueError("Only one of 'size' or 'basis' must not be None.") # Saves metadata if save_metadata: s_meta = [md.ObjectMetadata(s) for s in spectrograms] else: s_meta = [None for s in spectrograms] # Marks the limits of each spectrogram X_start = [0] for s in spectrograms: X_start.append(X_start[-1]+s.data.shape[1]) # Merges spectrograms X = numpy.hstack([s.data for s in spectrograms]) # If we have a basis, we only need to compute the activations if basis is not None: # Merges basis but keep track where each one starts so that it can # be used to characterize the activations B = [] B_start = [0] for k, data, metadata in basis.left(): B.append(data) B_start.append(B_start[-1]+data.shape[1]) B = numpy.hstack(B) # Saves metadata if save_metadata: b_meta = md.ObjectMetadata(B) else: b_meta = None # Initilizes activations A = numpy.ones((B.shape[1], X.shape[1])) # Computes the activation self.compute_activation(X, B, A, beta, min_delta, max_iterations) # Starts creating the decomposition object d = ld.LinearDecomposition() # Copy the left stuff from the basis, since they came from there d.data.left = basis.data.left d.metadata.left = basis.metadata.left # Cuts the activation. For each combination of basis and # spectrograms, we get an activation i = 0 for k, data, metadata in basis.left(): for j in range(len(spectrograms)): # Since spectrograms don't have name, we call it by its # sequence number s_name = (j,) # Cuts the activation A_cut = A[B_start[i]:B_start[i+1], X_start[j]:X_start[j+1]] # Merges the basis key with the spectrogram name to create a # key for the activation. Then stores a lot of metadata # about what was used to compute it. d.add(k+s_name, right=A_cut, right_metadata=md.Metadata( method="beta_nmf", beta=beta, min_delta=min_delta, max_iterations=max_iterations, spectrogram_input=s_meta[j], spectrogram=s.metadata, basis_input=b_meta, basis=metadata)) # Increase basis iterator i += 1 else: # Everyone gets the same matrices to work with every time, so we # avoid consistency problems. However, we can't have the same values # filling the matrices or the algorithm can't separate the basis and # activations (everyone keeps getting the same value). numpy.random.seed(0) B = numpy.random.rand(X.shape[0], size) A = numpy.random.rand(size, X.shape[1]) # Computes both basis and activations self.compute_both(X, B, A, beta, min_delta, max_iterations) # Key for the basis created key = (instrument, note) # Starts creating the decomposition object d = ld.LinearDecomposition() # Adds basis d.add(key, left=B, left_metadata=md.Metadata( method="beta_nmf", beta=beta, min_delta=min_delta, max_iterations=max_iterations, spectrogram_input=s_meta, spectrogram=[s.metadata for s in spectrograms])) # Adds the activations cutted to match the spectrograms for j in range(len(spectrograms)): # Since spectrograms don't have name, we call it by its sequence # number s = spectrograms[j] s_name = (j,) # Cuts the activation A_cut = A[:, X_start[j]:X_start[j+1]] # Merges the basis key with the spectrogram name to create a key # for the activation. Then stores a lot of metadata about what # was used to compute it. d.add(key+s_name, right=A_cut, right_metadata=md.Metadata( method="beta_nmf", beta=beta, min_delta=min_delta, max_iterations=max_iterations, spectrogram_input=s_meta[j], spectrogram=s.metadata)) return d def compute_both(self, X, B, A, beta=2., min_delta=0., max_iterations=100): """Computes both the basis and activation. Args: X: matrix to be approximated. B: initial guess for B. A: initial guess for A. beta: value of beta to be used. Default: 2. min_delta: minimum improvement necessary for the algorithm to continue. Default: 0. max_iterations: maximum number of iterations. Default: 100; Raises: ValueError: matrices have incompatible sizes. """ # Checks shapes match if X.shape[0] != B.shape[0] or X.shape[1] != A.shape[1]: raise ValueError("Incompatible matrix sizes: %r = %r * %r." % (X.shape, B.shape, A.shape)) # Makes decomposition self.beta_nmf(1e-6+X, # Avoids near-zero values B, A, beta=beta, update_B=True, update_A=True, min_delta=min_delta, max_iterations=max_iterations) def compute_activation(self, X, B, A, beta=2., min_delta=0., max_iterations=100): """Computes both the activation for a given basis. Args: X: matrix to be approximated. B: basis to be used. A: initial guess for A. beta: value of beta to be used. Default: 2. min_delta: minimum improvement necessary for the algorithm to continue. Default: 0. max_iterations: maximum number of iterations. Default: 100. Raises: ValueError: matrices have incompatible sizes. """ # Checks shapes match if X.shape[0] != B.shape[0] or X.shape[1] != A.shape[1]: raise ValueError("Incompatible matrix sizes: %r = %r * %r." % (X.shape, B.shape, A.shape)) # Computes 100 activations at the same time for speed # TODO: make this a parameter step = 100 for i in range(0,X.shape[1],step): self.beta_nmf(1e-6+X[:,i:i+step], # Avoids near-zero values B, A[:,i:i+step], beta=beta, update_B=False, update_A=True, min_delta=min_delta, max_iterations=max_iterations) def betadivergence(self, x, y, beta=2.0): """Computes the beta-divergence d(x|y). The beta-divergence, as defined by Eguchi and Kano [1], is given by: 1/(beta*(beta-1)))*(x**b + (beta-1)*y**(beta) - beta*x*(y**(beta-1))), if beta is not 0 or 1; x * log(x/y) + (y-x), if beta=1 (x/y) - log(x/y) - 1, if beta=0 The special cases for the beta divergence are: beta=0 -> Itakura-Saito divergence beta=1 -> Kullback-Leibler divergence beta=2 -> Euclidean distance Args: x: left side of the divergence y: right side of the divergence beta: value of beta used to compute. Default: 2. Returns: Divergence value. """ # Common values of beta with faster evaluation if beta == 1: return numpy.sum(x * numpy.log(x/y) + (y-x)) elif beta == 0: return numpy.sum((x/y) - numpy.log(x/y) - 1) elif beta == 2: return numpy.sum((x-y)**2)/2. # Magic formula for beta-divergence beta = float(beta) d = (1/(beta*(beta-1))) * \ numpy.sum((x**beta)+(beta-1)*(y**beta)-beta*x*(y**(beta-1))) return d def beta_nmf_step(self, X, B, A, beta=2.0, update_B=False, update_A=True): """Computes a step of a non-negative factorization towards X using B and A as initial conditions. X = B * A The matrices A and B are updated in place, so any previous value is destroyed. Because of convergence problems, only one update is performed at a time, with A update having priority. If you want to update both, call this twice. Returns B, A and the error after the step was taken. Uses the multiplicative approach as defined in: Cedric Fevotte and Jerome Idier: Algorithms for nonnegative matrix factorization with the beta-divergence (pg 13, eqs. 67 and 68) Download paper at http://arxiv.org/pdf/1010.1763v3.pdf Args: X: matrix to be approximated. B: initial guess for B. A: initial guess for A. beta: value of beta to be used. Default: 2. update_B: flag indicating that the value of B should be updated. Default: False. update_A: flag indicating that the value of A should be updated. Default: False. """ # Computes current approximation Xtil = numpy.dot(B,A) # Auxiliary variables for speed Xtil2 = Xtil**(beta-2) XtilNum = Xtil2*X XtilDen = Xtil2*Xtil if update_A: A_numerator = numpy.dot(B.transpose(), XtilNum) A_denominator = numpy.dot(B.transpose(), XtilDen) A *= A_numerator/A_denominator elif update_B: B_numerator = numpy.dot(XtilNum, A.transpose()) B_denominator = numpy.dot(XtilDen, A.transpose()) B *= B_numerator/B_denominator def beta_nmf(self, X, B, A, beta, update_B, update_A, min_delta, max_iterations): """Performs non-negative matrix factorization for X=BA using a beta-divergence. The algorithm stops if either the number of iterations exceed a maximum or the improvement is less the a threshold. If minDelta is 0, no beta divergence is computed and the algorithm may run faster! The values of B and A are updated in place. Args: X: matrix to be approximated. B: initial guess for B. A: initial guess for A. beta: value of beta to be used. updateB: flag indicating that the value of B should be updated. updateA: flag indicating that the value of A should be updated. minDelta: minimum improvement necessary for the algorithm to continue. maxIterations: maximum number of iterations """ # If tolerance is zero, we can skip beta divergence computation. This # may increase speed a lot min_delta_is_zero = (min_delta == 0) # If we have a tolerance, compute initial values to check for # convergence if not min_delta_is_zero: last_delta = 2*min_delta curr_err = self.betadivergence(X, numpy.dot(B,A), beta) n_iterations = 0 while (min_delta_is_zero or last_delta > min_delta) and \ n_iterations < max_iterations: # Update the chosen matrices if update_B and update_A: self.beta_nmf_step(X, B, A, beta, False, True) self.beta_nmf_step(X, B, A, beta, True, False) else: self.beta_nmf_step(X, B, A, beta, update_B, update_A) # If tolerance isn't zero, we need to check for convergence if not min_delta_is_zero: new_err = self.betadivergence(X, numpy.dot(B, A), beta) last_delta = curr_err-new_err curr_err = new_err n_iterations = n_iterations + 1

mit

slacker007/OFF-ToolKit

Modules/Correlation.py

1

1103

from Builders import wigile_query from Builders import kml_builder class ClassName(): #These are the options we will set def __init__(self): # Descriptions that are required!!! self.name = "Registry Network info corelation" self.description = "WIGLE Query your known BSSID" self.language = "python" self.extension = "py" self.rating = "Excellent" # options we require user interaction for- format is {Option : [Value, Description]]} self.required_options = {"bssid" : ['00:22:55:DF:C8:01', "Set BSSID or MAC of AP"], "user" : ['offtest', "Set Username to WIGLE"], "pass" : ['83128312', "Set Password to WIGLE"]} def startx(self): wa = wigile_query.WigleAgent(self.required_options["user"][0], self.required_options["pass"][0]) final = wa.get_lat_lng(self.required_options["bssid"][0]) print final kml = kml_builder.kml() kml.build(final["lat"], final["lng"], final["bssid"]) #Pass SSID name of network print "[*] Check output"

gpl-2.0

DayGitH/Python-Challenges

DailyProgrammer/DP20140718C.py

1

2012

""" [7/18/2014] Challenge #171 [Hard] Intergalatic Bitstream https://www.reddit.com/r/dailyprogrammer/comments/2b21mp/7182014_challenge_171_hard_intergalatic_bitstream/ #Description: Keeping with our "Bit" theme this week. We will look into the future. It is 2114. We have colonized the Galaxy. To communicate we send 140 character max messages using [A-Z0-9 ]. The technology to do this requires faster than light pulses to beam the messages to relay stations. Your challenge is to implement the compression for these messages. The design is very open and the solutions will vary. Your goals: * Compact 140 Bytes down to a stream of bits to send and then decompact the message and verify 100% data contained. * The goal is bit reduction. 140 bytes or less at 8 bits per byte so thats 1120 bits max. If you take a message of 140 bytes and compress it to 900 bits you have 220 less bits for 20% reduction. #Input: A text message of 140 or less characters that can be [A-Z0-9 ] #Output: Read Message of x Bytes. Compressing x*8 Bits into y Bits. (z% compression) Sending Message. Decompressing Message into x Bytes. Message Matches! * x - size of your message * x* 8 = bits of your message * z - the percentage of message compressed by * y bits of your bit stream for transmission So compress your tiny message and show some stats on it and then decompress it and verify it matches the original message. #Challenge Inputs: three messages to send: REMEMBER TO DRINK YOUR OVALTINE GIANTS BEAT DODGERS 10 TO 9 AND PLAY TOMORROW AT 1300 SPACE THE FINAL FRONTIER THESE ARE THE VOYAGES OF THE BIT STREAM DAILY PROGRAMMER TO SEEK OUT NEW COMPRESSION #Congrats! We are a trending subreddit for today 7-18-2014. Welcome to first time viewers of /r/dailyprogrammers checking out our cool subreddit. We have lots of programming challenges for you to take on in the past and many to look forward to in the future. """ def main(): pass if __name__ == "__main__": main()

mit

ContinuumIO/dask

setup.py

2

2210

#!/usr/bin/env python import sys from os.path import exists from setuptools import setup import versioneer # NOTE: These are tested in `continuous_integration/travis/test_imports.sh` If # you modify these, make sure to change the corresponding line there. extras_require = { "array": ["numpy >= 1.13.0", "toolz >= 0.8.2"], "bag": [ "cloudpickle >= 0.2.2", "fsspec >= 0.6.0", "toolz >= 0.8.2", "partd >= 0.3.10", ], "dataframe": [ "numpy >= 1.13.0", "pandas >= 0.23.0", "toolz >= 0.8.2", "partd >= 0.3.10", "fsspec >= 0.6.0", ], "distributed": ["distributed >= 2.0"], "diagnostics": ["bokeh >= 1.0.0"], "delayed": ["cloudpickle >= 0.2.2", "toolz >= 0.8.2"], } extras_require["complete"] = sorted({v for req in extras_require.values() for v in req}) install_requires = ["pyyaml"] packages = [ "dask", "dask.array", "dask.bag", "dask.bytes", "dask.dataframe", "dask.dataframe.io", "dask.dataframe.tseries", "dask.diagnostics", ] tests = [p + ".tests" for p in packages] # Only include pytest-runner in setup_requires if we're invoking tests if {"pytest", "test", "ptr"}.intersection(sys.argv): setup_requires = ["pytest-runner"] else: setup_requires = [] setup( name="dask", version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), description="Parallel PyData with Task Scheduling", url="https://github.com/dask/dask/", maintainer="Matthew Rocklin", maintainer_email="[email protected]", license="BSD", keywords="task-scheduling parallel numpy pandas pydata", classifiers=[ "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", ], packages=packages + tests, long_description=open("README.rst").read() if exists("README.rst") else "", python_requires=">=3.6", install_requires=install_requires, setup_requires=setup_requires, tests_require=["pytest"], extras_require=extras_require, include_package_data=True, zip_safe=False, )

bsd-3-clause

nkgilley/home-assistant

homeassistant/components/statistics/sensor.py

1

12228

"""Support for statistics for sensor values.""" from collections import deque import logging import statistics import voluptuous as vol from homeassistant.components.recorder.models import States from homeassistant.components.recorder.util import execute, session_scope from homeassistant.components.sensor import PLATFORM_SCHEMA from homeassistant.const import ( ATTR_UNIT_OF_MEASUREMENT, CONF_ENTITY_ID, CONF_NAME, EVENT_HOMEASSISTANT_START, STATE_UNAVAILABLE, STATE_UNKNOWN, ) from homeassistant.core import callback from homeassistant.helpers import config_validation as cv, event from homeassistant.helpers.entity import Entity from homeassistant.util import dt as dt_util _LOGGER = logging.getLogger(__name__) ATTR_AVERAGE_CHANGE = "average_change" ATTR_CHANGE = "change" ATTR_CHANGE_RATE = "change_rate" ATTR_COUNT = "count" ATTR_MAX_AGE = "max_age" ATTR_MAX_VALUE = "max_value" ATTR_MEAN = "mean" ATTR_MEDIAN = "median" ATTR_MIN_AGE = "min_age" ATTR_MIN_VALUE = "min_value" ATTR_SAMPLING_SIZE = "sampling_size" ATTR_STANDARD_DEVIATION = "standard_deviation" ATTR_TOTAL = "total" ATTR_VARIANCE = "variance" CONF_SAMPLING_SIZE = "sampling_size" CONF_MAX_AGE = "max_age" CONF_PRECISION = "precision" DEFAULT_NAME = "Stats" DEFAULT_SIZE = 20 DEFAULT_PRECISION = 2 ICON = "mdi:calculator" PLATFORM_SCHEMA = PLATFORM_SCHEMA.extend( { vol.Required(CONF_ENTITY_ID): cv.entity_id, vol.Optional(CONF_NAME, default=DEFAULT_NAME): cv.string, vol.Optional(CONF_SAMPLING_SIZE, default=DEFAULT_SIZE): vol.All( vol.Coerce(int), vol.Range(min=1) ), vol.Optional(CONF_MAX_AGE): cv.time_period, vol.Optional(CONF_PRECISION, default=DEFAULT_PRECISION): vol.Coerce(int), } ) async def async_setup_platform(hass, config, async_add_entities, discovery_info=None): """Set up the Statistics sensor.""" entity_id = config.get(CONF_ENTITY_ID) name = config.get(CONF_NAME) sampling_size = config.get(CONF_SAMPLING_SIZE) max_age = config.get(CONF_MAX_AGE) precision = config.get(CONF_PRECISION) async_add_entities( [StatisticsSensor(entity_id, name, sampling_size, max_age, precision)], True ) return True class StatisticsSensor(Entity): """Representation of a Statistics sensor.""" def __init__(self, entity_id, name, sampling_size, max_age, precision): """Initialize the Statistics sensor.""" self._entity_id = entity_id self.is_binary = self._entity_id.split(".")[0] == "binary_sensor" self._name = name self._sampling_size = sampling_size self._max_age = max_age self._precision = precision self._unit_of_measurement = None self.states = deque(maxlen=self._sampling_size) self.ages = deque(maxlen=self._sampling_size) self.count = 0 self.mean = self.median = self.stdev = self.variance = None self.total = self.min = self.max = None self.min_age = self.max_age = None self.change = self.average_change = self.change_rate = None self._update_listener = None async def async_added_to_hass(self): """Register callbacks.""" @callback def async_stats_sensor_state_listener(entity, old_state, new_state): """Handle the sensor state changes.""" self._unit_of_measurement = new_state.attributes.get( ATTR_UNIT_OF_MEASUREMENT ) self._add_state_to_queue(new_state) self.async_schedule_update_ha_state(True) @callback def async_stats_sensor_startup(_): """Add listener and get recorded state.""" _LOGGER.debug("Startup for %s", self.entity_id) event.async_track_state_change( self.hass, self._entity_id, async_stats_sensor_state_listener ) if "recorder" in self.hass.config.components: # Only use the database if it's configured self.hass.async_create_task(self._async_initialize_from_database()) self.hass.bus.async_listen_once( EVENT_HOMEASSISTANT_START, async_stats_sensor_startup ) def _add_state_to_queue(self, new_state): """Add the state to the queue.""" if new_state.state in [STATE_UNKNOWN, STATE_UNAVAILABLE]: return try: if self.is_binary: self.states.append(new_state.state) else: self.states.append(float(new_state.state)) self.ages.append(new_state.last_updated) except ValueError: _LOGGER.error( "%s: parsing error, expected number and received %s", self.entity_id, new_state.state, ) @property def name(self): """Return the name of the sensor.""" return self._name @property def state(self): """Return the state of the sensor.""" return self.mean if not self.is_binary else self.count @property def unit_of_measurement(self): """Return the unit the value is expressed in.""" return self._unit_of_measurement if not self.is_binary else None @property def should_poll(self): """No polling needed.""" return False @property def device_state_attributes(self): """Return the state attributes of the sensor.""" if not self.is_binary: return { ATTR_SAMPLING_SIZE: self._sampling_size, ATTR_COUNT: self.count, ATTR_MEAN: self.mean, ATTR_MEDIAN: self.median, ATTR_STANDARD_DEVIATION: self.stdev, ATTR_VARIANCE: self.variance, ATTR_TOTAL: self.total, ATTR_MIN_VALUE: self.min, ATTR_MAX_VALUE: self.max, ATTR_MIN_AGE: self.min_age, ATTR_MAX_AGE: self.max_age, ATTR_CHANGE: self.change, ATTR_AVERAGE_CHANGE: self.average_change, ATTR_CHANGE_RATE: self.change_rate, } @property def icon(self): """Return the icon to use in the frontend, if any.""" return ICON def _purge_old(self): """Remove states which are older than self._max_age.""" now = dt_util.utcnow() _LOGGER.debug( "%s: purging records older then %s(%s)", self.entity_id, dt_util.as_local(now - self._max_age), self._max_age, ) while self.ages and (now - self.ages[0]) > self._max_age: _LOGGER.debug( "%s: purging record with datetime %s(%s)", self.entity_id, dt_util.as_local(self.ages[0]), (now - self.ages[0]), ) self.ages.popleft() self.states.popleft() def _next_to_purge_timestamp(self): """Find the timestamp when the next purge would occur.""" if self.ages and self._max_age: # Take the oldest entry from the ages list and add the configured max_age. # If executed after purging old states, the result is the next timestamp # in the future when the oldest state will expire. return self.ages[0] + self._max_age return None async def async_update(self): """Get the latest data and updates the states.""" _LOGGER.debug("%s: updating statistics.", self.entity_id) if self._max_age is not None: self._purge_old() self.count = len(self.states) if not self.is_binary: try: # require only one data point self.mean = round(statistics.mean(self.states), self._precision) self.median = round(statistics.median(self.states), self._precision) except statistics.StatisticsError as err: _LOGGER.debug("%s: %s", self.entity_id, err) self.mean = self.median = STATE_UNKNOWN try: # require at least two data points self.stdev = round(statistics.stdev(self.states), self._precision) self.variance = round(statistics.variance(self.states), self._precision) except statistics.StatisticsError as err: _LOGGER.debug("%s: %s", self.entity_id, err) self.stdev = self.variance = STATE_UNKNOWN if self.states: self.total = round(sum(self.states), self._precision) self.min = round(min(self.states), self._precision) self.max = round(max(self.states), self._precision) self.min_age = self.ages[0] self.max_age = self.ages[-1] self.change = self.states[-1] - self.states[0] self.average_change = self.change self.change_rate = 0 if len(self.states) > 1: self.average_change /= len(self.states) - 1 time_diff = (self.max_age - self.min_age).total_seconds() if time_diff > 0: self.change_rate = self.change / time_diff self.change = round(self.change, self._precision) self.average_change = round(self.average_change, self._precision) self.change_rate = round(self.change_rate, self._precision) else: self.total = self.min = self.max = STATE_UNKNOWN self.min_age = self.max_age = dt_util.utcnow() self.change = self.average_change = STATE_UNKNOWN self.change_rate = STATE_UNKNOWN # If max_age is set, ensure to update again after the defined interval. next_to_purge_timestamp = self._next_to_purge_timestamp() if next_to_purge_timestamp: _LOGGER.debug( "%s: scheduling update at %s", self.entity_id, next_to_purge_timestamp ) if self._update_listener: self._update_listener() self._update_listener = None @callback def _scheduled_update(now): """Timer callback for sensor update.""" _LOGGER.debug("%s: executing scheduled update", self.entity_id) self.async_schedule_update_ha_state(True) self._update_listener = None self._update_listener = event.async_track_point_in_utc_time( self.hass, _scheduled_update, next_to_purge_timestamp ) async def _async_initialize_from_database(self): """Initialize the list of states from the database. The query will get the list of states in DESCENDING order so that we can limit the result to self._sample_size. Afterwards reverse the list so that we get it in the right order again. If MaxAge is provided then query will restrict to entries younger then current datetime - MaxAge. """ _LOGGER.debug("%s: initializing values from the database", self.entity_id) with session_scope(hass=self.hass) as session: query = session.query(States).filter( States.entity_id == self._entity_id.lower() ) if self._max_age is not None: records_older_then = dt_util.utcnow() - self._max_age _LOGGER.debug( "%s: retrieve records not older then %s", self.entity_id, records_older_then, ) query = query.filter(States.last_updated >= records_older_then) else: _LOGGER.debug("%s: retrieving all records.", self.entity_id) query = query.order_by(States.last_updated.desc()).limit( self._sampling_size ) states = execute(query, to_native=True, validate_entity_ids=False) for state in reversed(states): self._add_state_to_queue(state) self.async_schedule_update_ha_state(True) _LOGGER.debug("%s: initializing from database completed", self.entity_id)

apache-2.0

rjdp/Easynginedemoplugin

ee/core/mysql.py

1

4004

"""EasyEngine MySQL core classes.""" import pymysql import configparser from os.path import expanduser import sys import os from ee.core.logging import Log from ee.core.variables import EEVariables class EEMysql(): """Method for MySQL connection""" def execute(self, statement, errormsg='', log=True): """Get login details from ~/.my.cnf & Execute MySQL query""" config = configparser.RawConfigParser() cnfpath = expanduser("~")+"/.my.cnf" if [cnfpath] == config.read(cnfpath): user = config.get('client', 'user') passwd = config.get('client', 'password') try: host = config.get('client', 'host') except configparser.NoOptionError as e: host = 'localhost' try: port = config.get('client', 'port') except configparser.NoOptionError as e: port = '3306' try: conn = pymysql.connect(host=host, port=int(port), user=user, passwd=passwd) cur = conn.cursor() except Exception as e: if errormsg: Log.debug(self, '{0}' .format(e)) Log.error(self, '{0}' .format(errormsg)) else: Log.debug(self, '{0}' .format(e)) Log.error(self, 'Unable to connect to database: {0}' .format(e)) try: if log: Log.debug(self, "Executing MySQL statement: {0}" .format(statement)) cur.execute(statement) cur.close() conn.close() except Exception as e: cur.close() conn.close() Log.debug(self, "{0}".format(e)) if not errormsg: Log.error(self, 'Unable to execute statement') else: Log.error(self, '{0}'.format(errormsg)) def backupAll(self): import subprocess try: Log.info(self, "Backing up database at location: " "/var/ee-mysqlbackup") # Setup Nginx common directory if not os.path.exists('/var/ee-mysqlbackup'): Log.debug(self, 'Creating directory' '/var/ee-mysqlbackup') os.makedirs('/var/ee-mysqlbackup') db = subprocess.check_output(["mysql -Bse \'show databases\'"], universal_newlines=True, shell=True).split('\n') for dbs in db: if dbs == "": continue Log.info(self, "Backing up {0} database".format(dbs)) p1 = subprocess.Popen("mysqldump {0}" " --max_allowed_packet=1024M" " --single-transaction".format(dbs), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) p2 = subprocess.Popen("gzip -c > /var/ee-mysqlbackup/{0}{1}.s" "ql.gz".format(dbs, EEVariables.ee_date), stdin=p1.stdout, shell=True) # Allow p1 to receive a SIGPIPE if p2 exits p1.stdout.close() output = p1.stderr.read() p1.wait() if p1.returncode == 0: Log.debug(self, "done") else: Log.error(self, output.decode("utf-8")) except Exception as e: Log.error(self, "Error: process exited with status %s" % e)

mit

whtsky/catsup-docs-zh

catsup/generator/__init__.py

1

4323

import time import os import catsup.parser from catsup.logger import logger from catsup.generator.renderer import Renderer from catsup.reader import get_reader from catsup.options import g from catsup.utils import smart_copy from catsup.models import * class Generator(object): def __init__(self, config_path, local=False, base_url=None): self.config_path = config_path self.local = local self.base_url = base_url g.generator = self self.posts = [] self.pages = [] self.non_post_files = [] self.archives = [] self.tags = [] self.caches = [] self.config = {} self.renderer = None self.reset() def reset(self): self.posts = [] self.pages = [] self.non_post_files = [] self.archives = g.archives = Archives() self.tags = g.tags = Tags() self.load_config() self.load_posts() self.load_renderer() self.caches = { "static_url": {}, "url_for": {} } def load_config(self): self.config = g.config = catsup.parser.config( self.config_path, local=self.local, base_url=self.base_url ) def load_posts(self): for f in os.listdir(g.source): if f.startswith("."): # hidden file continue filename, ext = os.path.splitext(f) ext = ext.lower()[1:] reader = get_reader(ext) if reader is not None: logger.info('Loading file %s' % filename) path = os.path.join(g.source, f) post = reader(path) if post.type == "page": self.pages.append(post) else: self.posts.append(post) else: self.non_post_files.append(f) self.posts.sort( key=lambda x: x.datetime, reverse=True ) def load_renderer(self): templates_path = [ g.public_templates_path, os.path.join(g.theme.path, 'templates') ] self.renderer = Renderer( templates_path=templates_path, generator=self ) def generate_feed(self): feed = Feed(self.posts) feed.render(self.renderer) def generate_pages(self): page = Page(self.posts) page.render_all(self.renderer) def generate_posts(self): for post in self.posts: post.add_archive_and_tags() post.render(self.renderer) for page in self.pages: page.render(self.renderer) def generate_tags(self): self.tags.render(self.renderer) def generate_archives(self): self.archives.render(self.renderer) def generate_other_pages(self): NotFound().render(self.renderer) def copy_static_files(self): static_path = self.config.config.static_output smart_copy( os.path.join(g.theme.path, 'static'), static_path ) smart_copy( self.config.config.static_source, static_path ) for f in self.non_post_files: smart_copy( os.path.join(g.source, f), os.path.join(self.config.config.output, f) ) def generate(self): started_loading = time.time() self.reset() finish_loading = time.time() logger.info( "Loaded config and %s posts in %.3fs" % (len(self.posts), finish_loading - started_loading) ) if self.posts: self.generate_posts() self.generate_tags() self.generate_archives() self.generate_feed() self.generate_pages() else: logger.warning("Can't find any post.") self.generate_other_pages() self.copy_static_files() self.renderer.render_sitemap() finish_generating = time.time() logger.info( "Generated %s posts in %.3fs" % (len(self.posts), finish_generating - finish_loading) ) logger.info( "Generating finished in %.3fs" % (finish_generating - started_loading) )

mit

skygeek/skyproc

data_server/data/model_Archives.py

1

3610

# -*- coding: utf-8 -*- # Copyright 2012, Nabil SEFRIOUI # # This file is part of Skyproc. # # Skyproc is free software: you can redistribute it and/or modify # it under the terms of the GNU Affero General Public License as # published by the Free Software Foundation, either version 3 of # the License, or any later version. # # Skyproc is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU Affero General Public License for more details. # # You should have received a copy of the GNU Affero General Public # License along with Skyproc. If not, see <http://www.gnu.org/licenses/>. from django.db import models from django.db.models import Max from django.conf import settings import base import fields from choices import * class LoadLog(base.ArchiveModel): archive = True location = fields.UUIDField() aircraft = fields.UUIDField() pilot = fields.UUIDField() aircraft_reg = models.CharField(max_length=16) pilot_name = models.CharField(max_length=64) date = models.DateField() number = models.SmallIntegerField() total_slots = models.SmallIntegerField() prepaid_slots = models.SmallIntegerField() postpaid_slots = models.SmallIntegerField() unpaid_slots = models.SmallIntegerField() staff_slots = models.SmallIntegerField() prices = models.CharField(max_length=512) note = models.CharField(max_length=200, blank=True, null=True) class SlotLog(base.ArchiveModel): archive = True load = models.ForeignKey('LoadLog') jumper = fields.UUIDField(blank=True, null=True) jumper_name = models.CharField(max_length=64) is_worker = models.BooleanField(default=False) catalog_item = models.CharField(max_length=64) exit_order = models.SmallIntegerField() catalog_price = models.CharField(max_length=64, blank=True, null=True) payer = models.CharField(max_length=64, blank=True, null=True) payment = models.CharField(max_length=64) payment_type = models.CharField(max_length=16) class JumpLog(base.ArchiveModel): archive = True location = fields.UUIDField(blank=True, null=True) number = models.IntegerField(blank=True, null=True) location_name = models.CharField(max_length=64, blank=True, null=True) aircraft_type = models.CharField(max_length=32, blank=True, null=True) date = models.DateField() jump_type = models.CharField(max_length=32, blank=True, null=True) altitude = models.CharField(max_length=32, blank=True, null=True) note = models.CharField(max_length=100, blank=True, null=True) def save(self, *args, **kwargs): if not self.number: max_number = JumpLog.objects.filter(owner=self.owner).aggregate(Max('number'))['number__max'] if max_number is None: try: person = models.get_model(settings.DATA_APP, 'Person').objects.get_by_natural_key(self.owner) past_jumps = person.past_jumps except: past_jumps = 0 self.number = past_jumps+1 else: self.number = max_number+1 super(JumpLog, self).save(*args, **kwargs) class AccountOperationLog(base.ArchiveModel): archive = True location = fields.UUIDField() date = models.DateField() type = models.CharField(max_length=1, choices=ACCOUNT_OPERATIONS) amount = models.CharField(max_length=64) currency = models.CharField(max_length=5) note = models.CharField(max_length=100)

agpl-3.0

orting/emphysema-estimation

Experiments/02-ScalabilityOfClusteringAlgorithm/Scripts/RunScalability-1.py

1

2142

#!/usr/bin/python3 '''Run Scalability-1. See README.md for details. ''' import sys, subprocess, os.path from Util import intersperse def main(): skip = { 'Measure' : False, } basedir = '' dirs = { 'Instances' : os.path.join(basedir, 'Data', 'Instances'), 'Statistics' : os.path.join(basedir, 'Data', 'Statistics', 'Scalability-1'), 'Bin' : '../../Build', } files = { 'Instances' : [ os.path.join(dirs['Instances'], 'instances500.csv'), os.path.join(dirs['Instances'], 'instances1000.csv'), os.path.join(dirs['Instances'], 'instances2500.csv'), os.path.join(dirs['Instances'], 'instances5000.csv'), os.path.join(dirs['Instances'], 'instances7500.csv'), os.path.join(dirs['Instances'], 'instances10000.csv') ], } progs = { 'Scalability' : os.path.join(dirs['Bin'],'Experiments/02-ScalabilityOfClusteringAlgorithm/Scalability'), } params = { 'clusters' : [4, 8, 16, 32, 64], 'histograms' : 7*8, # 7 scales * 8 features 'burnin' : 10, 'iterations' : 100, 'branching' : 1, } if skip['Measure']: print( 'Skipping: Measure' ) else: print( 'Measuring' ) for instanceMatrix in files['Instances']: args = [ progs['Scalability'], '--input', instanceMatrix, '--nHistograms', "%d" % params['histograms'], '--output', os.path.join(dirs['Statistics'], 'stats_' + os.path.basename(instanceMatrix)), '--burnin', "%d" % params['burnin'], '--iterations', "%d" % params['iterations'], '--branching', "%d" % params['branching'] ] + list(intersperse('--clusters', ("%d" % k for k in params['clusters']))) print(' '.join(args)) if subprocess.call( args ) != 0: print( 'Error measuring', instanceMatrix ) return 1 return 0 if __name__ == '__main__': sys.exit( main() )

gpl-3.0

hideoussquid/aureus-12-bitcore

contrib/linearize/linearize-hashes.py

1

3034

#!/usr/bin/python # # linearize-hashes.py: List blocks in a linear, no-fork version of the chain. # # Copyright (c) 2013-2014 The Aureus Core developers # Distributed under the MIT software license, see the accompanying # file COPYING or http://www.opensource.org/licenses/mit-license.php. # from __future__ import print_function import json import struct import re import base64 import httplib import sys settings = {} class AureusRPC: def __init__(self, host, port, username, password): authpair = "%s:%s" % (username, password) self.authhdr = "Basic %s" % (base64.b64encode(authpair)) self.conn = httplib.HTTPConnection(host, port, False, 30) def execute(self, obj): self.conn.request('POST', '/', json.dumps(obj), { 'Authorization' : self.authhdr, 'Content-type' : 'application/json' }) resp = self.conn.getresponse() if resp is None: print("JSON-RPC: no response", file=sys.stderr) return None body = resp.read() resp_obj = json.loads(body) return resp_obj @staticmethod def build_request(idx, method, params): obj = { 'version' : '1.1', 'method' : method, 'id' : idx } if params is None: obj['params'] = [] else: obj['params'] = params return obj @staticmethod def response_is_error(resp_obj): return 'error' in resp_obj and resp_obj['error'] is not None def get_block_hashes(settings, max_blocks_per_call=10000): rpc = AureusRPC(settings['host'], settings['port'], settings['rpcuser'], settings['rpcpassword']) height = settings['min_height'] while height < settings['max_height']+1: num_blocks = min(settings['max_height']+1-height, max_blocks_per_call) batch = [] for x in range(num_blocks): batch.append(rpc.build_request(x, 'getblockhash', [height + x])) reply = rpc.execute(batch) for x,resp_obj in enumerate(reply): if rpc.response_is_error(resp_obj): print('JSON-RPC: error at height', height+x, ': ', resp_obj['error'], file=sys.stderr) exit(1) assert(resp_obj['id'] == x) # assume replies are in-sequence print(resp_obj['result']) height += num_blocks if __name__ == '__main__': if len(sys.argv) != 2: print("Usage: linearize-hashes.py CONFIG-FILE") sys.exit(1) f = open(sys.argv[1]) for line in f: # skip comment lines m = re.search('^\s*#', line) if m: continue # parse key=value lines m = re.search('^(\w+)\s*=\s*(\S.*)$', line) if m is None: continue settings[m.group(1)] = m.group(2) f.close() if 'host' not in settings: settings['host'] = '127.0.0.1' if 'port' not in settings: settings['port'] = 8332 if 'min_height' not in settings: settings['min_height'] = 0 if 'max_height' not in settings: settings['max_height'] = 313000 if 'rpcuser' not in settings or 'rpcpassword' not in settings: print("Missing username and/or password in cfg file", file=stderr) sys.exit(1) settings['port'] = int(settings['port']) settings['min_height'] = int(settings['min_height']) settings['max_height'] = int(settings['max_height']) get_block_hashes(settings)

mit

osgee/redigit

redigit/settings.py

1

2956

""" Django settings for redigit project. For more information on this file, see https://docs.djangoproject.com/en/1.7/topics/settings/ For the full list of settings and their values, see https://docs.djangoproject.com/en/1.7/ref/settings/ """ # Build paths inside the project like this: os.path.join(BASE_DIR, ...) import os BASE_DIR = os.path.dirname(os.path.dirname(__file__)) SETTINGS_PATH = os.path.realpath(os.path.dirname(__file__)) # Quick-start development settings - unsuitable for production # See https://docs.djangoproject.com/en/1.7/howto/deployment/checklist/ # SECURITY WARNING: keep the secret key used in production secret! SECRET_KEY = '7p8)$=frp+7336ak^oo1verce)=ywu(&of@qvrvylw4%!kpeak' # SECURITY WARNING: don't run with debug turned on in production! DEBUG = True TEMPLATE_DEBUG = True ALLOWED_HOSTS = [] SECURE_PROXY_SSL_HEADER = ('HTTP_X_FORWARDED_PROTO', 'https') # Application definition INSTALLED_APPS = ( 'django.contrib.admin', 'django.contrib.auth', 'django.contrib.contenttypes', 'django.contrib.sessions', 'django.contrib.messages', 'django.contrib.staticfiles', ) MIDDLEWARE_CLASSES = ( 'django.contrib.sessions.middleware.SessionMiddleware', 'django.middleware.common.CommonMiddleware', 'django.middleware.csrf.CsrfViewMiddleware', 'django.contrib.auth.middleware.AuthenticationMiddleware', 'django.contrib.auth.middleware.SessionAuthenticationMiddleware', 'django.contrib.messages.middleware.MessageMiddleware', 'django.middleware.clickjacking.XFrameOptionsMiddleware', ) ROOT_URLCONF = 'redigit.urls' WSGI_APPLICATION = 'redigit.wsgi.application' # Database # https://docs.djangoproject.com/en/1.7/ref/settings/#databases DATABASES = { 'default': { 'ENGINE': 'django.db.backends.sqlite3', 'NAME': os.path.join(BASE_DIR, 'db.sqlite3'), } } # Internationalization # https://docs.djangoproject.com/en/1.7/topics/i18n/ LANGUAGE_CODE = 'en-us' TIME_ZONE = 'UTC' USE_I18N = True USE_L10N = True USE_TZ = True # Static files (CSS, JavaScript, Images) # https://docs.djangoproject.com/en/1.7/howto/static-files/ STATIC_URL = '/static/' TEMPLATE_LOADERS = ( 'django.template.loaders.filesystem.Loader', 'django.template.loaders.app_directories.Loader', ) TEMPLATES = [ { 'BACKEND': 'django.template.backends.django.DjangoTemplates', 'DIRS': [os.path.join(BASE_DIR, 'redigit/templates')], 'APP_DIRS': True, 'OPTIONS': { 'context_processors': [ 'django.template.context_processors.debug', 'django.template.context_processors.request', 'django.contrib.auth.context_processors.auth', 'django.contrib.messages.context_processors.messages', ], }, }, ] TEMPLATE_DIRS = ( os.path.join(SETTINGS_PATH, 'templates'), ) STATICFILES_DIRS = ( os.path.join(BASE_DIR, "static"), )

apache-2.0

tobi-wan-kenobi/bumblebee-status

bumblebee_status/modules/contrib/twmn.py

1

1236

# pylint: disable=C0111,R0903 """Toggle twmn notifications. Requires the following executable: * systemctl contributed by `Pseudonick47 <https://github.com/Pseudonick47>`_ - many thanks! """ import core.module import core.widget import core.input import core.decorators import util.cli class Module(core.module.Module): @core.decorators.every(minutes=60) def __init__(self, config, theme): super().__init__(config, theme, core.widget.Widget("")) self.__paused = False # Make sure that twmn is currently not paused util.cli.execute("killall -SIGUSR2 twmnd", ignore_errors=True) core.input.register(self, button=core.input.LEFT_MOUSE, cmd=self.toggle_status) def toggle_status(self, event): self.__paused = not self.__paused try: if self.__paused: util.cli.execute("systemctl --user start twmnd") else: util.cli.execute("systemctl --user stop twmnd") except: self.__paused = not self.__paused # toggling failed def state(self, widget): if self.__paused: return ["muted"] return ["unmuted"] # vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4

mit

xArm-Developer/xArm-Python-SDK

example/wrapper/xarm7/2004-move_joint.py

1

2851

#!/usr/bin/env python3 # Software License Agreement (BSD License) # # Copyright (c) 2019, UFACTORY, Inc. # All rights reserved. # # Author: Vinman <[email protected]> <[email protected]> """ Description: Move Joint """ import os import sys import time import math sys.path.append(os.path.join(os.path.dirname(__file__), '../../..')) from xarm.wrapper import XArmAPI ####################################################### """ Just for test example """ if len(sys.argv) >= 2: ip = sys.argv[1] else: try: from configparser import ConfigParser parser = ConfigParser() parser.read('../robot.conf') ip = parser.get('xArm', 'ip') except: ip = input('Please input the xArm ip address:') if not ip: print('input error, exit') sys.exit(1) ######################################################## arm = XArmAPI(ip, is_radian=True) arm.motion_enable(enable=True) arm.set_mode(0) arm.set_state(state=0) arm.reset(wait=True) speed = 50 arm.set_servo_angle(servo_id=1, angle=90, speed=speed, is_radian=False, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=2, angle=-60, speed=speed, is_radian=False, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=3, angle=-30, speed=speed, is_radian=False, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=1, angle=0, speed=speed, is_radian=False, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=3, angle=0, speed=speed, is_radian=False, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=2, angle=0, speed=speed, is_radian=False, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.reset(wait=True) speed = math.radians(50) arm.set_servo_angle(servo_id=1, angle=math.radians(90), speed=speed, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=2, angle=math.radians(-60), speed=speed, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=3, angle=math.radians(-30), speed=speed, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=1, angle=0, speed=speed, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=3, angle=0, speed=speed, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.set_servo_angle(servo_id=2, angle=0, speed=speed, wait=True) print(arm.get_servo_angle(), arm.get_servo_angle(is_radian=False)) arm.reset(wait=True) arm.disconnect()

bsd-3-clause

laenderoliveira/exerclivropy

exercicios_resolvidos/capitulo 05/exercicio-05-28.py

1

1772

############################################################################## # Parte do livro Introdução à Programação com Python # Autor: Nilo Ney Coutinho Menezes # Editora Novatec (c) 2010-2014 # Primeira edição - Novembro/2010 - ISBN 978-85-7522-250-8 # Primeira reimpressão - Outubro/2011 # Segunda reimpressão - Novembro/1012 # Terceira reimpressão - Agosto/2013 # Segunda edição - Junho/2014 - ISBN 978-85-7522-408-3 # Site: http://python.nilo.pro.br/ # # Arquivo: exercicios_resolvidos\capitulo 05\exercicio-05-28.py ############################################################################## # Exercício 5.27 # Solução alternativa, usando apenas inteiros n = int(input ("Digite o número a verificar:")) # Com n é um número inteiro, vamos calcular sua # quantidade de dígitos, encontrado a primeira # potência de 10, superior a n. # Exemplo: 341 - primeira potência de 10 maior: 1000 = 10 ^ 4 # Utilizaremos 4 e não 3 para possibilitar o tratamento de números # com um só dígito. O ajuste é feito nas fórmulas abaixo q = 0 while 10 ** q < n: q = q + 1 i = q f = 0 nf = ni = n # Aqui nós copiamos n para ni e nf pi = pf = 0 # e fazemos pi = pf (para casos especiais) while i > f: pi = int(ni / (10 ** (i-1))) # Dígito mais à direita pf = nf % 10 # Dígito mais à esquerda if pi != pf: # Se são diferentes, saímos break f = f + 1 # Passamos para o próximo dígito a esqueda i = i - 1 # Passamos para o dígito a direita seguinte ni = ni - (pi * (10 ** i )) # Ajustamos ni de forma a retirar o dígito anterior nf = int(nf / 10) # Ajustamos nf para retirar o último dígito if pi == pf: print("%d é palíndromo" % n) else: print("%d não é palíndromo" % n)

mit

Tayamarn/socorro

socorro/unittest/processor/test_processor_2015.py

1

4727

import ujson from configman import ConfigurationManager from configman.dotdict import DotDict from mock import Mock, patch from socorro.lib.transform_rules import TransformRuleSystem from socorro.processor.processor_2015 import ( Processor2015, rule_sets_from_string ) from socorro.processor.general_transform_rules import ( CPUInfoRule, OSInfoRule ) from socorro.unittest.testbase import TestCase rule_set_01 = [ [ 'ruleset01', 'tag0.tag1', 'socorro.lib.transform_rules.TransformRuleSystem', 'apply_all_rules', 'socorro.processor.general_transform_rules.CPUInfoRule, ' 'socorro.processor.general_transform_rules.OSInfoRule ' ] ] rule_set_01_str = ujson.dumps(rule_set_01) class TestProcessor2015(TestCase): def test_rule_sets_from_string_1(self): rule_set_config = rule_sets_from_string(rule_set_01_str) rc = rule_set_config.get_required_config() assert 'ruleset01' in rc assert 'tag0.tag1' == rc.ruleset01.tag.default expected = 'socorro.lib.transform_rules.TransformRuleSystem' assert rc.ruleset01.rule_system_class.default == expected assert 'apply_all_rules' == rc.ruleset01.action.default expected = ( 'socorro.processor.general_transform_rules.CPUInfoRule, ' 'socorro.processor.general_transform_rules.OSInfoRule ' ) assert rc.ruleset01.rules_list.default == expected def test_Processor2015_init(self): cm = ConfigurationManager( definition_source=Processor2015.get_required_config(), values_source_list=[{'rule_sets': rule_set_01_str}], ) config = cm.get_config() config.logger = Mock() p = Processor2015(config) assert isinstance(p.rule_system, DotDict) assert len(p.rule_system) == 1 assert 'ruleset01' in p.rule_system assert isinstance(p.rule_system.ruleset01, TransformRuleSystem) trs = p.rule_system.ruleset01 assert trs.act == trs.apply_all_rules assert len(trs.rules) == 2 assert isinstance(trs.rules[0], CPUInfoRule) assert isinstance(trs.rules[1], OSInfoRule) def test_process_crash_no_rules(self): cm = ConfigurationManager( definition_source=Processor2015.get_required_config(), values_source_list=[{'rule_sets': '[]'}], ) config = cm.get_config() config.logger = Mock() config.processor_name = 'dwight' p = Processor2015(config) raw_crash = DotDict() raw_dumps = {} with patch('socorro.processor.processor_2015.utc_now') as faked_utcnow: faked_utcnow.return_value = '2015-01-01T00:00:00' processed_crash = p.process_crash( raw_crash, raw_dumps, DotDict() ) assert processed_crash.success assert processed_crash.started_datetime == '2015-01-01T00:00:00' assert processed_crash.startedDateTime == '2015-01-01T00:00:00' assert processed_crash.completed_datetime == '2015-01-01T00:00:00' assert processed_crash.completeddatetime == '2015-01-01T00:00:00' assert processed_crash.processor_notes == 'dwight; Processor2015' def test_process_crash_existing_processed_crash(self): cm = ConfigurationManager( definition_source=Processor2015.get_required_config(), values_source_list=[{'rule_sets': '[]'}], ) config = cm.get_config() config.logger = Mock() config.processor_name = 'dwight' p = Processor2015(config) raw_crash = DotDict() raw_dumps = {} processed_crash = DotDict() processed_crash.processor_notes = "we've been here before; yep" processed_crash.started_datetime = '2014-01-01T00:00:00' with patch('socorro.processor.processor_2015.utc_now') as faked_utcnow: faked_utcnow.return_value = '2015-01-01T00:00:00' processed_crash = p.process_crash( raw_crash, raw_dumps, processed_crash ) assert processed_crash.success assert processed_crash.started_datetime == '2015-01-01T00:00:00' assert processed_crash.startedDateTime == '2015-01-01T00:00:00' assert processed_crash.completed_datetime == '2015-01-01T00:00:00' assert processed_crash.completeddatetime == '2015-01-01T00:00:00' expected = ( "dwight; Processor2015; earlier processing: 2014-01-01T00:00:00; we've been here " "before; yep" ) assert processed_crash.processor_notes == expected

mpl-2.0

ToFuProject/tofu

tofu/tests/tests01_geom/test_03_core_data/WEST_Ves_VesOut_Notes.py

1

1355

#!/usr/bin/env python import os import argparse import numpy as np _save = True _here = os.path.abspath(os.path.dirname(__file__)) _Exp, _Cls, _name = os.path.split(__file__)[1].split('_')[:3] assert not any([any([ss in s for ss in ['Notes','.']]) for s in [_Exp, _Cls, _name]]) def get_notes(): # Notes from creoView (-X,Z,Y) notes = {'C': np.r_[2.465, 0.], 'r_in': 3.162/2., # r_out for later use (thick) 'r_out': 3.292/2.} return notes def make_Poly(save=_save, path=_here): notes = get_notes() C = notes['C'] nP = 100 theta = np.linspace(0.,2*np.pi, nP, endpoint=False) P = np.array([C[0]+notes['r_out']*np.cos(theta), C[1]+notes['r_out']*np.sin(theta)]) if save: cstr = '%s_%s_%s'%(_Exp,_Cls,_name) pathfilext = os.path.join(path, cstr+'_V0.txt') np.savetxt(pathfilext, P) return P, notes if __name__=='__main__': # Parse input arguments msg = 'Launch creation of polygons txt from bash' parser = argparse.ArgumentParser(description = msg) parser.add_argument('-save', type=bool, help='save ?', default=_save) parser.add_argument('-path', type=str, help='saving path ?', default=_here) args = parser.parse_args() # Call wrapper function make_Poly(save=args.save, path=args.path)

mit

miooim/project_hours

src/project_hours/driver/mongo_driver.py

1

2290

import datetime import pprint __author__ = 'michaell' import pymongo from tornado.options import options class ProjectHoursMongoDriver(object): """ Project hours mongo driver implementation """ @staticmethod def get_month_data(month, year, user): """ Get results from database :param month: month :type month: int :param year: year :type year: int :param user: user name :type user: str :return: result dictionary :rtype: dict """ query = { "$query": { 'month': int(month), 'year': int(year), 'user': user } } # print(options.mongodb, options.mongod_name, options.mongod_name) # pprint.pprint(query) collection = pymongo.MongoClient(host=options.mongodb)[options.mongod_name][options.mongod_name] return collection.find_one(query) @staticmethod def save(month, year, user, data): """ Saves data to mongod :param month: month :type month: int :param year: year :type year: int :param user: user name :type user: str :param data: data to save :type data: dict :return: true is success :rtype: bool """ for item in data: if 'no_work' in item: if item['no_work'] is True: item['projects'] = [] item['total'] = 0 result = ProjectHoursMongoDriver.get_month_data(month, year, user) if result: to_save = { '_id': result['_id'], 'month': int(month), 'year': int(year), 'user': user, "days": data, "timestamp": datetime.datetime.now(), } else: to_save = { 'month': int(month), 'year': int(year), 'user': user, "days": data, "timestamp": datetime.datetime.now(), } collection = pymongo.MongoClient(host=options.mongodb)[options.mongod_name][options.mongod_name] return collection.save(to_save=to_save, safe=True)

mit

asd43/Structural-Variation

popgen/getFeatureTable.py

1

2289

#!/usr/bin/env python3 # Copyright (c) 2017 Genome Research Ltd. # Author: Alistair Dunham # This program is free software: you can redistribute it and/or modify it under # the terms of the GNU General Public License as published by the Free Software # Foundation; either version 3 of the License , or (at your option) any later # version. # This program is distributed in the hope that it will be useful , but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU General Public License for more # details. # You should have received a copy of the GNU General Public License along with # this program. If not , see <http :// www.gnu.org/licenses/>. ## Script to convert bedtools cluster output of merged breakdancer calls into a feature table ## which has columns for each sample indicating the presence of each deletion import argparse import fileinput import re ## Read arguments parser = argparse.ArgumentParser(description="Transform bedtools cluster output for deletion calls into a feature table of 'genotypes'.") parser.add_argument('tenx',metavar='T',type=str,help="Bed file containing clustered deletion calls") parser.add_argument('--bd','-b',action='store_true',help="Expect BreakDancer formatted IDs. Otherwise expect 10X formatted IDs.") args = parser.parse_args() ## Determine function to use for setting sample ID depending on given source format if args.bd: def getSample(x): """Extract sample from BreakDancer formatted ID tags""" return(re.split("[_.]",x)[-2]) else: def getSample(x): """Extract sample from 10X formatted ID tags""" return(x.split('.')[0]) ## Extract each deletion call and its cluster number dels = [] samples = set() with fileinput.input(args.tenx) as bed: for li in bed: t = li.strip().split() s = getSample(t[3]) n = int(t[4]) samples.add(s) if len(dels) < n: dels.append(set([s])) else: dels[n - 1].add(s) ## Print feature table samples = sorted(list(samples)) print("Deletion",*samples,sep='\t') for n,delSamples in enumerate(dels): ## generate feature string feats = [(1 if i in delSamples else 0) for i in samples] print('_'.join(["del",str(n + 1)]),*feats,sep='\t')

gpl-3.0

2-B/etherpad-lite

bin/parsejson.py

1

1119

import json import re # Regular expression for comments comment_re = re.compile( '(^)?[^\S\n]*/(?:\*(.*?)\*/[^\S\n]*|/[^\n]*)($)?', re.DOTALL | re.MULTILINE ) def parse_json(filename): """ Parse a JSON file First remove comments and then use the json module package Comments look like : // ... or /* ... */ """ with open(filename) as f: content = ''.join(f.readlines()) ## Looking for comments match = comment_re.search(content) while match: # single line comment content = content[:match.start()] + content[match.end():] match = comment_re.search(content) #print content # Return json file return json.loads(content) if __name__ == '__main__': f = '../settings.json' data = parse_json(f) print "LOG="+data['log'] print "ERROR_HANDLING="+str(data['errorHandling']) print "EMAIL_ADDRESS="+data['emailAddress'] print "TIME_BETWEEN_EMAILS="+str(data['timeBetweenEmails']) print "NODEJS="+data['nodejs']

apache-2.0

bitwiseman/js-beautify

python/cssbeautifier/css/options.py

1

2360

# # The MIT License (MIT) # Copyright (c) 2007-2018 Einar Lielmanis, Liam Newman, and contributors. # Permission is hereby granted, free of charge, to any person # obtaining a copy of this software and associated documentation files # (the "Software"), to deal in the Software without restriction, # including without limitation the rights to use, copy, modify, merge, # publish, distribute, sublicense, and/or sell copies of the Software, # and to permit persons to whom the Software is furnished to do so, # subject to the following conditions: # The above copyright notice and this permission notice shall be # included in all copies or substantial portions of the Software. # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. from jsbeautifier.core.options import Options as BaseOptions class BeautifierOptions(BaseOptions): def __init__(self, options=None): BaseOptions.__init__(self, options, "css") self.selector_separator_newline = self._get_boolean( "selector_separator_newline", True ) self.newline_between_rules = self._get_boolean("newline_between_rules", True) brace_style_split = self._get_selection_list( "brace_style", ["collapse", "expand", "end-expand", "none", "preserve-inline"], ) self.brace_style = "collapse" for bs in brace_style_split: if bs != "expand": # default to collapse, as only collapse|expand is implemented for now self.brace_style = "collapse" else: self.brace_style = bs # deprecated space_around_selector_separator = self._get_boolean( "space_around_selector_separator" ) # Continue to accept deprecated option self.space_around_combinator = ( self._get_boolean("space_around_combinator") or space_around_selector_separator )

mit

openstack/python-heatclient

heatclient/osc/v1/software_deployment.py

1

13006

# Licensed under the Apache License, Version 2.0 (the "License"); you may # not use this file except in compliance with the License. You may obtain # a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, WITHOUT # WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the # License for the specific language governing permissions and limitations # under the License. # """Orchestration v1 Software Deployment action implementations""" import logging from osc_lib.command import command from osc_lib import exceptions as exc from osc_lib import utils from oslo_serialization import jsonutils from heatclient._i18n import _ from heatclient.common import deployment_utils from heatclient.common import format_utils from heatclient.common import utils as heat_utils from heatclient import exc as heat_exc class CreateDeployment(format_utils.YamlFormat): """Create a software deployment.""" log = logging.getLogger(__name__ + '.CreateDeployment') def get_parser(self, prog_name): parser = super(CreateDeployment, self).get_parser(prog_name) parser.add_argument( 'name', metavar='<deployment-name>', help=_('Name of the derived config associated with this ' 'deployment. This is used to apply a sort order to the ' 'list of configurations currently deployed to the server.') ) parser.add_argument( '--input-value', metavar='<key=value>', action='append', help=_('Input value to set on the deployment. This can be ' 'specified multiple times.') ) parser.add_argument( '--action', metavar='<action>', default='UPDATE', help=_('Name of an action for this deployment. This can be a ' 'custom action, or one of CREATE, UPDATE, DELETE, SUSPEND, ' 'RESUME. Default is UPDATE') ) parser.add_argument( '--config', metavar='<config>', help=_('ID of the configuration to deploy') ) parser.add_argument( '--signal-transport', metavar='<signal-transport>', default='TEMP_URL_SIGNAL', help=_('How the server should signal to heat with the deployment ' 'output values. TEMP_URL_SIGNAL will create a Swift ' 'TempURL to be signaled via HTTP PUT. ZAQAR_SIGNAL will ' 'create a dedicated zaqar queue to be signaled using the ' 'provided keystone credentials.NO_SIGNAL will result in ' 'the resource going to the COMPLETE state without waiting ' 'for any signal') ) parser.add_argument( '--container', metavar='<container>', help=_('Optional name of container to store TEMP_URL_SIGNAL ' 'objects in. If not specified a container will be created ' 'with a name derived from the DEPLOY_NAME') ) parser.add_argument( '--timeout', metavar='<timeout>', type=int, default=60, help=_('Deployment timeout in minutes') ) parser.add_argument( '--server', metavar='<server>', required=True, help=_('ID of the server being deployed to') ) return parser def take_action(self, parsed_args): self.log.debug('take_action(%s)', parsed_args) client = self.app.client_manager.orchestration config = {} if parsed_args.config: try: config = client.software_configs.get(parsed_args.config) except heat_exc.HTTPNotFound: msg = (_('Software configuration not found: %s') % parsed_args.config) raise exc.CommandError(msg) derived_params = deployment_utils.build_derived_config_params( parsed_args.action, config, parsed_args.name, heat_utils.format_parameters(parsed_args.input_value, False), parsed_args.server, parsed_args.signal_transport, signal_id=deployment_utils.build_signal_id(client, parsed_args) ) derived_config = client.software_configs.create(**derived_params) sd = client.software_deployments.create( config_id=derived_config.id, server_id=parsed_args.server, action=parsed_args.action, status='IN_PROGRESS' ) return zip(*sorted(sd.to_dict().items())) class DeleteDeployment(command.Command): """Delete software deployment(s) and correlative config(s).""" log = logging.getLogger(__name__ + '.DeleteDeployment') def get_parser(self, prog_name): parser = super(DeleteDeployment, self).get_parser(prog_name) parser.add_argument( 'deployment', metavar='<deployment>', nargs='+', help=_('ID of the deployment(s) to delete.') ) return parser def take_action(self, parsed_args): self.log.debug("take_action(%s)", parsed_args) hc = self.app.client_manager.orchestration failure_count = 0 for deploy_id in parsed_args.deployment: try: sd = hc.software_deployments.get(deployment_id=deploy_id) hc.software_deployments.delete( deployment_id=deploy_id) except Exception as e: if isinstance(e, heat_exc.HTTPNotFound): print(_('Deployment with ID %s not found') % deploy_id) else: print(_('Deployment with ID %s failed to delete') % deploy_id) failure_count += 1 continue # just try best to delete the corresponding config try: config_id = getattr(sd, 'config_id') hc.software_configs.delete(config_id=config_id) except Exception: print(_('Failed to delete the correlative config' ' %(config_id)s of deployment %(deploy_id)s') % {'config_id': config_id, 'deploy_id': deploy_id}) if failure_count: raise exc.CommandError(_('Unable to delete %(count)s of the ' '%(total)s deployments.') % {'count': failure_count, 'total': len(parsed_args.deployment)}) class ListDeployment(command.Lister): """List software deployments.""" log = logging.getLogger(__name__ + '.ListDeployment') def get_parser(self, prog_name): parser = super(ListDeployment, self).get_parser(prog_name) parser.add_argument( '--server', metavar='<server>', help=_('ID of the server to fetch deployments for') ) parser.add_argument( '--long', action='store_true', help=_('List more fields in output') ) return parser def take_action(self, parsed_args): self.log.debug("take_action(%s)", parsed_args) heat_client = self.app.client_manager.orchestration return _list_deployment(heat_client, args=parsed_args) def _list_deployment(heat_client, args=None): kwargs = {'server_id': args.server} if args.server else {} columns = ['id', 'config_id', 'server_id', 'action', 'status'] if args.long: columns.append('creation_time') columns.append('status_reason') deployments = heat_client.software_deployments.list(**kwargs) return ( columns, (utils.get_item_properties(s, columns) for s in deployments) ) class ShowDeployment(command.ShowOne): """Show SoftwareDeployment Details.""" log = logging.getLogger(__name__ + ".ShowSoftwareDeployment") def get_parser(self, prog_name): parser = super(ShowDeployment, self).get_parser(prog_name) parser.add_argument( 'deployment', metavar='<deployment>', help=_('ID of the deployment') ) parser.add_argument( '--long', action='store_true', help=_('Show more fields in output') ) return parser def take_action(self, parsed_args): self.log.debug("take_action(%s)", parsed_args) heat_client = self.app.client_manager.orchestration try: data = heat_client.software_deployments.get( deployment_id=parsed_args.deployment) except heat_exc.HTTPNotFound: raise exc.CommandError( _('Software Deployment not found: %s') % parsed_args.deployment) else: columns = [ 'id', 'server_id', 'config_id', 'creation_time', 'updated_time', 'status', 'status_reason', 'input_values', 'action', ] if parsed_args.long: columns.append('output_values') return columns, utils.get_item_properties(data, columns) class ShowMetadataDeployment(command.Command): """Get deployment configuration metadata for the specified server.""" log = logging.getLogger(__name__ + '.ShowMetadataDeployment') def get_parser(self, prog_name): parser = super(ShowMetadataDeployment, self).get_parser(prog_name) parser.add_argument( 'server', metavar='<server>', help=_('ID of the server to fetch deployments for') ) return parser def take_action(self, parsed_args): self.log.debug("take_action(%s)", parsed_args) heat_client = self.app.client_manager.orchestration md = heat_client.software_deployments.metadata( server_id=parsed_args.server) print(jsonutils.dumps(md, indent=2)) class ShowOutputDeployment(command.Command): """Show a specific deployment output.""" log = logging.getLogger(__name__ + '.ShowOutputDeployment') def get_parser(self, prog_name): parser = super(ShowOutputDeployment, self).get_parser(prog_name) parser.add_argument( 'deployment', metavar='<deployment>', help=_('ID of deployment to show the output for') ) parser.add_argument( 'output', metavar='<output-name>', nargs='?', default=None, help=_('Name of an output to display') ) parser.add_argument( '--all', default=False, action='store_true', help=_('Display all deployment outputs') ) parser.add_argument( '--long', action='store_true', default=False, help='Show full deployment logs in output', ) return parser def take_action(self, parsed_args): self.log.debug("take_action(%s)", parsed_args) heat_client = self.app.client_manager.orchestration if (not parsed_args.all and parsed_args.output is None or parsed_args.all and parsed_args.output is not None): raise exc.CommandError( _('Error: either %(output)s or %(all)s argument is needed.') % {'output': '<output-name>', 'all': '--all'}) try: sd = heat_client.software_deployments.get( deployment_id=parsed_args.deployment) except heat_exc.HTTPNotFound: raise exc.CommandError(_('Deployment not found: %s') % parsed_args.deployment) outputs = sd.output_values if outputs: if parsed_args.all: print('output_values:\n') for k in outputs: format_utils.print_software_deployment_output( data=outputs, name=k, long=parsed_args.long) else: if parsed_args.output not in outputs: msg = (_('Output %(output)s does not exist in deployment' ' %(deployment)s') % {'output': parsed_args.output, 'deployment': parsed_args.deployment}) raise exc.CommandError(msg) else: print('output_value:\n') format_utils.print_software_deployment_output( data=outputs, name=parsed_args.output)

apache-2.0

staneyffer/my_blog

config.py

1

1685

# -*- coding: UTF-8 -*- import os basedir = os.path.abspath(os.path.dirname(__file__)) class Config: SECRET_KEY = os.environ.get('SECRET_KEY') SQLALCHEMY_COMMIT_ON_TEARDOWN = True SQLALCHEMY_TRACK_MODIFICATIONS = True SQLALCHEMY_FOREIGN_KEY_CHECKS = False SQLALCHEMY_RECORD_QUERIES = True FLASKY_SLOW_DB_QUERY_TIME=0.5 FLASKY_ADMIN = '[email protected]' FLASKY_POSTS_PER_PAGE = 6 UPLOADED_FILES_DEST = os.getcwd()+'/app/static/images/' @staticmethod def init_app(app): pass class DevelopmentConfig(Config): DEBUG = True SQLALCHEMY_DATABASE_URI = os.environ.get('DEV_DATABASE_URL') class TestingConfig(Config): TESTING = True WTF_CSRF_ENABLED = False #在测试配置中禁用 CSRF 保护 #SQLALCHEMY_DATABASE_URI = os.environ.get('TEST_DATABASE_URL') or \ # 'sqlite:///' + os.path.join(basedir, 'data-test.sqlite') SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.join(basedir, 'data-test.sqlite') #测试采用sqlite class ProductionConfig(Config): SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL') or \ 'sqlite:///' + os.path.join(basedir, 'data.sqlite') class UnixConfig(ProductionConfig): @classmethod def init_app(cls, app): ProductionConfig.init_app(app) # log to syslog import logging from logging.handlers import SysLogHandler syslog_handler = SysLogHandler() syslog_handler.setLevel(logging.WARNING) app.logger.addHandler(syslog_handler) config = { 'development': DevelopmentConfig, 'testing': TestingConfig, 'production': ProductionConfig, 'default': DevelopmentConfig }

mit

masc3d/btrfs-sxbackup

btrfs_sxbackup/shell.py

1

2492

# Copyright (c) 2014 Marco Schindler # # This program is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by the Free # Software Foundation; either version 2 of the License, or (at your option) # any later version. import subprocess import logging _logger = logging.getLogger(__name__) def build_subprocess_args(cmd, url=None): """ Create subprocess arguments for shell command/args to be executed Internally Wraps command into ssh call if url host name is not None :param cmd: Shell command string or argument list :param url: url of remote host :return: Subprocess arguments """ # in case cmd is a regular value, convert to list cmd = cmd if isinstance(cmd, list) else [cmd] # wrap into bash or ssh command respectively # depending if command is executed locally (host==None) or remotely url_string = None ssh_args = ['ssh', '-o', 'ServerAliveInterval=5', '-o', 'ServerAliveCountMax=3'] if url is not None and url.hostname is not None: url_string = url.hostname if url.username is not None: url_string = '%s@%s' % (url.username, url.hostname) if url.port is not None: ssh_args += ['-p', '%s' % url.port] ssh_args += ['%s' % url_string] subprocess_args = ['bash', '-c'] + cmd if url_string is None else \ ssh_args + cmd _logger.debug(subprocess_args) return subprocess_args def exec_check_output(cmd, url=None) -> bytes: """ Wrapper for subprocess.check_output :param cmd: Command text :param url: URL :return: output """ return subprocess.check_output(build_subprocess_args(cmd, url), stderr=subprocess.STDOUT) def exec_call(cmd, url=None) -> int: """ Wrapper for subprocess.call :param cmd: Command text :param url: URL :return: """ return subprocess.call(build_subprocess_args(cmd, url), stderr=subprocess.PIPE, stdout=subprocess.PIPE) def exists(command, url=None): """ Check if shell command exists :param command: Command to verify :param url: url of remote host :return: True if location exists, otherwise False """ type_prc = subprocess.Popen(build_subprocess_args(['type ' + command], url), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=False) return type_prc.wait() == 0

gpl-2.0

Petr-By/qtpyvis

dltb/tool/adversarial.py

1

1626

"""Tools for creating and definding againts adversarial examples. """ # third party imports import numpy as np # Toolbox imports from ..datasource import Datasource from .tool import Tool from .classifier import Classifier, ClassIdentifier class Attacker(Tool): # pylint: disable=too-many-ancestors """An attacker can create adversarial attacks ("adversarial examples") for a given victim. Currently we assume that the victim is a classifier. """ def attack(self, victim: Classifier, example: np.ndarray, correct: ClassIdentifier, target: ClassIdentifier = None, **kwargs) -> np.ndarray: """ Perform an attack against a victim. Arguments --------- victim: Classifier The victim (classifier) to attack. example: np.ndarray The example that should be altered. correct: ClassIdentifier Correct class label for the example. target: ClassIdentifier Target label for the attack. If none is given, an untargeted attack is done. Result ------ adversarial_example: np.ndarray The adversarial example created by the attack. """ class Defender(Tool): # pylint: disable=too-many-ancestors """A :py:class:`Defender` aims at making a victim more robust against adversarial attacks. """ def defend(self, victim: Classifier, attacker: Attacker = None, datasource: Datasource = None, **kwargs) -> None: """Defend the victim against adversarial attacks. """

mit

Litetokens/liteblockd

armory_utxsvr.py

1

3736

#! /usr/bin/env python3 """ server for creating unsigned armory offline transactions """ import sys import logging import argparse import json import time import threading import flask from flask import request import jsonrpc from jsonrpc import dispatcher sys.path.append("/usr/lib/armory/") from armoryengine.ALL import * ARMORY_UTXSVR_PORT_MAINNET = 6590 ARMORY_UTXSVR_PORT_TESTNET = 6591 app = flask.Flask(__name__) @dispatcher.add_method def serialize_unsigned_tx(unsigned_tx_hex, public_key_hex): print("REQUEST(serialize_unsigned_tx) -- unsigned_tx_hex: '%s', public_key_hex: '%s'" % ( unsigned_tx_hex, public_key_hex)) try: unsigned_tx_bin = hex_to_binary(unsigned_tx_hex) pytx = PyTx().unserialize(unsigned_tx_bin) utx = UnsignedTransaction(pytx=pytx, pubKeyMap=hex_to_binary(public_key_hex)) unsigned_tx_ascii = utx.serializeAscii() except Exception, e: raise Exception("Could not serialize transaction: %s" % e) return unsigned_tx_ascii @dispatcher.add_method def convert_signed_tx_to_raw_hex(signed_tx_ascii): """Converts a signed tx from armory's offline format to a raw hex tx that litecoind can broadcast/use""" print("REQUEST(convert_signed_tx_to_raw_hex) -- signed_tx_ascii:\n'%s'\n" % (signed_tx_ascii,)) try: utx = UnsignedTransaction() utx.unserializeAscii(signed_tx_ascii) except Exception, e: raise Exception("Could not decode transaction: %s" % e) #see if the tx is signed if not utx.evaluateSigningStatus().canBroadcast: raise Exception("Passed transaction is not signed") try: pytx = utx.getSignedPyTx() raw_tx_bin = pytx.serialize() raw_tx_hex = binary_to_hex(raw_tx_bin) except Exception, e: raise Exception("Could not serialize transaction: %s" % e) return raw_tx_hex @app.route('/', methods=["POST",]) @app.route('/api/', methods=["POST",]) def handle_post(): request_json = flask.request.get_data().decode('utf-8') rpc_response = jsonrpc.JSONRPCResponseManager.handle(request_json, dispatcher) rpc_response_json = json.dumps(rpc_response.data).encode() response = flask.Response(rpc_response_json, 200, mimetype='application/json') return response class ArmoryBlockchainUpdaterThread(threading.Thread): def __init__(self): threading.Thread.__init__(self) def run(self): #loop to check for new blocks print("**** Polling for blockchain updates ...") while(True): prevTop = TheBDM.getTopBlockHeight() TheBDM.readBlkFileUpdate() newTop = TheBDM.getTopBlockHeight() if newTop > prevTop: print 'New blocks: %d (top: %d)' % (newTop-prevTop, newTop) time.sleep(1.0) # check every 1 second if __name__ == '__main__': print("**** Starting up ...") parser = argparse.ArgumentParser(description='Armory offline transaction generator daemon') parser.add_argument('--testnet', action='store_true', help='Run for testnet') args = parser.parse_args() ltcdir = "/home/xlt/.litecoin%s/" % ('-testnet/testnet3' if args.testnet else '') print("**** Initializing armory ...") #require armory to be installed, adding the configured armory path to PYTHONPATH TheBDM.ltcdir = ltcdir TheBDM.setBlocking(True) TheBDM.setOnlineMode(True) blockchainUpdaterThread = ArmoryBlockchainUpdaterThread() blockchainUpdaterThread.start() print("**** Initializing Flask (HTTP) server ...") app.run(host="127.0.0.1", port=ARMORY_UTXSVR_PORT_MAINNET if not args.testnet else ARMORY_UTXSVR_PORT_TESTNET, threaded=True) print("**** Ready to serve ...")

mit

cvandeplas/plaso

plaso/parsers/firefox_cache_test.py

1

6803

#!/usr/bin/python # -*- coding: utf-8 -*- # # Copyright 2014 The Plaso Project Authors. # Please see the AUTHORS file for details on individual authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """Tests for Firefox cache files parser.""" import unittest # pylint: disable=unused-import from plaso.formatters import firefox_cache as firefox_cache_formatter from plaso.lib import errors from plaso.lib import timelib_test from plaso.parsers import firefox_cache from plaso.parsers import test_lib __author__ = 'Petter Bjelland ([email protected])' class FirefoxCacheTest(test_lib.ParserTestCase): """A unit test for the FirefoxCacheParser.""" def setUp(self): self._parser = firefox_cache.FirefoxCacheParser() def VerifyMajorMinor(self, events): """Verify that valid Firefox cahce version is extracted.""" for event_object in events: self.assertEquals(event_object.major, 1) self.assertEquals(event_object.minor, 19) def testParseCache_InvalidFile(self): """Verify that parser do not accept small, invalid files.""" test_file = self._GetTestFilePath(['firefox_cache', 'invalid_file']) with self.assertRaises(errors.UnableToParseFile): _ = self._ParseFile(self._parser, test_file) def testParseCache_001(self): """Test Firefox 28 cache file _CACHE_001_ parsing.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox28', '_CACHE_001_']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(574, len(event_objects)) self.assertEquals(event_objects[1].url, 'HTTP:http://start.ubuntu.com/12.04/sprite.png') self.assertEquals(event_objects[1].timestamp, timelib_test.CopyStringToTimestamp('2014-04-21 14:13:35')) self.VerifyMajorMinor(event_objects) expected_msg = ( u'Fetched 2 time(s) ' u'[HTTP/1.0 200 OK] GET ' u'"HTTP:http://start.ubuntu.com/12.04/sprite.png"') expected_msg_short = ( u'[HTTP/1.0 200 OK] GET ' u'"HTTP:http://start.ubuntu.com/12.04/sprite.png"') self._TestGetMessageStrings(event_objects[1], expected_msg, expected_msg_short) def testParseCache_002(self): """Test Firefox 28 cache file _CACHE_002_ parsing.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox28', '_CACHE_002_']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(58, len(event_objects)) self.assertEquals(event_objects[2].url, ('HTTP:http://www.google-analytics.com/__utm.gif?utmwv=5.5.0&utms=' '1&utmn=1106893631&utmhn=www.dagbladet.no&utmcs=windows-1252&ut' 'msr=1920x1080&utmvp=1430x669&utmsc=24-bit&utmul=en-us&utmje=0&' 'utmfl=-&utmdt=Dagbladet.no%20-%20forsiden&utmhid=460894302&utm' 'r=-&utmp=%2F&utmht=1398089458997&utmac=UA-3072159-1&utmcc=__ut' 'ma%3D68537988.718312608.1398089459.1398089459.1398089459.1%3B%' '2B__utmz%3D68537988.1398089459.1.1.utmcsr%3D(direct)%7Cutmccn' '%3D(direct)%7Cutmcmd%3D(none)%3B&aip=1&utmu=qBQ~')) self.assertEquals(event_objects[1].timestamp, timelib_test.CopyStringToTimestamp('2014-04-21 14:10:58')) self.VerifyMajorMinor(event_objects) def testParseCache_003(self): """Test Firefox 28 cache file _CACHE_003_ parsing.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox28', '_CACHE_003_']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(4, len(event_objects)) self.assertEquals(event_objects[3].url, 'HTTP:https://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js') self.assertEquals(event_objects[3].timestamp, timelib_test.CopyStringToTimestamp('2014-04-21 14:11:07')) self.VerifyMajorMinor(event_objects) def testParseAlternativeFilename(self): """Test Firefox 28 cache 003 file with alternative filename.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox28', 'E8D65m01']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(4, len(event_objects)) def testParseLegacyCache_001(self): """Test Firefox 3 cache file _CACHE_001_ parsing.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox3', '_CACHE_001_']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(25, len(event_objects)) self.assertEquals(event_objects[0].timestamp, timelib_test.CopyStringToTimestamp('2014-05-02 14:15:03')) expected_msg = ( u'Fetched 1 time(s) ' u'[HTTP/1.1 200 OK] GET ' u'"HTTP:http://start.mozilla.org/en-US/"') expected_msg_short = ( u'[HTTP/1.1 200 OK] GET ' u'"HTTP:http://start.mozilla.org/en-US/"') self._TestGetMessageStrings(event_objects[0], expected_msg, expected_msg_short) def testParseLegacyCache_002(self): """Test Firefox 3 cache file _CACHE_002_ parsing.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox3', '_CACHE_002_']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(3, len(event_objects)) self.assertEquals(event_objects[1].timestamp, timelib_test.CopyStringToTimestamp('2014-05-02 14:25:55')) def testParseLegacyCache_003(self): """Test Firefox 3 cache file _CACHE_003_ parsing.""" test_file = self._GetTestFilePath(['firefox_cache', 'firefox3', '_CACHE_003_']) event_queue_consumer = self._ParseFile(self._parser, test_file) event_objects = self._GetEventObjectsFromQueue(event_queue_consumer) self.assertEquals(2, len(event_objects)) self.assertEquals(event_objects[1].timestamp, timelib_test.CopyStringToTimestamp('2014-05-02 14:15:07')) if __name__ == '__main__': unittest.main()

apache-2.0

Pikecillo/genna

external/PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py

1

2141

######################################################################## # # File Name: ParsedAbbreviatedRelativeLocationPath.py # # """ A parsed token that represents a abbreviated relative location path. WWW: http://4suite.org/XPATH e-mail: [email protected] Copyright (c) 2000-2001 Fourthought Inc, USA. All Rights Reserved. See http://4suite.org/COPYRIGHT for license and copyright information """ from xml.xpath import ParsedNodeTest from xml.xpath import ParsedPredicateList from xml.xpath import ParsedAxisSpecifier from xml.xpath import ParsedStep import Set class ParsedAbbreviatedRelativeLocationPath: def __init__(self,left,right): """ left can be a step or a relative location path right is only a step """ self._left = left self._right = right pnt = ParsedNodeTest.ParsedNodeTest('node','') ppl = ParsedPredicateList.ParsedPredicateList([]) pas = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') self._middle = ParsedStep.ParsedStep(pas, pnt, ppl) def evaluate(self, context): res = [] rt = self._left.select(context) l = len(rt) origState = context.copyNodePosSize() for ctr in range(l): context.setNodePosSize((rt[ctr],ctr+1,l)) subRt = self._middle.select(context) res = Set.Union(res,subRt) rt = res res = [] l = len(rt) for ctr in range(l): context.setNodePosSize((rt[ctr],ctr+1,l)) subRt = self._right.select(context) res = Set.Union(res,subRt) context.setNodePosSize(origState) return res select = evaluate def pprint(self, indent=''): print indent + str(self) self._left.pprint(indent + ' ') self._middle.pprint(indent + ' ') self._right.pprint(indent + ' ') def __str__(self): return '<AbbreviatedRelativeLocationPath at %x: %s>' % ( id(self), repr(self), ) def __repr__(self): return repr(self._left) + '//' + repr(self._right)

gpl-2.0

ntucllab/libact

libact/query_strategies/multiclass/tests/test_hierarchical_sampling.py

1

2717

""" HierarchicalSampling test """ import unittest import numpy as np from numpy.testing import assert_array_equal from sklearn import datasets from sklearn.utils import shuffle from libact.base.dataset import Dataset from libact.models import SVM from libact.query_strategies import UncertaintySampling from libact.query_strategies.multiclass import HierarchicalSampling as HS from ...tests.utils import run_qs class HierarchicalSamplingTestCase(unittest.TestCase): def setUp(self): iris = datasets.load_iris() X, y = shuffle(iris.data, iris.target, random_state=1126) self.X = X.tolist() self.y = y.tolist() self.classes = list(set(self.y)) def test_hs_random_selecting(self): ds = Dataset(self.X, self.y[:10] + [None] * (len(self.y) - 10)) qs = HS(ds, self.classes, active_selecting=False, random_state=1126) qseq = run_qs(ds, qs, self.y, len(self.y)-10) assert_array_equal( np.concatenate([qseq[:10], qseq[-10:]]), np.array([48, 143, 13, 142, 88, 130, 29, 87, 36, 28, 58, 137, 49, 105, 76, 71, 63, 47, 64, 55]) ) def test_hs_active_selecting(self): ds = Dataset(self.X, self.y[:10] + [None] * (len(self.y) - 10)) qs = HS(ds, self.classes, active_selecting=True, random_state=1126) qseq = run_qs(ds, qs, self.y, len(self.y)-10) assert_array_equal( np.concatenate([qseq[:10], qseq[-10:]]), np.array([48, 143, 13, 64, 101, 108, 51, 87, 36, 28, 43, 118, 47, 25, 81, 82, 95, 40, 67, 120]) ) def test_hs_subsampling(self): ds = Dataset(self.X, self.y[:10] + [None] * (len(self.y) - 10)) sub_qs = UncertaintySampling(ds, model=SVM(gamma='auto', decision_function_shape='ovr')) qs = HS(ds, self.classes, subsample_qs=sub_qs, random_state=1126) qseq = run_qs(ds, qs, self.y, len(self.y)-10) assert_array_equal( np.concatenate([qseq[:10], qseq[-10:]]), np.array([120, 50, 33, 28, 78, 133, 52, 124, 102, 109, 81, 108, 12, 10, 89, 114, 92, 126, 48, 25]) ) def test_hs_report_all_label(self): ds = Dataset(self.X, self.y) qs = HS(ds, self.classes, random_state=1126) y_report = qs.report_all_label() assert_array_equal(y_report, self.y) def test_hs_report_entry_label(self): ds = Dataset(self.X, self.y) qs = HS(ds, self.classes, random_state=1126) y_report = [] for i in range(len(self.y)): y_report.append(qs.report_entry_label(i)) assert_array_equal(y_report, self.y)

bsd-2-clause

b1r3k/recruitment-challanges

data-hacking/src/task1/classifier/channel.py

1

1678

''' * Author: Lukasz Jachym * Date: 9/14/13 * Time: 5:40 PM * * This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. * To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/. ''' from collections import namedtuple from branding import is_branded DIRECT = 1 PPC = 2 SEO = 3 Channel = namedtuple('Channel', ['type', 'keywords', 'branded']) def get_ppc_keywords(ppc_str): """ :param ppc_str: :return: keywords """ try: keywords = ppc_str.split('_')[2] except KeyError: raise ValueError return keywords def get_seo_keywords(seo_query): """ :param ppc_str: :return: keywords """ try: keywords = seo_query.split(' :: ')[2] except KeyError: raise ValueError return keywords def parse_source(source_str): if (source_str[0:3] == 'ppc'): channel_type = PPC keywords = get_ppc_keywords(source_str) channel_keywords = keywords channel_branded = is_branded(keywords) channel = Channel(channel_type, channel_keywords, channel_branded) else: if source_str[0:3] == 'seo': channel_type = SEO keywords = get_seo_keywords(source_str) channel_keywords = keywords channel_branded = is_branded(keywords) channel = Channel(channel_type, channel_keywords, channel_branded) else: channel_type = DIRECT channel_keywords = None channel_branded = False channel = Channel(channel_type, channel_keywords, channel_branded) return channel

mit

leriomaggio/pycon_site

p3/templatetags/p3.py

1

21562

# -*- coding: UTF-8 -*- from __future__ import absolute_import import mimetypes import os import os.path import re import random import sys import urllib from collections import defaultdict from datetime import datetime from itertools import groupby from django import template from django.conf import settings from django.core.urlresolvers import reverse from django.template import Context from django.template.defaultfilters import slugify from django.template.loader import render_to_string from django.utils.safestring import mark_safe from conference import dataaccess as cdataaccess from conference import models as ConferenceModels from conference.settings import STUFF_DIR, STUFF_URL from assopy import models as amodels from p3 import dataaccess from p3 import forms as p3forms from p3 import models from fancy_tag import fancy_tag mimetypes.init() register = template.Library() @register.inclusion_tag('p3/box_pycon_italia.html') def box_pycon_italia(): return {} @register.inclusion_tag('p3/box_newsletter.html', takes_context=True) def box_newsletter(context): return context @register.inclusion_tag('p3/box_cal.html', takes_context = True) def box_cal(context, limit=None): deadlines = ConferenceModels.Deadline.objects.valid_news() if limit: deadlines = deadlines[:int(limit)] return { 'deadlines': [ (d, d.content(context['LANGUAGE_CODE'])) for d in deadlines ] } @register.inclusion_tag('p3/render_cal.html', takes_context=True) def render_cal(context): return context @register.inclusion_tag('p3/box_download.html', takes_context = True) def box_download(context, fname, label=None): if '..' in fname: raise template.TemplateSyntaxError("file path cannot contains ..") if fname.startswith('/'): raise template.TemplateSyntaxError("file path cannot starts with /") if label is None: label = os.path.basename(fname) try: fpath = os.path.join(settings.STUFF_DIR, fname) stat = os.stat(fpath) except (AttributeError, OSError), e: fsize = ftype = None else: fsize = stat.st_size ftype = mimetypes.guess_type(fpath)[0] return { 'url': context['STUFF_URL'] + fname, 'label': label, 'fsize': fsize, 'ftype': ftype, } @register.inclusion_tag('p3/box_didyouknow.html', takes_context = True) def box_didyouknow(context): try: d = ConferenceModels.DidYouKnow.objects.filter(visible = True).order_by('?')[0] except IndexError: d = None return { 'd': d, 'LANGUAGE_CODE': context.get('LANGUAGE_CODE'), } @register.inclusion_tag('p3/box_googlemaps.html', takes_context = True) def box_googlemaps(context, what='', zoom=13): what = ','.join([ "'%s'" % w for w in what.split(',') ]) return { 'rand': random.randint(0, sys.maxint - 1), 'what': what, 'zoom': zoom } @register.inclusion_tag('p3/box_talks_conference.html', takes_context = True) def box_talks_conference(context, talks): """ mostra i talk passati raggruppati per conferenza """ conf = defaultdict(list) for t in talks: conf[t.conference].append(t) talks = [] for c in reversed(sorted(conf.keys())): talks.append((c, conf[c])) return { 'talks': talks } @register.inclusion_tag('p3/box_latest_tweets.html', takes_context=True) def box_latest_tweets(context): ctx = Context(context) ctx.update({ 'screen_name': settings.P3_TWITTER_USER, }) return ctx @register.filter def render_time(tweet, args=None): time = tweet["timestamp"] time = datetime.datetime.fromtimestamp(time) return time.strftime("%d-%m-%y @ %H:%M") @register.filter def check_map(page): """ controlla se la pagina passata richiede o meno una mappa """ if page: return '{% render_map' in page.expose_content() return False @register.inclusion_tag('p3/render_map.html', takes_context=True) def render_map(context): return {} @register.inclusion_tag('p3/fragments/render_ticket.html', takes_context=True) def render_ticket(context, ticket): from p3 import forms user = context['request'].user if ticket.fare.ticket_type == 'conference': try: inst = ticket.p3_conference except: inst = None form = forms.FormTicket( instance=inst, initial={ 'ticket_name': ticket.name, }, prefix='t%d' % (ticket.id,), single_day=ticket.fare.code[2] == 'D', ) if inst and inst.assigned_to: blocked = inst.assigned_to != user.email else: blocked = False elif ticket.fare.code in ('SIM01',): try: inst = ticket.p3_conference_sim except: inst = None form = forms.FormTicketSIM( instance=inst, initial={ 'ticket_name': ticket.name, }, prefix='t%d' % (ticket.id,), ) blocked = False elif ticket.fare.code.startswith('H'): # TicketRoom instances must exist, they're created by a listener inst = ticket.p3_conference_room form = forms.FormTicketRoom( instance=inst, initial={ 'ticket_name': ticket.name, }, prefix='t%d' % (ticket.id,), ) blocked = False else: form = forms.FormTicketPartner(instance=ticket, prefix='t%d' % (ticket.id,)) blocked = False ctx = Context(context) ctx.update({ 'ticket': ticket, 'form': form, 'user': user, 'blocked': blocked, }) return ctx @register.assignment_tag(takes_context=True) def fares_available(context, fare_type, sort=None): """ Restituisce l'elenco delle tariffe attive in questo momento per la tipologia specificata. """ assert fare_type in ('all', 'conference', 'goodies', 'partner', 'hotel-room', 'hotel-room-sharing', 'other') if not settings.P3_FARES_ENABLED(context['user']): return [] fares_list = filter(lambda f: f['valid'], cdataaccess.fares(settings.CONFERENCE_CONFERENCE)) if fare_type == 'conference': fares = [ f for f in fares_list if f['code'][0] == 'T' and f['ticket_type'] == 'conference' ] elif fare_type == 'hotel-room-sharing': fares = [ f for f in fares_list if f['code'].startswith('HB') ] elif fare_type == 'hotel-room': fares = [ f for f in fares_list if f['code'].startswith('HR') ] elif fare_type == 'other': fares = [ f for f in fares_list if f['ticket_type'] in ('other', 'event') and f['code'][0] != 'H' ] elif fare_type == 'partner': fares = [ f for f in fares_list if f['ticket_type'] in 'partner' ] elif fare_type == 'all': fares = fares_list if sort == "price": fares.sort(key=lambda x: x['price']) return fares @fancy_tag(register, takes_context=True) def render_cart_rows(context, fare_type, form): assert fare_type in ('conference', 'goodies', 'partner', 'hotel-room', 'hotel-room-sharing', 'other') ctx = Context(context) request = ctx['request'] try: company = request.user.assopy_user.account_type == 'c' except AttributeError: # anonymous user or without an assopy profile (impossible!) company = False ctx.update({ 'form': form, 'company': company, }) fares_list = filter(lambda f: f['valid'], cdataaccess.fares(settings.CONFERENCE_CONFERENCE)) if fare_type == 'conference': tpl = 'p3/fragments/render_cart_conference_ticket_row.html' # rendering "conference" tickets is a bit complex; each row in # the cart corresponds to multiple "fare" (student, private, copany) # # The prices must be sorted on time + ticket type + owner # early # full [Student, Private, Company] # lite (standard) [Student, Private, Company] # daily [Student, Private, Company] # regular (late) # ... # on desk # ... # # The correct time ordering is guaranteed implicitly by # excluding expired fares (it's not permitted to have overlaps # of validity periods). fares = dict((f['code'][2:], f) for f in fares_list if f['code'][0] == 'T') rows = [] for t in ('S', 'L', 'D'): # To simplify the template fares are packed in triplets: # student, private, company. # # Each raw is a tuple with three elements: # 1. Fare # 2. FormField # 3. Boolean flag telling if the price can be applied to the user row = [] for k in ('S', 'P', 'C'): try: f = fares[t+k] except KeyError: row.append((None, None, None)) else: # The price is valid if the time test is passed and if the # account type is compatible valid = not (company ^ (f['code'][-1] == 'C')) row.append((f, form.__getitem__(f['code']), valid)) rows.append(row) ctx['rows'] = rows elif fare_type == 'hotel-room-sharing': tpl = 'p3/fragments/render_cart_hotel_ticket_row.html' ctx['field'] = form['bed_reservations'] ctx['field'].field.widget._errors = ctx['field'].errors elif fare_type == 'hotel-room': tpl = 'p3/fragments/render_cart_hotel_ticket_row.html' ctx['field'] = form['room_reservations'] ctx['field'].field.widget._errors = ctx['field'].errors elif fare_type == 'other': tpl = 'p3/fragments/render_cart_og_ticket_row.html' fares = defaultdict(dict) order = ('p', 'c') columns = set() for f in fares_list: if f['ticket_type'] in ('other', 'event') and f['code'][0] != 'H': columns.add(f['recipient_type']) fares[f['name']][f['recipient_type']] = f ctx['fares'] = fares.values() ctx['recipient_types'] = sorted(columns, key=lambda v: order.index(v)) elif fare_type == 'partner': tpl = 'p3/fragments/render_cart_partner_ticket_row.html' ctx['fares'] = [ f for f in fares_list if f['ticket_type'] in 'partner' ] return render_to_string(tpl, ctx) @register.inclusion_tag('p3/box_image_gallery.html', takes_context=True) def box_image_gallery(context): images = [] for f in os.listdir(STUFF_DIR): images.append('%s%s' % (STUFF_URL, f)) context.update({ 'images': images, }) return context @fancy_tag(register, takes_context=True) def render_partner_program(context, conference=None): if conference is None: conference = settings.CONFERENCE_CONFERENCE from conference import dataaccess from conference.templatetags.conference import fare_blob fares = [ x for x in dataaccess.fares(conference) if x['ticket_type'] == 'partner' and x['valid'] ] fares.sort(key=lambda x: (slugify(x['name']), fare_blob(x, 'date'))) ctx = Context(context) ctx.update({ 'fares': [ (k, list(v)) for k, v in groupby(fares, key=lambda x: slugify(x['name'])) ], }) return render_to_string('p3/fragments/render_partner_program.html', ctx) @fancy_tag(register, takes_context=True) def event_partner_program(context, event): fare_id = re.search(r'f(\d+)', event.track) if fare_id is None: return '' from conference.templatetags.conference import _request_cache c = _request_cache(context['request'], 'fares') if not c: for f in ConferenceModels.Fare.objects.all(): c[str(f.id)] = f fare = c[fare_id.group(1)] return mark_safe('<a href="/partner-program/#%s">%s</a>' % (slugify(fare.name), event.custom,)) @register.filter def schedule_to_be_splitted(s): tracks = ConferenceModels.Track.objects.by_schedule(s) s = [] for t in tracks: if t.track.startswith('partner') or t.track.startswith('sprint'): s.append(t) return len(tracks) != len(s) @register.filter def tickets_url(user): """ ritorna la url più diretta per mandare l'utente sulla sua pagina ticket """ if user.assopy_user.token: u = reverse('p3-user', kwargs={'token': user.assopy_user.token}) else: u = reverse('p3-tickets') return settings.DEFAULT_URL_PREFIX + u @register.filter def ticket_user(ticket): try: p3c = ticket.p3_conference except models.TicketConference.DoesNotExist: p3c = None if p3c and p3c.assigned_to: from assopy.models import User return User.objects.get(user__email=p3c.assigned_to) else: return ticket.orderitem.order.user @register.filter def com_com_registration(user): url = 'https://hotspot.com-com.it/signup/?' name = user.name() try: fn, ln = name.split(' ', 1) except ValueError: fn = name ln = '' params = { 'autofill': 'yes', 'firstname': fn, 'lastname': ln, 'email': user.user.email, } if user.country: params['nationality'] = user.country.pk if user.phone and user.phone.startswith('+39'): params['ita_mobile'] = user.phone params['username'] = name.lower().replace(' ', '').replace('.', '')[:12] for k, v in params.items(): params[k] = v.encode('utf-8') return url + urllib.urlencode(params) @register.inclusion_tag('p3/box_next_events.html', takes_context=True) def box_next_events(context): from conference.templatetags import conference as ctags t = datetime.now() try: sch = ConferenceModels.Schedule.objects.get(date=t.date()) except ConferenceModels.Schedule.DoesNotExist: current = next = {} else: current = ctags.current_events(context, t) next = ctags.next_events(context, t) tracks = dict( (x, None) for x in ConferenceModels.Track.objects.by_schedule(sch) if x.outdoor == False ) for track in tracks: c = current.get(track) if c: if hasattr(c, 'evt'): c = c.evt.ref else: c = c.ref n = next.get(track) if n: n_time = n.time if hasattr(n, 'evt'): n = n.evt.ref else: n = n.ref else: n_time = None tracks[track] = { 'current': c, 'next': (n, n_time), } events = sorted(tracks.items(), key=lambda x: x[0].order) ctx = Context(context) ctx.update({ 'events': events, }) return ctx @fancy_tag(register) def p3_profile_data(uid): return dataaccess.profile_data(uid) @fancy_tag(register) def p3_profiles_data(uids): return dataaccess.profiles_data(uids) @fancy_tag(register) def p3_talk_data(tid): return dataaccess.talk_data(tid) @fancy_tag(register, takes_context=True) def get_form(context, name, bound="auto", bound_field=None): if '.' in name: from conference.utils import dotted_import fc = dotted_import(name) else: fc = getattr(p3forms, name) request = context['request'] if bound: if bound == 'auto': bound = request.method if bound == 'GET': data = request.GET elif bound == 'POST': data = request.POST else: from django.db.models import Model if isinstance(bound, Model): data = {} for name in fc.base_fields: data[name] = getattr(bound, name) else: data = bound if bound_field and bound_field not in data: data = None else: data = None form = fc(data=data) if data: form.is_valid() return form @fancy_tag(register) def pending_email_change(user): try: t = amodels.Token.objects.get(ctype='e', user=user) except amodels.Token.DoesNotExist: return None return t.payload @fancy_tag(register) def admin_ticketroom_overall_status(): status = models.TicketRoom.objects.overall_status() labels = dict(models.HOTELROOM_ROOM_TYPE) days = sorted(status.keys()) rooms = {} for day in days: dst = status[day] for room_type, dst in status[day].items(): try: r = rooms[room_type] except KeyError: r = rooms[room_type] = { 'type': room_type, 'label': labels.get(room_type, room_type), 'days': [], } r['days'].append(dst) return { 'days': days, 'rooms': rooms.values(), } @fancy_tag(register) def warmup_conference_cache(conference=None): """ """ if conference is None: conference = settings.CONFERENCE_CONFERENCE qs = ConferenceModels.TalkSpeaker.objects\ .filter(talk__conference=conference)\ .values_list('talk', 'speaker') talks = set() speakers = set() for row in qs: talks.add(row[0]) speakers.add(row[1]) return { 'speakers': dict([ (x['id'], x) for x in dataaccess.profiles_data(speakers) ]), 'talks': dict([ (x['id'], x) for x in cdataaccess.talks_data(talks) ]), } @register.filter def frozen_reason(ticket): if not ticket.frozen: return '' if amodels.RefundOrderItem.objects.filter(orderitem=ticket.orderitem).exists(): return 'refund pending' else: return '' @fancy_tag(register, takes_context=True) def all_user_tickets(context, uid=None, conference=None, status="complete", fare_type="conference"): if uid is None: uid = context['request'].user.id if conference is None: conference = settings.CONFERENCE_CONFERENCE tickets = dataaccess.all_user_tickets(uid, conference) if status == 'complete': tickets = filter(lambda x: x[3], tickets) elif status == 'incomplete': tickets = filter(lambda x: not x[3], tickets) if fare_type != "all": tickets = filter(lambda x: x[1] == fare_type, tickets) return tickets @fancy_tag(register) def p3_tags(): return dataaccess.tags() @fancy_tag(register) def p3_tags_for_talks(): conference = settings.CONFERENCE_CONFERENCE return dataaccess.tags_for_conference_talks(conference=conference) @fancy_tag(register, takes_context=True) def render_profile_box(context, profile, conference=None, user_message="auto"): if conference is None: conference = settings.CONFERENCE_CONFERENCE if isinstance(profile, int): profile = dataaccess.profile_data(profile) ctx = Context(context) ctx.update({ 'profile': profile, 'conference': conference, 'user_message': user_message if user_message in ('auto', 'always', 'none') else 'auto', }) return render_to_string('p3/fragments/render_profile_box.html', ctx) @register.inclusion_tag('p3/fragments/archive.html', takes_context=True) def render_archive(context, conference): ctx = Context(context) def match(e, exclude_tags=set(('partner0', 'partner1', 'sprint1', 'sprint2', 'sprint3'))): if e['tags'] & exclude_tags: return False if not e['talk']: return False return True events = { x['id']:x for x in filter(match, cdataaccess.events(conf=conference)) } talks = {} for e in events.values(): t = e['talk'] if t['id'] in talks: continue t['dates'] = sorted([ (events[x]['time'], events[x]['talk']['video_url']) for x in t['events_id'] ]) talks[t['id']] = t ctx.update({ 'conference': conference, 'talks': sorted(talks.values(), key=lambda x: x['title']), }) return ctx @register.filter def timetable_remove_first(timetable, tag): if not tag: return timetable start = None for time, events in timetable.iterOnTimes(): stop = False for e in events: if tag not in e['tags']: stop = True break start = time.time() if stop: break return timetable.slice(start=start) @register.assignment_tag def p3_voting_data(conference): from conference.templatetags.conference import voting_data from conference.utils import voting_results groups = defaultdict(list) results = voting_results() if results is not None: talk_ids = [ x[0] for x in results ] sub_community = dict( models.P3Talk.objects\ .filter(talk__conference=conference)\ .values_list('talk', 'sub_community')) for tid, type, language in results: community = sub_community.get(tid, '') groups[(type, community)].append(tid) results = voting_data(conference) results['groups'] = dict(groups) return results @fancy_tag(register, takes_context=True) def get_latest_conf_deadline(context, limit=None, not_expired=True): try: conf = ConferenceModels.Conference.objects.latest('code') return [conf.name, conf.code, conf.conference_start, conf.conference_end, datetime.today().date()] except IndexError: return []

bsd-2-clause

Semprini/cbe-retail

retail/store/models.py

1

2047

from django.db import models from django.contrib.contenttypes.fields import GenericRelation from cbe.location.models import Location, GeographicArea from cbe.party.models import Organisation, PartyRole from cbe.physical_object.models import Structure class Store(PartyRole): enterprise_id = models.IntegerField(unique=True) code = models.CharField(max_length=200, blank=True, null=True) description = models.TextField(blank=True, null=True) identifiers = GenericRelation('human_resources.Identification', object_id_field="party_role_object_id", content_type_field='party_role_content_type', related_query_name='store') store_type = models.CharField( max_length=100, null=True, blank=True, choices=(('mitre 10','mitre 10'),('mega','mega'),('hammer','hammer'),('trade','trade')) ) store_class = models.CharField( max_length=100, null=True, blank=True, choices=(('mega-1','mega-1'),('mega-2','mega-2'),('mega-3','mega-3'),('mega-r','mega-r'),('mitre10-small','mitre10-small'),('mitre10-medium','mitre10-medium'),('mitre10-large','mitre10-large'),('trade','trade')) ) opening_date = models.DateField(blank=True, null=True) location = models.ForeignKey(Location, on_delete=models.CASCADE, blank=True, null=True) trade_area = models.ForeignKey(GeographicArea, on_delete=models.CASCADE, related_name='store_trade_areas', blank=True, null=True) retail_area = models.ForeignKey(GeographicArea, on_delete=models.CASCADE, related_name='store_retail_areas', blank=True, null=True) national_area = models.ForeignKey(GeographicArea, on_delete=models.CASCADE, related_name='store_national_areas', blank=True, null=True) buildings = models.ManyToManyField(Structure, related_name='store') class Meta: ordering = ['id'] def __str__(self): return "%s" %(self.name ) def save(self, *args, **kwargs): if self.name == "": self.name = "Store" super(Store, self).save(*args, **kwargs)

apache-2.0

ytec/instaforex-web

app/open/migrations/0001_initial.py

1

1404

# -*- coding: utf-8 -*- from __future__ import unicode_literals from django.db import migrations, models class Migration(migrations.Migration): dependencies = [ ('cms', '0016_auto_20160608_1535'), ] operations = [ migrations.CreateModel( name='form', fields=[ ('cmsplugin_ptr', models.OneToOneField(primary_key=True, serialize=False, auto_created=True, related_name='open_form', parent_link=True, to='cms.CMSPlugin')), ('name', models.CharField(max_length=25, default='Demo')), ], options={ 'abstract': False, }, bases=('cms.cmsplugin',), ), migrations.CreateModel( name='OpenAccountAnonymous', fields=[ ('id', models.AutoField(verbose_name='ID', primary_key=True, serialize=False, auto_created=True)), ], ), migrations.CreateModel( name='OpenAccountDemo', fields=[ ('id', models.AutoField(verbose_name='ID', primary_key=True, serialize=False, auto_created=True)), ], ), migrations.CreateModel( name='OpenAccountReal', fields=[ ('id', models.AutoField(verbose_name='ID', primary_key=True, serialize=False, auto_created=True)), ], ), ]

gpl-3.0

AlexaProjects/Alexa2

ALEXA-IDE/core/ninja_tests/gui/test_status_bar.py

1

1869

# -*- coding: utf-8 -*- # # This file is part of NINJA-IDE (http://ninja-ide.org). # # NINJA-IDE is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or # any later version. # # NINJA-IDE is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with NINJA-IDE; If not, see <http://www.gnu.org/licenses/>. from __future__ import absolute_import from __future__ import unicode_literals import sys # Import this before Qt to set the correct API import ninja_ide # lint:ok from PyQt4.QtGui import QApplication from ninja_ide.gui import status_bar from ninja_ide.gui.main_panel import main_container from ninja_tests import BaseTest from ninja_tests import gui class StatusBarTestCase(BaseTest): def setUp(self): super(StatusBarTestCase, self).setUp() self.app = QApplication(sys.argv) self.parent = gui.FakeParent() self.patch(main_container.editor, 'Editor', gui.FakeEditor) self.main = main_container.MainContainer(None) self.main._parent = self.parent self.status = status_bar.StatusBar() def test_show(self): editor = self.main.add_editor() editor.setPlainText('ninja test') editor.selectAll() data = [] def fake_find_matches(*arg): data.append(arg) self.patch(self.status._searchWidget, 'find_matches', fake_find_matches) self.status.show() expected = [(editor, True)] self.assertEqual(data, expected)

gpl-3.0

josefschneider/switchboard

switchboard/__main__.py

1

1547

#!/usr/bin/env python '''The main entry point. Invoke as `switchboard' or `python -m switchboard'. ''' import argparse import sys from switchboard.config import SwitchboardConfig from switchboard.ws_ctrl_server import WSCtrlServer from switchboard.engine import SwitchboardEngine from switchboard.app_manager import AppManager from switchboard.cli import SwitchboardCli from switchboard.log import init_logging def main(): try: arg_parser = argparse.ArgumentParser() arg_parser.add_argument('-c', '--config', help='specify .json config file') args = arg_parser.parse_args() swb_config = SwitchboardConfig() if args.config: swb_config.load_config(args.config) init_logging(swb_config) ws_ctrl_server = WSCtrlServer(swb_config) swb = SwitchboardEngine(swb_config, ws_ctrl_server) with AppManager(swb_config, swb) as app_manager: cli = SwitchboardCli(swb, swb_config, app_manager) ws_ctrl_server.init_config() if args.config: swb.init_clients() # Only once the clients have been setup can we initialise the app manager app_manager.init_config() # And the modules go right at the end once we know all the devices swb.init_modules() ws_ctrl_server.set_dependencies(swb, app_manager) swb.start() sys.exit(cli.run()) except KeyboardInterrupt: pass if __name__ == '__main__': main()

mit

slideclick/toys

Simple/oMachine2.3.1-1.py

1

3469

# -* - coding: UTF-8 -* - ## Virtual Machine 2.3.1 ## 小步语义 -- 表达式 ## python 3.4 class Number(object): """ 数值符号类 """ def __init__(self, value): self.value = value def reducible(self): return False def to_s(self): return str(self.value) class Boolean(object): """ 布尔值符号类型 """ def __init__(self, value): self.value = value def reducible(self): return False def to_s(self): return str(self.value) class Add(object): """ 加法符号类 """ def __init__(self, left, right): self.left = left self.right = right def reducible(self): return True def reduce(self, environment): if self.left.reducible(): return Add(self.left.reduce(environment), self.right) elif self.right.reducible(): return Add(self.left, self.right.reduce(environment)) else: return Number(self.left.value + self.right.value) def to_s(self): return self.left.to_s() + ' + ' + self.right.to_s() class Multiply(object): """ 乘法符号类 """ def __init__(self, left, right): self.left = left self.right = right def reducible(self): return True def reduce(self, environment): if self.left.reducible(): return Multiply(self.left.reduce(environment), self.right) elif self.right.reducible(): return Multiply(self.left, self.right.reduce(environment)) else: return Number(self.left.value * self.right.value) def to_s(self): return self.left.to_s() + ' * ' + self.right.to_s() class LessThan(object): """ 小于符号类 """ def __init__(self, left, right): self.left = left self.right = right def reducible(self): return True def reduce(self, environment): if self.left.reducible(): return LessThan(self.left.reduce(environment), self.right) elif self.right.reducible(): return LessThan(self.left, self.right.reduce(environment)) else: return Boolean(self.left.value < self.right.value) def to_s(self): return self.left.to_s() + ' < ' + self.right.to_s() class Variable(object): """ 变量符号类 """ def __init__(self, name): self.name = name def reducible(self): return True def reduce(self, environment): return environment[self.name] def to_s(self): return str(self.name) class Machine(object): """ 虚拟机 """ def __init__(self, expression, environment): self.expression = expression self.environment = environment def step(self): self.expression = self.expression.reduce(self.environment) def run(self): while self.expression.reducible(): print(self.expression.to_s()) self.step() print(self.expression.value) ## test ## 在虚拟机中运行表达式 ##1 * 2 + 3 * 4 = 14 Machine(Add(Multiply(Number(1), Number(2)), Multiply(Number(3), Number(4))), {} ).run() print('') ##5 < 2 + 2 Machine( LessThan(Number(5), Add(Number(2), Number(2))), {} ).run() print('') ##x = 3; y = 4; x + y = 7 Machine( Add(Variable('x'), Variable('y')), {'x':Number(3), 'y':Number(4)} ).run()

gpl-2.0

jszopi/repESP

repESP/respin_format.py

1

19161

"""Parsing and writing ``resp`` program instruction file format ("respin")""" from dataclasses import dataclass, asdict from fortranformat import FortranRecordWriter as FW from itertools import zip_longest import io import math import re import sys from typing import Dict, List, Optional, TextIO, Tuple, Type, TypeVar, Union from repESP.exceptions import InputFormatError from repESP.equivalence import Equivalence from repESP.types import Atom, Molecule from repESP._util import get_line, zip_exact IvaryT = TypeVar('IvaryT', bound='Respin.Ivary') @dataclass class Respin: """Dataclass describing the ``resp`` program instructions Note that the functionality is currently limited to a single molecule and a single structure. Parameters ---------- title : str The title of the calculation to be performed. cntrl : Cntrl Dataclass representing the "cntrl" section of the input. subtitle : str Subtitle describing the considered molecular structure. charge : int The total charge of the molecule. molecule : Molecule[Atom] The molecule which charges are being fitted. Only atom identities are required. ivary : Ivary The "ivary" values for fitting the considered structure. These determine how the charge on each atom is allowed to vary during the fitting. Attributes ---------- title See initialization parameter cntrl See initialization parameter subtitle See initialization parameter charge See initialization parameter molecule See initialization parameter ivary See initialization parameter """ _ValueType = TypeVar("_ValueType", int, float, str) @staticmethod def _check_value( attr_name: str, attr_value: _ValueType, allowed_values: List[_ValueType] ) -> None: if attr_value not in allowed_values: raise ValueError( f"Invalid value for `{attr_name}`: {attr_value}." ) @dataclass class Cntrl: """Dataclass describing the "cntrl" section of a "respin" file See ``resp`` program documentation for more details. Parameters ---------- inopt : int, optional If equal to 1, ``resp`` will cycle through different "qwt" values from the file specified with the ``-w`` option. Defaults to 0. ioutopt : int, optional If equal to 1, ``resp`` will write restart info of new ESP field to the file specified with the ``-s`` option. Defaults to 0. iqopt : int, optional Controls setting initial charges. If equal to 1 (default), all initial charges will be set to zero. If equal to 2, initial charges are read from the file specified with the ``-q`` option. If equal to 3, charges are read as with the previous option and will additionally be averaged according to "ivary" values (normally not used). ihfree : int, optional If equal to 0, the charge magnitude restraint is applied to all charges. If equal to 1 (default), the restraint does not apply to hydrogen atoms. irstrnt : int, optional Controls the type of charge magnitude restraint. If equal to 0, harmonic restraints are used (old-style). If equal to 1 (default), hyperbolic restraints are used. If equal to 2, no charge fitting is carried out and only analysis of input charges is performed. qwt : float, optional The weight of the charge magnitude restraint to be used during the fitting. Defaults to 0.0 (no charge magnitude restraint). .. warning:: The default used here is different from the default used by ``resp``. That the ``resp`` documentation specifies that it uses the Amber force field values by default. However, it is not clear how it can determine the fitting stage. Thus, to remove the ambiguity, this dataclass assumes a weight of zero by default. .. note:: Amber force fields use values of 0.0005 and 0.001 for stages 1 and 2, respectively. The Glycam force field is derived with one stage fitting with a value of 0.01. Attributes ---------- inopt See initialization parameter ioutopt See initialization parameter iqopt See initialization parameter ihfree See initialization parameter irstrnt See initialization parameter qwt See initialization parameter """ inopt: int = 0 ioutopt: int = 0 iqopt: int = 1 ihfree: int = 1 irstrnt: int = 1 qwt: float = 0 @property def nmol(self) -> int: """Number of structures in a multiple structure fit. With the current implementation this will always be equal to 1. """ return 1 def __post_init__(self) -> None: Respin._check_value("inopt", self.inopt, [0, 1]) Respin._check_value("ioutopt", self.ioutopt, [0, 1]) Respin._check_value("iqopt", self.iqopt, [1, 2, 3]) Respin._check_value("ihfree", self.ihfree, [0, 1]) Respin._check_value("irstrnt", self.irstrnt, [0, 1, 2]) if self.qwt < 0: raise ValueError(f"Invalid value for `qwt`: {self.qwt}.") @dataclass class Ivary: """Dataclass representing per-atom fitting instructions for ``resp`` The fitting instructions are represented as a list of values stored in the `values` attribute. The length of this list must be the same as the number of atoms in the molecule it describes. Consecutive values refer to consecutive atoms of the molecule. The values determine how the charge on the atom can vary during the fitting and the allowed values are: * -1, meaning that the atom's charge is "frozen" at the initial value * 0, meaning that this atom will be varied freely * Larger than zero, representing the 1-based index of the atom in the molecule to which this atom is to be equivalenced. Example ------- Consider fitting RESP charges in a molecule of methylamine: >>> methylamine = Molecule([Atom(atomic_number) for atomic_number in [6, 1, 1, 1, 7, 1, 1]]) Fitting RESP charges consists of two stages. The ivary section for the second stage of the fitting for the methylamine molecule should be as follows: >>> ivary = Respin.Ivary([0, 0, 2, 2, -1, -1, -1]) The carbon atom is free to vary during the fitting. The first of the methyl hydrogens is equivalenced to the remaining two but they haven't been specified yet, so it also has a value of 0. These two hydrogen atoms are equivalenced to the first one, and thus are assigned its one-based index in the molecule, i.e. 2 (meaning "equivalenced to the second atom of the molecule"). The nitrogen atom and the two hydrogen atoms attached to it are frozen during the second stage of the fitting and are thus assigned values of -1. Parameters ---------- values : List[int] The per-atom instructions for the ``resp`` program. Attributes ---------- values See initialization parameter """ values: List[int] def __post_init__(self) -> None: for i, elem in enumerate(self.values): if elem < -1 or elem > len(self.values): raise ValueError( f"Value number {i} passed as `ivary` with value {elem}, " f"which is either lower than 0 or outside the list length." ) def describe(self, molecule: Optional[Molecule[Atom]]=None) -> str: """Verbosely report the "ivary" actions Example ------- >>> print(ivary.describe(methylamine)) Atom (C) number 1 Atom (H) number 2 Atom (H) number 3, equivalenced to atom 2 Atom (H) number 4, equivalenced to atom 2 Atom (N) number 5, frozen Atom (H) number 6, frozen Atom (H) number 7, frozen Parameters ---------- molecule : Optional[Molecule[Atom]], optional The molecule to which the ivary information refers. This argument is optional and defaults to None. If it is provided, atom identities will be included in the output. Raises ------ ValueError Raised when the number of atoms in the molecule does not match the length of the list of values in this object. Returns ------- str A verbose description of the "ivary" instructions. """ if molecule is not None and len(molecule.atoms) != len(self.values): raise ValueError( f"The number of atoms ({len(molecule.atoms)} is not the same " f"as the number of ivary values ({len(self.values)}." ) zipped = zip_longest(self.values, molecule.atoms if molecule is not None else []) f = io.StringIO() for i, (ivary, atom) in enumerate(zipped): atomic_number = atom.symbol if molecule is not None else None id_str = f" ({atomic_number})" if atomic_number is not None else "" if ivary < 0: # TODO: This could also report at what value if charges are provided ivary_str = ", frozen" elif ivary > 0: ivary_str = f", equivalenced to atom {ivary}" else: ivary_str = "" print(f"Atom{id_str} number {i+1}{ivary_str}", file=f) return f.getvalue() @classmethod def from_equivalence(cls: Type[IvaryT], equivalence: Equivalence) -> IvaryT: """Alternative initialization from equivalence information .. note: The resulting ivary instructions will correspond to fitting with equivalent atoms assigned identical charges. This may not be the type of fitting that you want to perform. Parameters ---------- equivalence : Equivalence Information about chemical equivalence of atoms in a molecule. """ return cls([0 if val is None else val + 1 for val in equivalence.values]) title: str cntrl: Cntrl subtitle: str charge: int molecule: Molecule[Atom] ivary: Ivary @property def wtmol(self) -> float: """Relative weight of the structure in a multistructure fitting. A value of 1.0 is always returned in the current implementation. """ return 1.0 @property def iuniq(self) -> int: """The number of atoms in the fitted structure""" return len(self.molecule.atoms) def __post_init__(self) -> None: if len(self.molecule.atoms) != len(self.ivary.values): raise ValueError( f"Number of atoms ({len(self.molecule.atoms)}) does not match number " f"of ivary values ({len(self.ivary.values)})." ) def _get_equivalence_from_ivary(ivary: Respin.Ivary) -> Equivalence: """Get atom equivalence information from an `Respin.Ivary` object This function is private as users probably mean to use the `get_equivalence` function instead. `Ivary` objects are specific to ``resp`` program input and thus may not provide information about atom equivalence. The "respin" file may have been generated to perform any custom fitting with ``resp``. Only use this function when you're certain that the "respin" file contains all the equivalence information that you need. """ return Equivalence([ None if ivary_value == 0 else ivary_value - 1 for ivary_value in ivary.values ]) def get_equivalence_from_two_stage_resp_ivary(ivary1: Respin.Ivary, ivary2: Respin.Ivary) -> Equivalence: """Get atom equivalence from input files for two 2-stage RESP Derive atom equivalence based on the data in two "respin" files (represented by the `Respin` objects) created for the purpose of two-stage RESP fitting with the ``resp`` program. The files can be generated with the ``respgen`` program with the following commands:: respgen -i methane.ac -o methane.respin1 -f resp1 respgen -i methane.ac -o methane.respin2 -f resp2 .. warning:: The correctness of this function relies on: 1. Antechamber and ``respgen`` correctly recognizing the symmetry relations between atoms. Fast-exchanging atoms may not be identified. 2. The author's understanding of how ``respgen`` generates the "respin" files for two-stage RESP fitting. Thus it is advised to always check that the result of this function agrees with the domain knowledge about the studied molecule. """ # The equivalence logic is explained somewhat inconsistently in the RESP # papers but I've additionally re-engineered the ``resp`` program's logic # to be sure that reading both the ``respin`` files will give the desired # behaviour. In fact, it's pretty simple. In the first stage atoms of the # methyl and methylene groups are free, while all the others are # equivalenced. In the second stage the former are equivalenced, while all # the others are frozen. return _get_equivalence_from_ivary(Respin.Ivary([ max(ivary1_value, ivary2_value) for ivary1_value, ivary2_value in zip_exact(ivary1.values, ivary2.values) ])) def _parse_cntrl(f: TextIO) -> Respin.Cntrl: line_re = re.compile(" (\w+) =\s+([0-9.]+)") kwargs: Dict[str, Union[int, float]] = {} for line in f: if line.rstrip('\n') == " &end": break if line.rstrip('\n') == "": continue line_match = line_re.match(line) if line_match is None: raise InputFormatError( f"Failed parsing cntrl section of respin file:\n{line}" ) key = line_match.group(1) value = line_match.group(2) kwargs[key] = float(value) if key == "qwt" else int(value) # nmol is not a parameter of Cntrl.__init__ and must be equal to 1. nmol = kwargs.pop("nmol", None) if nmol is not None and nmol != 1: raise InputFormatError("Parsing multiple structures is not supported") return Respin.Cntrl(**kwargs) # type: ignore # (not sure why not recognized) def parse_respin(f: TextIO) -> Respin: """Parse a file in the "respin" format (input format of ``resp``) Note that only files describing a single structure fit are currently supported. Parameters ---------- f : TextIO File object opened in read mode containing the "respin" file. Raises ------ InputFormatError Raised when the file does not follow the expected format. Returns ------- Respin Object representing the fitting instructions for the ``resp`` program. """ title = get_line(f) for line in f: if line == " &cntrl\n": break cntrl = _parse_cntrl(f) wtmol = get_line(f).strip() if not math.isclose(float(wtmol), 1.0, rel_tol=0, abs_tol=1e-6): raise InputFormatError( f"Encountered value of `wtmol` different from 1.0 ({wtmol}) but " f"parsing is supported only for single-structure respin files." ) subtitle = get_line(f) charge_and_iuniq = get_line(f) if len(charge_and_iuniq.split()) != 2: raise InputFormatError( f"Expected two ints for the line specifying charge and iuniq, found:\n{charge_and_iuniq}" ) charge = int(charge_and_iuniq.split()[0]) iuniq = int(charge_and_iuniq.split()[1]) atoms: List[Atom] = [] ivary = Respin.Ivary([]) for line in f: if line.rstrip('\n') == "": break if len(line.split()) != 2: raise InputFormatError( f"Expected two ints for the line specifying atom and ivary, found:\n{line}" ) atoms.append(Atom(int(line.split()[0]))) ivary_value = int(line.split()[1]) # `respgen` uses a value of -99 but internally we use -1 as per resp spec. ivary.values.append(ivary_value if ivary_value != -99 else -1) if len(atoms) != iuniq: raise InputFormatError( f"The value of `iuniq` ({iuniq}) is different from the number of" f"atoms in the described molecule ({len(atoms)})." ) return Respin( title, cntrl, subtitle, charge, Molecule(atoms), ivary ) def _write_cntrl(f: TextIO, cntrl: Respin.Cntrl, skip_defaults: bool) -> None: default_cntrl: Dict[str, Union[int, float]] = asdict(Respin.Cntrl()) default_cntrl["nmol"] = 1 dict_: Dict[str, Union[int, float]] = asdict(cntrl) dict_["nmol"] = cntrl.nmol print(" &cntrl\n", file=f) for key, value in dict_.items(): if key == "qwt": print(" {} = {:.5f},".format(key, value), file=f) else: if not skip_defaults or value != default_cntrl[key]: print(" {} = {},".format(key, value), file=f) print("\n &end", file=f) def write_respin(f: TextIO, respin: Respin, skip_cntrl_defaults: bool=True) -> None: """Write a "respin" file described by the given input data Parameters ---------- f : TextIO The file object to which the instructions are to be saved. The file must be opened for writing. respin : Respin The dataclass representing all the instructions needed by the ``resp`` program. skip_cntrl_defaults : bool, optional When this option is set to True (default), fitting options in the "cntrl" section with default values will not be written to the file. """ print(respin.title, file=f) print(file=f) _write_cntrl(f, respin.cntrl, skip_cntrl_defaults) print(FW("F7.1").write([respin.wtmol]), file=f) print(respin.subtitle, file=f) print(FW("2I5").write([respin.charge, respin.iuniq]), file=f) for atom, ivary in zip(respin.molecule.atoms, respin.ivary.values): print(FW("2I5").write([atom.atomic_number, ivary]), file=f) # According to the spec, a blank line is only for multi-structures but # `resp` fails without it. print(file=f)

gpl-3.0

senuido/stash-scanner

ui/ConfigEditor.py

1

40208

import copy import functools import os import pprint import threading from enum import Enum from tkinter import Toplevel, StringVar, BooleanVar, messagebox, IntVar from tkinter.constants import * import tkinter.font as tkfont from tkinter.ttk import Notebook, Frame, Label, Button, Style, Combobox, Entry, Checkbutton, Scale, LabelFrame from lib.CurrencyManager import cm from lib.FilterManager import fm from lib.ItemFilter import Filter from lib.Utility import logexception, AppException, config, AppConfiguration, ConfidenceLevel from ui.MyTreeview import EditableTreeview from ui.ScrollingFrame import AutoScrollbar from ui.TooltipEntry import TooltipEntry from ui.cmb_autocomplete import Combobox_Autocomplete from ui.entry_placeholder import PlaceholderEntry from ui.ttk_spinbox import Spinbox READONLY = 'readonly' ColEntry = EditableTreeview.ColEntry TAB_FPRICES = 'fprices' TAB_CURRENCY = 'currency' INVALID_PRICE = 'Price format is: <amount> <currency>\nExamples: 100 chaos, 20 ex, 5 divine' INVALID_PRICE_OVERRIDE = 'Price format is: <amount> <currency>\nExamples: 100 chaos, 20 ex, 5 divine\n' \ 'Prices can also be relative to their base.\n' \ 'Examples: / 3, * 0.5, +2.5 ex, -20 chaos' # class ConfigEditor(Toplevel): class ConfigEditor(Notebook): def __init__(self, master, app_main, **kwargs): super().__init__(master, **kwargs) # style = Style() # if we do this we also need to hide the #0 column because it adds indention for possible children # style.configure("Treeview.Heading", padding=(10, 0)) # self.protocol('WM_DELETE_WINDOW', self.onClose) # self.nb_tabs = Notebook(self) # self.create_iprice_tab() self.prices_editor = PricesEditor(self) self.currency_editor = CurrencyEditor(self) self.settings_editor = SettingsEditor(self, app_main) # self.add(self.frm_iprices_tab, text='Item Prices', sticky='nsew') self.add(self.settings_editor, text='General', sticky='nsew') self.add(self.prices_editor, text='Prices', sticky='nsew') self.add(self.currency_editor, text='Currency', sticky='nsew') self.bind('<<NotebookTabChanged>>', self.onTabChange) self.settings_editor_id, self.prices_tab_id, self.currency_tab_id = self.tabs() def loadCurrency(self, force=False): self.currency_editor.loadCurrency(force_reload=force) def loadPrices(self, force=False): self.prices_editor.loadPrices(force_reload=force) def loadSettings(self): self.settings_editor.loadSettings() def onTabChange(self, event=None): current_tab_id = self.select() if current_tab_id == self.currency_tab_id: self.loadCurrency(force=True) elif current_tab_id == self.prices_tab_id: self.loadPrices(force=True) elif current_tab_id == self.settings_editor_id: self.loadSettings() # def onClose(self): # self.destroy() leagueOptions = [ 'Harbinger', 'Hardcore Harbinger', 'Standard', 'Hardcore', # 'Beta Standard', # 'Beta Hardcore' ] scanModeOptions = ['Latest', 'Continue'] class SettingsEditor(Frame): def __init__(self, master, app_main, **kwargs): super().__init__(master, **kwargs) self.app = app_main self.create_settings_ui() def create_settings_ui(self): self.rowconfigure(0, weight=1) self.columnconfigure(0, weight=1) self.frm_settings = Frame(self) # self.frm_settings.rowconfigure(2, weight=1) # self.frm_settings.columnconfigure(0, weight=1) is_valid_req_delay = self.register(functools.partial(_is_number, min=0)) is_valid_duration = self.register(functools.partial(_is_number, min=0, max=20)) is_valid_history_retention = self.register(functools.partial(_is_number, min=0, max=100)) is_valid_max_conns = self.register(functools.partial(_is_number, min=1, max=20, integer=True)) is_valid_num_workers = self.register(functools.partial(_is_number, min=0, max=os.cpu_count() or 8, integer=True)) self.frm_settings.grid(padx=10, pady=10, sticky='nsew') frm_basic = LabelFrame(self.frm_settings, text='Basic') frm_basic.grid(padx=5, pady=5, sticky='nsew', row=0, column=0, ipadx=5) lbl = Label(frm_basic, text='League:') lbl.grid(row=0, column=0, padx=5, pady=3, sticky='w') self.cmb_league = Combobox(frm_basic, state=READONLY, values=leagueOptions) self.cmb_league.grid(row=0, column=1, pady=3, sticky='nsew') # lbl = Label(frm_basic, text='Minimum request delay(s):') # lbl.grid(row=1, column=0, padx=5, pady=3, sticky='w') # self.entry_req_delay = Entry(frm_basic, validate='all', validatecommand=(is_valid_req_delay, '%P')) # self.entry_req_delay.grid(row=1, column=1, pady=3, sticky='nsew') # lbl = Label(frm_basic, text='Scan mode:') # lbl.grid(row=2, column=0, padx=5, pady=3, sticky='w') # self.cmb_scan_mode = Combobox(frm_basic, state=READONLY, values=scanModeOptions) # self.cmb_scan_mode.grid(row=2, column=1, pady=3, sticky='nsew') lbl = Label(frm_basic, text='Notification duration(s):') lbl.grid(row=3, column=0, padx=5, pady=3, sticky='w') self.entry_notification_duration = Entry(frm_basic, validate='all', validatecommand=(is_valid_duration, '%P')) self.entry_notification_duration.grid(row=3, column=1, pady=3, sticky='nsew') frm = LabelFrame(self.frm_settings, text='Advanced') frm.grid(pady=5, sticky='nsew', row=0, column=1, ipadx=5) lbl = Label(frm, text='Scan mode:') lbl.grid(row=0, column=0, padx=5, pady=3, sticky='w') self.cmb_scan_mode = Combobox(frm, state=READONLY, values=scanModeOptions) self.cmb_scan_mode.grid(row=0, column=1, pady=3, sticky='nsew') lbl = Label(frm, text='Min. request delay:') lbl.grid(row=1, column=0, padx=5, pady=3, sticky='w') self.entry_req_delay = Entry(frm, validate='all', validatecommand=(is_valid_req_delay, '%P')) self.entry_req_delay.grid(row=1, column=1, pady=3, sticky='nsew') lbl = Label(frm, text='(seconds)') lbl.grid(row=1, column=2, padx=(5, 0), pady=3, sticky='w') lbl = Label(frm, text='Max connections:') lbl.grid(row=2, column=0, padx=5, pady=3, sticky='w') self.entry_max_conns = Entry(frm, validate='all', validatecommand=(is_valid_max_conns, '%P')) self.entry_max_conns.grid(row=2, column=1, pady=3, sticky='nsew') lbl = Label(frm, text='Parsers #:') lbl.grid(row=3, column=0, padx=5, pady=3, sticky='w') self.entry_num_workers = Entry(frm, validate='all', validatecommand=(is_valid_num_workers, '%P')) self.entry_num_workers.grid(row=3, column=1, pady=3, sticky='nsew') lbl = Label(frm, text='(0 = Auto)') lbl.grid(row=3, column=2, padx=(5, 0), pady=3, sticky='w') lbl = Label(frm, text='History retention:') lbl.grid(row=4, column=0, padx=5, pady=3, sticky='w') self.entry_history_retention = Entry(frm, validate='all', validatecommand=(is_valid_history_retention, '%P')) self.entry_history_retention.grid(row=4, column=1, pady=3, sticky='nsew') lbl = Label(frm, text='(days)') lbl.grid(row=4, column=2, padx=(5, 0), pady=3, sticky='w') frm = Frame(frm_basic) frm.grid(row=4, column=0) self.var_notify = BooleanVar() self.var_notify.trace_variable('w', lambda a, b, c: self._on_notify_option_change()) self.cb_notifications = Checkbutton(frm, text='Growl notifications', variable=self.var_notify) self.cb_notifications.grid(row=0, column=0, padx=5, pady=3, sticky='w') self.var_notify_copy = BooleanVar() self.cb_notify_copy = Checkbutton(frm, text='Copy message', variable=self.var_notify_copy) self.cb_notify_copy.grid(row=1, column=0, padx=5, pady=3, sticky='w') self.var_notify_play_sound = BooleanVar() self.cb_notify_play_sound = Checkbutton(frm, text='Play sound', variable=self.var_notify_play_sound) self.cb_notify_play_sound.grid(row=2, column=0, padx=5, pady=3, sticky='w') frm_btns = Frame(self.frm_settings) frm_btns.grid(row=2, columnspan=3, pady=(20, 5), sticky='w') self.btn_apply = Button(frm_btns, text='Apply', command=self.applyChanges) self.btn_apply.grid(row=0, column=0, padx=5) self.btn_reload = Button(frm_btns, text='Reload', command=self.loadSettings) self.btn_reload.grid(row=0, column=1) def _on_notify_option_change(self): state = NORMAL if self.var_notify.get() else DISABLED self.cb_notify_copy.config(state=state) self.cb_notify_play_sound.config(state=state) def applyChanges(self): cfg = AppConfiguration() cfg.league = self.cmb_league.get() or leagueOptions[0] cfg.notify = self.var_notify.get() cfg.notify_copy_msg = self.var_notify_copy.get() cfg.notify_play_sound = self.var_notify_play_sound.get() cfg.notification_duration = float(self.entry_notification_duration.get() or 4) cfg.request_delay = float(self.entry_req_delay.get() or 0.7) cfg.scan_mode = self.cmb_scan_mode.get() or scanModeOptions[0] cfg.history_retention = int(self.entry_history_retention.get() or 1) cfg.max_conns = int(self.entry_max_conns.get() or 8) cfg.num_workers = int(self.entry_num_workers.get() or 0) cfg.smooth_delay = config.smooth_delay self.app.update_configuration(cfg) def loadSettings(self): self.cmb_league.set(config.league) self.cmb_scan_mode.set(config.scan_mode) self.entry_notification_duration.delete(0, END) self.entry_notification_duration.insert(0, config.notification_duration) self.var_notify.set(config.notify) self.var_notify_copy.set(config.notify_copy_msg) self.var_notify_play_sound.set(config.notify_play_sound) self.entry_req_delay.delete(0, END) self.entry_req_delay.insert(0, config.request_delay) self.entry_history_retention.delete(0, END) self.entry_history_retention.insert(0, config.history_retention) self.entry_max_conns.delete(0, END) self.entry_max_conns.insert(0, config.max_conns) self.entry_num_workers.delete(0, END) self.entry_num_workers.insert(0, config.num_workers) class CurrencyColumn(Enum): Currency = 'Currency' Rate = 'Rate' Override = 'Override' EffectiveRate = 'Effective Rate' Filler = '' currencyColumns = [col.name for col in CurrencyColumn] class PricesColumn(Enum): Name = 'Name' ID = 'ID' ItemPrice = 'Item value' Override = 'Override' FilterPrice = 'Effective item value'#'Filter Price (c)' FilterOverride = 'Filter Override' EffectiveFilterPrice = 'Effective Filter Price (c)' FilterStateOverride = 'Filter State Override' Filler = '' pricesColumns = [col.name for col in PricesColumn] class FilterStateOption(Enum): Enable = True Disable = False filterStateOptions = [''] + [option.name for option in FilterStateOption] class PricesEditor(Frame): def __init__(self, master, **kwargs): super().__init__(master, **kwargs) self.create_prices_ui() self.initial_values = {} self.table_modified = False def create_prices_ui(self): self.rowconfigure(0, weight=1) self.columnconfigure(0, weight=1) self.frm_prices = Frame(self) self.frm_prices.rowconfigure(2, weight=1) self.frm_prices.columnconfigure(0, weight=1) self.frm_prices.grid(padx=10, pady=10, sticky='nsew') # Button Frame frm_btns = Frame(self.frm_prices, relief=SOLID, borderwidth=2) frm_btns.grid(row=0, column=0, pady=(0, 5), sticky='nsew') frm_btns.columnconfigure(10, weight=1) # self.entry_currency = \ # Combobox_Autocomplete(frm, list_of_items=['one of many currencies'], startswith_match=False) self.search_var = StringVar() self.entry_search = PlaceholderEntry(frm_btns, 'Search..', style='Default.TEntry', textvariable=self.search_var) self.search_var.trace_variable('w', lambda a, b, c: self.tree.search(self.entry_search.get_value())) self.entry_search.bind('<Return>', lambda event: self.tree.search(self.entry_search.get_value(), find_next=True)) self.btn_apply = Button(frm_btns, text='Apply', command=self.applyChanges) self.btn_reload = Button(frm_btns, text='Reload', command=lambda: self.loadPrices(force_reload=True)) self.entry_search.grid(row=2, column=0, pady=5, padx=5) self.btn_apply.grid(row=2, column=2, pady=5) # frm.columnconfigure(3, weight=1) self.btn_reload.grid(row=2, column=3, sticky='e', pady=5) self.var_advanced = BooleanVar(False) self.var_advanced.trace_variable('w', lambda a, b, c: self._on_view_option_change()) self.cb_advanced = Checkbutton(frm_btns, text='Advanced', variable=self.var_advanced) self.cb_advanced.grid(row=2, column=10, sticky='e', padx=10) frm_border = Frame(self.frm_prices, relief=SOLID, borderwidth=2) frm_border.grid(row=2, column=0, sticky='nsew') frm_border.rowconfigure(2, weight=1) frm_border.columnconfigure(0, weight=1) # Tree Frame self.frm_tree = Frame(frm_border) self.frm_tree.grid(row=2, column=0, sticky='nsew', padx=5, pady=(0, 0)) self.frm_tree.rowconfigure(0, weight=1) self.frm_tree.columnconfigure(0, weight=1) self.tree = EditableTreeview(self.frm_tree, on_cell_update=self.onCellUpdate) scrly = AutoScrollbar(self.frm_tree, command=self.tree.yview) scrlx = AutoScrollbar(self.frm_tree, command=self.tree.xview, orient=HORIZONTAL) self.tree.config(yscrollcommand=scrly.set, xscrollcommand=scrlx.set) self.tree.grid(row=0, column=0, sticky='nsew') scrly.grid(row=0, column=1, sticky='nsew') scrlx.grid(row=1, column=0, sticky='nsew') # Button Frame frm = Frame(frm_border) #, relief=SOLID, borderwidth=1) # frm = Frame(self.frm_prices) frm.grid(row=0, column=0, sticky='nsew') # self.entry_currency = \ # Combobox_Autocomplete(frm, list_of_items=['one of many currencies'], startswith_match=False) lbl = Label(frm, text='Item value threshold:') lbl.grid(row=0, column=0, padx=5, pady=5, sticky='w') self.var_threshold = StringVar() self.entry_threshold = TooltipEntry(frm, textvariable=self.var_threshold) self.entry_threshold.bind('<FocusOut>', lambda event: self._validate_threshold_entry()) self.entry_threshold.grid(row=0, column=1, padx=5, pady=5) self.var_threshold.trace('w', lambda a, b, c: self.on_entry_change(self.entry_threshold)) lbl = Label(frm, text='Budget:') lbl.grid(row=0, column=2, padx=5, pady=5) self.var_budget = StringVar() self.entry_budget = TooltipEntry(frm, textvariable=self.var_budget) self.entry_budget.bind('<FocusOut>', lambda event: self._validate_budget_entry()) self.entry_budget.grid(row=0, column=3, padx=5, pady=5) self.var_budget.trace('w', lambda a, b, c: self.on_entry_change(self.entry_budget)) lbl = Label(frm, text='Minimum price:') lbl.grid(row=0, column=4, padx=5, pady=5) self.var_min_price = StringVar() self.entry_min_price = TooltipEntry(frm, textvariable=self.var_min_price) self.entry_min_price.bind('<FocusOut>', lambda event: self._validate_min_price_entry()) self.entry_min_price.grid(row=0, column=5, padx=5, pady=5) self.var_min_price.trace('w', lambda a, b, c: self.on_entry_change(self.entry_min_price)) lbl = Label(frm, text='Default filter override:') lbl.grid(row=0, column=6, padx=5, pady=5) self.lbl_fprice_override = lbl self.var_fprice_override = StringVar() self.entry_fprice_override = TooltipEntry(frm, textvariable=self.var_fprice_override) self.entry_fprice_override.bind('<FocusOut>', lambda event: self._validate_fprice_override_entry()) self.entry_fprice_override.grid(row=0, column=7, padx=5, pady=5) self.var_fprice_override.trace('w', lambda a, b, c: self.on_entry_change(self.entry_fprice_override)) # Advanced lbl = Label(frm, text='Default item value override:') lbl.grid(row=1, column=0, padx=5, pady=(2, 5), sticky='w') self.lbl_price_override = lbl self.var_price_override = StringVar() self.entry_price_override = TooltipEntry(frm, textvariable=self.var_price_override) self.entry_price_override.bind('<FocusOut>', lambda event: self._validate_price_override_entry()) self.entry_price_override.grid(row=1, column=1, padx=5, pady=(2, 5)) self.var_price_override.trace('w', lambda a, b, c: self.on_entry_change(self.entry_price_override)) # Confidence Level lbl = Label(frm, text="Confidence level:") lbl.grid(row=1, column=2, padx=5, pady=(2, 5), sticky='w') self.lbl_confidence_lvl = lbl self.var_confidence_lvl = IntVar() self.entry_confidence_lvl = ConfidenceScale(frm, variable=self.var_confidence_lvl) self.entry_confidence_lvl.grid(row=1, column=3, padx=5, pady=(2, 5)) self.var_confidence_lvl.trace('w', lambda a, b, c: self.on_entry_change(self.entry_confidence_lvl)) self.var_5l_filters = BooleanVar(False) self.cb_5l_filters = VarCheckbutton(frm, text='Enable 5L filters', variable=self.var_5l_filters) self.cb_5l_filters.var = self.var_5l_filters self.cb_5l_filters.grid(row=1, column=4, padx=5, pady=(2, 5), columnspan=1) self.var_5l_filters.trace_variable('w', lambda a, b, c: self.on_entry_change(self.cb_5l_filters)) # Tree Config tree = self.tree def init_tree_column(col): col_name = pricesColumns[0] if col == '#0' else col tree.heading(col, text=PricesColumn[col_name].value, anchor=W, command=lambda col=col: tree.sort_col(col)) tree.column(col, width=140, stretch=False) # self.tree['columns'] = ('ID', 'Item Price', 'Override', 'Filter Price', 'Filter Override', 'Effective Filter Price', 'Filter State Override', '') self.tree['columns'] = pricesColumns[1:] self.tree.register_column(PricesColumn.Override.name, ColEntry(TooltipEntry(self.tree), func_validate=_validate_price_override)) self.tree.register_column(PricesColumn.FilterOverride.name, ColEntry(TooltipEntry(self.tree), func_validate=_validate_price_override)) self.tree.register_column(PricesColumn.FilterStateOverride.name, ColEntry(Combobox(self.tree, values=filterStateOptions, state=READONLY), accept_events=('<<ComboboxSelected>>', '<Return>'))) for col in (('#0', ) + tree['columns']): init_tree_column(col) tree.heading('#0', anchor=CENTER) tree.column('#0', width=200, stretch=False) tree.column(PricesColumn.Filler.name, stretch=True) tree.heading(PricesColumn.ItemPrice.name, command=lambda col=PricesColumn.ItemPrice.name: tree.sort_col(col, key=self._price_key)) tree.heading(PricesColumn.Override.name, command=lambda col=PricesColumn.Override.name: tree.sort_col(col, key=self._price_key)) tree.heading(PricesColumn.FilterOverride.name, command=lambda col=PricesColumn.FilterOverride.name: tree.sort_col(col, key=self._price_key)) tree.heading(PricesColumn.FilterPrice.name, command=lambda col=PricesColumn.FilterPrice.name: tree.sort_col(col, key=self._rate_key, default=0)) tree.heading(PricesColumn.EffectiveFilterPrice.name, command=lambda col=PricesColumn.EffectiveFilterPrice.name: tree.sort_col(col, key=self._rate_key, default=0)) self.bvar_modified = BooleanVar() self.bvar_modified.trace('w', lambda a, b, c: self._updateApplyState()) self.bvar_modified.set(False) self.var_advanced.set(False) def _rate_key(self, key): if key == 'N/A': return 0 return float(key) def _price_key(self, key): if key == '': return None # this means it will be ignored while sorting try: return cm.compilePrice(key, base_price=0) except Exception: return 0 def on_entry_change(self, entry): val = entry.get() if self.initial_values[entry] != val: self.bvar_modified.set(True) # def on_price_entry_focusout(self, widget): # valid = _validate_price(widget, accept_empty=False) # if valid and not self.bvar_modified.get() and self.initial_values[widget] != widget.get(): # self.bvar_modified.set(True) # return valid # # def on_override_entry_focusout(self, widget): # valid = _validate_price_override(widget, accept_empty=False) # if valid and not self.bvar_modified.get() and self.initial_values[widget] != widget.get(): # self.bvar_modified.set(True) # return valid def _validate_threshold_entry(self): return _validate_price(self.entry_threshold, accept_empty=False) def _validate_budget_entry(self): return _validate_price(self.entry_budget, accept_empty=True) def _validate_min_price_entry(self): return _validate_price(self.entry_min_price, accept_empty=True) def _validate_price_override_entry(self): return _validate_price_override(self.entry_price_override, accept_empty=False) def _validate_fprice_override_entry(self): return _validate_price_override(self.entry_fprice_override, accept_empty=False) def _update_modified(self): modified = any(entry.get() != self.initial_values[entry] for entry in self.initial_values) or self.table_modified self.bvar_modified.set(modified) def _updateApplyState(self): if self.bvar_modified.get(): self.btn_apply.config(state=NORMAL) else: self.btn_apply.config(state=DISABLED) def _validateForm(self): if not self._validate_threshold_entry(): return False if not self._validate_budget_entry(): return False if not self._validate_min_price_entry(): return False if not self._validate_price_override_entry(): return False if not self._validate_fprice_override_entry(): return False return True def applyChanges(self, event=None): if not self.bvar_modified.get() or not fm.initialized: return if not self._validateForm(): return price_threshold = self.entry_threshold.get() default_price_override = self.entry_price_override.get() default_fprice_override = self.entry_fprice_override.get() budget = self.entry_budget.get() min_price = self.entry_min_price.get() confidence_lvl = self.entry_confidence_lvl.get() or fm.DEFAULT_CONFIDENCE_LEVEL enable_5l_filters = self.var_5l_filters.get() price_overrides = {} filter_price_overrides = {} filter_state_overrides = {} for iid in self.tree.get_children(): id = self.tree.set(iid, PricesColumn.ID.name) iprice = self.tree.set(iid, PricesColumn.Override.name) if iprice: price_overrides[id] = iprice fprice = self.tree.set(iid, PricesColumn.FilterOverride.name) if fprice: filter_price_overrides[id] = fprice fstate = self.tree.set(iid, PricesColumn.FilterStateOverride.name) try: filter_state_overrides[id] = FilterStateOption[fstate].value except KeyError: pass ids = set([self.tree.set(iid, PricesColumn.ID.name) for iid in self.tree.get_children()]) # preserve unhandled ids configuration for key in (set(fm.price_overrides) - ids): price_overrides[key] = fm.price_overrides[key] for key in (set(fm.filter_price_overrides) - ids): filter_price_overrides[key] = fm.filter_price_overrides[key] for key in (set(fm.filter_state_overrides) - ids): filter_state_overrides[key] = fm.filter_state_overrides[key] try: fm.updateConfig(default_price_override, default_fprice_override, price_threshold, budget, min_price, price_overrides, filter_price_overrides, filter_state_overrides, int(confidence_lvl), enable_5l_filters) except AppException as e: messagebox.showerror('Validation error', 'Failed to update configuration:\n{}'.format(e), parent=self.winfo_toplevel()) except Exception as e: logexception() messagebox.showerror('Update error', 'Failed to apply changes, unexpected error:\n{}'.format(e), parent=self.winfo_toplevel()) else: # SHOULD always work since config is valid, main console will report any failures # background thread because schema validating takes a bit of time threading.Thread(target=fm.compileFilters).start() self._initFormState() def loadPrices(self, force_reload=False): if not cm.initialized or not fm.initialized: return if not force_reload: self._update_modified() # in case of reverted changes if self.bvar_modified.get(): # dont interrupt user changes return tree = self.tree tree.clear() table = {} for fltr in fm.autoFilters: # effective_rate = cm.crates.get(curr, '') # if effective_rate != '': # effective_rate = round(effective_rate, 3) fid = fltr.id fstate_override = fm.filter_state_overrides.get(fid, '') try: fstate_override = FilterStateOption(fstate_override).name except ValueError: fstate_override = '' table[fid] = (fltr.title, fid, fm.item_prices[fid], fm.price_overrides.get(fid, ''), _to_display_rate(fm.compiled_item_prices.get(fid, 'N/A')), fm.filter_price_overrides.get(fid, ''), _to_display_rate(fm.compiled_filter_prices.get(fid, 'N/A')), fstate_override) for fid in table: tree.insert('', END, '', text=table[fid][0], values=table[fid][1:]) # tree.sort_by('#0', descending=True) tree.sort_col('#0', reverse=False) self._initFormState() # def onItemPriceUpdate(self, iid, col, old, new): # print('IPrice update: iid {}, col {}'.format(iid, col)) def onCellUpdate(self, iid, col, old, new): if old != new: self.table_modified = True self.bvar_modified.set(True) # self._update_modified() def _initFormState(self): self.table_modified = False self.initial_values[self.entry_threshold] = fm.price_threshold self.initial_values[self.entry_budget] = fm.budget self.initial_values[self.entry_min_price] = fm.default_min_price self.initial_values[self.entry_price_override] = fm.default_price_override self.initial_values[self.entry_fprice_override] = fm.default_fprice_override self.initial_values[self.entry_confidence_lvl] = fm.confidence_level self.initial_values[self.cb_5l_filters] = fm.enable_5l_filters self.var_threshold.set(fm.price_threshold) self.var_budget.set(fm.budget) self.var_min_price.set(fm.default_min_price) self.var_price_override.set(fm.default_price_override) self.var_fprice_override.set(fm.default_fprice_override) self.var_confidence_lvl.set(fm.confidence_level) self.var_5l_filters.set(fm.enable_5l_filters) self.bvar_modified.set(False) def _on_view_option_change(self): advanced_widgets = [self.entry_price_override, self.lbl_price_override, self.lbl_confidence_lvl, self.entry_confidence_lvl, self.cb_5l_filters] if not self.var_advanced.get(): for w in advanced_widgets: w.grid_remove() self.tree.config(displaycolumn=[PricesColumn.FilterPrice.name, PricesColumn.FilterOverride.name, PricesColumn.EffectiveFilterPrice.name, PricesColumn.Filler.name]) else: for w in advanced_widgets: w.grid() self.tree.config(displaycolumn='#all') self.tree.on_entry_close() class CurrencyEditor(Frame): def __init__(self, master, **kwargs): super().__init__(master, **kwargs) self.bvar_modified = BooleanVar() self.create_currency_ui() def create_currency_ui(self): self.rowconfigure(0, weight=1) self.columnconfigure(0, weight=1) self.frm_currency = Frame(self) self.frm_currency.rowconfigure(2, weight=1) self.frm_currency.columnconfigure(0, weight=1) self.frm_currency.grid(padx=10, pady=10, sticky='nsew') # Tree Frame self.frm_tree = Frame(self.frm_currency) self.frm_tree.grid(row=2, sticky='nsew') self.frm_tree.rowconfigure(0, weight=1) self.frm_tree.columnconfigure(0, weight=1) self.tree = EditableTreeview(self.frm_tree, on_cell_update=self.onCellUpdate) scrly = AutoScrollbar(self.frm_tree, command=self.tree.yview) scrlx = AutoScrollbar(self.frm_tree, command=self.tree.xview, orient=HORIZONTAL) self.tree.config(yscrollcommand=scrly.set, xscrollcommand=scrlx.set) self.tree.grid(row=0, column=0, sticky='nsew') scrly.grid(row=0, column=1, sticky='nsew') scrlx.grid(row=1, column=0, sticky='nsew') self.tree.insert('', 0, text='Exalted Orb', values=('90', '85')) frm = Frame(self.frm_currency, relief=SOLID, borderwidth=2) frm.columnconfigure(10, weight=1) frm.grid(row=1, column=0, pady=(0, 5), sticky='nsew') # self.entry_currency = \ # Combobox_Autocomplete(frm, list_of_items=['one of many currencies'], startswith_match=False) self.search_var = StringVar() self.entry_search = PlaceholderEntry(frm, 'Search..', style='Default.TEntry', textvariable=self.search_var) self.search_var.trace_variable('w', lambda a, b, c: self.tree.search(self.entry_search.get_value())) self.entry_search.bind('<Return>', lambda event: self.tree.search(self.entry_search.get_value(), find_next=True)) # self.btn_currency_search = Button(frm, text='Search', command=lambda event: self.tree_currency.search(self.entry_currency_search.get_value(), find_next=True)) self.btn_apply = Button(frm, text='Apply', command=self.applyChanges) self.btn_reload = Button(frm, text='Reload', command=lambda: self.loadCurrency(force_reload=True)) self.entry_search.grid(row=2, column=0, pady=5, padx=5) # self.btn_currency_search.grid(row=2, column=1, pady=5) self.btn_apply.grid(row=2, column=2, pady=5) # frm.columnconfigure(3, weight=1) self.btn_reload.grid(row=2, column=3, sticky='e', pady=5) # Confidence Level lbl = Label(frm, text="Confidence level:") lbl.grid(row=2, column=10, padx=5, sticky='nse', pady=(3, 5)) self.lbl_confidence_lvl = lbl self.var_confidence_lvl = IntVar() self.entry_confidence_lvl = ConfidenceScale(frm, variable=self.var_confidence_lvl) self.entry_confidence_lvl.grid(row=2, column=11, padx=5, pady=5) self.var_confidence_lvl.trace('w', lambda a, b, c: self.on_entry_change(self.entry_confidence_lvl)) # Tree Config tree = self.tree tree['columns'] = currencyColumns[1:] tree.register_column('Override', ColEntry(TooltipEntry(tree), func_validate=_validate_price_override)) def init_tree_column(col): col_name = currencyColumns[0] if col == '#0' else col tree.heading(col, text=CurrencyColumn[col_name].value, anchor=W, command=lambda col=col: tree.sort_col(col)) tree.column(col, width=140, stretch=False) for col in ('#0', ) + tree['columns']: init_tree_column(col) tree.heading('#0', anchor=CENTER) tree.column('#0', width=250, stretch=False) tree.column(CurrencyColumn.Filler.name, stretch=True) tree.heading(CurrencyColumn.Rate.name, command=lambda col=CurrencyColumn.Rate.name: tree.sort_col(col, key=float, default=0)) tree.heading(CurrencyColumn.EffectiveRate.name, command=lambda col=CurrencyColumn.EffectiveRate.name: tree.sort_col(col, key=float, default=0)) tree.heading(CurrencyColumn.Override.name, command=lambda col=CurrencyColumn.Override.name: tree.sort_col(col, key=self._price_key)) self.bvar_modified.trace('w', lambda a, b, c: self._updateApplyState()) def _price_key(self, key): if key == '': return None # this means it will be ignored while sorting try: return cm.compilePrice(key, base_price=0) except Exception: return 0 def _updateApplyState(self): if self.bvar_modified.get(): self.btn_apply.config(state=NORMAL) else: self.btn_apply.config(state=DISABLED) def loadCurrency(self, force_reload=False): if not cm.initialized: return if not force_reload and self.bvar_modified.get(): return self.var_confidence_lvl.set(cm.confidence_level) tree = self.tree tree.clear() table = {} for curr in cm.shorts: effective_rate = cm.crates.get(curr, '0') table[curr] = (_to_display_rate(cm.rates.get(curr, '')), cm.overrides.get(curr, ''), _to_display_rate(effective_rate)) for curr in table: tree.insert('', END, '', text=curr, values=table[curr]) tree.sort_col(CurrencyColumn.EffectiveRate.name, key=float, default=0) self.bvar_modified.set(False) def applyChanges(self, event=None): if not self.bvar_modified.get() or not cm.initialized: return overrides = {} for iid in self.tree.get_children(): #TODO: hide #0 col and move names to a value column currency_name_col = '#0' # CurrencyColumn.Currency.name # id = self.tree.set(iid, currency_name_col) id = self.tree.item(iid, 'text') override = self.tree.set(iid, CurrencyColumn.Override.name) if override: overrides[id] = override # ids = set([self.tree.set(iid, currency_name_col) for iid in self.tree.get_children()]) ids = set([self.tree.item(iid, 'text') for iid in self.tree.get_children()]) # preserve unhandled ids configuration for key in (set(cm.overrides) - ids): overrides[key] = cm.overrides[key] cm.confidence_level = self.entry_confidence_lvl.get() try: cm.compile(overrides=overrides) if fm.initialized: threading.Thread(target=fm.compileFilters).start() self.bvar_modified.set(False) except AppException as e: messagebox.showerror('Update error', e, parent=self.winfo_toplevel()) except Exception as e: logexception() messagebox.showerror('Update error', 'Failed to apply changes, unexpected error:\n{}'.format(e), parent=self.winfo_toplevel()) def onCellUpdate(self, iid, col, old, new): if not self.bvar_modified.get() and old != new: self.bvar_modified.set(True) def on_entry_change(self, entry): self.bvar_modified.set(True) class VarCheckbutton(Checkbutton): def __init__(self, master, **kw): super().__init__(master, **kw) self.var = kw.get('variable', None) def configure(self, cnf=None, **kw): super().configure(cnf, **kw) if 'variable' in kw: self.var = kw['variable'] def get(self): if self.var: return self.var.get() return None class ConfidenceScale(Frame): def __init__(self, master, **kw): super().__init__(master) # self.grid_propagate(0) # self.columnconfigure(0, weight=1) # self.rowconfigure(0, weight=1) self.var = kw.get('variable', IntVar()) kw['variable'] = self.var kw['from_'] = ConfidenceLevel.Low.value kw['to'] = ConfidenceLevel.VeryHigh.value # kw['command'] = self.scale_change kw['orient'] = HORIZONTAL self.lbl_scale = Label(self) self.scale = Scale(self, **kw) self.scale_font = tkfont.nametofont(Style().lookup('TLabel', 'font')).copy() self.scale_font.config(weight=tkfont.BOLD, size=9) self.lbl_scale.config(font=self.scale_font, width=3, anchor=CENTER) self.var.trace_variable('w', lambda a, b, c: self.scale_change()) self.scale.grid(row=0, column=0, sticky='ns') self.lbl_scale.grid(row=0, column=1, sticky='ns', padx=(3, 0)) def scale_change(self): rval = self.get() if rval >= ConfidenceLevel.High: fg = '#4CAF50' elif rval >= ConfidenceLevel.Medium: fg = '#FF9800' else: fg = '#FF5722' self.lbl_scale.config(foreground=fg, text=str(rval)) def get(self): return round(float(self.var.get())) def _validate_price(widget, accept_empty=True): val = widget.get() valid, reason = _is_price_valid(val, accept_empty) if not valid: widget.showTooltip(reason) widget.focus() else: widget.hideTooltip() return valid def _is_price_valid(val, accept_empty=True): if accept_empty and val.strip() == '': return True, '' if not cm.initialized: return True, '' if not cm.isPriceValid(val): return False, INVALID_PRICE return True, '' def _validate_price_override(widget, accept_empty=True): val = widget.get() valid, reason = _is_price_override_valid(val, accept_empty) if not valid: widget.showTooltip(reason) widget.focus() else: widget.hideTooltip() return valid def _is_price_override_valid(val, accept_empty=True): if accept_empty and val.strip() == '': return True, '' if not cm.isOverridePriceValid(val): return False, INVALID_PRICE_OVERRIDE return True, '' def _to_display_rate(val): if val == 'N/A' or val == '': return val if int(val) == float(val): return int(val) return round(val, 2) def _is_number(text, min=None, max=None, accept_empty=True, integer=False): try: # text = text.strip() if text == '': return accept_empty if text.find(' ') != -1: return False if integer: num = int(text) else: num = float(text) if min is not None and num < min: return False if max is not None and num > max: return False return True except ValueError: return False

gpl-3.0

Azure/azure-sdk-for-python

sdk/network/azure-mgmt-network/azure/mgmt/network/v2016_12_01/aio/operations/_route_tables_operations.py

1

23236

# coding=utf-8 # -------------------------------------------------------------------------- # Copyright (c) Microsoft Corporation. All rights reserved. # Licensed under the MIT License. See License.txt in the project root for license information. # Code generated by Microsoft (R) AutoRest Code Generator. # Changes may cause incorrect behavior and will be lost if the code is regenerated. # -------------------------------------------------------------------------- from typing import Any, AsyncIterable, Callable, Dict, Generic, Optional, TypeVar, Union import warnings from azure.core.async_paging import AsyncItemPaged, AsyncList from azure.core.exceptions import ClientAuthenticationError, HttpResponseError, ResourceExistsError, ResourceNotFoundError, map_error from azure.core.pipeline import PipelineResponse from azure.core.pipeline.transport import AsyncHttpResponse, HttpRequest from azure.core.polling import AsyncLROPoller, AsyncNoPolling, AsyncPollingMethod from azure.mgmt.core.exceptions import ARMErrorFormat from azure.mgmt.core.polling.async_arm_polling import AsyncARMPolling from ... import models as _models T = TypeVar('T') ClsType = Optional[Callable[[PipelineResponse[HttpRequest, AsyncHttpResponse], T, Dict[str, Any]], Any]] class RouteTablesOperations: """RouteTablesOperations async operations. You should not instantiate this class directly. Instead, you should create a Client instance that instantiates it for you and attaches it as an attribute. :ivar models: Alias to model classes used in this operation group. :type models: ~azure.mgmt.network.v2016_12_01.models :param client: Client for service requests. :param config: Configuration of service client. :param serializer: An object model serializer. :param deserializer: An object model deserializer. """ models = _models def __init__(self, client, config, serializer, deserializer) -> None: self._client = client self._serialize = serializer self._deserialize = deserializer self._config = config async def _delete_initial( self, resource_group_name: str, route_table_name: str, **kwargs ) -> None: cls = kwargs.pop('cls', None) # type: ClsType[None] error_map = { 401: ClientAuthenticationError, 404: ResourceNotFoundError, 409: ResourceExistsError } error_map.update(kwargs.pop('error_map', {})) api_version = "2016-12-01" # Construct URL url = self._delete_initial.metadata['url'] # type: ignore path_format_arguments = { 'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'), 'routeTableName': self._serialize.url("route_table_name", route_table_name, 'str'), 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } url = self._client.format_url(url, **path_format_arguments) # Construct parameters query_parameters = {} # type: Dict[str, Any] query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str') # Construct headers header_parameters = {} # type: Dict[str, Any] request = self._client.delete(url, query_parameters, header_parameters) pipeline_response = await self._client._pipeline.run(request, stream=False, **kwargs) response = pipeline_response.http_response if response.status_code not in [200, 202, 204]: map_error(status_code=response.status_code, response=response, error_map=error_map) raise HttpResponseError(response=response, error_format=ARMErrorFormat) if cls: return cls(pipeline_response, None, {}) _delete_initial.metadata = {'url': '/subscriptions/{subscriptionId}/resourceGroups/{resourceGroupName}/providers/Microsoft.Network/routeTables/{routeTableName}'} # type: ignore async def begin_delete( self, resource_group_name: str, route_table_name: str, **kwargs ) -> AsyncLROPoller[None]: """Deletes the specified route table. :param resource_group_name: The name of the resource group. :type resource_group_name: str :param route_table_name: The name of the route table. :type route_table_name: str :keyword callable cls: A custom type or function that will be passed the direct response :keyword str continuation_token: A continuation token to restart a poller from a saved state. :keyword polling: Pass in True if you'd like the AsyncARMPolling polling method, False for no polling, or your own initialized polling object for a personal polling strategy. :paramtype polling: bool or ~azure.core.polling.AsyncPollingMethod :keyword int polling_interval: Default waiting time between two polls for LRO operations if no Retry-After header is present. :return: An instance of AsyncLROPoller that returns either None or the result of cls(response) :rtype: ~azure.core.polling.AsyncLROPoller[None] :raises ~azure.core.exceptions.HttpResponseError: """ polling = kwargs.pop('polling', True) # type: Union[bool, AsyncPollingMethod] cls = kwargs.pop('cls', None) # type: ClsType[None] lro_delay = kwargs.pop( 'polling_interval', self._config.polling_interval ) cont_token = kwargs.pop('continuation_token', None) # type: Optional[str] if cont_token is None: raw_result = await self._delete_initial( resource_group_name=resource_group_name, route_table_name=route_table_name, cls=lambda x,y,z: x, **kwargs ) kwargs.pop('error_map', None) kwargs.pop('content_type', None) def get_long_running_output(pipeline_response): if cls: return cls(pipeline_response, None, {}) path_format_arguments = { 'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'), 'routeTableName': self._serialize.url("route_table_name", route_table_name, 'str'), 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } if polling is True: polling_method = AsyncARMPolling(lro_delay, path_format_arguments=path_format_arguments, **kwargs) elif polling is False: polling_method = AsyncNoPolling() else: polling_method = polling if cont_token: return AsyncLROPoller.from_continuation_token( polling_method=polling_method, continuation_token=cont_token, client=self._client, deserialization_callback=get_long_running_output ) else: return AsyncLROPoller(self._client, raw_result, get_long_running_output, polling_method) begin_delete.metadata = {'url': '/subscriptions/{subscriptionId}/resourceGroups/{resourceGroupName}/providers/Microsoft.Network/routeTables/{routeTableName}'} # type: ignore async def get( self, resource_group_name: str, route_table_name: str, expand: Optional[str] = None, **kwargs ) -> "_models.RouteTable": """Gets the specified route table. :param resource_group_name: The name of the resource group. :type resource_group_name: str :param route_table_name: The name of the route table. :type route_table_name: str :param expand: Expands referenced resources. :type expand: str :keyword callable cls: A custom type or function that will be passed the direct response :return: RouteTable, or the result of cls(response) :rtype: ~azure.mgmt.network.v2016_12_01.models.RouteTable :raises: ~azure.core.exceptions.HttpResponseError """ cls = kwargs.pop('cls', None) # type: ClsType["_models.RouteTable"] error_map = { 401: ClientAuthenticationError, 404: ResourceNotFoundError, 409: ResourceExistsError } error_map.update(kwargs.pop('error_map', {})) api_version = "2016-12-01" accept = "application/json, text/json" # Construct URL url = self.get.metadata['url'] # type: ignore path_format_arguments = { 'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'), 'routeTableName': self._serialize.url("route_table_name", route_table_name, 'str'), 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } url = self._client.format_url(url, **path_format_arguments) # Construct parameters query_parameters = {} # type: Dict[str, Any] query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str') if expand is not None: query_parameters['$expand'] = self._serialize.query("expand", expand, 'str') # Construct headers header_parameters = {} # type: Dict[str, Any] header_parameters['Accept'] = self._serialize.header("accept", accept, 'str') request = self._client.get(url, query_parameters, header_parameters) pipeline_response = await self._client._pipeline.run(request, stream=False, **kwargs) response = pipeline_response.http_response if response.status_code not in [200]: map_error(status_code=response.status_code, response=response, error_map=error_map) raise HttpResponseError(response=response, error_format=ARMErrorFormat) deserialized = self._deserialize('RouteTable', pipeline_response) if cls: return cls(pipeline_response, deserialized, {}) return deserialized get.metadata = {'url': '/subscriptions/{subscriptionId}/resourceGroups/{resourceGroupName}/providers/Microsoft.Network/routeTables/{routeTableName}'} # type: ignore async def _create_or_update_initial( self, resource_group_name: str, route_table_name: str, parameters: "_models.RouteTable", **kwargs ) -> "_models.RouteTable": cls = kwargs.pop('cls', None) # type: ClsType["_models.RouteTable"] error_map = { 401: ClientAuthenticationError, 404: ResourceNotFoundError, 409: ResourceExistsError } error_map.update(kwargs.pop('error_map', {})) api_version = "2016-12-01" content_type = kwargs.pop("content_type", "application/json") accept = "application/json, text/json" # Construct URL url = self._create_or_update_initial.metadata['url'] # type: ignore path_format_arguments = { 'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'), 'routeTableName': self._serialize.url("route_table_name", route_table_name, 'str'), 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } url = self._client.format_url(url, **path_format_arguments) # Construct parameters query_parameters = {} # type: Dict[str, Any] query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str') # Construct headers header_parameters = {} # type: Dict[str, Any] header_parameters['Content-Type'] = self._serialize.header("content_type", content_type, 'str') header_parameters['Accept'] = self._serialize.header("accept", accept, 'str') body_content_kwargs = {} # type: Dict[str, Any] body_content = self._serialize.body(parameters, 'RouteTable') body_content_kwargs['content'] = body_content request = self._client.put(url, query_parameters, header_parameters, **body_content_kwargs) pipeline_response = await self._client._pipeline.run(request, stream=False, **kwargs) response = pipeline_response.http_response if response.status_code not in [200, 201]: map_error(status_code=response.status_code, response=response, error_map=error_map) raise HttpResponseError(response=response, error_format=ARMErrorFormat) if response.status_code == 200: deserialized = self._deserialize('RouteTable', pipeline_response) if response.status_code == 201: deserialized = self._deserialize('RouteTable', pipeline_response) if cls: return cls(pipeline_response, deserialized, {}) return deserialized _create_or_update_initial.metadata = {'url': '/subscriptions/{subscriptionId}/resourceGroups/{resourceGroupName}/providers/Microsoft.Network/routeTables/{routeTableName}'} # type: ignore async def begin_create_or_update( self, resource_group_name: str, route_table_name: str, parameters: "_models.RouteTable", **kwargs ) -> AsyncLROPoller["_models.RouteTable"]: """Create or updates a route table in a specified resource group. :param resource_group_name: The name of the resource group. :type resource_group_name: str :param route_table_name: The name of the route table. :type route_table_name: str :param parameters: Parameters supplied to the create or update route table operation. :type parameters: ~azure.mgmt.network.v2016_12_01.models.RouteTable :keyword callable cls: A custom type or function that will be passed the direct response :keyword str continuation_token: A continuation token to restart a poller from a saved state. :keyword polling: Pass in True if you'd like the AsyncARMPolling polling method, False for no polling, or your own initialized polling object for a personal polling strategy. :paramtype polling: bool or ~azure.core.polling.AsyncPollingMethod :keyword int polling_interval: Default waiting time between two polls for LRO operations if no Retry-After header is present. :return: An instance of AsyncLROPoller that returns either RouteTable or the result of cls(response) :rtype: ~azure.core.polling.AsyncLROPoller[~azure.mgmt.network.v2016_12_01.models.RouteTable] :raises ~azure.core.exceptions.HttpResponseError: """ polling = kwargs.pop('polling', True) # type: Union[bool, AsyncPollingMethod] cls = kwargs.pop('cls', None) # type: ClsType["_models.RouteTable"] lro_delay = kwargs.pop( 'polling_interval', self._config.polling_interval ) cont_token = kwargs.pop('continuation_token', None) # type: Optional[str] if cont_token is None: raw_result = await self._create_or_update_initial( resource_group_name=resource_group_name, route_table_name=route_table_name, parameters=parameters, cls=lambda x,y,z: x, **kwargs ) kwargs.pop('error_map', None) kwargs.pop('content_type', None) def get_long_running_output(pipeline_response): deserialized = self._deserialize('RouteTable', pipeline_response) if cls: return cls(pipeline_response, deserialized, {}) return deserialized path_format_arguments = { 'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'), 'routeTableName': self._serialize.url("route_table_name", route_table_name, 'str'), 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } if polling is True: polling_method = AsyncARMPolling(lro_delay, path_format_arguments=path_format_arguments, **kwargs) elif polling is False: polling_method = AsyncNoPolling() else: polling_method = polling if cont_token: return AsyncLROPoller.from_continuation_token( polling_method=polling_method, continuation_token=cont_token, client=self._client, deserialization_callback=get_long_running_output ) else: return AsyncLROPoller(self._client, raw_result, get_long_running_output, polling_method) begin_create_or_update.metadata = {'url': '/subscriptions/{subscriptionId}/resourceGroups/{resourceGroupName}/providers/Microsoft.Network/routeTables/{routeTableName}'} # type: ignore def list( self, resource_group_name: str, **kwargs ) -> AsyncIterable["_models.RouteTableListResult"]: """Gets all route tables in a resource group. :param resource_group_name: The name of the resource group. :type resource_group_name: str :keyword callable cls: A custom type or function that will be passed the direct response :return: An iterator like instance of either RouteTableListResult or the result of cls(response) :rtype: ~azure.core.async_paging.AsyncItemPaged[~azure.mgmt.network.v2016_12_01.models.RouteTableListResult] :raises: ~azure.core.exceptions.HttpResponseError """ cls = kwargs.pop('cls', None) # type: ClsType["_models.RouteTableListResult"] error_map = { 401: ClientAuthenticationError, 404: ResourceNotFoundError, 409: ResourceExistsError } error_map.update(kwargs.pop('error_map', {})) api_version = "2016-12-01" accept = "application/json, text/json" def prepare_request(next_link=None): # Construct headers header_parameters = {} # type: Dict[str, Any] header_parameters['Accept'] = self._serialize.header("accept", accept, 'str') if not next_link: # Construct URL url = self.list.metadata['url'] # type: ignore path_format_arguments = { 'resourceGroupName': self._serialize.url("resource_group_name", resource_group_name, 'str'), 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } url = self._client.format_url(url, **path_format_arguments) # Construct parameters query_parameters = {} # type: Dict[str, Any] query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str') request = self._client.get(url, query_parameters, header_parameters) else: url = next_link query_parameters = {} # type: Dict[str, Any] request = self._client.get(url, query_parameters, header_parameters) return request async def extract_data(pipeline_response): deserialized = self._deserialize('RouteTableListResult', pipeline_response) list_of_elem = deserialized.value if cls: list_of_elem = cls(list_of_elem) return deserialized.next_link or None, AsyncList(list_of_elem) async def get_next(next_link=None): request = prepare_request(next_link) pipeline_response = await self._client._pipeline.run(request, stream=False, **kwargs) response = pipeline_response.http_response if response.status_code not in [200]: map_error(status_code=response.status_code, response=response, error_map=error_map) raise HttpResponseError(response=response, error_format=ARMErrorFormat) return pipeline_response return AsyncItemPaged( get_next, extract_data ) list.metadata = {'url': '/subscriptions/{subscriptionId}/resourceGroups/{resourceGroupName}/providers/Microsoft.Network/routeTables'} # type: ignore def list_all( self, **kwargs ) -> AsyncIterable["_models.RouteTableListResult"]: """Gets all route tables in a subscription. :keyword callable cls: A custom type or function that will be passed the direct response :return: An iterator like instance of either RouteTableListResult or the result of cls(response) :rtype: ~azure.core.async_paging.AsyncItemPaged[~azure.mgmt.network.v2016_12_01.models.RouteTableListResult] :raises: ~azure.core.exceptions.HttpResponseError """ cls = kwargs.pop('cls', None) # type: ClsType["_models.RouteTableListResult"] error_map = { 401: ClientAuthenticationError, 404: ResourceNotFoundError, 409: ResourceExistsError } error_map.update(kwargs.pop('error_map', {})) api_version = "2016-12-01" accept = "application/json, text/json" def prepare_request(next_link=None): # Construct headers header_parameters = {} # type: Dict[str, Any] header_parameters['Accept'] = self._serialize.header("accept", accept, 'str') if not next_link: # Construct URL url = self.list_all.metadata['url'] # type: ignore path_format_arguments = { 'subscriptionId': self._serialize.url("self._config.subscription_id", self._config.subscription_id, 'str'), } url = self._client.format_url(url, **path_format_arguments) # Construct parameters query_parameters = {} # type: Dict[str, Any] query_parameters['api-version'] = self._serialize.query("api_version", api_version, 'str') request = self._client.get(url, query_parameters, header_parameters) else: url = next_link query_parameters = {} # type: Dict[str, Any] request = self._client.get(url, query_parameters, header_parameters) return request async def extract_data(pipeline_response): deserialized = self._deserialize('RouteTableListResult', pipeline_response) list_of_elem = deserialized.value if cls: list_of_elem = cls(list_of_elem) return deserialized.next_link or None, AsyncList(list_of_elem) async def get_next(next_link=None): request = prepare_request(next_link) pipeline_response = await self._client._pipeline.run(request, stream=False, **kwargs) response = pipeline_response.http_response if response.status_code not in [200]: map_error(status_code=response.status_code, response=response, error_map=error_map) raise HttpResponseError(response=response, error_format=ARMErrorFormat) return pipeline_response return AsyncItemPaged( get_next, extract_data ) list_all.metadata = {'url': '/subscriptions/{subscriptionId}/providers/Microsoft.Network/routeTables'} # type: ignore

mit

Azure/azure-sdk-for-python

sdk/cosmos/azure-cosmos/test/test_diagnostics.py

1

1357

import unittest import pytest import azure.cosmos.diagnostics as m _common = { 'x-ms-activity-id', 'x-ms-session-token', 'x-ms-item-count', 'x-ms-request-quota', 'x-ms-resource-usage', 'x-ms-retry-after-ms', } _headers = dict(zip(_common, _common)) _headers['other'] = 'other' class BaseUnitTests(unittest.TestCase): def test_init(self): rh = m.RecordDiagnostics() assert rh.headers == {} def test_headers(self): rh = m.RecordDiagnostics() rh(_headers, "body") assert rh.headers == _headers assert rh.headers is not _headers def test_headers_case(self): rh = m.RecordDiagnostics() rh(_headers, "body") rh_headers = rh.headers for key in rh.headers.keys(): assert key.upper() in rh_headers assert key.lower() in rh_headers def test_common_attrs(self): rh = m.RecordDiagnostics() rh(_headers, "body") for name in _common: assert rh.headers[name] == name attr = name.replace('x-ms-', '').replace('-', '_') assert getattr(rh, attr) == name def test_other_attrs(self): rh = m.RecordDiagnostics() rh(_headers, "body") assert rh.headers['other'] == 'other' with pytest.raises(AttributeError): rh.other

mit

Storj/pyp2p

tests/test_sock.py

1

15565

""" * Test whether multiple recvs on the same connection (non-blocking) will eventually have the connection closed (use another net instance.) * Test whether multiple sends on the same connection (non-blocking) will eventually lead to the connection being closed (use a net instance with no recvs! and loop over the cons) (Not implemented for now since these will greatly slow the build.) """ import hashlib import os import tempfile from threading import Thread from unittest import TestCase from pyp2p.net import rendezvous_servers from pyp2p.rendezvous_client import RendezvousClient from pyp2p.sock import * if sys.version_info >= (3, 0, 0): from urllib.parse import urlparse import socketserver as SocketServer from http.server import HTTPServer from http.server import SimpleHTTPRequestHandler else: from urlparse import urlparse import SocketServer from BaseHTTPServer import HTTPServer from SimpleHTTPServer import SimpleHTTPRequestHandler class ThreadingSimpleServer( SocketServer.ThreadingMixIn, HTTPServer ): pass def md5sum(fname): my_hash = hashlib.md5() with open(fname, "rb") as f: for chunk in iter(lambda: f.read(4096), b""): my_hash.update(chunk) return my_hash.hexdigest() class SockDownload: def __init__(self, url, expected_hash, file_size, blocking=0, encoding="ascii"): """ Download a file from a HTTP URL and compare it to an MD5 hash. Uses the sock.py module for testing. :param url: URL to download :param expected_hash: MD5 hash of file (md5sum file from term) :param file_size: size in bytes of the file to download :param blocking: use blocking or non-blocking sockets :return: """ url = urlparse(url) location = url.netloc.split(":") if len(location) == 1: port = 80 host, = location else: host, port = location con = Sock(host, port, blocking=blocking, debug=1) req = self.build_request(host, url.path) con.send(req, send_all=1) buf = u"" eof = u"\r\n\r\n" while buf != eof and con.connected: ch = con.recv(1) if len(ch): buf += ch eq = 0 for i in range(0, len(buf)): if buf[i] != eof[eq]: eq = 0 else: eq += 1 # Reset buf. if eq == len(eof): break fp, path = tempfile.mkstemp() os.close(fp) remaining = file_size with open(path, "ab") as fp: future = time.time() + 30 # Slow connections are slow. while con.connected and remaining: data = con.recv(remaining, encoding=encoding) print(type(data)) if len(data): remaining -= len(data) fp.write(data) time.sleep(0.0002) # Fail safe: if time.time() >= future: break found_hash = md5sum(path) os.remove(path) if expected_hash is not None: assert(found_hash == expected_hash) def build_request(self, host, resource): req = "GET %s HTTP/1.1\r\n" % resource req += "Host: %s\r\n\r\n" % host return req class SockUpload: def __init__(self, upload_size, blocking=0): host = u"185.86.149.128" port = 80 resource = u"/upload_test.php" content = self.build_content(upload_size) con = Sock(host, port, blocking=blocking, debug=1) req = self.build_request(host, resource, content) con.send(req, send_all=1, timeout=6) # Now do the actual upload. remaining = upload_size chunk_size = 4096 while con.connected and remaining: sent = upload_size - remaining msg = content[sent:sent + chunk_size] sent = con.send(msg) if sent: remaining -= sent # Get response. con.set_blocking(1) ret = con.recv(1024) # Check response. expected_hash = hashlib.sha256(content).hexdigest() assert(expected_hash in ret) def build_request(self, host, resource, content): req = "POST %s HTTP/1.1\r\n" % resource req += "Host: %s\r\n" % host req += "User-Agent: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:42.0) " req += "Gecko/20100101 Firefox/42.0\r\n" req += "Accept: text/html," req += "application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8\r\n" req += "Accept-Language: en-US,en;q=0.5\r\n" req += "Accept-Encoding: gzip, deflate\r\n" req += "Connection: keep-alive\r\n" req += "Content-Type: application/x-www-form-urlencoded\r\n" req += "Content-Length: %d\r\n\r\n" % (len(content) + 5) req += "test=" # Hence the extra + 5. return req def build_content(self, upload_size): content = b"8" * upload_size return content def simple_server(): s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) s.bind(('localhost', 9000)) s.listen(0) (clientsocket, address) = s.accept() time.sleep(2) s.close() class TestSock(TestCase): def test_http_upload_post(self): SockUpload(1000 * 100) def test_http_download(self): SockDownload( "http://mirror.internode.on.net/pub/test/1meg.test", "e6527b4d5db05226f40f9f2e7750abfb", 1000000 ) def test_blocking_mode(self): x = Sock() blocking = x.s.gettimeout() if x.blocking: assert(blocking >= 1 or blocking is None) else: assert(blocking == 0.0) x.close() x = Sock(blocking=1) blocking = x.s.gettimeout() if x.blocking: assert(blocking >= 1 or blocking is None) else: assert(blocking == 0.0) x.close() x = Sock("www.example.com", 80, timeout=10) blocking = x.s.gettimeout() if x.blocking: assert(blocking >= 1 or blocking is None) else: assert(blocking == 0.0) x.close() x = Sock("www.example.com", 80, blocking=1, timeout=10) blocking = x.s.gettimeout() if x.blocking: assert(blocking >= 1 or blocking is None) else: assert(blocking == 0.0) x.close() def test_blocking_timeout(self): client = RendezvousClient(nat_type="preserving", rendezvous_servers=rendezvous_servers) s = client.server_connect() t = time.time() s.recv_line(timeout=1) if time.time() - t >= 4: print("Manual timeout failed.") assert 0 s.close() def test_non_blocking_timeout(self): client = RendezvousClient(nat_type="preserving", rendezvous_servers=rendezvous_servers) s = client.server_connect() assert(s.recv_line() == u"") assert(s.recv(1) == u"") s.close() def test_encoding(self): client = RendezvousClient(nat_type="preserving", rendezvous_servers=rendezvous_servers) s = client.server_connect() s.send_line("SOURCE TCP 50") ret = s.recv(1, encoding="ascii") if sys.version_info >= (3, 0, 0): assert(type(ret) == bytes) else: assert(type(ret) == str) assert(ret == b"R") ret = s.recv_line() assert(u"EMOTE" in ret) s.send_line("SOURCE TCP 50") ret = s.recv(1, encoding="unicode") if sys.version_info >= (3, 0, 0): assert(type(ret) == str) else: assert(type(ret) == unicode) s.close() def test_0000001_sock(self): client = RendezvousClient(nat_type="preserving", rendezvous_servers=rendezvous_servers) s = client.server_connect() assert s.connected s.send_line("SOURCE TCP 323") assert s.connected line = s.recv_line() assert ("REMOTE" in line) s = Sock("www.example.com", 80, blocking=0, timeout=10) data = "GET / HTTP/1.1\r\n" data += "Connection: close\r\n" data += "Host: www.example.com\r\n\r\n" s.send(data, send_all=1) replies = "" while s.connected: for reply in s: # Output should be unicode. if sys.version_info >= (3, 0, 0): assert (type(reply) == str) else: assert (type(reply) == unicode) replies += reply print(reply) assert (s.connected != 1) assert (replies != "") s.close() s.reconnect() s.close() s = Sock("www.example.com", 80, blocking=1, timeout=10) s.send_line("GET / HTTP/1.1") s.send_line("Host: www.example.com\r\n") line = s.recv_line() print(line) print(type(line)) print(s.buf) print(type(s.buf)) assert (line, "HTTP/1.1 200 OK") if sys.version_info >= (3, 0, 0): assert (type(line) == str) else: assert (type(line) == unicode) s.close() s = Sock() s.buf = b"\r\nx\r\n" x = s.parse_buf() assert (x[0] == "x") s.buf = b"\r\n" x = s.parse_buf() assert (x == []) s.buf = b"\r\n\r\n" x = s.parse_buf() assert (x == []) s.buf = b"\r\r\n\r\n" x = s.parse_buf() assert (x[0] == "\r") s.buf = b"\r\n\r\n\r\nx" x = s.parse_buf() assert (x == []) s.buf = b"\r\n\r\nx\r\nsdfsdfsdf\r\n" x = s.parse_buf() assert (x[0] == "x" and x[1] == "sdfsdfsdf") s.buf = b"sdfsdfsdf\r\n" s.parse_buf() s.buf += b"abc\r\n" x = s.parse_buf() assert (x[0] == "abc") s.buf += b"\r\ns\r\n" x = s.parse_buf() assert (x[0] == "s") s.buf = b"reply 1\r\nreply 2\r\n" s.replies = [] s.update() assert (s.pop_reply(), "reply 1") assert (s.replies[0], "reply 2") def test_keep_alive(self): old_system = platform.system for os in ["Darwin", "Windows", "Linux"]: def system_wrapper(): return os platform.system = system_wrapper sock = Sock() # Sock option error - not supported on this OS. try: sock.set_keep_alive(sock.s) except socket.error as e: valid_errors = (10042, 22) if e.errno not in valid_errors: raise e except AttributeError: pass sock.close() platform.system = old_system assert 1 def test_non_default_iface(self): sock = Sock(interface="eth12") try: sock.connect("www.example.com", 80, timeout=10) except (TypeError, socket.error) as e: pass sock.close() assert 1 def test_ssl(self): s = Sock( "www.example.com", 443, blocking=0, timeout=10, use_ssl=1 ) data = "GET / HTTP/1.1\r\n" data += "Connection: close\r\n" data += "Host: www.example.com\r\n\r\n" s.send(data, send_all=1) replies = "" while s.connected: for reply in s: # Output should be unicode. if sys.version_info >= (3, 0, 0): assert (type(reply) == str) else: assert (type(reply) == unicode) replies += reply print(reply) assert (s.connected != 1) assert (replies != "") def test_ssl_blocking_error(self): # Blocking. s = Sock( "www.example.com", 443, blocking=1, timeout=2, use_ssl=1, debug=1 ) s.get_chunks() s.close() # Non-blocking. s = Sock( "www.example.com", 443, blocking=0, timeout=2, use_ssl=1, debug=1 ) s.get_chunks() s.close() def test_decoding_error(self): SockDownload( "http://mirror.internode.on.net/pub/test/1meg.test", expected_hash=None, file_size=1000, blocking=0, encoding="unicode" ) def test_broken_send_con(self): # Can't monkey patch socket on Linux. if platform.system != "Windows": return port = 10121 server = ThreadingSimpleServer(('', port), SimpleHTTPRequestHandler) sock = Sock("127.0.0.1", port, debug=1, timeout=6) server.server_close() print(sock.send(b"test")) sock.close() server = ThreadingSimpleServer(('', port), SimpleHTTPRequestHandler) def close_server(): time.sleep(1) server.server_close() sock = Sock("127.0.0.1", port, debug=1, timeout=6) Thread(target=close_server).start() for i in range(0, 5): print(sock.send(b"test")) time.sleep(0.5) sock.close # Simulate send timeout! sock = Sock(debug=1, blocking=1) def raise_timeout(): time.sleep(1) original_send = sock.s.send def fake_send(data): raise socket.timeout("timed out") sock.s.send = fake_send time.sleep(1) sock.s.send = original_send Thread(target=raise_timeout).start() sock.connect("www.example.com", 80) # You want to fill up the entire networking buffer # so that it times out without the needed recv. buf_size = sock.s.getsockopt(socket.SOL_SOCKET, socket.SO_SNDBUF) + 1 buf_size *= 2 sock.chunk_size = buf_size total = 0 for i in range(0, 4): x = sock.send(b"x" * buf_size) total += x if x < buf_size: break time.sleep(2.2) sock.close() # Test broken connection. sock = Sock(debug=1, blocking=1) def raise_timeout(): time.sleep(1) original_send = sock.s.send def fake_send(data): return 0 sock.s.send = fake_send time.sleep(1) Thread(target=raise_timeout).start() sock.connect("www.example.com", 80) # You want to fill up the entire networking buffer # so that it times out without the needed recv. x = 1 timeout = time.time() + 10 while x and time.time() < timeout: x = sock.send(b"x") time.sleep(2.2) sock.close() def test_magic(self): sock = Sock() sock.replies = ["a", "b", "c"] assert(len(sock) == 3) assert(sock[0] == "a") del sock[0] assert(sock[0] == "b") sock[0] = "x" assert(sock[0] == "x") y = list(reversed(sock)) assert(y == ["x", "c"])

mit

julython/julython.org

july/people/migrations/0010_auto__add_userbadge.py

1

9221

# -*- coding: utf-8 -*- from south.utils import datetime_utils as datetime from south.db import db from south.v2 import SchemaMigration from django.db import models class Migration(SchemaMigration): def forwards(self, orm): # Adding model 'UserBadge' db.create_table(u'people_userbadge', ( (u'id', self.gf('django.db.models.fields.AutoField')(primary_key=True)), ('user', self.gf('django.db.models.fields.related.ForeignKey')(to=orm['july.User'])), ('badges', self.gf('jsonfield.fields.JSONField')(null=True, blank=True)), )) db.send_create_signal(u'people', ['UserBadge']) def backwards(self, orm): # Deleting model 'UserBadge' db.delete_table(u'people_userbadge') models = { u'auth.group': { 'Meta': {'object_name': 'Group'}, u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'name': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '80'}), 'permissions': ('django.db.models.fields.related.ManyToManyField', [], {'to': u"orm['auth.Permission']", 'symmetrical': 'False', 'blank': 'True'}) }, u'auth.permission': { 'Meta': {'ordering': "(u'content_type__app_label', u'content_type__model', u'codename')", 'unique_together': "((u'content_type', u'codename'),)", 'object_name': 'Permission'}, 'codename': ('django.db.models.fields.CharField', [], {'max_length': '100'}), 'content_type': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['contenttypes.ContentType']"}), u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '50'}) }, u'contenttypes.contenttype': { 'Meta': {'ordering': "('name',)", 'unique_together': "(('app_label', 'model'),)", 'object_name': 'ContentType', 'db_table': "'django_content_type'"}, 'app_label': ('django.db.models.fields.CharField', [], {'max_length': '100'}), u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'model': ('django.db.models.fields.CharField', [], {'max_length': '100'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '100'}) }, u'july.user': { 'Meta': {'object_name': 'User'}, 'date_joined': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), 'email': ('django.db.models.fields.EmailField', [], {'max_length': '75', 'blank': 'True'}), 'first_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), 'groups': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Group']"}), u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'is_active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), 'is_staff': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), 'is_superuser': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), 'last_login': ('django.db.models.fields.DateTimeField', [], {'default': 'datetime.datetime.now'}), 'last_name': ('django.db.models.fields.CharField', [], {'max_length': '30', 'blank': 'True'}), 'location': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'location_members'", 'null': 'True', 'to': u"orm['people.Location']"}), 'password': ('django.db.models.fields.CharField', [], {'max_length': '128'}), 'picture_url': ('django.db.models.fields.URLField', [], {'max_length': '200', 'null': 'True', 'blank': 'True'}), 'projects': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'to': u"orm['people.Project']", 'null': 'True', 'blank': 'True'}), 'team': ('django.db.models.fields.related.ForeignKey', [], {'blank': 'True', 'related_name': "'team_members'", 'null': 'True', 'to': u"orm['people.Team']"}), 'url': ('django.db.models.fields.URLField', [], {'max_length': '200', 'null': 'True', 'blank': 'True'}), 'user_permissions': ('django.db.models.fields.related.ManyToManyField', [], {'symmetrical': 'False', 'related_name': "u'user_set'", 'blank': 'True', 'to': u"orm['auth.Permission']"}), 'username': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '30'}) }, u'people.commit': { 'Meta': {'ordering': "['-timestamp']", 'object_name': 'Commit'}, 'author': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), 'created_on': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), 'email': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), 'files': ('jsonfield.fields.JSONField', [], {'null': 'True', 'blank': 'True'}), 'hash': ('django.db.models.fields.CharField', [], {'unique': 'True', 'max_length': '255'}), u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'message': ('django.db.models.fields.CharField', [], {'max_length': '2024', 'blank': 'True'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), 'project': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['people.Project']", 'null': 'True', 'blank': 'True'}), 'timestamp': ('django.db.models.fields.DateTimeField', [], {}), 'url': ('django.db.models.fields.CharField', [], {'max_length': '512', 'blank': 'True'}), 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['july.User']", 'null': 'True', 'blank': 'True'}) }, u'people.language': { 'Meta': {'object_name': 'Language'}, u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '64'}) }, u'people.location': { 'Meta': {'object_name': 'Location'}, 'approved': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '64'}), 'slug': ('django.db.models.fields.SlugField', [], {'max_length': '50', 'primary_key': 'True'}), 'total': ('django.db.models.fields.IntegerField', [], {'default': '0'}) }, u'people.project': { 'Meta': {'object_name': 'Project'}, 'active': ('django.db.models.fields.BooleanField', [], {'default': 'True'}), 'created_on': ('django.db.models.fields.DateTimeField', [], {'auto_now_add': 'True', 'blank': 'True'}), 'description': ('django.db.models.fields.TextField', [], {'blank': 'True'}), 'forked': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), 'forks': ('django.db.models.fields.IntegerField', [], {'default': '0'}), u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), 'parent_url': ('django.db.models.fields.CharField', [], {'max_length': '255', 'blank': 'True'}), 'repo_id': ('django.db.models.fields.IntegerField', [], {'null': 'True', 'blank': 'True'}), 'service': ('django.db.models.fields.CharField', [], {'default': "''", 'max_length': '30', 'blank': 'True'}), 'slug': ('django.db.models.fields.SlugField', [], {'max_length': '50'}), 'updated_on': ('django.db.models.fields.DateTimeField', [], {'auto_now': 'True', 'blank': 'True'}), 'url': ('django.db.models.fields.CharField', [], {'max_length': '255'}), 'watchers': ('django.db.models.fields.IntegerField', [], {'default': '0'}) }, u'people.team': { 'Meta': {'object_name': 'Team'}, 'approved': ('django.db.models.fields.BooleanField', [], {'default': 'False'}), 'name': ('django.db.models.fields.CharField', [], {'max_length': '64'}), 'slug': ('django.db.models.fields.SlugField', [], {'max_length': '50', 'primary_key': 'True'}), 'total': ('django.db.models.fields.IntegerField', [], {'default': '0'}) }, u'people.userbadge': { 'Meta': {'object_name': 'UserBadge'}, 'badges': ('jsonfield.fields.JSONField', [], {'null': 'True', 'blank': 'True'}), u'id': ('django.db.models.fields.AutoField', [], {'primary_key': 'True'}), 'user': ('django.db.models.fields.related.ForeignKey', [], {'to': u"orm['july.User']"}) } } complete_apps = ['people']

mit

astromme/classify-handwritten-characters

utils/gnt.py

1

1587

#!/usr/bin/env python3 import os import sys import numpy as np from .tagcode import tagcode_to_unicode def samples_from_gnt(f): header_size = 10 # read samples from f until no bytes remaining while True: header = np.fromfile(f, dtype='uint8', count=header_size) if not header.size: break sample_size = header[0] + (header[1]<<8) + (header[2]<<16) + (header[3]<<24) tagcode = header[5] + (header[4]<<8) width = header[6] + (header[7]<<8) height = header[8] + (header[9]<<8) assert header_size + width*height == sample_size bitmap = np.fromfile(f, dtype='uint8', count=width*height).reshape((height, width)) yield bitmap, tagcode def read_gnt_in_directory(gnt_dirpath): for file_name in os.listdir(gnt_dirpath): if file_name.endswith('.gnt'): file_path = os.path.join(gnt_dirpath, file_name) with open(file_path, 'rb') as f: for bitmap, tagcode in samples_from_gnt(f): yield bitmap, tagcode def main(): import png if len(sys.argv) != 3: print("usage: {} gntfile outputdir".format(sys.argv[0])) _, gntfile, outputdir = sys.argv try: os.makedirs(outputdir) except FileExistsError: pass with open(gntfile) as f: for i, (bitmap, tagcode) in enumerate(samples_from_gnt(f)): character = tagcode_to_unicode(tagcode) png.from_array(bitmap, 'L').save(os.path.join(outputdir, '{} {}.png'.format(character, i))) if __name__ == "__main__": main()

mit

ppolewicz/logfury

setup.py

1

3132

from codecs import open import os.path from setuptools import setup, find_packages import sys ################################################################### yapf: disable NAME = 'logfury' VERSION = '0.1.2' AUTHOR = 'Pawel Polewicz' AUTHOR_EMAIL = '[email protected]' DESCRIPTION = 'Toolkit for responsible, low-boilerplate logging of library method calls', LICENSE = 'BSD' KEYWORDS = ['logging', 'tracing'] URL = 'https://github.com/ppolewicz/logfury' DOWNLOAD_URL_TEMPLATE = URL + '/tarball/%s' CLASSIFIERS = [ 'Development Status :: 4 - Beta', 'Intended Audience :: Developers', 'Topic :: Software Development :: Libraries :: Python Modules', 'Topic :: System :: Logging', 'Natural Language :: English', 'License :: OSI Approved :: BSD License', 'Operating System :: OS Independent', 'Programming Language :: Python', 'Programming Language :: Python :: 2', 'Programming Language :: Python :: 2.6', 'Programming Language :: Python :: 2.7', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.3', 'Programming Language :: Python :: 3.4', 'Programming Language :: Python :: 3.5', 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: Implementation :: CPython', 'Programming Language :: Python :: Implementation :: Jython', 'Programming Language :: Python :: Implementation :: PyPy', ] ################################################################### yapf: enable if __name__ == '__main__': here = os.path.abspath(os.path.dirname(__file__)) def read_file_contents(filename): with open(os.path.join(here, filename), 'rb', encoding='utf-8') as f: return f.read() long_description = read_file_contents('README.rst') requirements_install = read_file_contents('requirements.txt').splitlines() if sys.version_info == (2, 6): requirements_install.append('ordereddict') requirements_test = read_file_contents('requirements-test.txt').splitlines() setup( name = NAME, version = VERSION, url = URL, download_url = DOWNLOAD_URL_TEMPLATE % (VERSION,), author = AUTHOR, author_email = AUTHOR_EMAIL, maintainer = AUTHOR, maintainer_email = AUTHOR_EMAIL, packages = find_packages(where='src'), license = LICENSE, description = DESCRIPTION, long_description = long_description, keywords = KEYWORDS, package_dir = {'': 'src'}, zip_safe = False, classifiers = CLASSIFIERS, install_requires = requirements_install, tests_require = requirements_test, package_data = { NAME: [ 'requirements.txt', 'requirements-test.txt', ] }, # to install: pip install -e .[dev,test] extras_require = { 'test': requirements_test, }, ) # yapf: disable

bsd-3-clause

crawfordsm/pyspectrograph

PySpectrograph/WavelengthSolution/WavelengthSolution.py

1

3169

"""Wavelength Solution is a task describing the functional form for transforming pixel position to wavelength. The inputs for this task are the given pixel position and the corresponding wavelength. The user selects an input functional form and order for that form. The task then calculates the coefficients for that form. Possible options for the wavelength solution include polynomial, legendre, spline. HISTORY 20090915 SMC Initially Written by SM Crawford LIMITATIONS 20090915 SMC Need to add legendre, spline functions """ import numpy as np from .LineSolution import LineSolution from .ModelSolution import ModelSolution class WavelengthSolution: """Wavelength Solution is a task describing the functional form for transforming pixel position to wavelength. """ func_options = ['poly', 'polynomial', 'spline', 'legendre', 'chebyshev', 'model'] def __init__(self, x, w, function='poly', order=3, niter=5, thresh=3, sgraph=None, cfit='both', xlen=3162, yval=0): self.sgraph = sgraph self.function = function self.order = order self.niter = niter self.thresh = thresh self.cfit = cfit self.xlen = xlen self.yval = yval self.set_array(x, w) self.set_func() def set_array(self, x, w): self.x_arr = x self.w_arr = w def set_thresh(self, thresh): self.thresh = thresh def set_niter(self, niter): self.niter = niter def set_func(self): if self.function in ['poly', 'polynomial', 'spline', 'legendre', 'chebyshev']: self.func = LineSolution(self.x_arr, self.w_arr, function=self.function, order=self.order, niter=self.niter, thresh=self.thresh) if self.function == 'model': self.func = ModelSolution(self.x_arr, self.w_arr, sgraph=self.sgraph, xlen=self.xlen, yval=self.yval, order=self.order) def fit(self): if self.function in ['poly', 'polynomial', 'spline', 'legendre', 'chebyshev']: self.func.interfit() self.coef = self.func.coef if self.function in ['model']: self.func.fit(cfit=self.cfit) self.coef = np.array([c() for c in self.func.coef]) # self.set_coef(coef) def set_coef(self, coef): if self.function in ['poly', 'polynomial', 'spline', 'legendre', 'chebyshev']: self.func.coef = coef self.coef = self.func.coef if self.function in ['model']: for i in range(len(self.func.coef)): self.func.coef[i].set(coef[i]) self.coef = np.array([c() for c in self.func.coef]) def value(self, x): return self.func.value(x) def invvalue(self, w): """Given a wavelength, return the pixel position """ return w def sigma(self, x, y): """Return the RMS of the fit """ return (((y - self.value(x)) ** 2).mean()) ** 0.5 def chisq(self, x, y, err): """Return the chi^2 of the fit""" return (((y - self.value(x)) / err) ** 2).sum()

bsd-3-clause

Guokr1991/ProstateSensitivityAnalysis

convert_histology_txt_json.py

1

2295

def main(): hist_txt_to_json() def hist_txt_to_json(): j = open('HistologyLesions.json', 'w') j.write('{\n') index = True benign = False with open('HistologyLesions.txt', 'r') as t: tfile = t.readlines() num_lesions = len(tfile) global td # define globally for ece_extent_writer method for nl, td in enumerate(tfile): td = td[:-1] if 'pca' in td and index: j.write('\t"pca": [\n') j.write('\t\t{\n\t\t\t"region": "%s",\n' % td.split(',')[1][1:]) j.write('\t\t\t"volume_cc": %.1f,\n' % float(td.split(',')[2])) j.write('\t\t\t"Gleason": %i,\n' % float(td.split(',')[3])) j.write('\t\t\t"Staging": "%s",\n' % td.split(',')[4][1:4]) j.write('\t\t\t"ECE_extent": "%s",\n' % ece_extent_writer()) j.write('\t\t\t"index": true\n\t\t}') index = False if (nl+1) == num_lesions: j.write(']\n') elif 'pca' in td and not index: j.write(',\n') j.write('\t\t{\n\t\t\t"region": "%s",\n' % td.split(',')[1][1:]) j.write('\t\t\t"volume_cc": %.1f,\n' % float(td.split(',')[2])) j.write('\t\t\t"Gleason": %i,\n' % float(td.split(',')[3])) j.write('\t\t\t"Staging": "%s",\n' % td.split(',')[4][1:4]) j.write('\t\t\t"ECE_extent": "%s",\n' % ece_extent_writer()) j.write('\t\t\t"index": false\n\t\t}') if (nl+1) == num_lesions: j.write(']\n') elif ('atrophy' in td) or ('bph' in td): if not benign: j.write('],\n') else: j.write(',\n') num_regions = len(td.split(',')[1:]) j.write('\t"%s": {\n\t\t"regions": [' % td.split(',')[0]) for n, r in enumerate(td.split(',')[1:]): if n < (num_regions-1): j.write('"%s", ' % r[1:]) else: j.write('"%s"]\n\t\t}' % r[1:]) benign = True j.write('\n}') def ece_extent_writer(): if td.split(',')[4][-1] == 'E': return "Established" elif td.split(',')[4][-1] == 'F': return "Focal" else: return "None" if __name__ == '__main__': main()

apache-2.0

harlowja/speedlimit

speedlimit/__init__.py

1

3653

# vim: tabstop=4 shiftwidth=4 softtabstop=4 # Copyright 2010 United States Government as represented by the # Administrator of the National Aeronautics and Space Administration. # All Rights Reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); you may # not use this file except in compliance with the License. You may obtain # a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, WITHOUT # WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the # License for the specific language governing permissions and limitations # under the License. import math import time from monotonic import monotonic as _now class SpeedLimit(object): """Speed/limiting iterator wrapper object. A wrapper object that uses the `token bucket`_ algorithm to limit the rate at which values comes out of an iterable. This can be used to limit the consumption speed of iteration of some other iterator (or iterable). .. _token bucket: http://en.wikipedia.org/wiki/Token_bucket """ def __init__(self, # How many items to yield from the provided # wrapped iterator (per second). items_per_second, # Used to simulate a thread with its own 'tic rate'. Making # this smaller affects the accuracy of the 'tic' calculation, # which affects the accuracy of consumption (and delays). refresh_rate_seconds=0.01, # How *full* the initial bucket is. initial_bucket_size=1, # Made a keyword argument, so one could replace this # with a eventlet.sleep or other idling function... sleep_func=time.sleep): self._refresh_rate_seconds = refresh_rate_seconds self._bucket = (items_per_second * refresh_rate_seconds * initial_bucket_size) self._items_per_tic = items_per_second * refresh_rate_seconds self._next_fill = _now() + refresh_rate_seconds self._sleep = sleep_func def _check_fill(self): # Fill the bucket based on elapsed time. # # This simulates a background thread... now = _now() if now > self._next_fill: d = now - self._next_fill tics = int(math.ceil(d / self._refresh_rate_seconds)) self._bucket += tics * self._items_per_tic self._next_fill += tics * self._refresh_rate_seconds def speed_limit_iter(self, itr, chunk_size_cb=None): """Return an iterator/generator which limits after each iteration. :param itr: an iterator to wrap :param chunk_size_cb: a function that can calculate the size of each chunk (if none provided this defaults to 1) """ for chunk in itr: if chunk_size_cb is None: sz = 1 else: sz = chunk_size_cb(chunk) self._check_fill() if sz > self._bucket: now = _now() tics = int((sz - self._bucket) / self._items_per_tic) tm_diff = self._next_fill - now secs = tics * self._refresh_rate_seconds if tm_diff > 0: secs += tm_diff self._sleep(secs) self._check_fill() self._bucket -= sz yield chunk

apache-2.0

stopthatcow/zazu

zazu/scm_host.py

1

1275

# -*- coding: utf-8 -*- """Source code management (SCM) host related classes.""" __author__ = 'Nicholas Wiles' __copyright__ = 'Copyright 2018' class ScmHost(object): """Parent of all ScmHost objects.""" class ScmHostError(Exception): """Parent of all ScmHost errors.""" class ScmHostRepo(object): """Parent of all SCM repos.""" @property def name(self): """Get the name of the repo.""" raise NotImplementedError('Must implement name') @property def id(self): """Get the id of the repo.""" raise NotImplementedError('Must implement id') @property def description(self): """Get the description of the repo.""" raise NotImplementedError('Must implement description') @property def browse_url(self): """Get the url to open to display the repo.""" raise NotImplementedError('Must implement browse_url') @property def ssh_url(self): """Get the ssh url to clone the repo.""" raise NotImplementedError('Must implement ssh_url') def __str__(self): """Return the id as the string representation.""" return self.id def __repr__(self): """Return the id as the string representation.""" return self.id

mit

randy3k/AutoWrap

tests/test_longline.py

1

2204

import sublime from unittesting import DeferrableTestCase Lorem = ("""Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod""" """tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam,""" """quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo""" """consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse""" """cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non""" """proident, sunt in culpa qui officia deserunt mollit anim id est \nlaborum.""") class TestLongline(DeferrableTestCase): def setUp(self): # make sure we have a window to work with s = sublime.load_settings("Preferences.sublime-settings") s.set("close_windows_when_empty", False) self.view = sublime.active_window().new_file() self.view.settings().set("auto_wrap", True) self.view.settings().set("auto_wrap_width", 80) def tearDown(self): if self.view: self.view.set_scratch(True) self.view.window().focus_view(self.view) self.view.window().run_command("close_file") def setText(self, string): self.view.run_command("insert", {"characters": string}) def getRow(self, row): return self.view.substr(self.view.line(self.view.text_point(row, 0))) def test_long_line_end(self): self.setText(Lorem) self.view.sel().clear() self.view.sel().add(sublime.Region(433, 433)) for c in "apple is orange": self.setText(c) yield 10 self.assertEqual(self.getRow(5), "culpa qui officia deserunt mollit anim id est apple is orange") self.assertEqual(self.getRow(6), "laborum.") def test_long_line_middle(self): self.setText(Lorem) self.view.sel().clear() self.view.sel().add(sublime.Region(200, 200)) for c in "apple is orange": self.setText(c) yield 10 self.assertEqual( self.getRow(1), "incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam,quis" )

mit

dubourg/openturns

python/test/t_FisherSnedecor_std.py

1

4992

#! /usr/bin/env python from __future__ import print_function from openturns import * from cmath import * TESTPREAMBLE() RandomGenerator.SetSeed(0) try: # Instanciate one distribution object distribution = FisherSnedecor(5.5, 10.5) print("Distribution ", repr(distribution)) print("Distribution ", distribution) # Is this distribution elliptical ? print("Elliptical = ", distribution.isElliptical()) # Is this distribution continuous ? print("Continuous = ", distribution.isContinuous()) # Test for realization of distribution oneRealization = distribution.getRealization() print("oneRealization=", repr(oneRealization)) # Test for sampling size = 10000 oneSample = distribution.getSample(size) print("oneSample first=", repr( oneSample[0]), " last=", repr(oneSample[size - 1])) print("mean=", repr(oneSample.computeMean())) print("covariance=", repr(oneSample.computeCovariance())) size = 100 for i in range(2): msg = '' if FittingTest.Kolmogorov(distribution.getSample(size), distribution).getBinaryQualityMeasure(): msg = "accepted" else: msg = "rejected" print( "Kolmogorov test for the generator, sample size=", size, " is", msg) size *= 10 # Define a point point = NumericalPoint(distribution.getDimension(), 1.0) print("Point= ", repr(point)) # Show PDF and CDF of point eps = 1e-5 # derivative of PDF with regards its arguments DDF = distribution.computeDDF(point) # print "ddf =" , repr(DDF) # by the finite difference technique # print "ddf (FD)=" ,repr(NumericalPoint(1, (distribution.computePDF( # point + NumericalPoint(1, eps) ) - distribution.computePDF( point + # NumericalPoint(1, -eps) )) / (2.0 * eps))) # PDF value LPDF = distribution.computeLogPDF(point) print("log pdf=%.6f" % LPDF) PDF = distribution.computePDF(point) print("pdf =%.6f" % PDF) # by the finite difference technique from CDF print("pdf (FD)=%.6f" % ((distribution.computeCDF(point + NumericalPoint(1, eps)) - distribution.computeCDF(point + NumericalPoint(1, -eps))) / (2.0 * eps))) # derivative of the PDF with regards the parameters of the distribution CDF = distribution.computeCDF(point) print("cdf=%.6f" % CDF) CCDF = distribution.computeComplementaryCDF(point) print("ccdf=%.6f" % CCDF) CF = distribution.computeCharacteristicFunction(point[0]) print("characteristic function=(%.6f+%.6fj)" % (CF.real, CF.imag)) ## PDFgr = distribution.computePDFGradient( point ) # print "pdf gradient =" , repr(PDFgr) # by the finite difference technique ## PDFgrFD = NumericalPoint(2) ## PDFgrFD[0] = (FisherSnedecor(distribution.getLambda() + eps, distribution.getGamma()).computePDF(point) - FisherSnedecor(distribution.getLambda() - eps, distribution.getGamma()).computePDF(point)) / (2.0 * eps) ## PDFgrFD[1] = (FisherSnedecor(distribution.getLambda(), distribution.getGamma() + eps).computePDF(point) - FisherSnedecor(distribution.getLambda(), distribution.getGamma() - eps).computePDF(point)) / (2.0 * eps) # print "pdf gradient (FD)=" , repr(PDFgrFD) # derivative of the PDF with regards the parameters of the distribution ## CDFgr = distribution.computeCDFGradient( point ) # print "cdf gradient =" , repr(CDFgr) ## CDFgrFD = NumericalPoint(2) ## CDFgrFD[0] = (FisherSnedecor(distribution.getLambda() + eps, distribution.getGamma()).computeCDF(point) - FisherSnedecor(distribution.getLambda() - eps, distribution.getGamma()).computeCDF(point)) / (2.0 * eps) ## CDFgrFD[1] = (FisherSnedecor(distribution.getLambda(), distribution.getGamma() + eps).computeCDF(point) - FisherSnedecor(distribution.getLambda(), distribution.getGamma() - eps).computeCDF(point)) / (2.0 * eps) # print "cdf gradient (FD)=", repr(CDFgrFD) # quantile quantile = distribution.computeQuantile(0.95) print("quantile=", repr(quantile)) print("cdf(quantile)=%.6f" % distribution.computeCDF(quantile)) mean = distribution.getMean() print("mean=", repr(mean)) standardDeviation = distribution.getStandardDeviation() print("standard deviation=", repr(standardDeviation)) skewness = distribution.getSkewness() print("skewness=", repr(skewness)) kurtosis = distribution.getKurtosis() print("kurtosis=", repr(kurtosis)) covariance = distribution.getCovariance() print("covariance=", repr(covariance)) parameters = distribution.getParametersCollection() print("parameters=", repr(parameters)) for i in range(6): print("standard moment n=", i, " value=", distribution.getStandardMoment(i)) print("Standard representative=", distribution.getStandardRepresentative()) except: import sys print("t_FisherSnedecor_std.py", sys.exc_info()[0], sys.exc_info()[1])

gpl-3.0

Fuchai/Philosophy-Machine

knowledgeframework/playground2.py

1

3640

from knowledgeframework.kf2 import * kf=KF() pred1 = Predicate(id="male") pred2 = Predicate(id="single") pred4 = Predicate(id="bachelor") pred5 = Predicate(id="thief") pred6 = Predicate(id="steals") pred7 = Predicate(id="female") pred8 = Predicate(id="human") kf.add_node(pred1, name="male") kf.add_node(pred2, name="man") kf.add_node(pred4, name="bachelor") pred3 = Analytical(kf, lambda x, y: x and y, (pred1, pred2), id="AND") kf.add_node(pred3) kf.add_node(pred6, name="thief") kf.add_node(pred5, name="steals") kf.add_edge(pred5, pred6) kf.add_node(pred7) kf.add_node(pred8) kf.make_dimension(pred8) # pred8 human is a dimension kf.add_edge_to_instance(pred1) # known man kf.add_edge_to_instance(pred2) # known male print(kf.consistency_search_through_dimensions(kf.get_instance())) pred9=Predicate(id="dummy") kf.add_node(pred9) kf.add_edge_to_instance(pred7) print(kf.consistency_search_through_dimensions(kf.get_instance())) print(kf.static_proof("bachelor")) print(kf.dynamic_eval("bachelor")) # pred1=Predicate(id="1") # pred2=Predicate(id="2") # pred4=Predicate(id="4") # pred5=Predicate(id="5") # pred6=Predicate(id="6") # pred7=Predicate(id="7") # # # # knowledgeframework.add_node(pred1,name="male") # knowledgeframework.add_node(pred2,name="man") # pred3=Analytical(knowledgeframework,lambda x,y: x and y,(pred1,pred2),id="3") # # knowledgeframework.add_node(pred3) # bachelor analytical # knowledgeframework.add_node(pred4,name="bachelor") # knowledgeframework.add_edge(pred3,pred4) # # knowledgeframework.add_node(pred6,name="thief") # knowledgeframework.add_node(pred5,name="steals") # knowledgeframework.add_edge(pred5,pred6) # knowledgeframework.add_node(pred7) # # knowledgeframework.add_edge_to_instance(pred1) # known man # knowledgeframework.add_edge_to_instance(pred2) # known male # # # if pred3.eval()==True: # # knowledgeframework.add_edge_to_instance(pred3) # # print(knowledgeframework.static_proof(pred4)) # print(knowledgeframework.hybrid_eval_I(pred4)) # True! # knowledgeframework=KF() # pred1=Predicate() # pred2=Predicate() # # knowledgeframework.add_node(pred1,name="red") # knowledgeframework.add_node(pred2,name="apple") # knowledgeframework.add_edge(pred2,pred1) # # print(1,knowledgeframework.nodes()) # print(knowledgeframework.edges()) # print(2,knowledgeframework.find_name("apple")) # print(3,knowledgeframework.find_name("red")) # print(4,knowledgeframework.predecessors_set(knowledgeframework.find_name("apple"))) # #print(knowledgeframework.predecessors(knowledgeframework[knowledgeframework.find_name("apple")[0]])) # # # # Noteworthy:"apple"'s successor is the "name" labels, and the predecessors return all the names. This is an interesting # # operation, since it basically returns everything that has some directly overlapped properties. # print(knowledgeframework.predecessors_set(knowledgeframework.successors_set(["apple"]))) # # dummy1=knowledgeframework.nodes()[3] # dummy2=knowledgeframework.nodes()[4] # # # Example of a proof that an apple is red # print(5,knowledgeframework.get_node_from_hash("instance") in knowledgeframework.nodes()) # knowledgeframework.add_edge(knowledgeframework.get_node_from_hash("instance"),knowledgeframework.find_name("apple")[0]) # print(networkx.shortest_path(knowledgeframework,knowledgeframework.get_instance(),knowledgeframework.find_name("red")[0])) # # # Fast query # knowledgeframework.static_proof(knowledgeframework.find_name_unqiue("red")) # # # def hello(*args): # for i in args: # print(i) # # print (type(args)) # # # def ya(i, *args): # print("starting") # hello(*args) # # # # ya(2, 3, 4, 5)

apache-2.0

tensorflow/privacy

tensorflow_privacy/privacy/estimators/multi_label_head.py

1

6457

# Copyright 2020, The TensorFlow Authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """Multiclass head for Estimator that allow integration with TF Privacy.""" from __future__ import absolute_import from __future__ import division from __future__ import print_function import tensorflow as tf from tensorflow.python.keras.utils import losses_utils # pylint: disable=g-direct-tensorflow-import from tensorflow_estimator.python.estimator import model_fn from tensorflow_estimator.python.estimator.canned import prediction_keys from tensorflow_estimator.python.estimator.export import export_output from tensorflow_estimator.python.estimator.head import base_head from tensorflow_estimator.python.estimator.mode_keys import ModeKeys class DPMultiLabelHead(tf.estimator.MultiLabelHead): """Creates a TF Privacy-enabled version of MultiLabelHead.""" def __init__(self, n_classes, weight_column=None, thresholds=None, label_vocabulary=None, loss_reduction=tf.keras.losses.Reduction.SUM_OVER_BATCH_SIZE, loss_fn=None, classes_for_class_based_metrics=None, name=None): if loss_reduction == tf.keras.losses.Reduction.NONE: loss_reduction = tf.keras.losses.Reduction.SUM_OVER_BATCH_SIZE super(DPMultiLabelHead, self).__init__( n_classes=n_classes, weight_column=weight_column, thresholds=thresholds, label_vocabulary=label_vocabulary, loss_reduction=tf.keras.losses.Reduction.SUM_OVER_BATCH_SIZE, loss_fn=loss_fn, classes_for_class_based_metrics=classes_for_class_based_metrics, name=name) def loss(self, labels, logits, features=None, mode=None, regularization_losses=None): """Returns regularized training loss. See `base_head.Head` for details.""" del mode # Unused for this head. with tf.compat.v1.name_scope( 'losses', values=(logits, labels, regularization_losses, features)): logits = base_head.check_logits_final_dim(logits, self.logits_dimension) labels = self._processed_labels(logits, labels) unweighted_loss, weights = self._unweighted_loss_and_weights( logits, labels, features) vector_training_loss = losses_utils.compute_weighted_loss( unweighted_loss, sample_weight=weights, reduction=tf.keras.losses.Reduction.NONE) regularization_loss = tf.math.add_n( regularization_losses) if regularization_losses is not None else None vector_regularized_training_loss = ( tf.add(vector_training_loss, regularization_loss) if regularization_loss is not None else vector_training_loss) return vector_regularized_training_loss def _create_tpu_estimator_spec(self, features, mode, logits, labels=None, optimizer=None, trainable_variables=None, train_op_fn=None, update_ops=None, regularization_losses=None): """See superclass for description.""" with tf.compat.v1.name_scope(self._name, 'head'): # Predict. pred_keys = prediction_keys.PredictionKeys predictions = self.predictions(logits) if mode == ModeKeys.PREDICT: probabilities = predictions[pred_keys.PROBABILITIES] classifier_output = base_head.classification_output( scores=probabilities, n_classes=self._n_classes, label_vocabulary=self._label_vocabulary) return model_fn._TPUEstimatorSpec( # pylint: disable=protected-access mode=ModeKeys.PREDICT, predictions=predictions, export_outputs={ base_head.DEFAULT_SERVING_KEY: classifier_output, base_head.CLASSIFY_SERVING_KEY: classifier_output, base_head.PREDICT_SERVING_KEY: export_output.PredictOutput(predictions) }) regularized_training_loss = self.loss( logits=logits, labels=labels, features=features, mode=mode, regularization_losses=regularization_losses) scalar_loss = tf.reduce_mean(regularized_training_loss) # Eval. if mode == ModeKeys.EVAL: eval_metrics = self.metrics(regularization_losses=regularization_losses) return model_fn._TPUEstimatorSpec( # pylint: disable=protected-access mode=ModeKeys.EVAL, predictions=predictions, loss=scalar_loss, eval_metrics=base_head.create_eval_metrics_tuple( self.update_metrics, { 'eval_metrics': eval_metrics, 'features': features, 'logits': logits, 'labels': labels, 'regularization_losses': regularization_losses })) # Train. train_op = base_head.create_estimator_spec_train_op( head_name=self._name, optimizer=optimizer, train_op_fn=train_op_fn, update_ops=update_ops, trainable_variables=trainable_variables, regularized_training_loss=regularized_training_loss, loss_reduction=self._loss_reduction) # Create summary. base_head.create_estimator_spec_summary( regularized_training_loss=scalar_loss, regularization_losses=regularization_losses, summary_key_fn=self._summary_key) return model_fn._TPUEstimatorSpec( # pylint: disable=protected-access mode=ModeKeys.TRAIN, predictions=predictions, loss=scalar_loss, train_op=train_op)

apache-2.0

DentonJC/virtual_screening

moloi/descriptors/morgan_descriptor.py

1

1427

#!/usr/bin/env python """ https://github.com/kudkudak """ import numpy as np from rdkit import Chem from rdkit.Chem import AllChem def smiles_to_morgan(smi, hashed=True, radius=2, n_bits=300): mol = Chem.MolFromSmiles(smi) if hashed: try: vect = AllChem.GetHashedMorganFingerprint(mol=mol, radius=radius, nBits=n_bits) vect = vect.GetNonzeroElements() vect_keys = list(vect.keys()) vect_values = list(vect.values()) # Not sure how to transform it better vect_dense = np.zeros(shape=(n_bits,)) vect_dense[vect_keys] = vect_values return vect_dense except: print("Failed computing morgan fingerprint for %s", smi) return np.zeros(shape=(n_bits,)) else: try: mol = Chem.MolFromSmiles(smi) vect = AllChem.GetMorganFingerprintAsBitVect(mol=mol, radius=radius, nBits=n_bits) return np.array(vect) except: print("Failed computing morgan fingerprint for %s", smi) return np.zeros(shape=(n_bits,)) if __name__ == "__main__": features = smiles_to_morgan("CC") print(features)

gpl-3.0

maym2104/ift6266-h17-project

lib/updates.py

1

9422

""" Copyright (c) 2017 - Philip Paquette Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ # Modified from https://raw.githubusercontent.com/Newmu/dcgan_code/master/lib/updates.py # MIT License import theano import theano.tensor as T from .utils import floatX from .layers import l2norm # ------------------------ # Regularization # ------------------------ def clip_norm(grad, clip, norm): if clip > 0: grad = T.switch(T.ge(norm, clip), grad * clip / norm, grad) return grad def clip_norms(grads, clip): norm = T.sqrt(sum([T.sum(grad ** 2) for grad in grads])) return [clip_norm(grad, clip, norm) for grad in grads] # Base regularizer class Regularizer(object): def __init__(self, l1=0., l2=0., maxnorm=0., l2norm=False, frobnorm=False): self.__dict__.update(locals()) def max_norm(self, param, maxnorm): if maxnorm > 0: norms = T.sqrt(T.sum(T.sqr(param), axis=0)) desired = T.clip(norms, 0, maxnorm) param = param * (desired / (1e-7 + norms)) return param def l2_norm(self, param): return param / l2norm(param, axis=0) def frob_norm(self, param, nrows): return (param / T.sqrt(T.sum(T.sqr(param)))) * T.sqrt(nrows) def gradient_regularize(self, param, grad): grad += param * self.l2 grad += T.sgn(param) * self.l1 return grad def weight_regularize(self, param): param = self.max_norm(param, self.maxnorm) if self.l2norm: param = self.l2_norm(param) if self.frobnorm > 0: param = self.frob_norm(param, self.frobnorm) return param # ------------------------ # Updates # ------------------------ class Update(object): def __init__(self, regularizer=Regularizer(), clipnorm=0.): self.__dict__.update(locals()) def __call__(self, params, grads): raise NotImplementedError # Stochastic Gradient Descent class SGD(Update): def __init__(self, lr=0.01, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) updated_param = param - self.lr * grad updated_param = self.regularizer.weight_regularize(updated_param) updates.append((param, updated_param)) return updates # SGD with momentum class Momentum(Update): def __init__(self, lr=0.01, momentum=0.9, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) m = theano.shared(param.get_value() * 0.) v = (self.momentum * m) - (self.lr * grad) updates.append((m, v)) updated_param = param + v updated_param = self.regularizer.weight_regularize(updated_param) updates.append((param, updated_param)) return updates # SGD with Nesterov Accelerated Gradient class Nesterov(Update): def __init__(self, lr=0.01, momentum=0.9, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) m = theano.shared(param.get_value() * 0.) v = (self.momentum * m) - (self.lr * grad) updated_param = param + self.momentum * v - self.lr * grad updated_param = self.regularizer.weight_regularize(updated_param) updates.append((m, v)) updates.append((param, updated_param)) return updates # RMS Prop class RMSprop(Update): def __init__(self, lr=0.001, rho=0.9, epsilon=1e-6, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) acc = theano.shared(param.get_value() * 0.) acc_new = self.rho * acc + (1 - self.rho) * grad ** 2 updates.append((acc, acc_new)) updated_param = param - self.lr * (grad / T.sqrt(acc_new + self.epsilon)) updated_param = self.regularizer.weight_regularize(updated_param) updates.append((param, updated_param)) return updates # Adam class Adam(Update): def __init__(self, lr=0.001, b1=0.9, b2=0.999, e=1e-8, l=1 - 1e-8, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) t = theano.shared(floatX(1.)) b1_t = self.b1 * self.l ** (t - 1) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) m = theano.shared(param.get_value() * 0.) v = theano.shared(param.get_value() * 0.) m_t = b1_t * m + (1 - b1_t) * grad v_t = self.b2 * v + (1 - self.b2) * grad ** 2 m_c = m_t / (1 - self.b1 ** t) v_c = v_t / (1 - self.b2 ** t) p_t = param - (self.lr * m_c) / (T.sqrt(v_c) + self.e) p_t = self.regularizer.weight_regularize(p_t) updates.append((m, m_t)) updates.append((v, v_t)) updates.append((param, p_t)) updates.append((t, t + 1.)) return updates # AdaGrad class Adagrad(Update): def __init__(self, lr=0.01, epsilon=1e-6, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) acc = theano.shared(param.get_value() * 0.) acc_t = acc + grad ** 2 updates.append((acc, acc_t)) p_t = param - (self.lr / T.sqrt(acc_t + self.epsilon)) * grad p_t = self.regularizer.weight_regularize(p_t) updates.append((param, p_t)) return updates # AdeDelta class Adadelta(Update): def __init__(self, lr=0.5, rho=0.95, epsilon=1e-6, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] grads = T.grad(cost, params) grads = clip_norms(grads, self.clipnorm) for param, grad in zip(params, grads): grad = self.regularizer.gradient_regularize(param, grad) acc = theano.shared(param.get_value() * 0.) acc_delta = theano.shared(param.get_value() * 0.) acc_new = self.rho * acc + (1 - self.rho) * grad ** 2 updates.append((acc, acc_new)) update = grad * T.sqrt(acc_delta + self.epsilon) / T.sqrt(acc_new + self.epsilon) updated_param = param - self.lr * update updated_param = self.regularizer.weight_regularize(updated_param) updates.append((param, updated_param)) acc_delta_new = self.rho * acc_delta + (1 - self.rho) * update ** 2 updates.append((acc_delta, acc_delta_new)) return updates # No updates class NoUpdate(Update): def __init__(self, lr=0.01, momentum=0.9, *args, **kwargs): Update.__init__(self, *args, **kwargs) self.__dict__.update(locals()) def __call__(self, params, cost): updates = [] for param in params: updates.append((param, param)) return updates

mit

Stunkymonkey/passworts

calc.py

1

2206

#!/usr/bin/env python3 import os.path from collections import defaultdict import pickle from optparse import OptionParser import sys n = 3 def analyse(counts, text, n): """analyse text with n chars markov state, update the counts""" text = '^' * n + text + '$' * n for i in range(len(text) - n): st = i, text[i:i + n] next = text[i + n] counts[st][next] += 1 return counts def compute_prob(counts): """compute ranges in [0 .. 1) of the given words""" for c1 in counts: total = float(sum(counts[c1][c2] for c2 in counts[c1])) base = 0.0 for c2 in counts[c1]: prob = counts[c1][c2] / total base = base + prob counts[c1][c2] = base return counts def text_import(dict_path, source): """reads a file to analyse""" try: with open(dict_path + source, "r", encoding="ISO-8859-1") as f: text = set(f.read().split()) except FileNotFoundError as e: raise SystemExit("Could not open text file: " + str(e)) return text def dd(): return defaultdict(int) def calculate(source): print("reading...") dict_path = os.path.join(os.path.abspath(".") + r"/dict/") text = text_import(dict_path, source) source = source.split(".")[0] print("analysing text...") counts = defaultdict(dd) for word in text: counts = analyse(counts, word, n) print("calculating...") counts = compute_prob(counts) # print(type(counts)) # print(counts) # save to file print("write...") with open((dict_path + source + '.pickle'), 'wb') as handle: pickle.dump(counts, handle) print("checking file...") with open((dict_path + source + '.pickle'), 'rb') as handle: written = pickle.load(handle) if written == counts: print("Calucation was sucessfull") else: print("Something went wrong") sys.exit(1) if __name__ == '__main__': parser = OptionParser() parser.add_option("-f", "--file", type="string", dest="filename", help="Name of the input file") (options, args) = parser.parse_args() calculate(options.filename)

mit

wolfsonliu/crispr

pycas/script/pycasanalysis.py

1

3253

#! /bin/env python3 __all__ = ['pycaspattern'] # ------------------ # Libraries # ------------------ import argparse import os import sys sys.path.append('/gpfs/user/liuzh/Code/crispr') import pandas as pd from pycas.analysis import Screening from pycas.utils.decorator import helpstring from pycas.utils.decorator import AppendHelp # ------------------ # Functions # ------------------ def pycasanalysis(filename, ctrl_label, exp_label, method, hasbarcode, out_dir): file_type = 'csv' if filename.split('.')[-1] == 'txt': sep = '\t' file_type = 'txt' elif filename.split('.')[-1] == 'csv': sep = ',' file_type = 'csv' else: raise ValueError('Input data file should be txt or csv') if file_type == 'csv': data = pd.read_csv(filename, header=0) else: data = pd.read_table(filename, header=0, sep='\t') for x in ['gene', 'guide', 'barcode']: if x not in data.columns: raise ValueError('Input data file should contain column named as: ' + x) if len(ctrl_label) != len(exp_label): raise ValueError('Input control labels and treatment labels should be of the same length.') if out_dir != '' and not os.path.exists(out_dir): os.mkdir(out_dir) if method not in ['sunbird', 'mw']: raise ValueError('The test method should be in: sunbird mw.') analysis = Screening(data, ctrl_label, exp_label, hasbarcode=hasbarcode) if method == 'sunbird': analysis.sunbird(10) analysis.test['sunbird'].to_csv( os.path.join(out_dir, 'pycas_analysis_sunbird.csv') ) else: pass # ------------------ # Main # ------------------ if __name__ == '__main__': parser = argparse.ArgumentParser( prog='pycasanalysis', description='Analysis the library screening result.' ) parser.add_argument( '-i', '--input', required=True, help='Input data file path, with columns: gene, guide <, barcode>, [labels]. (column names should be in the csv file).' ) parser.add_argument( '-c', '--control-label', nargs='+', help='Control experiment labels, separeted by space.' ) parser.add_argument( '-t', '--treat-label', nargs='+', help='Treatment experiment labels, separeted by space.' ) parser.add_argument( '-m', '--method', default='sunbird', help='Method to be used in the analysis: sunbird, mw.' ) parser.add_argument( '--has-barcode', action='store_true', help='Input data should be tested consider barcodes.' ) parser.add_argument( '--out-dir', default='', help='Result output directory，default is current work directory.' ) args = parser.parse_args() def analysis(**args): pycasanalysis( filename=args['input'], ctrl_label=args['control_label'], exp_label=args['treat_label'], method=args['method'], hasbarcode=args['has_barcode'], out_dir=args['out_dir'] ) analysis(**vars(args)) # ------------------ # EOF # ------------------

gpl-3.0

alberthdev/cihelper

cihelper/download.py

1

2101

#!/usr/bin/env python3 import os import requests import time from collections import namedtuple from urllib3.util.retry import Retry from requests.adapters import HTTPAdapter class TimeoutRequestsSession(requests.Session): def __init__(self, *args, **kwargs): self.__default_timeout = None if 'timeout' in kwargs: self.__default_timeout = kwargs.pop('timeout') super().__init__(*args, **kwargs) def request(self, *args, **kwargs): if self.__default_timeout: kwargs.setdefault('timeout', self.__default_timeout) return super(TimeoutRequestsSession, self).request(*args, **kwargs) SessionSettings = namedtuple("SessionSettings", ["total_retries", "timeout", "backoff_factor", "status_forcelist"]) cached_sessions = {} def get_session(total_retries=5, timeout=60, backoff_factor=1, status_forcelist=None): if not status_forcelist: status_forcelist = (500, 502, 503, 504) settings = SessionSettings(total_retries=total_retries, timeout=timeout, backoff_factor=backoff_factor, status_forcelist=status_forcelist) if settings in cached_sessions: return cached_sessions[settings] session = TimeoutRequestsSession(timeout=timeout) retries = Retry(total=total_retries, backoff_factor=backoff_factor, status_forcelist=status_forcelist) session.mount("http://", HTTPAdapter(max_retries=retries)) session.mount("httsp://", HTTPAdapter(max_retries=retries)) cached_sessions[settings] = session return session def check_url(session, url): response = session.get(url) return response.status_code < 400 def download_file(session, url, dest=None, chunk_size=8192): dl_attempts = 0 dest = dest or os.path.basename(url) with session.get(url, stream=True) as response: response.raise_for_status() with open(dest, 'wb') as fh: for chunk in r.iter_content(chunk_size=chunk_size): fh.write(chunk) return dest

mit

kennt/fixtest

simple/logon_controller.py

1

4782

""" Simple client/server controller for testing. Copyright (c) 2014 Kenn Takara See LICENSE for details """ import logging from fixtest.base.asserts import * from fixtest.base.controller import TestCaseController from fixtest.fix.constants import FIX from fixtest.fix.messages import logon_message, logout_message from fixtest.fix.transport import FIXTransportFactory class LogonController(TestCaseController): """ The base class for FIX-based TestCaseControllers. This creates a client and a server that will communicate with each other. So they will use the same link config. """ def __init__(self, **kwargs): super(LogonController, self).__init__(**kwargs) self.testcase_id = 'Simple-1' self.description = 'Test of the command-line tool' config = kwargs['config'] self.server_config = config.get_role('test-server') self.server_config.update({'name': 'server-9940'}) self.server_link_config = config.get_link('client', 'test-server') self.server_link_config.update({ 'sender_compid': self.server_link_config['test-server'], 'target_compid': self.server_link_config['client'], }) self.client_config = config.get_role('client') self.client_config.update({'name': 'client-9940'}) self.client_link_config = config.get_link('client', 'test-server') self.client_link_config.update({ 'sender_compid': self.client_link_config['client'], 'target_compid': self.client_link_config['test-server'], }) self._servers = dict() self._clients = dict() factory = FIXTransportFactory('server-9940', self.server_config, self.server_link_config) factory.filter_heartbeat = False server = { 'name': 'server-9940', 'port': self.server_link_config['port'], 'factory': factory, } self._servers[server['name']] = server # In the client case we do not need to provide a # factory, Just need a transport. client = { 'name': 'client-9940', 'host': self.client_link_config['host'], 'port': self.client_link_config['port'], 'node': factory.create_transport('client-9940', self.client_config, self.client_link_config), } self._clients[client['name']] = client self._logger = logging.getLogger(__name__) def clients(self): """ The clients that need to be started """ return self._clients def servers(self): """ The servers that need to be started """ return self._servers def setup(self): """ For this case, wait until our servers are all connected before continuing with the test. """ # at this point the servers should be waiting # so startup the clients self.wait_for_client_connections(10) self.wait_for_server_connections(10) def teardown(self): pass def run(self): """ This test is a demonstration of logon and heartbeat/TestRequest processing. Usually the logon process should be done from setup(). """ client = self._clients['client-9940']['node'] client.protocol.heartbeat = 5 # We only have a single server connection server = self._servers['server-9940']['factory'].servers[0] server.protocol.heartbeat = 5 # client -> server client.send_message(logon_message(client)) # server <- client message = server.wait_for_message(title='waiting for logon') assert_is_not_none(message) assert_tag(message, [(35, FIX.LOGON)]) # server -> client server.send_message(logon_message(server)) server.start_heartbeat(True) # client <- server message = client.wait_for_message(title='waiting for logon ack') client.start_heartbeat(True) assert_is_not_none(message) assert_tag(message, [(35, FIX.LOGON)]) # Logout client.send_message(logout_message(client)) message = server.wait_for_message(title='waiting for logout') assert_is_not_none(message) assert_tag(message, [(35, FIX.LOGOUT)]) server.send_message(logout_message(server)) server.start_heartbeat(False) message = client.wait_for_message('waiting for logout ack') client.start_heartbeat(False) assert_is_not_none(message) assert_tag(message, [(35, FIX.LOGOUT)])

mit

gwob/Maarifa

twpm/manage.py

1

5250

from csv import DictReader from datetime import datetime from pprint import pprint from flask.ext.script import Manager from taarifa_api import add_document, delete_documents, get_schema from taarifa_waterpoints import app from taarifa_waterpoints.schemas import facility_schema, service_schema manager = Manager(app) def check(response, success=201, print_status=True): data, _, _, status = response if status == success: if print_status: print " Succeeded" return True print "Failed with status", status pprint(data) return False @manager.option("resource", help="Resource to show the schema for") def show_schema(resource): """Show the schema for a given resource.""" pprint(get_schema(resource)) @manager.command def list_routes(): """List all routes defined for the application.""" import urllib for rule in sorted(app.url_map.iter_rules(), key=lambda r: r.endpoint): methods = ','.join(rule.methods) print urllib.unquote("{:40s} {:40s} {}".format(rule.endpoint, methods, rule)) @manager.command def create_facility(): """Create facility for waterpoints.""" check(add_document('facilities', facility_schema)) @manager.command def create_service(): """Create service for waterpoints.""" check(add_document('services', service_schema)) @manager.command def delete_facilities(): """Delete all facilities.""" check(delete_documents('facilities'), 200) @manager.command def delete_services(): """Delete all services.""" check(delete_documents('services'), 200) @manager.command def delete_requests(): """Delete all requests.""" check(delete_documents('requests'), 200) @manager.option("filename", help="CSV file to upload (required)") @manager.option("--skip", type=int, default=0, help="Skip a number of records") @manager.option("--limit", type=int, help="Only upload a number of records") def upload_waterpoints(filename, skip=0, limit=None): """Upload waterpoints from a CSV file.""" # Use sys.stdout.write so waterpoints can be printed nicely and succinctly import sys date_converter = lambda s: datetime.strptime(s, "%Y-%m-%dT%H:%M:%SZ") bool_converter = lambda s: s == "T" status_map = { "non functional": "not functional", "functional needs repair": "needs repair" } status_converter = lambda s: status_map.get(s.lower(), s.lower()) convert = { 'latitude': float, 'longitude': float, 'gid': int, 'objectid': int, 'valid_from': date_converter, 'valid_to': date_converter, 'amount_tsh': float, 'breakdown_year': int, 'date_recorded': date_converter, 'gps_height': float, 'x_wgs84': float, 'y_wgs84': float, 'num_privcon': int, 'pop_served': int, 'public_meeting': bool_converter, 'construction_year': int, 'status_group': status_converter, 'region_code': int, 'district_code': int, 'ward_code': int } def print_flush(msg): sys.stdout.write(msg) sys.stdout.flush() facility_code = "wpf001" print_every = 1000 print_flush("Adding waterpoints. Please be patient.") with open(filename, 'rU') as f: reader = DictReader(f) for i in range(skip): reader.next() for i, d in enumerate(reader): actual_index = i + skip + 2 do_print = actual_index % print_every == 0 try: d = dict((k, convert.get(k, str)(v)) for k, v in d.items() if v) coords = [d.pop('longitude'), d.pop('latitude')] d['location'] = {'type': 'Point', 'coordinates': coords} d['facility_code'] = facility_code if not check(add_document('waterpoints', d), 201, False): raise Exception() if do_print: print_flush(".") except Exception as e: print "Error adding waterpoint", e pprint(d) exit() if limit and i >= limit: break # Create a 2dsphere index on the location field for geospatial queries app.data.driver.db['resources'].ensure_index([('location', '2dsphere')]) print "Waterpoints uploaded!" @manager.command def ensure_indexes(): """Make sure all important database indexes are created.""" print "Ensuring resources:location 2dsphere index is created ..." app.data.driver.db['resources'].ensure_index([('location', '2dsphere')]) print "Done!" @manager.option("status", help="Status (functional or non functional)") @manager.option("wp", help="Waterpoint id") def create_request(wp, status): """Create an example request reporting a broken waterpoint""" r = {"service_code": "wps001", "attribute": {"waterpoint_id": wp, "status": status}} check(add_document("requests", r)) @manager.command def delete_waterpoints(): """Delete all existing waterpoints.""" print delete_documents('waterpoints') if __name__ == "__main__": manager.run()

apache-2.0

kevinah95/bmc-sequence-alignment

algorithms/needleman_wunsch/plot_nw.py

1

3189

import matplotlib.pyplot as plt import matplotlib.ticker as ticker import numpy as np import datetime from Bio.Seq import Seq if __name__ == '__main__': from needleman_wunsch import needleman_wunsch else: from .needleman_wunsch import needleman_wunsch #------------------------------- def plot_nw(seq_alpha_col,seq_beta_row,p_penalty): if not seq_alpha_col or not seq_beta_row: print("Alguna de las secuencias está vacía.") return plt.rcParams["figure.figsize"] = 20, 20 param = {"grid.linewidth": 1.6, "grid.color": "lightgray", "axes.linewidth": 1.6, "axes.edgecolor": "lightgray", "font.size": 8} plt.rcParams.update(param) # Data headh = seq_alpha_col headv = seq_beta_row score_matrix, pt_mat, arrows = needleman_wunsch(seq_alpha_col,seq_beta_row,p_penalty,score_only=False) # Plot fig, ax = plt.subplots() ax.set_xlim(-1.5, score_matrix.shape[1] - .5) ax.set_ylim(-1.5, score_matrix.shape[0] - .5) ax.invert_yaxis() for i in range(score_matrix.shape[0]): for j in range(score_matrix.shape[1]): ax.text(j, i, score_matrix[i, j], ha="center", va="center") for i, l in enumerate(headh): ax.text(i + 1, -1, l, ha="center", va="center", fontweight="semibold") for i, l in enumerate(headv): ax.text(-1, i + 1, l, ha="center", va="center", fontweight="semibold") ax.xaxis.set_minor_locator(ticker.FixedLocator( np.arange(-1.5, score_matrix.shape[1] - .5, 1))) ax.yaxis.set_minor_locator(ticker.FixedLocator( np.arange(-1.5, score_matrix.shape[1] - .5, 1))) plt.tick_params(axis='both', which='both', bottom='off', top='off', left="off", right="off", labelbottom='off', labelleft='off') #-----------ax.set_aspect('auto') ax.grid(True, which='minor') arrowprops = dict(facecolor='blue', alpha=0.5, lw=0, shrink=0.2, width=2, headwidth=7, headlength=7) # all path for i in range(1,pt_mat.shape[0]): for j in range(1,pt_mat.shape[1]): if(pt_mat[i][j]['left'] != ''): ax.annotate("", xy=(j-1,i), xytext=(j,i), arrowprops=arrowprops) if(pt_mat[i][j]['diagonal'] != ''): ax.annotate("", xy=(j-1,i-1), xytext=(j,i), arrowprops=arrowprops) if(pt_mat[i][j]['up'] != ''): ax.annotate("", xy=(j,i-1), xytext=(j,i), arrowprops=arrowprops) # optimal path arrowprops.update(facecolor='crimson') for i in range(arrows.shape[0]): ax.annotate("", xy=arrows[i, 2:], # origin xytext=arrows[i, :2], arrowprops=arrowprops) #------------ plt.gca().set_aspect('auto') time = '{:%Y-%m-%d_%H-%M-%S}'.format(datetime.datetime.now()) plt.savefig("output/needleman_wunsch/output-nw_"+time+".pdf", dpi=600) #plt.show() if __name__ == '__main__': alpha = Seq("ACTCA") beta = Seq("TTCAT") penalty = {'MATCH': 1, 'MISMATCH': -1, 'GAP': -2} plot_nw(alpha,beta,penalty)

mit

cchampet/TuttleOFX

doc/scripts/plaintext2html.py

1

3911

#!/usr/bin/env python from __future__ import with_statement import re import cgi colorcodes = {'bold':{True:'\033[1m',False:'\033[22m'}, 'cyan':{True:'\033[1;36m',False:'\033[0;0m'}, #'#8E4429':{True:'\033[1;33m',False:'\033[0;0m'}, '#8E4429':{True:'\033[0;33m',False:'\033[0;0m'}, #'#8E4429':{True:'\033[33m',False:'\033[0;0m'}, '#0000B0':{True:'\033[1;34m',False:'\033[0;0m'}, '#B63A11':{True:'\033[1;31m',False:'\033[0;0m'}, 'magenta':{True:'\033[1;35m',False:'\033[0;0m'}, #'green':{True:'\033[1;32m',False:'\033[0;0m'}, 'green':{True:'\033[0;32m',False:'\033[0;0m'}, #'green':{True:'\033[32m',False:'\033[0;0m'}, 'underline':{True:'\033[1;4m',False:'\033[0;0m'}} def recolor(color, text): regexp = "(?:%s)(.*?)(?:%s)" % (colorcodes[color][True], colorcodes[color][False]) regexp = regexp.replace('[', r'\[') return re.sub(regexp, r'''<span style="color: %s">\1</span>''' % color, text) def resinglecolor(color, text, intxt): regexp = "(?:\033\[1;32m%s)(.*?)" % intxt return re.sub(regexp, r'<span style="color: green">%s\1</span>'% intxt, text) def removestdcolor(text): regexp = "(?:\033\[0;0m)(.*?)" return re.sub(regexp, r'', text) def bold(text): regexp = "(?:%s)(.*?)(?:%s)" % (colorcodes['bold'][True], colorcodes['bold'][False]) regexp = regexp.replace('[', r'\[') return re.sub(regexp, r'<span style="font-weight:bold">\1</span>', text) def underline(text): regexp = "(?:%s)(.*?)(?:%s)" % (colorcodes['underline'][True], colorcodes['underline'][False]) regexp = regexp.replace('[', r'\[') return re.sub(regexp, r'<span style="text-decoration: underline">\1</span>', text) def removebells(text): return text.replace('\07', '') def removebackspaces(text): backspace_or_eol = r'(.\010)|(\033\[K)' n = 1 while n > 0: text, n = re.subn(backspace_or_eol, '', text, 1) return text template = '''\ <html> <head> </head> <body> %s </body> </html> ''' re_string = re.compile(r'(?P<htmlchars>[<&>])|(?P<space>^[ \t]+)|(?P<lineend>\r\n|\r|\n)|(?P<protocal>(^|\s|\[)((http|ftp)://.*?))(\s|$|\])', re.S|re.M|re.I) def plaintext2html(text, tabstop=4): def do_sub(m): c = m.groupdict() if c['htmlchars']: return cgi.escape(c['htmlchars']) if c['lineend']: return '<br>' elif c['space']: t = m.group().replace('\t', '&nbsp;'*tabstop) t = t.replace(' ', '&nbsp;') return t elif c['space'] == '\t': return ' '*tabstop; else: url = m.group('protocal') #print url if url.startswith('['): prefix = '[' suffix = ']' url = url[1:] else: prefix = '' suffix = '' last = m.groups()[-1] if last in ['\n', '\r', '\r\n']: last = '<br>' return '%s<a href=%s>%s</a>%s' % (prefix, url, url, suffix) result = re.sub(re_string, do_sub, text) result = result.replace(' ', '&nbsp;') result = result.replace('\t', '&nbsp;'*tabstop) result = recolor('cyan', result) result = recolor('#8E4429', result) result = recolor('#0000B0', result) result = recolor('#B63A11', result) result = recolor('magenta', result) result = recolor('green', result) result = resinglecolor('green', result, 'Source') result = resinglecolor('green', result, 'Output') result = bold(result) result = underline(result) result = removebells(result) result = removebackspaces(result) result = removestdcolor(result) return template % result if __name__ == '__main__': import sys with open(sys.argv[-1]) as f: text = f.read() print plaintext2html(text)

gpl-3.0

mantarayforensics/mantaray

Tools/Python/extract_ntfs_artifacts_mr.py

1

15861

#!/usr/bin/env python3 #This program extracts NTFS artifacts ($MFT, $Logfile, $USRJRNL) (Overt, Deleted #Shadow Volumes) #Use to extract files when using Triforce ANJP NTFS Journal Parser | Triforce (David Cohen) #########################COPYRIGHT INFORMATION############################ #Copyright (C) 2013 [email protected] # #This program is free software: you can redistribute it and/or modify # #it under the terms of the GNU General Public License as published by # #the Free Software Foundation, either version 3 of the License, or # #(at your option) any later version. # # #This program is distributed in the hope that it will be useful, # #but WITHOUT ANY WARRANTY; without even the implied warranty of # #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # #GNU General Public License for more details. # # #You should have received a copy of the GNU General Public License # #along with this program. If not, see http://www.gnu.org/licenses/. # #########################COPYRIGHT INFORMATION############################ from easygui import * from get_case_number import * from get_output_location import * from select_file_to_process import * from parted import * from mount import * from mount_ewf import * from done import * from unix2dos import * from remove_dupes_module_noask import * from mmls import * from Windows_Time_Converter_module import * from check_for_folder import * import os from os.path import join import re import io import sys import string import subprocess import datetime import shutil import struct ### GET BLOCK SIZE ############################################################################################## def get_block_size_mmls(Image_Path, outfile): block_size = subprocess.check_output(['mmls -i raw ' + Image_Path + " | grep Units | awk '{print $4}' | sed s/-byte//"], shell=True, universal_newlines=True) block_size = block_size.strip() print("The block size is: " + str(block_size)) outfile.write("The block size is: " + str(block_size) + "\n\n") return block_size def get_block_size_parted(outfile, temp_time): block_size_command = "sudo cat /tmp/timeline_partition_info_" + temp_time +".txt | grep -a " + "'"+"Sector size"+"'" + " | awk {'print $4'} | sed s_B/.*__" outfile.write("The block_size command is: " + block_size_command + "\n") block_size = subprocess.check_output([block_size_command], shell=True, universal_newlines=True) block_size = block_size.strip() print("The block size is: " + str(block_size)) outfile.write("The block size is: " + str(block_size) + "\n\n") return block_size ### END GET BLOCK SIZE ########################################################################################## ### PROCESS FLS OUTPUT ###### ############################################################ def process_fls_output(value, key, Image_Path, block_size, folder_path, item, file_type, outfile, temp_file): #divide offset by block size so it is in correct format for fls key_bytes = int(key)//int(block_size) #open FLS output file fls_output_file = open("/tmp/fls_output_ntfs_" + temp_file + ".txt", 'r') for line in fls_output_file: #print current line for debugging purposes #print(line) newList=[] #strip carriage returns line = line.strip() line_split = line.split('/') #print(line_split) for i in line_split: newList.append(i.split('\t')[0]) #print (newList) #assign items in newList to variables inode_number_temp = newList[1] #strip alpha chars from inode & leading space inode_number = re.sub('[a-z]','',inode_number_temp) inode_number = re.sub('^ +','', inode_number) #get file_name file_name = newList[-1] if(item == "NO"): if(re.search('OrphanFiles', line)): #copy files out using icat icat_command = "icat -r -i raw -f " + value + " -o " + str(key_bytes) + " -b " + block_size + " " + Image_Path + " " + inode_number + " > " + "'" + folder_path + "/" + inode_number + "_Partition_" + str(key) + "_" + file_type +"_DELETED" + "'" else: #get user profile name icat_command = "icat -r -i raw -f " + value + " -o " + str(key_bytes) + " -b " + block_size + " " + Image_Path + " " + inode_number + " > " + "'" + folder_path + "/" + inode_number + "_Partition_" + str(key) + "_OVERT_" + file_type + "'" else: #these are the shadow volume files if(re.search('OrphanFiles', line)): #copy files out using icat icat_command = "icat -r -i raw -f " + value + " -o " + str(key_bytes) + " -b " + block_size + " " + Image_Path + " " + inode_number + " > " + "'" + folder_path + "/" + inode_number + "_Partition_" + str(key) + "_DELETED_" + file_type + "_" + item + "'" else: #get user profile name icat_command = "icat -r -i raw -f " + value + " -o " + str(key_bytes) + " -b " + block_size + " " + Image_Path + " " + inode_number + " > " + "'" + folder_path + "/" + inode_number + "_Partition_" + str(key) + "_" + file_type + "_" + item + "'" print("File Name: " + file_name.ljust(10) + "\t" "Inode number: " + inode_number.ljust(10)) outfile.write("The icat command is: " + icat_command + "\n") #run icat command subprocess.call([icat_command], shell=True) #close file fls_output_file.close() ########################################################################################## ### PROCESS OVERT / DELETED HIVES ############################################################################## def process_overt_deleted_files(value, key, Image_Path, outfile, folder_path, block_size, item, temp_time): #divide offset by block size so it is in correct format for fls key_bytes = int(key)//int(block_size) #run fls to get information for MFT files fls_command = "fls -Fpr -f ntfs -i raw -o " + str(key_bytes) + " " + Image_Path + " | grep -i '\$MFT$' | sed s/:// | sed s/*// > /tmp/fls_output_ntfs_" + temp_time + ".txt" #print ("\nThe fls command is: " + fls_command + "\n") print("\nSearching for $MFT files") outfile.write("The fls command is: " + fls_command + "\n") #run fls command subprocess.call([fls_command], shell=True) #process fls output process_fls_output(value, key, Image_Path, block_size, folder_path, item, "MFT", outfile, temp_time) #run fls to get information for Logfiles files fls_command = "fls -Fpr -f ntfs -i raw -o " + str(key_bytes) + " " + Image_Path + " | grep -i '\$LogFile$' | sed s/:// | sed s/*// > /tmp/fls_output_ntfs_" + temp_time +".txt" #print ("\nThe fls command is: " + fls_command + "\n") print("\nSearching for $LogFiles files") outfile.write("The fls command is: " + fls_command + "\n") #run fls command subprocess.call([fls_command], shell=True) #process fls output process_fls_output(value, key, Image_Path, block_size, folder_path, item, "LogFile", outfile, temp_time) #run fls to get information for $UsrJrnl files fls_command = "fls -Fpr -f ntfs -i raw -o " + str(key_bytes) + " " + Image_Path + " | grep -i '\$UsnJrnl.\$J$' | sed s/:// | sed s/*// > /tmp/fls_output_ntfs_" + temp_time + ".txt" #print ("\nThe fls command is: " + fls_command + "\n") print("\nSearching for $UsrJrnl files") outfile.write("The fls command is: " + fls_command + "\n") #run fls command subprocess.call([fls_command], shell=True) #process fls output process_fls_output(value, key, Image_Path, block_size, folder_path, item, "UsnJrnl", outfile, temp_time) ### END PROCESS OVERT / DELETED HIVES ############################################################################## ### CHECK FOR SHADOW VOLUMES ################################################ def check_for_shadow_volumes(Image_Path, key, block_size, outfile, folder_path, temp_time): #set shadow volume variables has_shadow_volumes = "NULL" vssvolume_mnt = "NULL" #divide offset by block size so it is in correct format for vshadowinfo key_bytes = int(key)//int(block_size) key_bytes_disk_offset = int(key) * int(block_size) image_no_quotes = Image_Path.replace("'","") print("\nChecking: " + Image_Path + " for shadow volumes") f = open('/tmp/dump_' + temp_time + '.txt', 'w+t') try: vshadow_info_command = "vshadowinfo -v -o " + str(key) + " " + Image_Path# + " > /tmp/dump.txt" #print("The vshadow_command is: " + vshadow_info_command) outfile.write("The vshadow_command is: " + vshadow_info_command) subprocess.call([vshadow_info_command], shell=True, stdout = f, stderr=subprocess.STDOUT) #vshadow_output = subprocess.check_output([vshadow_info_command], shell=True, stderr=subprocess.STDOUT) #f.close() f =open('/tmp/dump_' + temp_time + '.txt', 'rt') #print("try succedded") for line in f: line = line.strip() print(line) if (re.search("No Volume Shadow Snapshots found", line)): has_shadow_volumes = "NO" if(has_shadow_volumes != "NO"): print("Partition at offset: " + str(key_bytes) + " has shadow volumes.") outfile.write("Partition at offset: " + str(key_bytes) + " has shadow volumes.") #check for existence of folder vssvolume_mnt = check_for_folder("/mnt/vssvolume", outfile) #mount shadow volumes for partition mount_shadow_command = "sudo vshadowmount -o " + str(key) + " " + Image_Path + " " + vssvolume_mnt print("The mount_shadow_command is: " + mount_shadow_command) subprocess.call(["sudo vshadowmount -o " + str(key) + " " + Image_Path + " " + vssvolume_mnt], shell=True, stderr=subprocess.STDOUT) #pass vssvolume mount point to mount_shadow_volume for mounting mount_shadow_volumes(vssvolume_mnt, outfile, folder_path) elif(has_shadow_volumes == "NO"): print("Partition at offset: " + str(key) + " has no shadow volumes") f.close() except: print("The vshadow_info command for partition: " + str(key) + " failed") return vssvolume_mnt ############################################################################# #### MOUNT INDIVIDUAL SHADOW VOLUMES ######################################## def mount_shadow_volumes(vssvolume_mnt, outfile, folder_path): print("Inside mount_shadow_volumes sub") print("Vssvolume_mnt: " + vssvolume_mnt) #check for existence of folder vss_mount = check_for_folder("/mnt/vss_mount", outfile) vss_volumes = os.listdir(vssvolume_mnt) print(vss_volumes) for item in vss_volumes: print("About to process Shadow Volume: " + item) #call parted function partition_info_dict, temp_time = parted(outfile, vssvolume_mnt + "/"+item) block_size = get_block_size_parted(outfile, temp_time) for key,value in partition_info_dict.items(): print("About to process registry hives from: " + item) process_overt_deleted_files(value, key, vssvolume_mnt+"/"+item, outfile, folder_path, block_size, item, temp_time) ############################################################################# ### MAIN PROGRAM ######################################################################################################################## def extract_ntfs_artifacts_mr(item_to_process, case_number, root_folder_path, evidence): print("The item to process is: " + item_to_process) print("The case_name is: " + case_number) print("The output folder is: " + root_folder_path) print("The evidence to process is: " + evidence) #get datetime now = datetime.datetime.now() #set Mount Point mount_point = "/mnt/" + now.strftime("%Y-%m-%d_%H_%M_%S") #create output folder path folder_path = root_folder_path + "/" + "NTFS_Artifacts" check_for_folder(folder_path, "NONE") #open a log file for output log_file = folder_path + "/NTFS_Artifacts_logfile.txt" outfile = open(log_file, 'wt+') Image_Path = '"' + evidence + '"' #set item variable to tell functions whether data is from shadow volumes item = "NO" #check if Image file is in Encase format if re.search(".E01", Image_Path): #set mount point mount_point = "/mnt/"+case_number+"_unallocated" Image_Path = mount_ewf(Image_Path, outfile, mount_point) #call mmls function partition_info_dict, temp_time = mmls(outfile, Image_Path) partition_info_dict_temp = partition_info_dict #get filesize of mmls_output.txt file_size = os.path.getsize("/tmp/mmls_output_" + temp_time + ".txt") #if filesize of mmls output is 0 then run parted if(file_size == 0): print("mmls output was empty, running parted\n") outfile.write("mmls output was empty, running parted\n") #call parted function partition_info_dict, temp_time = parted(outfile, Image_Path) block_size = get_block_size_parted(outfile, temp_time) else: #get block_size since mmls was successful block_size = get_block_size_mmls(Image_Path, outfile) #read through the mmls output and look for GUID Partition Tables (used on MACS) mmls_output_file = open("/tmp/mmls_output_" + temp_time + ".txt", 'r') for line in mmls_output_file: if re.search("GUID Partition Table", line): print("We found a GUID partition table, need to use parted") outfile.write("We found a GUID partition table, need to use parted\n") #call parted function partition_info_dict, temp_time = parted(outfile, Image_Path) #loop through the dictionary containing the partition info (filesystem is VALUE, offset is KEY) for key,value in partition_info_dict.items(): #process overt registy hives if(value =="ntfs") or (value=="fat32"): if not os.path.exists(folder_path + "/Partition_" + str(key)): os.makedirs(folder_path + "/Partition_" + str(key)) #print("Just created output folder: " + folder_path + "/Partition_" + str(key)) outfile.write("Just created output folder: " + folder_path + "/Partition_" + str(key) + "\n\n") else: print("Output folder: " + folder_path +"/Partition_" + str(key) + " already exists") outfile.write("Output folder: " + folder_path +"/Partition_" + str(key) + " already exists\n\n") process_overt_deleted_files(value, key, Image_Path, outfile, folder_path, block_size, item, temp_time) vssvolume_mnt = check_for_shadow_volumes(Image_Path, key, block_size, outfile, folder_path, temp_time) else: print("This partition is not formatted NTFS or FAT32") outfile.write("This partition is not formatted NTFS or FAT32\n\n") #run fdupes against output path to eliminate dupes remove_dupes_module_noask(folder_path, outfile, str(key)) #chdir to output foler os.chdir(folder_path) #unmount shadow volumes if(vssvolume_mnt != "NULL"): print("Unmounting: " + vssvolume_mnt) outfile.write("Unmounting: " + vssvolume_mnt + "\n") subprocess.call(['sudo umount -f ' + vssvolume_mnt], shell=True) os.rmdir(vssvolume_mnt) #unmount and remount points if re.search(".E01", Image_Path): if(os.path.exists(mount_point+"_ewf")): subprocess.call(['sudo umount -f ' + mount_point + "_ewf"], shell=True) os.rmdir(mount_point+"_ewf") #remove empty directories for root, dirs, files in os.walk(folder_path, topdown = False): for directory in dirs: dir_path = os.path.join(root, directory) if not os.listdir(dir_path): outfile.write("Removing empty folder: " + dir_path + "\n") os.rmdir(dir_path) #close outfiles outfile.close() #delete temp files os.remove('/tmp/fls_output_ntfs_' + temp_time + '.txt') #run text files through unix2dos for root, dirs, files in os.walk(folder_path): for filenames in files: #get file extension fileName, fileExtension = os.path.splitext(filenames) if(fileExtension.lower() == ".txt"): full_path = os.path.join(root,filenames) quoted_full_path = "'" +full_path+"'" print("Running Unix2dos against file: " + filenames) unix2dos_command = "sudo unix2dos " + quoted_full_path subprocess.call([unix2dos_command], shell=True)

gpl-3.0

vlegoff/tsunami

src/secondaires/auberge/editeurs/aubedit/__init__.py

1

3826

# -*-coding:Utf-8 -* # Copyright (c) 2010-2017 LE GOFF Vincent # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # * Redistributions of source code must retain the above copyright notice, this # list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above copyright notice, # this list of conditions and the following disclaimer in the documentation # and/or other materials provided with the distribution. # * Neither the name of the copyright holder nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT # OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. """Package contenant l'éditeur d'auberge 'aubedit'. Si des redéfinitions de contexte-éditeur standard doivent être faites, elles seront placées dans ce package Note importante : ce package contient la définition d'un éditeur, mais celui-ci peut très bien être étendu par d'autres modules. Au quel cas, les extensions n'apparaîtront pas ici. """ from primaires.interpreteur.editeur.presentation import Presentation from primaires.interpreteur.editeur.uniligne import Uniligne from secondaires.auberge.editeurs.aubedit.edt_chambres import EdtChambres class EdtAubedit(Presentation): """Classe définissant l'éditeur d'auberge.""" nom = "aubedit" def __init__(self, personnage, auberge): """Constructeur de l'éditeur""" if personnage: instance_connexion = personnage.instance_connexion else: instance_connexion = None Presentation.__init__(self, instance_connexion, auberge) if personnage and auberge: self.construire(auberge) def __getnewargs__(self): return (None, None) def construire(self, auberge): """Construction de l'éditeur""" # Titre titre = self.ajouter_choix("titre", "t", Uniligne, auberge, "titre") titre.parent = self titre.prompt = "Titre de l'auberge : " titre.apercu = "{objet.titre}" titre.aide_courte = \ "Entrez le |ent|titre|ff| de l'auberge ou |cmd|/|ff| pour " \ "revenir à la fenêtre parente.\n\nTitre actuel : " \ "|bc|{objet.titre}|ff|" # Clé de l'aubergiste cle = self.ajouter_choix("clé de l'aubergiste", "a", Uniligne, auberge, "cle_aubergiste") cle.parent = self cle.prompt = "Clé du prototype de l'aubergiste : " cle.apercu = "{objet.cle_aubergiste}" cle.aide_courte = \ "Entrez la |ent|clé de l'aubergiste|ff| ou |cmd|/|ff| pour " \ "revenir à la fenêtre parente.\n\nClé actuelle : " \ "|bc|{objet.cle_aubergiste}|ff|" # Chambres chambres = self.ajouter_choix("chambres", "c", EdtChambres, auberge) chambres.parent = self chambres.apercu = "\n{objet.aff_chambres}"

bsd-3-clause