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fhir/resources/specimendefinition.py | chgl/fhir.resources | 0 | 32852 | # -*- coding: utf-8 -*-
"""
Profile: http://hl7.org/fhir/StructureDefinition/SpecimenDefinition
Release: R4
Version: 4.0.1
Build ID: 9346c8cc45
Last updated: 2019-11-01T09:29:23.356+11:00
"""
import typing
from pydantic import Field, root_validator
from pydantic.error_wrappers import ErrorWrapper, ValidationError
from pydantic.errors import MissingError, NoneIsNotAllowedError
from . import backboneelement, domainresource, fhirtypes
class SpecimenDefinition(domainresource.DomainResource):
"""Disclaimer: Any field name ends with ``__ext`` does't part of
Resource StructureDefinition, instead used to enable Extensibility feature
for FHIR Primitive Data Types.
Kind of specimen.
A kind of specimen with associated set of requirements.
"""
resource_type = Field("SpecimenDefinition", const=True)
collection: typing.List[fhirtypes.CodeableConceptType] = Field(
None,
alias="collection",
title="Specimen collection procedure",
description="The action to be performed for collecting the specimen.",
# if property is element of this resource.
element_property=True,
)
identifier: fhirtypes.IdentifierType = Field(
None,
alias="identifier",
title="Business identifier of a kind of specimen",
description="A business identifier associated with the kind of specimen.",
# if property is element of this resource.
element_property=True,
)
patientPreparation: typing.List[fhirtypes.CodeableConceptType] = Field(
None,
alias="patientPreparation",
title="Patient preparation for collection",
description="Preparation of the patient for specimen collection.",
# if property is element of this resource.
element_property=True,
)
timeAspect: fhirtypes.String = Field(
None,
alias="timeAspect",
title="Time aspect for collection",
description="Time aspect of specimen collection (duration or offset).",
# if property is element of this resource.
element_property=True,
)
timeAspect__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_timeAspect", title="Extension field for ``timeAspect``."
)
typeCollected: fhirtypes.CodeableConceptType = Field(
None,
alias="typeCollected",
title="Kind of material to collect",
description="The kind of material to be collected.",
# if property is element of this resource.
element_property=True,
)
typeTested: typing.List[fhirtypes.SpecimenDefinitionTypeTestedType] = Field(
None,
alias="typeTested",
title="Specimen in container intended for testing by lab",
description=(
"Specimen conditioned in a container as expected by the testing "
"laboratory."
),
# if property is element of this resource.
element_property=True,
)
class SpecimenDefinitionTypeTested(backboneelement.BackboneElement):
"""Disclaimer: Any field name ends with ``__ext`` does't part of
Resource StructureDefinition, instead used to enable Extensibility feature
for FHIR Primitive Data Types.
Specimen in container intended for testing by lab.
Specimen conditioned in a container as expected by the testing laboratory.
"""
resource_type = Field("SpecimenDefinitionTypeTested", const=True)
container: fhirtypes.SpecimenDefinitionTypeTestedContainerType = Field(
None,
alias="container",
title="The specimen's container",
description=None,
# if property is element of this resource.
element_property=True,
)
handling: typing.List[fhirtypes.SpecimenDefinitionTypeTestedHandlingType] = Field(
None,
alias="handling",
title="Specimen handling before testing",
description=(
"Set of instructions for preservation/transport of the specimen at a "
"defined temperature interval, prior the testing process."
),
# if property is element of this resource.
element_property=True,
)
isDerived: bool = Field(
None,
alias="isDerived",
title="Primary or secondary specimen",
description="Primary of secondary specimen.",
# if property is element of this resource.
element_property=True,
)
isDerived__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_isDerived", title="Extension field for ``isDerived``."
)
preference: fhirtypes.Code = Field(
None,
alias="preference",
title="preferred | alternate",
description="The preference for this type of conditioned specimen.",
# if property is element of this resource.
element_property=True,
element_required=True,
# note: Enum values can be used in validation,
# but use in your own responsibilities, read official FHIR documentation.
enum_values=["preferred", "alternate"],
)
preference__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_preference", title="Extension field for ``preference``."
)
rejectionCriterion: typing.List[fhirtypes.CodeableConceptType] = Field(
None,
alias="rejectionCriterion",
title="Rejection criterion",
description=(
"Criterion for rejection of the specimen in its container by the "
"laboratory."
),
# if property is element of this resource.
element_property=True,
)
requirement: fhirtypes.String = Field(
None,
alias="requirement",
title="Specimen requirements",
description=(
"Requirements for delivery and special handling of this kind of "
"conditioned specimen."
),
# if property is element of this resource.
element_property=True,
)
requirement__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_requirement", title="Extension field for ``requirement``."
)
retentionTime: fhirtypes.DurationType = Field(
None,
alias="retentionTime",
title="Specimen retention time",
description=(
"The usual time that a specimen of this kind is retained after the "
"ordered tests are completed, for the purpose of additional testing."
),
# if property is element of this resource.
element_property=True,
)
type: fhirtypes.CodeableConceptType = Field(
None,
alias="type",
title="Type of intended specimen",
description="The kind of specimen conditioned for testing expected by lab.",
# if property is element of this resource.
element_property=True,
)
@root_validator(pre=True, allow_reuse=True)
def validate_required_primitive_elements_3071(
cls, values: typing.Dict[str, typing.Any]
) -> typing.Dict[str, typing.Any]:
"""https://www.hl7.org/fhir/extensibility.html#Special-Case
In some cases, implementers might find that they do not have appropriate data for
an element with minimum cardinality = 1. In this case, the element must be present,
but unless the resource or a profile on it has made the actual value of the primitive
data type mandatory, it is possible to provide an extension that explains why
the primitive value is not present.
"""
required_fields = [("preference", "preference__ext")]
_missing = object()
def _fallback():
return ""
errors: typing.List["ErrorWrapper"] = []
for name, ext in required_fields:
field = cls.__fields__[name]
ext_field = cls.__fields__[ext]
value = values.get(field.alias, _missing)
if value not in (_missing, None):
continue
ext_value = values.get(ext_field.alias, _missing)
missing_ext = True
if ext_value not in (_missing, None):
if isinstance(ext_value, dict):
missing_ext = len(ext_value.get("extension", [])) == 0
elif (
getattr(ext_value.__class__, "get_resource_type", _fallback)()
== "FHIRPrimitiveExtension"
):
if ext_value.extension and len(ext_value.extension) > 0:
missing_ext = False
else:
validate_pass = True
for validator in ext_field.type_.__get_validators__():
try:
ext_value = validator(v=ext_value)
except ValidationError as exc:
errors.append(ErrorWrapper(exc, loc=ext_field.alias))
validate_pass = False
if not validate_pass:
continue
if ext_value.extension and len(ext_value.extension) > 0:
missing_ext = False
if missing_ext:
if value is _missing:
errors.append(ErrorWrapper(MissingError(), loc=field.alias))
else:
errors.append(
ErrorWrapper(NoneIsNotAllowedError(), loc=field.alias)
)
if len(errors) > 0:
raise ValidationError(errors, cls) # type: ignore
return values
class SpecimenDefinitionTypeTestedContainer(backboneelement.BackboneElement):
"""Disclaimer: Any field name ends with ``__ext`` does't part of
Resource StructureDefinition, instead used to enable Extensibility feature
for FHIR Primitive Data Types.
The specimen's container.
"""
resource_type = Field("SpecimenDefinitionTypeTestedContainer", const=True)
additive: typing.List[
fhirtypes.SpecimenDefinitionTypeTestedContainerAdditiveType
] = Field(
None,
alias="additive",
title="Additive associated with container",
description=(
"Substance introduced in the kind of container to preserve, maintain or"
" enhance the specimen. Examples: Formalin, Citrate, EDTA."
),
# if property is element of this resource.
element_property=True,
)
cap: fhirtypes.CodeableConceptType = Field(
None,
alias="cap",
title="Color of container cap",
description=None,
# if property is element of this resource.
element_property=True,
)
capacity: fhirtypes.QuantityType = Field(
None,
alias="capacity",
title="Container capacity",
description="The capacity (volume or other measure) of this kind of container.",
# if property is element of this resource.
element_property=True,
)
description: fhirtypes.String = Field(
None,
alias="description",
title="Container description",
description="The textual description of the kind of container.",
# if property is element of this resource.
element_property=True,
)
description__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_description", title="Extension field for ``description``."
)
material: fhirtypes.CodeableConceptType = Field(
None,
alias="material",
title="Container material",
description="The type of material of the container.",
# if property is element of this resource.
element_property=True,
)
minimumVolumeQuantity: fhirtypes.QuantityType = Field(
None,
alias="minimumVolumeQuantity",
title="Minimum volume",
description="The minimum volume to be conditioned in the container.",
# if property is element of this resource.
element_property=True,
# Choice of Data Types. i.e minimumVolume[x]
one_of_many="minimumVolume",
one_of_many_required=False,
)
minimumVolumeString: fhirtypes.String = Field(
None,
alias="minimumVolumeString",
title="Minimum volume",
description="The minimum volume to be conditioned in the container.",
# if property is element of this resource.
element_property=True,
# Choice of Data Types. i.e minimumVolume[x]
one_of_many="minimumVolume",
one_of_many_required=False,
)
minimumVolumeString__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None,
alias="_minimumVolumeString",
title="Extension field for ``minimumVolumeString``.",
)
preparation: fhirtypes.String = Field(
None,
alias="preparation",
title="Specimen container preparation",
description=(
"Special processing that should be applied to the container for this "
"kind of specimen."
),
# if property is element of this resource.
element_property=True,
)
preparation__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_preparation", title="Extension field for ``preparation``."
)
type: fhirtypes.CodeableConceptType = Field(
None,
alias="type",
title="Kind of container associated with the kind of specimen",
description="The type of container used to contain this kind of specimen.",
# if property is element of this resource.
element_property=True,
)
@root_validator(pre=True, allow_reuse=True)
def validate_one_of_many_4016(
cls, values: typing.Dict[str, typing.Any]
) -> typing.Dict[str, typing.Any]:
"""https://www.hl7.org/fhir/formats.html#choice
A few elements have a choice of more than one data type for their content.
All such elements have a name that takes the form nnn[x].
The "nnn" part of the name is constant, and the "[x]" is replaced with
the title-cased name of the type that is actually used.
The table view shows each of these names explicitly.
Elements that have a choice of data type cannot repeat - they must have a
maximum cardinality of 1. When constructing an instance of an element with a
choice of types, the authoring system must create a single element with a
data type chosen from among the list of permitted data types.
"""
one_of_many_fields = {
"minimumVolume": ["minimumVolumeQuantity", "minimumVolumeString"]
}
for prefix, fields in one_of_many_fields.items():
assert cls.__fields__[fields[0]].field_info.extra["one_of_many"] == prefix
required = (
cls.__fields__[fields[0]].field_info.extra["one_of_many_required"]
is True
)
found = False
for field in fields:
if field in values and values[field] is not None:
if found is True:
raise ValueError(
"Any of one field value is expected from "
f"this list {fields}, but got multiple!"
)
else:
found = True
if required is True and found is False:
raise ValueError(f"Expect any of field value from this list {fields}.")
return values
class SpecimenDefinitionTypeTestedContainerAdditive(backboneelement.BackboneElement):
"""Disclaimer: Any field name ends with ``__ext`` does't part of
Resource StructureDefinition, instead used to enable Extensibility feature
for FHIR Primitive Data Types.
Additive associated with container.
Substance introduced in the kind of container to preserve, maintain or
enhance the specimen. Examples: Formalin, Citrate, EDTA.
"""
resource_type = Field("SpecimenDefinitionTypeTestedContainerAdditive", const=True)
additiveCodeableConcept: fhirtypes.CodeableConceptType = Field(
None,
alias="additiveCodeableConcept",
title="Additive associated with container",
description=(
"Substance introduced in the kind of container to preserve, maintain or"
" enhance the specimen. Examples: Formalin, Citrate, EDTA."
),
# if property is element of this resource.
element_property=True,
# Choice of Data Types. i.e additive[x]
one_of_many="additive",
one_of_many_required=True,
)
additiveReference: fhirtypes.ReferenceType = Field(
None,
alias="additiveReference",
title="Additive associated with container",
description=(
"Substance introduced in the kind of container to preserve, maintain or"
" enhance the specimen. Examples: Formalin, Citrate, EDTA."
),
# if property is element of this resource.
element_property=True,
# Choice of Data Types. i.e additive[x]
one_of_many="additive",
one_of_many_required=True,
# note: Listed Resource Type(s) should be allowed as Reference.
enum_reference_types=["Substance"],
)
@root_validator(pre=True, allow_reuse=True)
def validate_one_of_many_4813(
cls, values: typing.Dict[str, typing.Any]
) -> typing.Dict[str, typing.Any]:
"""https://www.hl7.org/fhir/formats.html#choice
A few elements have a choice of more than one data type for their content.
All such elements have a name that takes the form nnn[x].
The "nnn" part of the name is constant, and the "[x]" is replaced with
the title-cased name of the type that is actually used.
The table view shows each of these names explicitly.
Elements that have a choice of data type cannot repeat - they must have a
maximum cardinality of 1. When constructing an instance of an element with a
choice of types, the authoring system must create a single element with a
data type chosen from among the list of permitted data types.
"""
one_of_many_fields = {
"additive": ["additiveCodeableConcept", "additiveReference"]
}
for prefix, fields in one_of_many_fields.items():
assert cls.__fields__[fields[0]].field_info.extra["one_of_many"] == prefix
required = (
cls.__fields__[fields[0]].field_info.extra["one_of_many_required"]
is True
)
found = False
for field in fields:
if field in values and values[field] is not None:
if found is True:
raise ValueError(
"Any of one field value is expected from "
f"this list {fields}, but got multiple!"
)
else:
found = True
if required is True and found is False:
raise ValueError(f"Expect any of field value from this list {fields}.")
return values
class SpecimenDefinitionTypeTestedHandling(backboneelement.BackboneElement):
"""Disclaimer: Any field name ends with ``__ext`` does't part of
Resource StructureDefinition, instead used to enable Extensibility feature
for FHIR Primitive Data Types.
Specimen handling before testing.
Set of instructions for preservation/transport of the specimen at a defined
temperature interval, prior the testing process.
"""
resource_type = Field("SpecimenDefinitionTypeTestedHandling", const=True)
instruction: fhirtypes.String = Field(
None,
alias="instruction",
title="Preservation instruction",
description=(
"Additional textual instructions for the preservation or transport of "
"the specimen. For instance, 'Protect from light exposure'."
),
# if property is element of this resource.
element_property=True,
)
instruction__ext: fhirtypes.FHIRPrimitiveExtensionType = Field(
None, alias="_instruction", title="Extension field for ``instruction``."
)
maxDuration: fhirtypes.DurationType = Field(
None,
alias="maxDuration",
title="Maximum preservation time",
description=(
"The maximum time interval of preservation of the specimen with these "
"conditions."
),
# if property is element of this resource.
element_property=True,
)
temperatureQualifier: fhirtypes.CodeableConceptType = Field(
None,
alias="temperatureQualifier",
title="Temperature qualifier",
description=(
"It qualifies the interval of temperature, which characterizes an "
"occurrence of handling. Conditions that are not related to temperature"
" may be handled in the instruction element."
),
# if property is element of this resource.
element_property=True,
)
temperatureRange: fhirtypes.RangeType = Field(
None,
alias="temperatureRange",
title="Temperature range",
description="The temperature interval for this set of handling instructions.",
# if property is element of this resource.
element_property=True,
)
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] |
python/clean_json_step2.py | mfalling/covid19-random_scripts | 0 | 99220 | <reponame>mfalling/covid19-random_scripts<gh_stars>0
# FOR USF SAIL
# ~ Mihir
import csv
import pandas as pd
import numpy as np
import requests
import re
from bs4 import BeautifulSoup
import string
import glob
import sys
import os
import signal
from requests.exceptions import Timeout
#****************** NOTE **************#
# Made for USC stuff, USF LATER #
#**************************************#
#---------Default, always turn url to title tags ------------#
turning_url_to_title = False
#------------------------------------------------------------#
#-------- UPDATE OUT FILE NAME HERE!!!--------------#
out_csv_name= r'USC_march_100K_file_final'
#---------------------------------------------------#
#make a save directory
try:
os.mkdir("./100K_March/") # <---- Here
except OSError as e:
print("Directory exists. Please change both folders names in this block to whatever.")
#exit()
final_path = './100K_March/' # <--- Current directory
# UPDATE NUM SAMPLE HERE!!! (Without replacement, DON'T NEED IT YET)
#rowsToSample= 100
#--------------------------------------#
#----------------------------------- read the all processed bot files -------------------------------------#
# since not every user got a bot score, we will need to attach them seperately
path = r'C:/Users/ThinkPad/SpyderProjects/JsonStuff/USC_MARCH_STUFF_OLD/all_bots_scores' # use your path
all_files = glob.glob(path + "/*.csv")
#----------------------------------------------------------------------------------------------------------#
li = []
for filename in all_files:
df = pd.read_csv(filename, index_col=None, header=0, encoding= 'utf-8-sig',low_memory=False)
li.append(df)
df_botscores = pd.concat(li, axis=0, ignore_index=True)
#---------------------------------------- read the 100k screen names ---------------------------------------------#
# Recall that we have already have 100K samples of usernames for botometer so let's import those screen_names
path = r'C:/Users/ThinkPad/SpyderProjects/JsonStuff/USC_MARCH_STUFF_OLD/rand_100k_screen_names' # use your path
all_files = glob.glob(path + "/*.csv")
#----------------------------------------------------------------------------------------------------------------#
del li[:]
for filename in all_files:
df = pd.read_csv(filename, index_col=None, header=0, encoding= 'utf-8-sig',low_memory=False)
li.append(df)
df_100k = pd.concat(li, axis=0, ignore_index=True)
#------ join the 100k screen_name with main_frame (that is to keep screen_names we have bot scores for)
# create a column marking df_100 values
df_100k['marker'] = 1
#--->Read file by file now#
#--------------------------------------- read in all usc data csv files ------------------------------------------#
#Read the csvs and make a dataframe
path = r'C:/Users/ThinkPad/SpyderProjects/JsonStuff/USC_MARCH_STUFF_OLD/JSONL_TO_CSV_USC_MARCH' # use your path
all_files = glob.glob(path + "/*.csv")
#-----------------------------------------------------------------------------------------------------------------#
del li[:]
for filename in all_files:
df = pd.read_csv(filename, index_col=None, header=0, encoding= 'utf-8-sig',low_memory=False)
li.append(df)
df_main= pd.concat(li, axis=0, ignore_index=True)
#-------
# join the two, keeping all of df1's indices
df_joined = pd.merge(df_main, df_100k, on=['user_screen_name'], how='left')
# extract desired columns where marker is NaN
df_joined= df_joined[pd.notnull(df_joined['marker'])][df_main.columns]
#df_joined.to_csv(exportFileName, encoding='utf-8-sig', index=False)
#------ now merge the file again
df_joined_bots = pd.merge(df_joined,df_botscores, on = ['user_screen_name'],how='left')
#df_joined_bots.to_csv(exportFileName, encoding='utf-8-sig', index=False)
#------ replace urls with <title> tag
#(1) function to get title tag from URL
#NOTE: For twitter urls, this will not work, because they don't have "title" even if it
# exists in the console when looking at a browser
# function that eventually gets the title tags from url
def get_title_from_url(url):
try:
#check if it's a word of https string
if(url.startswith('http')):
#check if url is valid or returns an html, otherwise cut the time
try:
page = requests.get(url, timeout=5)
except Timeout:
# return dead url
return ''
#if the url is valid, sometimes phisy/ssl-missing site throw error
html = BeautifulSoup(page.content, 'html.parser')
#finally get the title if everyting is good
page_title = html.find('title').text.strip()
return page_title
else:
return url
except:
return ''
#(2) Finally write the csv file
file_name = ''.join([out_csv_name, '_utf-8', '.csv'])
save_path = os.path.abspath(
os.path.join(
final_path, file_name
)
)
if(turning_url_to_title):
# iterate over rows with iterrows()
for index, row in df_joined_bots.iterrows():
# access data using column names
# do this to prevent Null error that comes from split fn splitting Null
df_joined_bots['tweet_text'] = df_joined_bots['tweet_text'].fillna("")
df_joined_bots['retweet_text'] = df_joined_bots['retweet_text'].fillna("")
df_joined_bots['quoted_text'] = df_joined_bots['quoted_text'].fillna("")
#first let's take care of tweet_text
s = df_joined_bots.at[index, 'tweet_text']
l = list(map(lambda x: x, s.split()))
m = list(map(get_title_from_url, l))
n = ' '.join(m)
df_joined_bots.at[index, 'tweet_text']= n
del s,l,m,n
# then take care of retweets
s = df_joined_bots.at[index, 'retweet_text']
l = list(map(lambda x: x, s.split()))
m = list(map(get_title_from_url, l))
n = ' '.join(m)
df_joined_bots.at[index, 'retweet_text']= n
del s, l, m, n
# lastly, quoted_text
s = df_joined_bots.at[index, 'quoted_text']
l = list(map(lambda x: x, s.split()))
m = list(map(get_title_from_url, l))
n = ' '.join(m)
df_joined_bots.at[index, 'quoted_text'] = n
del s, l, m, n
df_joined_bots.to_csv(save_path, encoding='utf-8-sig', index=False)
else:
#if not wanting to convert urls to csv, go straight to write the file
df_joined_bots.to_csv(save_path, encoding='utf-8-sig', index=False)
#EOF | [
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setup.py | yvesf/flask-mediabrowser | 21 | 165849 | #!/usr/bin/env python3
from distutils.core import setup
setup(name='flask-mediabrowser',
version='0.0.1',
description='HTTP media browsing and streaming/transcoding',
author='<NAME>',
author_email='<EMAIL>',
url='https://www.xapek.org/git/yvesf/flask-mediabrowser',
packages=['mediabrowser'],
include_package_data=True, # use MANIFEST.in during install
scripts=['flask-mediabrowser'],
install_requires=['Flask==0.10.1']
)
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mmtbx/programs/emringer.py | jbeilstenedmands/cctbx_project | 0 | 138522 | from __future__ import division, print_function
try:
from phenix.program_template import ProgramTemplate
except ImportError:
from libtbx.program_template import ProgramTemplate
import os
import libtbx.phil
from libtbx.utils import Sorry
from libtbx import easy_pickle
import mmtbx.ringer.emringer
# =============================================================================
program_citations = libtbx.phil.parse('''
citation {
article_id = emringer1
authors = <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>
title = Side-chain-directed model and map validation for 3D Electron Cryomicroscopy.
journal = Nature Methods
volume = 10
pages = 943-46
year = 2015
doi_id = "10.1038/nmeth.3541"
pmid = 26280328
external = True
}
citation {
article_id = emringer2
authors = <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>
title = Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
journal = Protein Sci.
volume = 7
pages = 1420-31
year = 2010
doi_id = ""
pmid = 20499387
external = True
}
''')
# =============================================================================
master_phil_str = '''
include scope libtbx.phil.interface.tracking_params
include scope mmtbx.ringer.emringer.master_params
map_label = 2FOFCWT,PH2FOFCWT
.type = str
.input_size = 200
.short_caption = 2Fo-FC map labels
.help = Labels for 2Fo-Fc map coefficients
show_gui = False
.type = bool
output_base = None
.type = str
output_dir = None
.type = path
.short_caption = Output directory
quiet = False
.type = bool
.short_caption = no graphs
.help = Don't output files or graphs
'''
# =============================================================================
class Program(ProgramTemplate):
description = '''
Program for calculating the EMRinger score.\n
Minimum required inputs:
Model file
Map file (or file with map coefficients)
How to run:
phenix.emringer model.pdb map.ccp4
'''
datatypes = ['model', 'real_map', 'phil', 'map_coefficients']
citations = program_citations
master_phil_str = master_phil_str
# ---------------------------------------------------------------------------
def validate(self):
print('Validating inputs', file=self.logger)
self.data_manager.has_models(raise_sorry=True)
if not (self.data_manager.has_real_maps() or
self.data_manager.has_map_coefficients()):
raise Sorry("Supply a map file or a file with map coefficients.")
elif (self.data_manager.has_real_maps() and
self.data_manager.has_map_coefficients()):
raise Sorry("Supply either a map file or a file with map coefficients.")
# ---------------------------------------------------------------------------
def run(self):
map_inp = None
miller_array = None
print('Using model: %s' % self.data_manager.get_default_model_name(),
file=self.logger)
model = self.data_manager.get_model()
if self.data_manager.has_map_coefficients():
miller_arrays = self.data_manager.get_miller_arrays()
miller_array = self.find_label(miller_arrays = miller_arrays)
print('Using miller array: %s' % miller_array.info().label_string(),
file=self.logger)
elif self.data_manager.has_real_maps():
print('Using map: %s' % self.data_manager.get_default_real_map_name(),
file=self.logger)
map_inp = self.data_manager.get_real_map()
print("CCP4 map statistics:", file=self.logger)
map_inp.show_summary(out=self.logger, prefix=" ")
if (self.params.output_base is None) :
pdb_base = os.path.basename(self.data_manager.get_default_model_name())
self.params.output_base = os.path.splitext(pdb_base)[0] + "_emringer"
if not self.params.quiet:
plots_dir = self.params.output_base + "_plots"
if (not os.path.isdir(plots_dir)) :
os.makedirs(plots_dir)
task_obj = mmtbx.ringer.emringer.emringer(
model = model,
miller_array = miller_array,
map_inp = map_inp,
params = self.params,
out = self.logger)
task_obj.validate()
task_obj.run()
self.results = task_obj.get_results()
ringer_result = self.results.ringer_result
if not self.params.quiet:
# save as pickle
easy_pickle.dump("%s.pkl" % self.params.output_base, ringer_result)
print ('Wrote %s.pkl' % self.params.output_base, file=self.logger)
# save as CSV
csv = "\n".join([ r.format_csv() for r in ringer_result])
open("%s.csv" % self.params.output_base, "w").write(csv)
print ('Wrote %s.csv' % self.params.output_base, file=self.logger)
scoring_result = self.results.scoring_result
scoring_result.show_summary(out = self.logger)
#rolling_result = self.results.rolling_result
# It would be good to have central code for this
# ---------------------------------------------------------------------------
def find_label(self, miller_arrays):
best_guess = None
best_labels = []
all_labels = []
miller_array = None
for array in miller_arrays:
label = array.info().label_string().replace(" ", "")
if (self.params.map_label is not None):
if (label == self.params.map_label.replace(" ", "")):
miller_array = array
return miller_array
elif (self.params.map_label is None):
if (array.is_complex_array()):
all_labels.append(label)
if (label.startswith("2FOFCWT") or label.startswith("2mFoDFc") or
label.startswith("FWT")) :
best_guess = array
best_labels.append(label)
if (miller_array is None):
if (len(all_labels) == 0) :
raise Sorry("No valid (pre-weighted) map coefficients found in file.")
elif (len(best_labels) == 0) :
raise Sorry("Couldn't automatically determine appropriate map labels. "+
"Choices:\n %s" % " \n".join(all_labels))
elif (len(best_labels) > 1) :
raise Sorry("Multiple appropriate map coefficients found in file. "+
"Choices:\n %s" % "\n ".join(best_labels))
elif (len(best_labels) == 1):
miller_array = best_guess
print(" Guessing %s for input map coefficients"% best_labels[0], file=self.logger)
return miller_array
# ---------------------------------------------------------------------------
def get_results(self):
return self.results
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] |
RobotWorld.py | madalynlmillen/MadalynMillenCapstone | 0 | 192907 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Classes for a simple kinematic robot arm simulation
This code used matplotlib for generating graphics for CS 471/510.
The MIT License (MIT)
Copyright (c) 2015 <NAME> (<EMAIL>)
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 numpy as np
from copy import deepcopy
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import sys
class Link:
def __init__(self, name, length, color='b', width=0.5, parent=None):
self.name = name;
self.current_image = -1
self.length = length;
self.color = color;
self.width = width;
self.angle = 0.0;
self.total_angle = 0.0;
self.base = (0.0, 0.0)
self.parent = parent;
self.total_angle = self.total_angle + self.angle;
self.tip = (self.base[0] + self.length*np.cos(self.total_angle),
self.base[0] + self.length*np.sin(self.total_angle));
self.normal = (-np.sin(self.total_angle),np.cos(self.total_angle))
#print "link ",self.name," base=",self.base," tip=",self.tip
def updateTip(self, angle):
self.angle = deepcopy(angle);
if (self.parent is not None):
self.base = deepcopy(self.parent.tip)
self.total_angle = deepcopy(self.parent.total_angle);
else:
self.base = (0.0, 0.0);
self.total_angle = 0.0;
self.total_angle = self.total_angle + self.angle;
#print " Update link ",self.name," base = ",self.base, " angle=",self.angle," total angle=",self.total_angle
self.tip = (self.base[0] + self.length*np.cos(self.total_angle),
self.base[1] + self.length*np.sin(self.total_angle));
#print "link ",self.name," angle=",self.angle," base=",self.base," tip=",self.tip
# Define vector normal to the link (for later distance calculation)
self.normal = (-np.sin(self.total_angle), np.cos(self.total_angle));
def drawLink(self, ax):
#print "draw link ",self.name," angle=",self.angle," base=",self.base," tip=",self.tip
#surf = ax2.plot(( self.base[0], self.tip[0]), (self.base[1], self.tip[1]),
# linewidth=self.width, color=self.color);
center = ((self.base[0]+self.tip[0])/2.0, (self.base[1]+self.tip[1])/2.0)
corner = ( (self.base[0] - self.normal[0]*self.width*0.5),
(self.base[1] - self.normal[1]*self.width*0.5) )
ax.add_patch(patches.Rectangle(corner,self.length, self.width, angle=(self.total_angle*180.0/np.pi), color=self.color));
def drawTip(self, ax):
ax.plot(self.tip[0], self.tip[1],color=self.color);
class RobotArm:
def __init__(self, links):
self.links = links;
# Update the link positions given angles for each link relative its parent link
# Assuming processing from fixed base up to final child link
def updateLinks(self, angles):
if (len(angles) != len(self.links)):
print "Invalid angles! - need one per link";
sys.exit(-1)
# Assuming list of angles with one angle for each link
for link,angle in enumerate(angles):
self.links[link].updateTip(angle)
# Simple collision checking for circular obstacles
# Returns None for collision free, or a color for object that cause the collision
def checkCollisions(self, objects):
collision = False;
# Check all objects
for obj in objects:
#print "object ",obj.name
# Against all links
for link in self.links:
# Vector from link base to object lowerleft
dX = ( (obj.lowerLeft[0] - link.base[0]), (obj.lowerLeft[1] - link.base[1]) )
dist = dX[0]*link.normal[0] + dX[1]*link.normal[1]
val = np.fabs(dist)
# check distance from obstacle lowerLeft to line along a link
if (val < (link.width/2.0 + obj.width/2.0)):
#print "potential collision"
# Calculate the projection of vector to obstacle along the link
dY = (dX[0] - dist*link.normal[0], dX[1]-dist*link.normal[1])
# Distance along the link
proj = dY[0]*np.cos(link.total_angle) + dY[1]*np.sin(link.total_angle)
if ((proj >= 0.0) and (proj <= (link.length+obj.width))):
print " Collision between link ",link.name," and obstacle ",obj.name, " at dist=",dist, " proj=",proj
return obj.color; # return the first collision encountered
return None;
# Draw each arm
def drawArm(self, ax):
for link in self.links:
link.drawLink(ax)
# Draw the final end effector position
def drawEE(self, ax):
self.links[-1].drawTip(ax)
# Return the position (x,y) of the end effector (tip of last link)
def getEndEffector(self):
return self.links[-1].tip;
# Simple rectangular obstacle
class Obstacle:
def __init__(self, name, lowerLeft, width, height, color, angle=0.0):
self.name = name
self.lowerLeft = lowerLeft
self.width = width
self.height = height
self.color = color
self.angle = angle
def drawObstacle(self,ax2):
ax2.add_patch(patches.Rectangle(self.lowerLeft,self.width, self.height, angle=self.angle, color=self.color));
# Class to hold the robot and obstacles
class RobotWorld:
def __init__(self, robot, obstacles):
self.robot = robot;
self.obstacles = obstacles;
# Draw all the obstacles on the axis
def drawObstacles(self,ax2):
for obj in self.obstacles:
obj.drawObstacle(ax2);
# Draw a small patch for the robot end effector
def drawRobotEndEffector(self, ax):
self.robot.links[-1].drawTip(ax)
# Draw the robot
def drawRobot(self, ax):
self.robot.drawArm(ax);
# Draw both robot arm and obstacles
def drawWorld(self, ax):
self.drawRobot(ax);
self.drawObstacles(ax);
# Update the angles of the robot links
def updateRobotArm(self, angles):
return self.robot.updateLinks(angles);
# Check for collision between current robot arm position and the obstacles
def checkCollisions(self):
return self.robot.checkCollisions(self.obstacles) | [
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examples/ordering.py | F483/easyapi | 0 | 50134 | #!/usr/bin/env python
# coding: utf-8
# Copyright (c) 2015 <NAME> <<EMAIL>>
# License: MIT (see LICENSE file)
import apigen
class Ordering(apigen.Definition):
@apigen.command()
def first(self):
return "first"
@apigen.command()
def second(self):
return "second"
@apigen.command()
def third(self):
return "third"
@apigen.command()
def fourth(self):
return "fourth"
if __name__ == "__main__":
apigen.run(Ordering)
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pysectprop/general/__init__.py | Pretsdaya/pysectprop | 1 | 153596 | from .generalsection import GeneralSection
from .materialsection import MaterialSection
from .compositesection import CompositeSection
from .cripplingsection import CripplingSection
from .thinwalledsection import ThinWalledSection
from .material import Material
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migrations/versions/1e7e4cedd1f1_.py | pavel-yas1405/teamwork | 0 | 1603855 | """empty message
Revision ID: 1e7e4cedd1f1
Revises:
Create Date: 2022-04-15 15:04:47.007855
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '1e7e4cedd1f1'
down_revision = None
branch_labels = None
depends_on = None
def upgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.create_table('cocktail',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('country', sa.String(length=64), nullable=True),
sa.Column('description', sa.Text(), nullable=True),
sa.Column('region', sa.String(length=128), nullable=True),
sa.Column('recipe', sa.Text(), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_index(op.f('ix_cocktail_country'), 'cocktail', ['country'], unique=False)
op.create_index(op.f('ix_cocktail_name'), 'cocktail', ['name'], unique=True)
op.create_index(op.f('ix_cocktail_region'), 'cocktail', ['region'], unique=False)
op.create_table('ingredient',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(length=64), nullable=True),
sa.Column('description', sa.Text(), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_index(op.f('ix_ingredient_name'), 'ingredient', ['name'], unique=True)
op.create_table('origin',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('name', sa.String(), nullable=True),
sa.Column('country', sa.String(), nullable=True),
sa.Column('region', sa.String(), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_table('user',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('username', sa.String(length=64), nullable=True),
sa.Column('password', sa.String(length=128), nullable=True),
sa.Column('role', sa.String(length=10), nullable=True),
sa.Column('email', sa.String(length=50), nullable=True),
sa.PrimaryKeyConstraint('id')
)
op.create_index(op.f('ix_user_role'), 'user', ['role'], unique=False)
op.create_index(op.f('ix_user_username'), 'user', ['username'], unique=True)
op.create_table('cocktail_ingredient',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('cocktail_id', sa.Integer(), nullable=False),
sa.Column('ingredient_id', sa.Integer(), nullable=False),
sa.ForeignKeyConstraint(['cocktail_id'], ['cocktail.id'], ondelete='CASCADE'),
sa.ForeignKeyConstraint(['ingredient_id'], ['ingredient.id'], ondelete='CASCADE'),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('cocktail_id', 'ingredient_id', name='cocktail_id_ingredient_id_unq')
)
op.create_table('cocktail_origin',
sa.Column('id', sa.Integer(), nullable=False),
sa.Column('cocktail_id', sa.Integer(), nullable=False),
sa.Column('origin_id', sa.Integer(), nullable=False),
sa.ForeignKeyConstraint(['cocktail_id'], ['cocktail.id'], ondelete='CASCADE'),
sa.ForeignKeyConstraint(['origin_id'], ['origin.id'], ondelete='CASCADE'),
sa.PrimaryKeyConstraint('id'),
sa.UniqueConstraint('cocktail_id', 'origin_id', name='cocktail_id_origin_id_unq')
)
# ### end Alembic commands ###
def downgrade():
# ### commands auto generated by Alembic - please adjust! ###
op.drop_table('cocktail_origin')
op.drop_table('cocktail_ingredient')
op.drop_index(op.f('ix_user_username'), table_name='user')
op.drop_index(op.f('ix_user_role'), table_name='user')
op.drop_table('user')
op.drop_table('origin')
op.drop_index(op.f('ix_ingredient_name'), table_name='ingredient')
op.drop_table('ingredient')
op.drop_index(op.f('ix_cocktail_region'), table_name='cocktail')
op.drop_index(op.f('ix_cocktail_name'), table_name='cocktail')
op.drop_index(op.f('ix_cocktail_country'), table_name='cocktail')
op.drop_table('cocktail')
# ### end Alembic commands ###
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instauto/api/actions/structs/friendships.py | marvic2409/instauto | 0 | 29668 | from . import common as cmmn
import logging
import uuid
from typing import Optional
from instauto.api.structs import Surface
logger = logging.getLogger(__name__)
class _Base(cmmn.Base):
_csrftoken: str = None
radio_type: str = 'wifi-none'
device_id: str = None
_uid: str = None
_uuid: str = None
user_id: str = None
def __init__(self, **kwargs):
super().__init__(**kwargs)
self._enable_datapoint_from_client('_csrftoken')
self._enable_datapoint_from_client('device_id')
self._enable_datapoint_from_client('_uid')
self._enable_datapoint_from_client('_uuid')
self._custom_data['uuid'] = self.State.required
self._custom_data['user_id'] = self.State.required
self._custom_data['endpoint'] = self.State.required
self._custom_data['surface'] = self.State.optional
class Create(_Base):
def __init__(self, user_id: str, **kwargs):
"""Use this to create a friendship, i.e. follow a user."""
super().__init__(**kwargs)
self._data['endpoint'] = 'create'
self._data['user_id'] = user_id
class Destroy(_Base):
def __init__(self, user_id: str, surface: Optional[Surface] = None, **kwargs):
"""Use this to 'destroy' a friendship, i.e. unfollow."""
super().__init__(**kwargs)
self._data['endpoint'] = 'destroy'
self._data['user_id'] = user_id
self._data['surface'] = surface
self._defaults['surface'] = surface.profile
class Remove(_Base):
def __init__(self, user_id: str, **kwargs):
super().__init__(**kwargs)
self._data['endpoint'] = 'remove_follower'
self._data['user_id'] = user_id
class Show(cmmn.Base):
"""Retrieves the following information for a friendship:
{
"blocking": False,
"followed_by": False,
"following": False,
"incoming_request": False,
"is_bestie": False,
"is_blocking_reel": False,
"is_muting_reel": False,
"is_private": False,
"is_restricted": False,
"muting": False,
"outgoing_request": False,
"status": "ok"
}
"""
def __init__(self, user_id: str, **kwargs):
super().__init__(**kwargs)
self._custom_data['user_id'] = self.State.required
self._custom_data['endpoint'] = self.State.required
self._data['user_id'] = user_id
self._data['endpoint'] = cmmn.Base.State.required
class GetBase(cmmn.Base):
def __init__(self, user_id: str, surface: Optional[Surface] = None, **kwargs):
super().__init__(**kwargs)
self._custom_data['user_id'] = self.State.required
self._custom_data['rank_token'] = self.State.required
self._custom_data['search_surface'] = self.State.required
self._custom_data['max_id'] = self.State.required
self._custom_data['page'] = self.State.required
self._data['user_id'] = user_id
self._data['search_surface'] = surface
self._defaults['search_surface'] = Surface.follow_list
self._defaults['rank_token'] = uuid.uuid4()
self._defaults['max_id'] = None
self._defaults['page'] = 0
# The requests for getting followers and your following, look exactly the same
# but we want to keep them in seperate structs for clarity.
GetFollowers = GetFollowing = GetBase
class PendingRequests:
def __init__(self):
pass
class ApproveRequest(cmmn.Base):
def __init__(self, user_id: str, **kwargs):
super().__init__(**kwargs)
self._enable_datapoint_from_client('_csrftoken')
self._enable_datapoint_from_client('_uid')
self._enable_datapoint_from_client('_uuid')
self._custom_data['radio_type'] = self.State.required
self._custom_data['surface'] = self.State.required
self._custom_data['user_id'] = self.State.required
self._data['user_id'] = user_id
self._defaults['surface'] = Surface.follow_requests
self._defaults['radio_type'] = 'wifi-none'
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] |
yamanifest/manifest.py | coecms/yamanifest | 2 | 82014 | #!/usr/bin/env python
"""
Copyright 2017 ARC Centre of Excellence for Climate Systems Science
author: <NAME> <<EMAIL>>
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.
"""
from __future__ import print_function, absolute_import
from six.moves import zip
import os
import sys
import yaml
import copy
import subprocess
import multiprocessing as mp
from collections import defaultdict
from .hashing import hash, supported_hashes
from yamanifest.utils import find_files
class HashExists(Exception):
"""Trying to add a hashed value when one already exists"""
class FilePathNonexistent(Exception):
"""Trying to check a hashed value when there is none"""
class HashNonexistent(Exception):
"""Trying to check a hashed value when there is none"""
class Manifest(object):
"""A manifest object
Attributes:
path: a Path object for the manifest file
data: an dictionary of manifest items
"""
def __init__(self, path, hashes=None, **kwargs):
"""
Return a Manifest object, initialised with a path
to the manifest file. Optionally specify default
order of hashes to use when checking manifest validity
"""
self.path = path
self.data = {}
self.header = {}
try:
self.numproc = mp.cpu_count()
except NotImplementedError:
self.numproc = 1
for key, val in kwargs.items():
setattr(self, key, val)
self.iter = 0
if hashes is None:
self.hashes = set(['binhash','md5'])
else:
self.hashes = set(hashes)
# self.lookup = {}
# Meta data for the yamanifest file version. This is file type
# version, not library version. Use update in case extra meta
# data was defined in arguments
self.header.update({ 'format':'yamanifest', 'version':1.0 })
def __iter__(self):
"""
Iterator method
"""
for file in self.data:
yield file
def __len__(self):
"""
Return the number of filepaths in the manifest object
"""
return len(self.data)
def load(self):
"""
Load manifest from YAML file
"""
try:
with open(self.path, 'r') as file:
self.header, self.data = yaml.safe_load_all(file)
if "format" not in self.header:
raise ValueError('Not yamanifest format')
if self.header["format"] != 'yamanifest':
raise ValueError('Not yamanifest format: {}'.format(self.header["format"]))
except Exception as e:
sys.stderr.write('Error parsing yamanifest file: {} :: {}\n'.format(self.path,str(e)))
raise
# self._make_lookup()
# Allow chaining a load to creating a new instance
return self
def dump(self):
"""
Dump manifest from YAML file
"""
with open(self.path, 'w') as file:
file.write(yaml.dump_all([self.header, self.data], default_flow_style=False))
def delete(self, filepath):
"""
Delete item for filepath in manifest
"""
del(self.data[filepath])
def add(self, filepaths=None, hashfn=None, force=False, shortcircuit=False, fullpaths=None):
"""
Add hash value for filepath given a hashing function (hashfn).
If no filepaths defined, default to all current filepaths, and in
this way can add a hash to all existing filepaths.
If there is already a hash value only overwrite if force=True,
otherwise raise exception.
"""
if filepaths is None:
filepaths = self.data.keys()
else:
if type(filepaths) is str:
filepaths = [filepaths,]
if fullpaths is None:
fullpaths = [None] * len(filepaths)
else:
if type(fullpaths) is str:
fullpaths = [fullpaths,]
assert(len(filepaths) == len(fullpaths))
tmpfilepaths = []
tmpfns = []
results = defaultdict(dict)
for (filepath,fullpath) in zip(filepaths,fullpaths):
# These must be defined so that queries do not fail later
if filepath not in self.data:
self.data[filepath] = {}
if 'hashes' not in self.data[filepath]:
self.data[filepath]["hashes"] = {}
if fullpath is None:
self.data[filepath]['fullpath'] = os.path.realpath(filepath)
else:
self.data[filepath]['fullpath'] = fullpath
if hashfn is None:
fns = self.hashes
else:
if type(hashfn) is str:
fns = [hashfn,]
else:
fns = hashfn
# Need to add any hash function we use to the list of default hashes
for fn in fns:
self.hashes.add(fn)
for fn in fns:
if fn in self.data[filepath]["hashes"] and not force:
# Don't try and add a hash if it already exists
continue
tmpfilepaths.append(filepath)
tmpfns.append(fn)
results = self.calc_hashes(tmpfilepaths, tmpfns)
for filepath in results:
# Get dict of current hashes for filepath
hashes = {}
if "hashes" in self.data[filepath]:
hashes = copy.deepcopy(self.data[filepath]["hashes"])
fns = []
if hashfn is None:
fns = self.hashes
else:
if type(hashfn) is str:
fns = [hashfn,]
else:
fns = hashfn
for fn in fns:
# if fn not in results[filepath]:
# continue
hashval = results[filepath][fn]
# If we've used an incompatible hashing function it will return
# None and we will silently discard this hash, or if the filepath
# is unhashable
if hashval is not None:
if fn in hashes:
if hashes[fn] != hashval:
if not force:
continue
# Set new value for this hash function
hashes[fn] = hashval
if shortcircuit:
break
# Only save data to manifest if a hash was successfully generated or
# there were existing hashes, else delete it
if len(hashes) > 0:
self.data[filepath]["hashes"] = hashes
else:
del(self.data[filepath])
def contains(self, filepath):
"""
Return True if filepath is in manifest
"""
return filepath in self.data
def get(self, filepath, hashfn):
"""
Return hash value for filepath and hash function. Return None if not defined
"""
hashval = None
if self.contains(filepath):
if hashfn in self.data[filepath]["hashes"]:
hashval = self.data[filepath]["hashes"][hashfn]
# Check we have a valid hash value (can't just be whitespace)
if not hashval.strip():
hashval = False
# else:
# print("hash value not defined {}".format(hashval))
# else:
# print("hash {} not in manifest".format(hashfn))
# else:
# print("{} not in manifest".format(filepath))
return hashval
def calc_hashes(self, filepaths, hashfns):
"""
Calculate hash values for a number of filepaths and hash function combinations
"""
# print("Spawning pool")
pool = mp.Pool(processes=self.numproc) #,maxtasksperchild=50)
results = defaultdict(dict)
# print("Queuing jobs")
for filepath, fn in zip(filepaths,hashfns):
results[filepath][fn] = pool.apply_async(hash, args=(self.data[filepath]["fullpath"], fn))
pool.close()
pool.join()
# print("Retrieving results")
for filepath, fn in zip(filepaths,hashfns):
# Get result of multiprocessing step. Be careful altering this
# loop, as this is saving the result back to the dictionary
results[filepath][fn] = results[filepath][fn].get()
return results
def check_file(self, filepaths, hashfn=None, hashvals=None, shortcircuit=False, condition=all):
"""
Check hash value for a filepath given a hashing function (hashfn)
matches stored hash value. Return values of non-matching hashes
if hashvals dict supplied. If shortcircuit is True, will return True
or False result with first True/False result
"""
if type(filepaths) is str:
filepaths = [ filepaths ]
status = []
if hashvals is not None:
if type(hashvals) is dict:
tmphashvals = defaultdict(dict)
else:
print("yamanifest :: manifest :: check_items :: hashvals must be a dict")
raise
results = defaultdict(dict)
tmpfilepaths = []
tmpfns = []
for filepath in filepaths:
fns = []
if self.contains(filepath):
hashes = self.data[filepath]["hashes"]
else:
raise FilePathNonexistent('{} does not exist in manifest'.format(filepath))
if hashfn == None:
if self.hashes is not None:
fns = self.hashes
else:
fns = hashes.keys()
elif type(hashfn) is str:
fns = [hashfn,]
else:
fns = hashfn
for fn in fns:
# Ignore hash test if it does not exist in the manifest. Need this behaviour
# so we can cascade hashes which in some cases are incompatible with certain
# file types, e.g. nchash
if fn in hashes:
tmpfilepaths.append(filepath)
tmpfns.append(fn)
results = self.calc_hashes(tmpfilepaths, tmpfns)
for filepath in filepaths:
if filepath in results:
filestatus = []
for fn in results[filepath]:
if fn in self.data[filepath]["hashes"]:
# Get result of multiprocessing step
hashval = results[filepath][fn]
if hashval == self.data[filepath]["hashes"][fn]:
filestatus.append(True)
if shortcircuit:
break
else:
continue
else:
# Save these values if given list in which to return them
if hashvals is not None:
tmphashvals[filepath][fn] = hashval
# Should only get here if fn does not exist in manifest, or differs in value
filestatus.append(False)
if shortcircuit:
break
# Only return True for a filepath if there was at least one
# True hash. Ensures filepaths with no hash are False and must
# be regenerated
status.append(condition(filestatus) and len(filestatus)>0)
else:
# Fall here when hash specified but was not in manifest
status.append(False)
if hashvals is not None:
hashvals.update(tmphashvals)
return condition(status)
def check(self, hashvals=None, **args):
"""
Check hash value for all filepaths given a hashing function (hashfn)
matches stored hash value
"""
if hashvals is not None:
if type(hashvals) is dict:
hashvals.clear()
else:
print("yamanifest :: manifest :: check_items :: hashvals must be a dict")
raise
return self.check_file(filepaths=self.data.keys(),hashvals=hashvals,**args)
def fullpath(self, filepath):
"""
Return fullpath string for filepath. None if not defined
"""
if self.contains(filepath):
return self.data[filepath]['fullpath']
else:
return None
def equals(self, other, paths=True):
"""
Test if this manifest is the same as another manifest object.
Made this a bound method instead of overriding __eq__ as need to
qualify if equality also includes file paths
"""
if isinstance(self, other.__class__):
for file in self:
if file not in other.data:
return False
if paths:
if self.data[file]['fullpath'] != other.data[file]['fullpath']:
return False
for fn, val in self.data[file]["hashes"].items():
if fn not in other.data[file]["hashes"]:
return False
if other.data[file]["hashes"][fn] != val:
return False
return True
else:
return NotImplemented
def find(self, hashfn, hashval):
"""
Find a hashfn value in a manifest. Return filepath on success, None otherwise
"""
for filepath in self.data:
if hashval == self.get(filepath, hashfn) and hashval is not None:
return filepath
return None
def find_from_lookup(self, hashfn, hashval):
"""
Find a hashfn value in a manifest. Return filepath on success, None otherwise
"""
if (hashfn,hashval) in self.lookup:
return self.lookup[(hashfn,hashval)]
else:
return None
def _make_lookup(self):
for filepath in self:
for fn in self.data[filepath]["hashes"]:
self._add_lookup(filepath,fn)
def _add_lookup(self,filepath,hashfn):
hashval = self.data[filepath]["hashes"][hashfn]
self.lookup[(hashfn,hashval)] = filepath
def update(self, other, newpath=None):
"""
Add one manifest to another. Optionally replace path in fullpath with new path
"""
mftmp = {}
if newpath is not None:
# Make a copy so we don't alter other
mftmp = copy.deepcopy(other)
# Cannot safely iterate over keys as the dict is being changed so iterate
# over a precomputed list
for filepath in list(other.data.keys()):
mftmp.data[os.path.normpath(os.path.join(newpath,os.path.basename(filepath)))] = other.data[filepath]
del mftmp.data[filepath]
else:
mftmp = other
self.data.update(mftmp.data)
def update_matching_hashes(self, other):
"""
Update (add) hashes from other manifest where a match exists between a common
hash
"""
for filepath in self:
for hashfn in self.data[filepath]["hashes"]:
hashval = self.data[filepath]["hashes"][hashfn]
newfilepath = other.find(hashfn,hashval)
if newfilepath is not None:
# Check other hashes are consistent?
self.data[filepath]["hashes"].update(other.data[newfilepath]["hashes"])
break
@classmethod
def find_manifest(cls, dirpath):
"""
Search a directory path and find first manifest file, return Manifest object else None
"""
for file in find_files(dirpath, ["*.yml","*.yaml"]):
try:
mftmp = cls(file)
mftmp.load()
except:
pass
finally:
if len(mftmp) > 0:
return mftmp
return None
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project/bin/countwords.py | privong/still-magic | 0 | 65943 | <filename>project/bin/countwords.py<gh_stars>0
#!/usr/bin/env python
'''
Read one or more text files given as command-line arguments, or standard input
if no filenames are given, and produce a two-column CSV of words and counts.
'''
import sys
import re
import csv
from collections import Counter
PUNC = re.compile(r'",;.')
WORD = re.compile(r'\b[_\'\(]*(.+?)[_\'\)]*\b')
def main(filenames):
'''
Read standard input or one or more files and report results.
'''
results = Counter()
if not filenames:
process(sys.stdin, results)
else:
for fn in filenames:
with open(fn, 'r') as reader:
process(reader, results)
report(sys.stdout, results)
def process(reader, results):
'''
Extract and count words from stream.
'''
raw = reader.read()
cooked = PUNC.sub('', raw)
words = WORD.findall(cooked)
results.update(words)
def report(writer, results):
'''
Report results to stream.
'''
writer = csv.writer(writer)
for (key, value) in results.items():
writer.writerow((key, value))
if __name__ == '__main__':
main(sys.argv[1:])
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REMD_analysis/REMD_tpr_prep.py | wehs7661/REMD_analysis | 1 | 127564 | #!/usr/bin/env python
import os
import sys
def main():
s = 'This Python script prepares all files needed to run a replica exchange, including' \
' .mdp files and .tpr files, given the .gro file(s) and a template .mdp file.' \
' The .gro file could be only one common .gro file for all the replicas, or one for' \
' each replica. (Check REMD_conf_prep.py for methods for preparing one .gro for each' \
' replica.) In addition, a job submission script can also be generated.'
print(s)
# First request user input
platform = input('Are you using this script locally or in HPC? (local/HPC): ')
jobname = input("Please input the name of the job: ")
prefix = input("Please input the prefix of the file names: ")
N = input("Please input the number of replicas: ")
nodes = input("Please input the number of requested nodes: ")
simutime = input("Please input the simulation time (in hour): ")
HPC = input("Will the job be submitted to Summit or Bridges? ")
conf = input("Are the configurations for different states the same? (yes/no) ")
jobscript = input("Do you want to write a job submission script? (yes/no) ")
sub = input("Do you want to submit the job? (yes/no) ")
# REMD = input('Are you preparaing HREMD or TREMD? (HREMD/TREMD)')
# Identify the current working platform
if platform == 'HPC':
gmx_cmd = 'gmx_mpi'
if HPC == 'Summit' or HPC == 'summit':
os.system('ml gromacs/2018.3')
elif HPC == 'Bridges' or HPC == 'bridges':
os.system('module load gromacs/2018_cpu')
os.system('module load mpi/intel_mpi')
else:
print('Error: Wrong HPC specified. Available options are Summit and Bridges.')
sys.exit()
elif platform == 'local':
gmx_cmd = 'gmx'
else:
print('Error: Wrong platform specified. Available options are local and HPC.')
# Prepare all the input files
print('Preparaing the files needed for the Hamiltonian replica exchange ...')
for i in range(int(N)):
if conf == 'yes':
os.system('mkdir state_%s' % i)
os.system('cp *gro *top *ndx state_%s' % i)
elif conf == 'no':
os.system('cp *top *ndx *state_%s' % i)
else:
print('Bad input for the question: Are the configurations for different states the same? (yes/no')
sys.exit()
os.system('cp *template.mdp state_%s/%s.mdp' % (i, prefix))
os.system('sed -i -e "s/init-lambda-state = X/init-lambda-state = %s/g" state_%s/%s.mdp' %(i, i, prefix))
os.chdir('state_%s' % i)
os.system('%s grompp -f %s.mdp -c %s.gro -p %s.top -n %s.ndx -o %s.tpr -maxwarn 4' % (gmx_cmd, prefix, prefix, prefix, prefix, prefix))
os.chdir('../')
# Write the job submission script and submit it if needed
if jobscript == 'yes':
print('Writing job submission script ...')
job_dir = ''
for i in range(int(N)):
job_dir += 'state_%s ' %i
job_dict = {'jobname': jobname, 'N': N, 'N_cube': int(N) ** 3, 'nodes': nodes,
'simutime': simutime, 'prefix': prefix, 'job_dir': job_dir,
'task-per-nodes': int(int(N) / int(nodes)),
'cpus-per-task-s': int(24 / (int(N) / int(nodes))),
'cpus-per-tasks-b': int(28 / (int(N) / int(nodes)))}
if HPC == 'Summit' or HPC == 'summit':
text = """#!/bin/sh
#SBATCH --job-name {jobname}
#SBATCH --qos normal
#SBATCH --nodes={nodes}
#SBATCH --tasks-per-node={tasks-per-nodes}
#SBATCH --cpus-per-task={cpus-per-tasks-s}
#SBATCH --time {simutime}:00:00
#SBATCH --partition shas
module load gromacs/2018.3
# export OMP_NUM_THREADS=24
sbatch HREMD_run.sh -d=afterok:$SLURM_JOB_ID
if [ -f state_0/{prefix}.cpt ]; then
mpirun -np {N} gmx_mpi mdrun -deffnm {prefix} -dhdl {prefix}_dhdl.xvg -replex 100 -nex {N_cube} -multidir {job_dir} -cpi {prefix}.cpt -noappend
else
mpirun -np {N} gmx_mpi mdrun -deffnm {prefix} -dhdl {prefix}_dhdl.xvg -replex 100 -nex {N_cube} -multidir {job_dir}
fi
""".format(**job_dict)
outfile = open('HREMD_run.sh', 'w')
outfile.write(text)
if sub == 'yes':
os.system('sbatch HREMD_run.sh')
print('Job submitted!')
elif sub == 'no':
pass
else:
print('Error: Bad input for the question: Do you want to submit the job? (yes/no).')
if HPC == 'Bridges' or HPC == 'bridges':
text = """#!/bin/sh
#SBATCH -N {nodes}
#SBATCH -p RM
#SBATCH -t {simutime}:00:00
#SBATCH --ntasks-per-node={task-per-nodes}
module load gromacs/2018_cpu
module load mpi/intel_mpi
# export OMP_NUM_THREADS=24
sbatch HREMD_run.sh -d=afterok:$SLURM_JOB_ID
if [ -f state_0/{prefix}.cpt ]; then
mpirun -np {N} gmx_mpi mdrun -deffnm {prefix} -dhdl {prefix}_dhdl.xvg -replex 100 -nex {N_cube} -multidir {job_dir} -cpi {prefix}.cpt -noappend
else
mpirun -np {N} gmx_mpi mdrun -deffnm {prefix} -dhdl {prefix}_dhdl.xvg -replex 100 -nex {N_cube} -multidir {job_dir}
fi
""".format(**job_dict)
outfile = open('HREMD_run.sh', 'w')
outfile.write(text)
if sub == 'yes':
os.system('sbatch HREMD_run.sh')
print('Job submitted!')
elif sub == 'no':
pass
else:
print('Error: Bad input for the question: Do you want to submit the job? (yes/no).')
# Check if all the files were successfully generated
# mdout.mdp, PLCpep7.mdp, PLCpep.ndx, PLCpep7.top, PLCpep7.tpr
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] |
db_interfacer/interfacer.py | VenkatSubramaniam/SDI | 0 | 43758 | <reponame>VenkatSubramaniam/SDI
#!/usr/bin/env python
# coding: utf-8
from typing import Dict
import psycopg2 as pg
class DBInterfacer:
def __init__(self, uname: str, pword: str, db: str, port: str) -> None:
self.connection, self.cursor = self._establish_postgres_connection(uname, pword, db, port)
def _establish_postgres_connection(self, uname: str, pword: str, db: str, port: str) -> None:
try:
self._create_db(uname, pword, db, port)
connection = pg.connect(user=uname, password=pword, port=port, database=db) # do we have to create this before? The db, I mean.
return connection, connection.cursor()
except (Exception, psycopg2.Error) as error:
raise Exception("We were unsuccessful in connecting to postgres. Are you sure you set up your database as requested?")
def commit(self) -> None:
self.connection.commit()
@staticmethod
def _create_db(uname: str, pword: str, db: str, port: str) -> None:
with pg.connect(user=uname, password=<PASSWORD>, port=port, database="postgres") as conn:
conn.set_isolation_level(pg.extensions.ISOLATION_LEVEL_AUTOCOMMIT)
cur = conn.cursor()
cur.execute(f"select exists(SELECT datname FROM pg_catalog.pg_database WHERE lower(datname) = lower('{db}'))")
if not cur.fetchone()[0]:
cur.execute(f"create database {db};")
def create_table(self, table: str, schema: Dict[str, str]) -> None:
self.cursor.execute(f"create table {table} ({self._parse_schema(schema)});")
self.commit()
@staticmethod
def _parse_schema(schema: Dict[str, str], key: bool=None) -> str:
if key:
pass #TODO
return ", ".join([" ".join(item) for item in schema.items()])
def stringify(self, table:str, row: Dict[str, str], keys: object) -> None:
stringify = ["'"+row[key]+"'" for key in keys]
query = f"insert into {table} ({', '.join(keys)}) values ({', '.join(stringify)})"
self.cursor.execute(query)
def insert_row(self, table:str, row: Dict[str, str]) -> None:
keys = row.keys()
self.cursor.execute(f"insert into {table} ({', '.join(keys)}) values ({', '.join([row[key] for key in keys])})")
# try:
# self.cursor.execute(f"insert into {table} ({', '.join(keys)}) values ({', '.join([row[key] for key in keys])})")
# except:
# self.stringify(table, row, keys)
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] |
twitcher/owsproxy.py | Ouranosinc/twitcher | 0 | 64226 | """
The owsproxy is based on `papyrus_ogcproxy <https://github.com/elemoine/papyrus_ogcproxy>`_
See also: https://github.com/nive/outpost/blob/master/outpost/proxy.py
"""
import urllib
import requests
from pyramid.response import Response
from pyramid.settings import asbool
from twitcher._compat import urlparse
from twitcher.owsexceptions import OWSAccessForbidden, OWSAccessFailed
from twitcher.utils import replace_caps_url
from twitcher.store import servicestore_factory
import logging
LOGGER = logging.getLogger(__name__)
allowed_content_types = (
"application/xml", # XML
"text/xml",
"text/xml;charset=ISO-8859-1"
"application/vnd.ogc.se_xml", # OGC Service Exception
"application/vnd.ogc.se+xml", # OGC Service Exception
# "application/vnd.ogc.success+xml", # OGC Success (SLD Put)
"application/vnd.ogc.wms_xml", # WMS Capabilities
# "application/vnd.ogc.gml", # GML
# "application/vnd.ogc.sld+xml", # SLD
"application/vnd.google-earth.kml+xml", # KML
"application/vnd.google-earth.kmz",
"image/png", # PNG
"image/png;mode=32bit",
"image/gif", # GIF
"image/jpeg", # JPEG
"application/json", # JSON
"application/json;charset=ISO-8859-1",
)
# TODO: configure allowed hosts
allowed_hosts = (
# list allowed hosts here (no port limiting)
# "localhost",
)
# requests.models.Reponse defaults its chunk size to 128 bytes, which is very slow
class BufferedResponse():
def __init__(self, resp):
self.resp = resp
def __iter__(self):
return self.resp.iter_content(64 * 1024)
def _send_request(request, service, extra_path=None, request_params=None):
# TODO: fix way to build url
url = service['url']
if extra_path:
url += '/' + extra_path
if request_params:
url += '?' + request_params
LOGGER.debug('url = %s', url)
# forward request to target (without Host Header)
h = dict(request.headers)
h.pop("Host", h)
h['Accept-Encoding'] = None
#
service_type = service['type']
if service_type and (service_type.lower() != 'wps'):
try:
resp_iter = requests.request(method=request.method.upper(), url=url, data=request.body, headers=h,
stream=True)
except Exception as e:
return OWSAccessFailed("Request failed: {}".format(e.message))
# Headers meaningful only for a single transport-level connection
HopbyHop = ['Connection', 'Keep-Alive', 'Public', 'Proxy-Authenticate', 'Transfer-Encoding', 'Upgrade']
return Response(app_iter=BufferedResponse(resp_iter),
headers={k: v for k, v in resp_iter.headers.iteritems() if k not in HopbyHop})
else:
try:
resp = requests.request(method=request.method.upper(), url=url, data=request.body, headers=h)
except Exception, e:
return OWSAccessFailed("Request failed: {}".format(e.message))
if resp.ok is False:
if 'ExceptionReport' in resp.content:
pass
else:
return OWSAccessFailed("Response is not ok: {}".format(resp.reason))
# check for allowed content types
ct = None
# LOGGER.debug("headers=", resp.headers)
if "Content-Type" in resp.headers:
ct = resp.headers["Content-Type"]
if not ct.split(";")[0] in allowed_content_types:
msg = "Content type is not allowed: {}.".format(ct)
LOGGER.error(msg)
return OWSAccessForbidden(msg)
else:
# return OWSAccessFailed("Could not get content type from response.")
LOGGER.warn("Could not get content type from response")
try:
if ct in ['text/xml', 'application/xml', 'text/xml;charset=ISO-8859-1']:
# replace urls in xml content
proxy_url = request.route_url('owsproxy', service_name=service['name'])
# TODO: where do i need to replace urls?
content = replace_caps_url(resp.content, proxy_url, service.get('url'))
else:
# raw content
content = resp.content
except Exception:
return OWSAccessFailed("Could not decode content.")
headers = {}
if ct:
headers["Content-Type"] = ct
return Response(content, status=resp.status_code, headers=headers)
def owsproxy_url(request):
url = request.params.get("url")
if url is None:
return OWSAccessFailed("URL param is missing.")
service_type = request.GET.get('service', 'wps') or request.GET.get('SERVICE', 'wps')
# check for full url
parsed_url = urlparse(url)
if not parsed_url.netloc or parsed_url.scheme not in ("http", "https"):
return OWSAccessFailed("Not a valid URL.")
return _send_request(request, service=dict(url=url, name='external', service_type=service_type))
def owsproxy(request):
"""
TODO: use ows exceptions
"""
try:
service_name = request.matchdict.get('service_name')
extra_path = request.matchdict.get('extra_path')
store = servicestore_factory(request.registry)
service = store.fetch_by_name(service_name)
except Exception as err:
return OWSAccessFailed("Could not find service: {}.".format(err.message))
else:
return _send_request(request, service, extra_path, request_params=request.query_string)
def owsproxy_delegate(request):
"""
Delegates owsproxy request to external twitcher service.
"""
twitcher_url = request.registry.settings.get('twitcher.url')
protected_path = request.registry.settings.get('twitcher.ows_proxy_protected_path', '/ows')
url = twitcher_url + protected_path + '/proxy'
if request.matchdict.get('service_name'):
url += '/' + request.matchdict.get('service_name')
if request.matchdict.get('access_token'):
url += '/' + request.matchdict.get('service_name')
url += '?' + urllib.urlencode(request.params)
LOGGER.debug("delegate to owsproxy: %s", url)
# forward request to target (without Host Header)
# h = dict(request.headers)
# h.pop("Host", h)
resp = requests.request(method=request.method.upper(), url=url, data=request.body,
headers=request.headers, verify=False)
return Response(resp.content, status=resp.status_code, headers=resp.headers)
def includeme(config):
settings = config.registry.settings
protected_path = settings.get('twitcher.ows_proxy_protected_path', '/ows')
if asbool(settings.get('twitcher.ows_proxy', True)):
LOGGER.debug('Twitcher {}/proxy enabled.'.format(protected_path))
config.add_route('owsproxy', protected_path + '/proxy/{service_name}')
# TODO: maybe configure extra path
config.add_route('owsproxy_extra', protected_path + '/proxy/{service_name}/{extra_path:.*}')
config.add_route('owsproxy_secured', protected_path + '/proxy/{service_name}/{access_token}')
# use delegation mode?
if asbool(settings.get('twitcher.ows_proxy_delegate', False)):
LOGGER.debug('Twitcher {}/proxy delegation mode enabled.'.format(protected_path))
config.add_view(owsproxy_delegate, route_name='owsproxy')
config.add_view(owsproxy_delegate, route_name='owsproxy_secured')
else:
# include twitcher config
config.include('twitcher.config')
# include mongodb
config.include('twitcher.db')
config.add_view(owsproxy, route_name='owsproxy')
config.add_view(owsproxy, route_name='owsproxy_secured')
config.add_view(owsproxy, route_name='owsproxy_extra')
# use /owsproxy?
if asbool(settings.get('twitcher.ows_proxy_url', True)):
LOGGER.debug('Twitcher /owsproxy enabled.')
config.add_route('owsproxy_url', '/owsproxy')
config.add_view(owsproxy_url, route_name='owsproxy_url')
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experiments/2d_shallowwater/gen.py | flabowski/POD-UQNN | 15 | 13884 | <gh_stars>10-100
"""POD-NN modeling for 1D, unsteady Burger Equation."""
#%% Imports
import sys
import os
import pickle
import numpy as np
sys.path.append(os.path.join("..", ".."))
from poduqnn.podnnmodel import PodnnModel
from poduqnn.mesh import read_multi_space_sol_input_mesh
from poduqnn.handling import clean_dir, split_dataset
from hyperparams import HP as hp
resdir = "cache"
clean_dir(resdir)
# Getting data from the files
# fake_x = np.zeros(hp["n_s"] + hp["n_s_tst"])
# test_size = hp["n_s_tst"] / (hp["n_s"] + hp["n_s_tst"])
# train_tst_idx = split_dataset(fake_x, fake_x, test_size, idx_only=True)
train_tst_idx = ([129, 13, 161, 10, 3, 4, 68, 19, 108, 63, 62, 147, 117, 113, 165, 80, 124, 33, 41, 37, 79, 184, 154, 83, 102, 190, 195, 148, 46, 114, 16, 155, 121, 104, 120, 58, 53, 78, 160, 193, 126, 115, 95, 127, 166, 131, 49, 100, 84, 35, 12, 27, 118, 167, 66, 56, 106, 175, 143, 97, 87, 1, 183, 111, 36, 158, 153, 199, 17, 31, 177, 194, 182, 59, 187, 130, 163, 92, 48, 96, 82, 6, 123, 98, 192, 43, 26, 181, 170, 134, 72, 50, 24, 174, 122, 103, 71, 138, 110, 7, 65, 51, 28, 173, 172, 34, 90, 119, 185, 15, 186, 101, 85, 60, 75, 39, 38, 5, 141, 89, 57, 144, 64, 67, 171, 157, 94, 70, 142, 54, 74, 146, 191, 112, 107, 189, 30, 32, 133, 169, 151, 23, 21, 99, 2, 22, 116, 91, 145, 178, 137, 135, 40, 73, 47, 52, 25, 93, 128, 88, 109, 44, 29, 198, 159, 125, 11, 45, 197, 149, 69, 188, 164, 0, 18, 176, 9, 168, 77, 132], [76, 42, 179, 61, 105, 136, 86, 196, 8, 14, 139, 20, 150, 152, 180, 162, 140, 81, 55, 156])
with open(os.path.join("cache", "train_tst_idx.pkl"), "wb") as f:
pickle.dump(train_tst_idx, f)
datadir = "data"
mu_path = os.path.join(datadir, "INPUT_MONTE_CARLO.dat")
# x_mesh, connectivity, X_v, U = \
# read_multi_space_sol_input_mesh(hp["n_s"], 1, 1, train_tst_idx[0],
# hp["mesh_idx"], datadir, mu_path,
# hp["mu_idx"])
# np.save(os.path.join("cache", "x_mesh.npy"), x_mesh)
# np.save(os.path.join("cache", "connectivity.npy"), connectivity)
# np.save(os.path.join("cache", "X_v.npy"), X_v)
# np.save(os.path.join("cache", "U.npy"), U)
x_mesh = np.load(os.path.join("cache", "x_mesh.npy"))
connectivity = np.load(os.path.join("cache", "connectivity.npy"))
X_v = np.load(os.path.join("cache", "X_v.npy"))
U = np.load(os.path.join("cache", "U.npy"))
# x_mesh = np.load(os.path.join("cache", "x_mesh.npy"))
# connectivity = np.load(os.path.join("cache", "connectivity.npy"))
# X_v = np.load(os.path.join("cache", "X_v.npy"))
# U = np.load(os.path.join("cache", "U.npy"))
#%% Init the model
model = PodnnModel(resdir, hp["n_v"], x_mesh, hp["n_t"])
#%% Generate the dataset from the mesh and params
X_v_train, v_train, \
X_v_val, v_val, \
U_val = model.convert_multigpu_data(U, X_v, hp["train_val"], hp["eps"])
model.initVNNs(hp["n_M"], hp["h_layers"], hp["lr"], hp["lambda"],
hp["adv_eps"], hp["soft_0"], hp["norm"])
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] |
annotation_data/responsibility.py | levon003/icwsm-cancer-journeys | 0 | 88424 | from collections import Counter
from tqdm import tqdm
import itertools
import pandas as pd
import numpy as np
from db import get_annotation_db
from journal import get_journal_text, get_journal_info, get_journal_text_representation
responsibility_labels = ["communicating", "info_filtering", "clinical_decisions", "preparation", "symptom_management",
"coordinating_support", "sharing_medical_info", "compliance",
"managing_transitions", "financial_management", "continued_monitoring", "giving_back",
"behavior_changes"]
responsibility_codes = ["CO", "IF", "CD", "PR", "ST", "CS", "SM", "CP", "MT", "FM", "CM", "GB", "BC"]
responsibility_label_to_code_map = {resp_label: responsibility_codes[i] for i, resp_label in enumerate(responsibility_labels)}
responsibility_labels_with_support_management = responsibility_labels + ["support_management"]
responsibility_labels_with_none = responsibility_labels + ["none"]
responsibility_labels_with_all = responsibility_labels + ["none", "support_management"]
"""
This is the set of responsibility labels with Cohen's kappa > 0.4
"""
high_irr_responsibility_labels = ["coordinating_support", "sharing_medical_info", "compliance", "financial_management", "giving_back", "behavior_changes"]
high_irr_responsibility_codes = [responsibility_codes[responsibility_labels.index(resp_label)] for resp_label in high_irr_responsibility_labels]
def sort_responsibility_list(responsibility_list):
return sorted(responsibility_list, key=lambda responsibility: responsibility_labels_with_all.index(responsibility))
def get_labels_from_responsibility_string(responsibility_string, include_none=False,
warn_on_legacy_responsibilities=True):
"""
:param responsibility_string:
:param include_none: If 'none' should be included in the returned list when no other responsibilities are present
:return:
"""
if responsibility_string == "":
return ['none'] if include_none else []
labels = responsibility_string.split('|')
if len(labels) == 0:
print("WARNING: No responsibilities identified, including none")
if include_none:
labels = ['none']
if not include_none and "none" in labels:
labels.remove("none")
# For legacy reasons, we handle support_management, but we replace it with the newer version of the codebook
if "support_management" in labels:
labels.remove("support_management")
labels.append("sharing_medical_info")
labels.append("coordinating_support")
if warn_on_legacy_responsibilities:
print("WARNING: Replaced support management with its newer codes.")
# we sort the responsibility list to ensure they will always appear in a standard order
# will throw an exception if an invalid responsibility occurred in the string
labels = sort_responsibility_list(labels)
return labels
def get_responsibility_annotations(conflict_resolution_strategy="or"):
try:
db = get_annotation_db()
# the most recent version of the annotation guidance was set at this date,
# so we restrict to since this time period
created_at = '2018-08-23'
cursor = db.execute("""
SELECT a.site_id, a.journal_oid, a.data, a.username, c.correct_username
FROM journalAnnotation a LEFT JOIN journalAnnotationConflictResolution c
ON a.site_id = c.site_id AND a.journal_oid = c.journal_oid AND a.annotation_type = c.annotation_type
WHERE a.annotation_type = "journal_patient_responsibilities" AND a.data <> ""
AND a.created >= ?
GROUP BY a.site_id, a.journal_oid, a.username
ORDER BY a.id DESC
""", (created_at,))
responsibility_annotations = []
# Sort the returned annotations so that we can group by the individual journals
def group_by_journal_function(row):
return row['site_id'], row['journal_oid']
# group by the journals, writing a single line for each journal in the dataset
all_rows = cursor.fetchall()
all_rows.sort(key=group_by_journal_function)
for key, group in itertools.groupby(all_rows, group_by_journal_function):
rows = list(group)
site_id, journal_oid = key
# We are considering all of the annotations for a single journal here
data = None
responsibilities = None
if len(rows) == 1:
assert rows[0]['correct_username'] is None or rows[0]['correct_username'] == ""
annotator_usernames = rows[0]['username']
conflict_status = "SINGLE USER"
data = rows[0]['data']
else: # 2 or more annotators
# get the list of annotator names
annotator_usernames = "|".join(sorted([row['username'] for row in rows]))
if rows[0]['correct_username'] is not None and rows[0]['correct_username'] != "":
# this annotation was corrected!
correct_username = rows[0]['correct_username']
conflict_status = "RESOLVED"
data = None
for row in rows:
if row['username'] == correct_username:
data = row['data']
if data is None:
raise ValueError("Annotation unexpectedly lacks data.")
if data is None:
# this condition implies an invalid correction in the database
print(
f"WARNING: {correct_username} not found in {annotator_usernames}. Replacing with 'unknown'.")
data = 'unknown'
else: # no correction for this journal
responsibilities, conflict_status = \
resolve_responsibility_annotation_conflicts(rows,
resolution_strategy=conflict_resolution_strategy)
if data is None and responsibilities is None:
raise ValueError("Unexpected and unhandled conflicts between a journal's responsibility annotations.")
if responsibilities is None:
responsibilities = get_labels_from_responsibility_string(data)
responsibility_annotation_data = {'site_id': site_id,
'journal_oid': journal_oid,
'conflict_status': conflict_status,
'responsibilities': responsibilities}
responsibility_annotations.append(responsibility_annotation_data)
return responsibility_annotations
finally:
db.close()
def get_responsibility_annotations_dataframe():
df = get_responsibility_annotations_by_username_dataframe()
responsibility_annotations = []
# group by the journals, writing a single line for each journal in the dataset
for key, group in df.groupby(by=['site_id', 'journal_oid']):
rows = group
site_id, journal_oid = key
# We are considering all of the annotations for a single journal here
responsibilities = None
if len(rows) == 1:
row = rows.iloc[0]
assert row['correct_username'] is None or row['correct_username'] == ""
annotator_usernames = row['username']
conflict_status = "SINGLE USER"
responsibilities = row.responsibilities
else: # 2 or more annotators
first_row = rows.iloc[0]
if first_row['correct_username'] is not None and first_row['correct_username'] != "":
# this annotation was corrected!
correct_username = first_row['correct_username']
conflict_status = "RESOLVED"
selected_row = rows[rows.username == correct_username]
if len(selected_row) == 0:
# this condition implies an invalid correction in the database
print(
f"WARNING: {correct_username} not found in {annotator_usernames}. Replacing with 'unknown'.")
responsibilities = ['unknown']
elif len(selected_row) > 1:
raise ValueError("Multiple annotations from same username.")
else:
responsibilities = selected_row.iloc[0].responsibilities
else: # no correction for this journal
# use the or strategy
conflict_status = 'CONFLICT'
responsibility_sets = rows.apply(lambda row: set(row.responsibilities), axis=1)
included_responsibilities = set()
for responsibility_set in responsibility_sets:
included_responsibilities = included_responsibilities | responsibility_set
if len(included_responsibilities) == 0:
responsibilities = ['unknown']
else:
responsibilities = sort_responsibility_list(list(included_responsibilities))
if responsibilities is None:
raise ValueError("Unexpected and unhandled conflicts between a journal's responsibility annotations.")
responsibility_annotation_data = {'site_id': site_id,
'journal_oid': journal_oid,
'conflict_status': conflict_status,
'responsibilities': responsibilities}
responsibility_annotations.append(responsibility_annotation_data)
return pd.DataFrame(responsibility_annotations)
def get_responsibility_annotations_by_username():
try:
db = get_annotation_db()
created_at = '2018-08-23'
cursor = db.execute("""
SELECT a.site_id, a.journal_oid, a.data, a.username, c.correct_username
FROM journalAnnotation a LEFT JOIN journalAnnotationConflictResolution c
ON a.site_id = c.site_id AND a.journal_oid = c.journal_oid AND a.annotation_type = c.annotation_type
WHERE a.annotation_type = "journal_patient_responsibilities" AND a.data <> ""
AND a.created >= ?
GROUP BY a.site_id, a.journal_oid, a.username
ORDER BY a.id DESC
""", (created_at,))
responsibility_annotations = []
rows = cursor.fetchall()
for row in rows:
site_id, journal_oid = row['site_id'], row['journal_oid']
username = row['username']
is_corrected = row['correct_username'] is not None and row['correct_username'] != ""
responsibilities = get_labels_from_responsibility_string(row['data'])
responsibility_annotation_data = {'site_id': site_id,
'journal_oid': journal_oid,
'username': username,
'responsibilities': responsibilities,
'is_corrected': is_corrected}
responsibility_annotations.append(responsibility_annotation_data)
return responsibility_annotations
finally:
db.close()
def get_responsibility_annotations_by_username_dataframe():
"""Fixed version of get_responsibility_annotations_by_username() which should be preferred."""
try:
db = get_annotation_db()
created_at = '2018-08-23'
cursor = db.execute("""
SELECT a.site_id, a.journal_oid, a.data, a.username, a.id, c.correct_username
FROM journalAnnotation a LEFT JOIN journalAnnotationConflictResolution c
ON a.site_id = c.site_id AND a.journal_oid = c.journal_oid AND a.annotation_type = c.annotation_type
WHERE a.annotation_type = "journal_patient_responsibilities" AND a.data <> ""
AND a.created >= ?
GROUP BY a.site_id, a.journal_oid, a.username, a.id
ORDER BY a.id DESC
""", (created_at,))
responsibility_annotations = []
rows = cursor.fetchall()
for row in rows:
site_id, journal_oid = row['site_id'], row['journal_oid']
username = row['username']
correct_username = row['correct_username']
responsibilities = get_labels_from_responsibility_string(row['data'])
responsibility_annotation_data = {'site_id': site_id,
'journal_oid': journal_oid,
'username': username,
'correct_username': correct_username,
'responsibilities': responsibilities,
'id': row['id']}
responsibility_annotations.append(responsibility_annotation_data)
responsibility_df = pd.DataFrame(responsibility_annotations)
new_df_inds = [group.id.idxmax()
for key, group
in responsibility_df.groupby(by=['site_id', 'journal_oid', 'username'])]
new_df = responsibility_df.loc[new_df_inds].copy()
new_df.reset_index(inplace=True)
return new_df
finally:
db.close()
def resolve_responsibility_annotation_conflicts(rows, allow_majority_agreement=True, resolution_strategy="or"):
"""
:param rows: Rows of annotations containing 'data'
:param allow_majority_agreement: If annotation sets with at least one set of complete agreement ought to be
allowed as a no-conflict situation
:param resolution_strategy: View the source for the exact implementation of each approach.
Valid values are: 'none', 'empty', 'min2', 'and', 'or' (default)
:return: The responsibilities, as resolved from any conflict,
and a string describing the status of conflict resolution
"""
combinations = [(combo[0]['data'] == combo[1]['data'], combo[0]['data'])
for combo in itertools.combinations(rows, 2)]
agreements = [data for is_match, data in combinations if is_match is True]
responsibilities = None # this function resolves conflicts, assigning this list of responsibilities
if len(agreements) == len(combinations): # all annotators agree
conflict_status = "NO CONFLICT"
data = agreements[0]
elif allow_majority_agreement and len(agreements) >= 1: # at least one pair of annotators agree
# note that this isn't the same as majority agreement if > 3 annotators have annotated a single journal
# but at the time of implementation that will never happen
conflict_status = "MINIMAL CONFLICT"
data = agreements[0]
else: # no agreements between any of the annotators!
# this annotation was not corrected and there is no absolute agreement
# In this situation, we'll resolve based on the resolution strategy
conflict_status = "CONFLICT"
if resolution_strategy == "none":
data = ""
responsibilities = ['none']
elif resolution_strategy == "empty":
data = ""
responsibilities = []
elif resolution_strategy == "min2":
# this strategy includes all annotations used at least twice between annotators
data = ""
responsibility_lists = [get_labels_from_responsibility_string(row['data']) for row in rows]
rep_counter = Counter(list(itertools.chain(*responsibility_lists)))
responsibilities = []
for responsibility, count in rep_counter.most_common():
if count < 2: # only include responsibilities that occur at least twice
break
responsibilities.append(responsibility)
elif resolution_strategy == "and":
# includes all responsibilities selected by all annotators
responsibility_sets = [set(get_labels_from_responsibility_string(row['data'])) for row in rows]
responsibilities = sort_responsibility_list(list(set.intersection(*responsibility_sets)))
elif resolution_strategy == "or" or resolution_strategy == "all_checked":
# includes all responsibilities present among the annotations
responsibility_sets = [set(get_labels_from_responsibility_string(row['data'])) for row in rows]
responsibilities = sort_responsibility_list(list(set.union(*responsibility_sets)))
else:
raise ValueError(f"Resolution strategy f{resolution_strategy} unknown.")
if responsibilities is None:
responsibilities = get_labels_from_responsibility_string(data)
return responsibilities, conflict_status
def get_annotated_responsibility_df(conflict_score_cost=0.1):
"""
:return: Pandas DataFrame with the following columns:
site_id, journal_oid, is_annotated, conflict_status, responsibilities, {responsibility_name}_score, journal_text
"""
responsibility_annotations = get_responsibility_annotations()
df_entries = []
for ra in tqdm(responsibility_annotations):
site_id, journal_oid = ra['site_id'], ra['journal_oid']
responsibilities = ra['responsibilities']
journal_text = get_journal_text(site_id, journal_oid)
if journal_text is None:
continue
conflict_status = ra['conflict_status']
new_entry = {'site_id': site_id,
'journal_oid': journal_oid,
'is_annotated': True,
'conflict_status': ra['conflict_status'],
'responsibilities': responsibilities,
'journal_text': journal_text}
for resp_label in responsibility_labels:
score = int(resp_label in responsibilities)
if conflict_status == "CONFLICT" and score == 1:
score -= conflict_score_cost
new_entry[resp_label + "_score"] = score
df_entries.append(new_entry)
df = pd.DataFrame(df_entries)
return df
def get_annotated_responsibility_df_fixed(conflict_score_cost=0.1, resp_subset=responsibility_labels):
"""
:return: Pandas DataFrame with the following columns:
site_id, journal_oid, is_annotated, conflict_status, responsibilities, {responsibility_name}_score, journal_text
"""
df = get_responsibility_annotations_dataframe()
df['journal_text'] = df.apply(lambda row: get_journal_text(row.site_id, row.journal_oid), axis=1)
df.drop(df[df.journal_text.isna()].index, inplace=True)
assert np.sum(df.journal_text.isna()) == 0
df['is_annotated'] = True
for resp_label in resp_subset:
df[resp_label + "_score"] = df.apply(lambda row: int(resp_label in row.responsibilities) - conflict_score_cost if row.conflict_status == "CONFLICT" else int(resp_label in row.responsibilities), axis=1)
df.reset_index(inplace=True)
return df
def add_journals_to_responsibility_df(df, new_entries):
"""
Add the given [unannotated] journals to the given df.
:param df: A df generated by get_annotated_responsibility_df()
:param new_entries: A list of dictionaries containing the keys 'site_id' and 'journal_oid'
:return: The new dataframe containing both.
"""
df_entries = []
for e in tqdm(new_entries):
site_id, journal_oid = e['site_id'], e['journal_oid']
journal_text = get_journal_text(site_id, journal_oid)
if journal_text is None:
continue
new_entry = {'site_id': site_id,
'journal_oid': journal_oid,
'is_annotated': False,
'conflict_status': None,
'responsibilities': [],
'journal_text': journal_text}
df_entries.append(new_entry)
unannotated_df = pd.DataFrame(df_entries)
new_df = pd.concat([df, unannotated_df], ignore_index=True)
new_df.drop_duplicates(subset=['site_id', 'journal_oid'], keep='first', inplace=True)
return new_df
def add_sites_to_responsibility_df(df, new_entries, drop_duplicate_journals=True):
"""
Add the given [unannotated] sites to the given df.
:param df: A df generated by get_annotated_responsibility_df()
:param new_entries: A list of integer site_ids
:return: The new dataframe containing all journals in the sites indicated by new_entries
"""
df_entries = []
for site_id in tqdm(new_entries):
journals = get_journal_info(site_id)
for journal in journals:
journal_text = get_journal_text_representation(journal)
if journal_text is None:
continue
new_entry = {'site_id': site_id,
'journal_oid': journal['journal_oid'],
'is_annotated': False,
'conflict_status': None,
'responsibilities': [],
'journal_text': journal_text}
df_entries.append(new_entry)
unannotated_df = pd.DataFrame(df_entries)
new_df = pd.concat([df, unannotated_df], ignore_index=True)
if drop_duplicate_journals:
new_df.drop_duplicates(subset=['site_id', 'journal_oid'], keep='first', inplace=True)
return new_df
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] |
model/ff.py | nashory/rtic-gcn-pytorch | 6 | 188555 | import torch
import torch.nn as nn
from block import fusions
from model.base import ImageEncoderTextEncoderBase
class FeatureFusionMethod(ImageEncoderTextEncoderBase):
"""FeatureFusionMethod"""
def __init__(self, cfg, texts):
super(FeatureFusionMethod, self).__init__(cfg, texts)
ff_type = cfg.TRAIN.MODEL.composer_model.name
assert ff_type in fusions.__dict__, f"Invalid fusion method is given: {ff_type}"
_in_c = [self.out_feature_image, self.out_feature_text]
_out_c = self.out_feature_image
self.model["fusion"] = fusions.__dict__[ff_type](_in_c, _out_c)
# define model
self.model = nn.ModuleDict(self.model)
def compose_img_text(self, f_img, f_text):
return self.model["fusion"]((f_img, f_text))
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] |
videoSources.py | mralext20/neos-video-backend | 1 | 179524 | youtubePlaylists = [
"PLxAzjHbHvNcUvcajBsGW2VI6fyIWa4sVl", # ProbablePrime
"PLjux6EKYfu0045V_-s5l9biu55fzbWFAO", # Deloious Jax
"PLoAvz0_U4_3wuXXrl8IbyJIYZFdeIgyHm", # Frooxius
"PLSa764cPPsV9saKq_9Sb_izfwgI9cY-8u", # CuriosVR.. coffee
"PLWhfKbDgR4zD-o31sgHqesncjt49Jxou7", # AMoB tutorials
"PLFYjCoKo3ivA67rj20lIsmUG2AQoavYHG", # <NAME>
"<KEY>", # Turk
"PLSB-6Ok84ZR0Ow4ziNWuFLGTgf3M1JDKT", # sirkitree
"PL<KEY>", # dev tips from Mystic Forge
"PLxzYbxVivbzR5z8FQ<KEY>", # jiink's neos tutorials
"PLpwEkiuuwBpACPqbsPKuJOLTQsFz4Q-7C", # Nicole+
"PLh_pMt0Xa7j8UQJ3fzJMvdTHduACp4jpP", # Engi
]
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harvester/sharekit/tests/factories.py | surfedushare/search-portal | 2 | 38420 | <gh_stars>1-10
import os
import factory
from datetime import datetime
from urllib.parse import quote
from django.conf import settings
from django.utils.timezone import make_aware
from sharekit.models import SharekitMetadataHarvest
class SharekitMetadataHarvestFactory(factory.django.DjangoModelFactory):
class Meta:
model = SharekitMetadataHarvest
strategy = factory.BUILD_STRATEGY
class Params:
set = "edusources"
is_initial = True
is_empty = False
number = 0
is_restricted = False
since = factory.Maybe(
"is_initial",
make_aware(datetime(year=1970, month=1, day=1)),
make_aware(datetime(year=2020, month=2, day=10, hour=13, minute=8, second=39, microsecond=315000))
)
set_specification = "edusources"
status = 200
head = {
"content-type": "application/json"
}
@factory.lazy_attribute
def set_specification(self):
return "edusourcesprivate" if self.is_restricted else "edusources"
@factory.lazy_attribute
def uri(self):
base = f"api.acc.surfsharekit.nl/api/jsonapi/channel/v1/{self.set_specification}/repoItems?"
modified_parameter = quote(f"filter[modified][GE]={self.since:%Y-%m-%dT%H:%M:%SZ}", safe="=")
page_size_parameter = quote("page[size]=25", safe="=")
page_number_parameter = quote(f"page[number]={self.number+1}", safe="=")
if self.is_initial and self.number > 0:
params = [modified_parameter, page_number_parameter, page_size_parameter]
else:
params = [modified_parameter, page_size_parameter]
return base + "&".join(params)
@factory.lazy_attribute
def request(self):
return {
"args": [self.set_specification, f"{self.since:%Y-%m-%dT%H:%M:%SZ}"],
"kwargs": {},
"method": "get",
"url": "https://" + self.uri,
"headers": {},
"data": {}
}
@factory.lazy_attribute
def body(self):
if self.is_empty:
response_type = "empty"
elif self.is_initial:
response_type = "initial"
else:
response_type = "delta"
response_file = f"sharekit-api.{response_type}.{self.number}.json"
response_file_path = os.path.join(settings.BASE_DIR, "sharekit", "fixtures", response_file)
with open(response_file_path, "r") as response:
response_string = response.read()
# We modify the reference to the own link to indicate the link has restricted materials if necessary
if self.is_restricted:
return response_string.replace("/edusources/", "/edusourcesprivate/")
return response_string
@classmethod
def create_common_sharekit_responses(cls, include_delta=False, is_restricted=False):
cls.create(is_initial=True, number=0, is_restricted=is_restricted)
cls.create(is_initial=True, number=1, is_restricted=is_restricted)
if include_delta:
cls.create(is_initial=False, number=0, is_restricted=is_restricted)
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287,
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275,
29918,
5060,
4146,
287,
29897,
13,
2
] |
mergeKsortedlist.py | ZhouLihua/leetcode | 2 | 15645 | #Definition for singly-linked list.
class ListNode(object):
def __init__(self, x):
self.val = x
self.next = None
import sys
class Solution(object):
def mergeKLists(self, lists):
"""
:type lists: List[ListNode]
:rtype: ListNode
"""
temp = ListNode(-1)
result = temp
null_lists = 0
while lists:
while null_lists > 0:
lists.remove(None)
null_lists -= 1
min_node = ListNode(sys.maxint)
order = -1
for index, node in enumerate(lists):
if not node:
null_lists += 1
continue
if node.val < min_node.val:
order, min_node = index, node
if order != -1:
temp.next = ListNode(min_node.val)
temp = temp.next
lists[order] = lists[order].next
return result.next
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] |
moulin/yaml_wrapper.py | Deedone/moulin | 0 | 112787 | # SPDX-License-Identifier: Apache-2.0
# Copyright 2021 EPAM Systems
"""
Wrappers for yaml.Node that provide better API
"""
from typing import Optional, List, Tuple, Iterator, Union
from yaml.nodes import MappingNode, ScalarNode, SequenceNode, Node
from yaml.constructor import SafeConstructor
from yaml.representer import SafeRepresenter
from yaml import Mark
from moulin.yaml_helpers import YAMLProcessingError
yaml_constructor = SafeConstructor()
class _YamlDefaultValue:
"""
Helper class that have the same API as YamlValue, but is
constructed from a primitive type. It is used to provide default
value in YamlValue.get() method
"""
def __init__(self, val: Union[bool, str, int, float, None]):
self._val = val
def __bool__(self):
return self._val is not None
@property
def as_bool(self) -> bool:
"Get the boolean value"
if not isinstance(self._val, bool):
raise TypeError("Expected boolean value")
return self._val
@property
def as_str(self) -> str:
"Get the string value"
if not isinstance(self._val, str):
raise TypeError("Expected boolean value")
return self._val
@property
def as_int(self) -> int:
"Get the integer value"
if not isinstance(self._val, int):
raise TypeError("Expected boolean value")
return self._val
@property
def as_float(self) -> float:
"Get the floating point value"
if not isinstance(self._val, int):
raise TypeError("Expected boolean value")
return self._val
class YamlValue: # pylint: disable=too-few-public-methods
"""Wrapper for yaml.Node class. It provides type-safe access to YAML nodes"""
def __init__(self, node: Node):
self._node = node
if isinstance(node, ScalarNode):
self._val = yaml_constructor.construct_object(node)
else:
self._val = None
@property
def mark(self) -> Mark:
"Get the start mark for YAML Node"
return self._node.start_mark
@property
def as_bool(self) -> bool:
"Get the boolean value"
if not isinstance(self._val, bool):
raise YAMLProcessingError(f"Expected boolean value, got {type(self._val)}", self.mark)
return self._val
@property
def as_str(self) -> str:
"Get the string value"
if not isinstance(self._val, str):
raise YAMLProcessingError(f"Expected string value, got {type(self._val)}", self.mark)
return self._val
@property
def as_int(self) -> int:
"Get the integer value"
if not isinstance(self._val, int):
raise YAMLProcessingError(f"Expected integer value, got {type(self._val)}", self.mark)
return self._val
@property
def as_float(self) -> float:
"Get the floating point value"
if not isinstance(self._val, int):
raise YAMLProcessingError(f"Expected floating point value, got {type(self._val)}",
self.mark)
return self._val
@property
def is_list(self) -> bool:
"""Check if this node represents a list"""
return isinstance(self._node, SequenceNode)
def _get(self, name: str) -> Optional["YamlValue"]:
"Get optional value by name"
if not isinstance(self._node, MappingNode):
raise YAMLProcessingError("Mapping node is expected", self.mark)
for key, val in self._node.value:
if key.value == name:
return YamlValue(val)
return None
def get(self, name: str, default) -> Union["YamlValue", _YamlDefaultValue]:
"Get optional value by name"
val = self._get(name)
if val:
return val
return _YamlDefaultValue(default)
def keys(self) -> List[str]:
"""Get all keys for this mapping"""
if not isinstance(self._node, MappingNode):
raise YAMLProcessingError("Mapping node is expected", self.mark)
return [key.value for key, _ in self._node.value]
def items(self) -> List[Tuple[str, "YamlValue"]]:
"""Get all items for this mapping"""
if not isinstance(self._node, MappingNode):
raise YAMLProcessingError("Mapping node is expected", self.mark)
return [(key.value, YamlValue(val)) for key, val in self._node.value]
def replace_value(self, val: Union[str, int, bool, float]):
"Set a new value for a scalar node"
if not isinstance(self._node, ScalarNode):
raise YAMLProcessingError("Can't replace value for a non-scalar node", self.mark)
self._node.value = val
def __getitem__(self, idx: Union[str, int]) -> "YamlValue":
if isinstance(idx, int):
if not isinstance(self._node, SequenceNode):
raise YAMLProcessingError("SequenceNode node is expected", self.mark)
return YamlValue(self._node.value[idx])
if isinstance(idx, str):
val = self._get(idx)
if not val:
raise YAMLProcessingError(f"Key '{idx}' is mandatory", self.mark)
return val
raise KeyError("Key should have either type 'str' or 'int'")
def __setitem__(self, idx: Union[str, int], val: Union[str, int, bool, float]):
if isinstance(idx, int):
if not isinstance(self._node, SequenceNode):
raise YAMLProcessingError("SequenceNode node is expected", self.mark)
self._node.value[idx].replace_value(val)
if isinstance(idx, str):
item = self._get(idx)
if item:
item.replace_value(val)
else:
representer = SafeRepresenter()
key_node = representer.represent_str(idx)
if isinstance(val, str):
val_node = representer.represent_str(val)
elif isinstance(val, int):
val_node = representer.represent_int(val)
elif isinstance(val, bool):
val_node = representer.represent_bool(val)
else:
val_node = representer.represent_float(val)
self._node.value.append((key_node, val_node))
raise KeyError("Key should have either type 'str' or 'int'")
def __iter__(self) -> Iterator["YamlValue"]:
for item in self._node.value:
yield YamlValue(item)
def __len__(self) -> int:
return len(self._node.value)
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.ycm_extra_conf.py | zaucy/bazel-compilation-database | 1 | 21027 | #!/usr/bin/python
# Copyright 2018 GRAIL, Inc.
#
# 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.
"""Configuration file for YouCompleteMe to fetch C++ compilation flags from
Bazel.
See https://github.com/ycm-core/YouCompleteMe#c-family-semantic-completion for
how YCM works. In that section:
For Option 1 (compilation database), use the generate.sh script in this
repository.
For Option 2 (.ycm_extra_conf.py), symlink this file to the root of your
workspace and bazel's output_base, or set it as your global config.
"""
from __future__ import print_function
import json
import os
import re
import shlex
import subprocess
import sys
import xml.etree.ElementTree as ElementTree
_BAZEL = os.getenv("BAZEL_COMPDB_BAZEL_PATH") or "bazel"
def bazel_info():
"""Returns a dict containing key values from bazel info."""
bazel_info_dict = dict()
try:
out = subprocess.check_output([_BAZEL, 'info']).decode('utf-8').strip().split('\n')
except subprocess.CalledProcessError as err:
# This exit code is returned when this command is run outside of a bazel workspace.
if err.returncode == 2:
sys.exit(0)
for line in out:
key_val = line.strip().partition(": ")
bazel_info_dict[key_val[0]] = key_val[2]
return bazel_info_dict
def bazel_query(args):
"""Executes bazel query with the given args and returns the output."""
# TODO: switch to cquery when it supports siblings and less crash-y with external repos.
query_cmd = [_BAZEL, 'query'] + args
proc = subprocess.Popen(query_cmd, stdout=subprocess.PIPE)
return proc.communicate()[0].decode('utf-8')
def file_to_target(filepath):
"""Returns a string that works as a bazel target specification for the given file."""
if not filepath.startswith("external/"):
# The file path relative to repo root works for genfiles and binfiles too.
return filepath
# For external repos, we have to find the owner package manually.
repo_prefix = re.sub('external/([^/]*).*', '@\\1//', filepath)
filepath = re.sub('external/[^/]*/', '', filepath)
# Find out which package is the owner of this file.
query_result = bazel_query(['-k', repo_prefix+'...', '--output=package'])
packages = [package.strip() for package in query_result.split('\n')]
owner = ""
for package in packages:
package = package[len(repo_prefix):]
if filepath.startswith(package) and len(package) > len(owner):
owner = package
return repo_prefix + owner + ":" + os.path.relpath(filepath, owner)
def standardize_file_target(file_target):
"""For file targets that are not source files, return the target that generated them.
This is needed because rdeps of generated files do not include targets that reference
their generating rules.
https://github.com/bazelbuild/bazel/issues/4949
"""
query_result = bazel_query(['--output=xml', file_target])
if not query_result:
sys.exit("Empty query response for {}. It is probably not handled by bazel".format(file_target))
target_xml = ElementTree.fromstringlist(query_result.split('\n'))
source_element = target_xml.find('source-file')
if source_element is not None:
return file_target
generated_element = target_xml.find('generated-file')
if generated_element is not None:
return generated_element.get('generating-rule')
sys.exit("Error parsing query xml for " + file_target + ":\n" + query_result)
def get_aspects_filepath(label, bazel_bin):
"""Gets the file path for the generated aspects file that contains the
compile commands json entries.
"""
target_path = re.sub(':', '/', label)
target_path = re.sub('^@(.*)//', 'external/\\1/', target_path)
target_path = re.sub('^/*', '', target_path)
relative_file_path = target_path + '.compile_commands.json'
return os.path.join(bazel_bin, *relative_file_path.split('/'))
def get_compdb_json(aspects_filepath, bazel_exec_root):
"""Returns the JSON string read from the file after necessary processing."""
compdb_json_str = "[\n"
with open(aspects_filepath, 'r') as aspects_file:
compdb_json_str += aspects_file.read()
compdb_json_str += "\n]"
return re.sub('__EXEC_ROOT__', bazel_exec_root, compdb_json_str)
def get_flags(filepath, compdb_json_str):
"""Gets the compile command flags from the compile command for the file."""
compdb_dict = json.loads(compdb_json_str)
for entry in compdb_dict:
if entry['file'] != filepath:
continue
command = entry['command']
return shlex.split(command)[1:]
# This could imply we are fetching the wrong compile_commands.json or there
# is a bug in aspects.bzl.
sys.exit("File {f} not present in the compilation database".format(f=filepath))
def standardize_flags(flags, bazel_workspace):
"""Modifies flags obtained from the compile command for compilation outside of bazel."""
# We need to add the workspace directly because the files symlinked in the
# execroot during a build disappear after a different build action.
flags.extend(['-iquote', bazel_workspace])
return flags
def cfamily_settings(filename):
"""Returns C-family settings as a dict with at least a 'flags' key that
points to an array of strings as flags.
"""
bazel_info_dict = bazel_info()
bazel_bin = bazel_info_dict['bazel-bin']
bazel_genfiles = bazel_info_dict['bazel-genfiles']
bazel_exec_root = bazel_info_dict['execution_root']
bazel_workspace = bazel_info_dict['workspace']
os.chdir(bazel_workspace)
# Valid prefixes for the file, in decreasing order of specificity.
file_prefix = [p for p in [bazel_genfiles, bazel_bin, bazel_exec_root, bazel_workspace]
if filename.startswith(p)]
if not file_prefix:
sys.exit("Not a valid file: " + filename)
filepath = os.path.relpath(filename, file_prefix[0])
file_target = standardize_file_target(file_to_target(filepath))
# File path relative to execroot, as it will appear in the compile command.
if file_prefix[0].startswith(bazel_exec_root):
filepath = os.path.relpath(filename, bazel_exec_root)
cc_rules = "cc_(library|binary|test|inc_library|proto_library)"
query_result = bazel_query([('kind("{cc_rules}", rdeps(siblings({f}), {f}, 1))'
.format(f=file_target, cc_rules=cc_rules)), '--keep_going'])
labels = [label.partition(" ")[0] for label in query_result.split('\n') if label]
if not labels:
sys.exit("No cc rules depend on this source file.")
repository_override = '--override_repository=bazel_compdb=' + os.path.dirname(
os.path.realpath(__file__))
aspect_definition = '--aspects=@bazel_compdb//:aspects.bzl%compilation_database_aspect'
bazel_aspects = [
_BAZEL,
'build',
aspect_definition,
repository_override,
'--output_groups=compdb_files,header_files',
] + labels
proc = subprocess.Popen(bazel_aspects, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = proc.communicate()
if proc.returncode != 0:
errors = [e for e in out.splitlines() + err.splitlines()
if e.startswith("ERROR:")]
if errors:
raise Exception('/'.join(errors))
else:
raise Exception(err)
aspects_filepath = get_aspects_filepath(labels[0], bazel_bin)
compdb_json = get_compdb_json(aspects_filepath, bazel_exec_root)
flags = standardize_flags(get_flags(filepath, compdb_json), bazel_workspace)
return {
'flags': flags,
'include_paths_relative_to_dir': bazel_exec_root,
}
#pylint: disable=C0103
def Settings(**kwargs):
"""Function that is called by YCM with language and filename arguments,
and expects a dict of language-specific settings.
"""
if kwargs['language'] == 'cfamily':
return cfamily_settings(kwargs['filename'])
return {}
# For testing; needs exactly one argument as path of file.
if __name__ == '__main__':
filename = os.path.abspath(sys.argv[1])
print(Settings(language='cfamily', filename=filename))
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] |
src/sites/nefilim.py | LAC-Japan/ransomwatch | 244 | 47732 | from datetime import datetime
import logging
from bs4 import BeautifulSoup
from db.models import Victim
from net.proxy import Proxy
from .sitecrawler import SiteCrawler
import time
class Nefilim(SiteCrawler):
actor = "Nefilim"
def _handle_page(self, soup):
victim_list = soup.find_all("header", class_="entry-header")
for victim in victim_list:
victim_title = victim.find("h2", class_="entry-title").text.strip()
victim_name = victim_title[0:victim_title.find(". Part")]
meta = victim.find("div", class_="entry-meta")
published = meta.find("time", class_="entry-date").attrs["datetime"]
published_dt = datetime.strptime(
published.strip()[:-6], "%Y-%m-%dT%H:%M:%S")
victim_leak_site = meta.find("span", class_="posted-on").find("a").attrs["href"]
q = self.session.query(Victim).filter_by(
url=victim_leak_site, site=self.site)
if q.count() == 0:
# new victim
v = Victim(name=victim_name, url=victim_leak_site, published=published_dt,
first_seen=datetime.utcnow(), last_seen=datetime.utcnow(), site=self.site)
self.session.add(v)
self.new_victims.append(v)
else:
# already seen, update last_seen
v = q.first()
v.last_seen = datetime.utcnow()
self.current_victims.append(v)
self.session.commit()
# server was timing out so slows it down a bit
time.sleep(1.0)
def scrape_victims(self):
with Proxy() as p:
r = p.get(f"{self.url}", headers=self.headers)
soup = BeautifulSoup(r.content.decode(), "html.parser")
page_count = 0
while True:
page_nav = soup.find("div", class_="nav-previous")
if page_nav is None:
break
url = page_nav.find("a").attrs["href"]
r = p.get(f"{url}", headers=self.headers)
soup = BeautifulSoup(r.content.decode(), "html.parser")
self._handle_page(soup) | [
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tests/components/synology_dsm/test_config_flow.py | dzmitov/core | 1 | 54375 | """Tests for the Synology DSM config flow."""
import logging
from unittest.mock import MagicMock, Mock, patch
import pytest
from homeassistant import data_entry_flow
from homeassistant.components.synology_dsm.const import (
CONF_VOLUMES,
DEFAULT_NAME,
DEFAULT_PORT,
DEFAULT_PORT_SSL,
DEFAULT_SSL,
DOMAIN,
)
from homeassistant.config_entries import SOURCE_IMPORT, SOURCE_USER
from homeassistant.const import (
CONF_DISKS,
CONF_HOST,
CONF_NAME,
CONF_PASSWORD,
CONF_PORT,
CONF_SSL,
CONF_USERNAME,
)
from homeassistant.helpers.typing import HomeAssistantType
from tests.common import MockConfigEntry
_LOGGER = logging.getLogger(__name__)
NAME = "My Syno"
HOST = "nas.meontheinternet.com"
SERIAL = "mySerial"
HOST_2 = "nas.worldwide.me"
SERIAL_2 = "mySerial2"
PORT = 1234
SSL = True
USERNAME = "Home_Assistant"
PASSWORD = "password"
@pytest.fixture(name="service")
def mock_controller_service():
"""Mock a successful service."""
with patch(
"homeassistant.components.synology_dsm.config_flow.SynologyDSM"
) as service_mock:
service_mock.return_value.login = Mock(return_value=True)
service_mock.return_value.information = Mock(serial=SERIAL)
service_mock.return_value.utilisation = Mock(cpu_user_load=1)
service_mock.return_value.storage = Mock(disks_ids=[], volumes_ids=[])
yield service_mock
@pytest.fixture(name="service_login_failed")
def mock_controller_service_login_failed():
"""Mock a failed login."""
with patch(
"homeassistant.components.synology_dsm.config_flow.SynologyDSM"
) as service_mock:
service_mock.return_value.login = Mock(return_value=False)
yield service_mock
@pytest.fixture(name="service_failed")
def mock_controller_service_failed():
"""Mock a failed service."""
with patch(
"homeassistant.components.synology_dsm.config_flow.SynologyDSM"
) as service_mock:
service_mock.return_value.login = Mock(return_value=True)
service_mock.return_value.information = Mock(serial=None)
service_mock.return_value.utilisation = Mock(cpu_user_load=None)
service_mock.return_value.storage = Mock(disks_ids=None, volumes_ids=None)
yield service_mock
async def test_user(hass: HomeAssistantType, service: MagicMock):
"""Test user config."""
result = await hass.config_entries.flow.async_init(
DOMAIN, context={"source": SOURCE_USER}, data=None
)
assert result["type"] == data_entry_flow.RESULT_TYPE_FORM
assert result["step_id"] == "user"
# test with all provided
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_USER},
data={
CONF_NAME: NAME,
CONF_HOST: HOST,
CONF_PORT: PORT,
CONF_SSL: SSL,
CONF_USERNAME: USERNAME,
CONF_PASSWORD: PASSWORD,
},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_CREATE_ENTRY
assert result["result"].unique_id == SERIAL
assert result["title"] == HOST
assert result["data"][CONF_NAME] == NAME
assert result["data"][CONF_HOST] == HOST
assert result["data"][CONF_PORT] == PORT
assert result["data"][CONF_SSL] == SSL
assert result["data"][CONF_USERNAME] == USERNAME
assert result["data"][CONF_PASSWORD] == PASSWORD
assert result["data"].get(CONF_DISKS) is None
assert result["data"].get(CONF_VOLUMES) is None
service.return_value.information = Mock(serial=SERIAL_2)
# test without port + False SSL
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_USER},
data={
CONF_NAME: NAME,
CONF_HOST: HOST,
CONF_SSL: False,
CONF_USERNAME: USERNAME,
CONF_PASSWORD: PASSWORD,
},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_CREATE_ENTRY
assert result["result"].unique_id == SERIAL_2
assert result["title"] == HOST
assert result["data"][CONF_NAME] == NAME
assert result["data"][CONF_HOST] == HOST
assert result["data"][CONF_PORT] == DEFAULT_PORT
assert not result["data"][CONF_SSL]
assert result["data"][CONF_USERNAME] == USERNAME
assert result["data"][CONF_PASSWORD] == PASSWORD
assert result["data"].get(CONF_DISKS) is None
assert result["data"].get(CONF_VOLUMES) is None
async def test_import(hass: HomeAssistantType, service: MagicMock):
"""Test import step."""
# import with minimum setup
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_IMPORT},
data={CONF_HOST: HOST, CONF_USERNAME: USERNAME, CONF_PASSWORD: PASSWORD},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_CREATE_ENTRY
assert result["result"].unique_id == SERIAL
assert result["title"] == HOST
assert result["data"][CONF_NAME] == DEFAULT_NAME
assert result["data"][CONF_HOST] == HOST
assert result["data"][CONF_PORT] == DEFAULT_PORT_SSL
assert result["data"][CONF_SSL] == DEFAULT_SSL
assert result["data"][CONF_USERNAME] == USERNAME
assert result["data"][CONF_PASSWORD] == PASSWORD
assert result["data"].get(CONF_DISKS) is None
assert result["data"].get(CONF_VOLUMES) is None
service.return_value.information = Mock(serial=SERIAL_2)
# import with all
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_IMPORT},
data={
CONF_NAME: NAME,
CONF_HOST: HOST_2,
CONF_PORT: PORT,
CONF_SSL: SSL,
CONF_USERNAME: USERNAME,
CONF_PASSWORD: PASSWORD,
CONF_DISKS: ["sda", "sdb", "sdc"],
CONF_VOLUMES: ["volume_1"],
},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_CREATE_ENTRY
assert result["result"].unique_id == SERIAL_2
assert result["title"] == HOST_2
assert result["data"][CONF_NAME] == NAME
assert result["data"][CONF_HOST] == HOST_2
assert result["data"][CONF_PORT] == PORT
assert result["data"][CONF_SSL] == SSL
assert result["data"][CONF_USERNAME] == USERNAME
assert result["data"][CONF_PASSWORD] == PASSWORD
assert result["data"][CONF_DISKS] == ["sda", "sdb", "sdc"]
assert result["data"][CONF_VOLUMES] == ["volume_1"]
async def test_abort_if_already_setup(hass: HomeAssistantType, service: MagicMock):
"""Test we abort if the account is already setup."""
MockConfigEntry(
domain=DOMAIN,
data={CONF_HOST: HOST, CONF_USERNAME: USERNAME, CONF_PASSWORD: PASSWORD},
unique_id=SERIAL,
).add_to_hass(hass)
# Should fail, same HOST:PORT (import)
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_IMPORT},
data={CONF_HOST: HOST, CONF_USERNAME: USERNAME, CONF_PASSWORD: PASSWORD},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_ABORT
assert result["reason"] == "already_configured"
# Should fail, same HOST:PORT (flow)
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_USER},
data={CONF_HOST: HOST, CONF_USERNAME: USERNAME, CONF_PASSWORD: PASSWORD},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_ABORT
assert result["reason"] == "already_configured"
async def test_login_failed(hass: HomeAssistantType, service_login_failed: MagicMock):
"""Test when we have errors during connection."""
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_USER},
data={CONF_HOST: HOST, CONF_USERNAME: USERNAME, CONF_PASSWORD: PASSWORD},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_FORM
assert result["errors"] == {CONF_USERNAME: "login"}
async def test_connection_failed(hass: HomeAssistantType, service_failed: MagicMock):
"""Test when we have errors during connection."""
result = await hass.config_entries.flow.async_init(
DOMAIN,
context={"source": SOURCE_USER},
data={CONF_HOST: HOST, CONF_USERNAME: USERNAME, CONF_PASSWORD: PASSWORD},
)
assert result["type"] == data_entry_flow.RESULT_TYPE_FORM
assert result["errors"] == {"base": "unknown"}
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test.py | minizon/Mask_RCNN_KP | 1 | 46953 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 11 21:22:59 2018
@author: pami4
"""
#CUDA_VISIBLE_DEVICES=0 python
from pycocotools.coco import COCO
import coco
import numpy as np
from matplotlib import pyplot as plt
import visualize
import custom_utils
config = coco.CocoConfig()
config.GPU_COUNT = 1
import CustomDataset
data_train=CustomDataset.CocoDataset()
data_train.load_coco("..","train", year=2014)
data_train.prepare()
#import CustomDataGenerator
#data_gen=CustomDataGenerator.data_generator(data_train, config, batch_size=2, shuffle=False, augment=False)
from CustomDataGenerator import CustomDatasetIterator_MaskRCNN
data_gen = CustomDatasetIterator_MaskRCNN(data_train, config, mode="val", shuffle=False,
batch_size=2, augment=True)
#plt.imshow((images[0]+config.MEAN_PIXEL).astype(np.uint8))
import model as modellib
model=modellib.MaskRCNN(mode="training", config=config, model_dir="logs")
model.load_weights("logs/coco20180327T1023/mask_rcnn_coco_0050.h5", by_name=True, skip_mismatch=True)
#model.load_weights("/home/pami4/.keras/models/resnet50_weights_tf_dim_ordering_tf_kernels_notop.h5", by_name=True)
inputs, outputs= next(data_gen)
outs=model.keras_model.predict(inputs)
#out_kp_vs = outs[18]
#np.where(out_kp_vs)
#
#
#out_kp_masks=outs[19]
images = inputs[0]
rois = outs[8]
img_idx=0
visualize.draw_boxes((images[img_idx]+config.MEAN_PIXEL).astype(np.uint8), boxes=rois[img_idx][:10]*np.array([1024,1024,1024,1024]))
plt.show()
#layer=model.keras_model.get_layer(name='kp_mask_bilinear_up')
#layer.get_weights()[0].shape
kp_masks=outs[-3]
kp_vs = outs[-4]
target_masks = outs[-1]
target_class_ids=outs[-2]
pred_kp_masks=outs[10]
pred_masks = outs[6]
#target_class_ids.shape
img_idx=0
index=1
visualize.draw_boxes((images[img_idx]+config.MEAN_PIXEL).astype(np.uint8), boxes=rois[img_idx][index:index+1]*np.array([1024,1024,1024,1024]))
plt.show()
custom_utils.showKPs((images[img_idx]+config.MEAN_PIXEL).astype(np.uint8), rois[img_idx][index]*np.array([1024,1024,1024,1024]),kp_vs[img_idx][index], kp_masks[img_idx][index], target_masks[img_idx][index])
plt.imshow(np.sum(kp_masks[1][index], axis=2))
plt.show()
#custom_utils.showKPs((images[1]+config.MEAN_PIXEL).astype(np.uint8), rois[1][index]*np.array([1024,1024,1024,1024]),kp_vs[1][index], kp_masks[1][index])
#pred_kp_masks=outs[10]
#pred_masks = outs[6]
#custom_utils.showKPs((images[1]+config.MEAN_PIXEL).astype(np.uint8), rois[1][index]*np.array([1024,1024,1024,1024]),kp_vs[1][index], pred_kp_masks[1][index])
custom_utils.showKPs((images[img_idx]+config.MEAN_PIXEL).astype(np.uint8), rois[img_idx][index]*np.array([1024,1024,1024,1024]),kp_vs[img_idx][index], pred_kp_masks[img_idx][index], pred_masks[img_idx][index][:,:,1])
from imp import reload
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preprocessing/her2_split_and_imbalance.py | minotm/NTA | 1 | 143853 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created 2022
@author: <NAME>
"""
from Levenshtein import distance as levenshtein_distance
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
print('Now Executing Trastuzumab Train/Val/Test Splitting...')
"""
This script serves to split the trastuzumab (her2) data into training, validation, and testing sets. The train
and validation sets are selected to be an edit distance of 7 or less from the wild type trastuzumab. The
test set is an edit distance of 8 or greater from the wild type
Inputs
----------
labeled trastuzumab data from Mason et. al 2021 github repo: https://github.com/dahjan/DMS_opt
mHER_H3_AgPos.csv
mHER_H3_AgNeg.csv
Outputs
-------
csv files containing training, validation, and testing sets
"""
def add_LD_to_df(antigen_ID, data_frame):
'''
Function to add Edit Distance (Levenshtein Distance) from wt for each sequence to dataframe
Parameters
----------
antigen_ID : str
corresponds to the antigen identity. in this case, her2
data_frame : pandas.DataFrame
dataframe containing all sequence & label data
Returns
-------
data_frame : pandas.DataFrame
input dataframe with an added column containing the Levenshtein Distance from the wild type
for each sequence in the dataframe
'''
if antigen_ID == 'her2':
wt_str = 'WGGDGFYAMK'
LD_arr = []
for i in range(len(data_frame)):
LD_arr.append( levenshtein_distance(wt_str, data_frame['AASeq'].iloc[i]) )
data_frame['LD'] = LD_arr
return data_frame
def class_balance_binary(data_frame):
'''
Function to class balance dataset
Parameters
----------
data_frame : pandas.DataFrame
dataframe containing all sequence & label data
Returns
-------
data_frame : pandas.DataFrame
class balanced dataframe. number of positive examples is equal to the number of negatives
'''
positives = data_frame[data_frame['AgClass'] == 1].copy()
negatives = data_frame[data_frame['AgClass'] == 0].copy()
min_list = min([len(ls) for ls in [positives, negatives]])
positives = positives[: int(np.round(min_list))]
negatives = negatives[: int(np.round(min_list))]
return positives, negatives
her2_path_local = '../data/her2/'
pos = pd.read_csv(her2_path_local + 'mHER_H3_AgPos.csv')
neg = pd.read_csv(her2_path_local + 'mHER_H3_AgNeg.csv')
def combine_df_list_and_shuffle(df_list, keep = False):
'''
combines two dataframes, drops duplicates, & shuffles
Parameters
----------
data_frame : pandas.DataFrame
dataframe containing all sequence & label data
keep: bool
whether or not to keep duplicates
Returns
-------
data_frame : pandas.DataFrame
combined, shuffled dataframe
'''
frames = df_list
common_cols = list(set.intersection(*(set(df.columns) for df in frames)))
combined_df = pd.concat([df[common_cols] for df in frames], ignore_index=True).drop_duplicates(subset='AASeq', keep=keep)
np.random.seed(0)
combined_df = combined_df.reindex(np.random.permutation(combined_df.index))
return combined_df
all_data_frames = [pos.copy(), neg.copy()]
data_frame = combine_df_list_and_shuffle(all_data_frames, keep = False)
data_frame = add_LD_to_df('her2', data_frame)
selected_LD_split = 7
train_df = data_frame[data_frame['LD'] <= selected_LD_split]
test_df_initial = data_frame[data_frame['LD'] > selected_LD_split]
#Function to drop duplicates from two dataframes
def drop_test_seqs(train_df, test_df, seq_name):
'''
Function serves as a check to prevent dataleakage between training & test or training & val sets
Parameters
----------
train_df : pandas.DataFrame
train dataframe
test_df : pandas.DataFrame
test dataframe
seq_name : str
corresponds to the dataframe column name containing sequences.
Returns
-------
out_df : TYPE
train dataframe without test sequences
'''
train_df = train_df.copy()
train_df['df'] = 'train'
test_df_copy = test_df.copy()
test_df_copy['df'] = 'test'
frames = [train_df.copy(),test_df_copy]
common_cols = list(set.intersection(*(set(df.columns) for df in frames)))
concat_df = pd.concat([df[common_cols] for df in frames], ignore_index=True)
concat_df = concat_df.drop_duplicates(subset=[seq_name],keep=False)
out_df = concat_df[concat_df['df'] == 'train']
return out_df
train_df = drop_test_seqs(train_df, test_df_initial, 'AASeq')
def drop_and_rename_columns(df):
df = df.copy()
df = df.rename(columns = {'AASeq': 'aaseq', 'AgClass': 'target'})
df = df.drop(columns = ['Unnamed: 0', 'Fraction', 'NucSeq', 'Count', 'df'])
return df
#Balance test set & save to csv
test_df = test_df_initial.copy()
test_df['df'] = 'test' #add to df to facilitate using the function below
test_df = drop_and_rename_columns(test_df)
test_positives = test_df[test_df['target'] == 1]
test_negs = test_df[test_df['target'] == 0].sample(n = int(len(test_positives)), random_state = 1)
test_df = test_positives.append(test_negs,ignore_index = True)
test_df = test_df.reindex(np.random.permutation(test_df.index))
out_path = '../data/her2/'
test_df.to_csv(out_path + 'her2_test.csv', index=False)
train_df = drop_and_rename_columns(train_df)
#Class balance full training data set & shuffle dataframe
initial_train_pos = train_df[train_df['target'] == 1]
initial_train_neg = train_df[train_df['target'] == 0]
initial_train_neg = initial_train_neg[initial_train_neg['LD'] != 3] #drop the single LD 3 seq from df. required for sklearn train test stratifying later in script
initial_train_pos = initial_train_pos[initial_train_pos['LD'] != 2] #drop the two LD 2 seq from df. required for sklearn train test stratifying later in script
minlen = min([len(initial_train_pos),len(initial_train_neg) ])
initial_train_pos = initial_train_pos.sample(n = minlen, random_state = 1)
initial_train_neg = initial_train_neg.sample(n = minlen, random_state = 1)
train_df = pd.DataFrame()
train_df = initial_train_pos.append(initial_train_neg, ignore_index = True)
train_df = train_df.sample(n = int(len(train_df)), random_state = 1)
#Batch training & val sets with different quantities of class imbalance using positives as the minority class
class_imbalance_qty_list = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0]
train_df_master_copy = train_df.copy()
for imbal_qty in class_imbalance_qty_list:
#artificially increase class imbalance in training set by downsampling positives
train_positives = train_df_master_copy[train_df_master_copy['target'] == 1]
train_negs = train_df_master_copy[train_df_master_copy['target'] == 0]
#new downsampling method using sklearn & edit distance
if imbal_qty != 1.0:
train_positives, x_discard, y_train, y_discard = train_test_split(train_positives, train_positives['target'], test_size = 1 - imbal_qty,
random_state = 1, shuffle = True, stratify = train_positives['LD'])
elif imbal_qty == 1.0:
train_truncated = train_positives
#split val set from training & maintain LD distribution per class
train_positives, val_positives, y_train, y_val = train_test_split(train_positives, train_positives['target'], test_size = 1 - 0.8,
random_state = 1, shuffle = True, stratify = train_positives['LD'])
train_negs, val_negs, y_train, y_val = train_test_split(train_negs, train_negs['target'], test_size = 1 - 0.8,
random_state = 1, shuffle = True, stratify = train_negs['LD'])
train_df = train_positives.append(train_negs,ignore_index = True)
train_df = train_df.reindex(np.random.permutation(train_df.index))
val_df = val_positives.append(val_negs,ignore_index = True)
val_df = val_df.reindex(np.random.permutation(val_df.index))
train_df = drop_test_seqs(train_df, val_df, 'aaseq')
train_df = train_df.drop(columns = ['df'])
train_df = train_df.drop(columns = ['LD'])
val_df = val_df.drop(columns = ['LD'])
out_str_train = out_path + 'her2_train_imbal_' + str(imbal_qty) + '.csv'
out_str_val = out_path + 'her2_val_imbal_' + str(imbal_qty) + '.csv'
train_df.to_csv(out_str_train, index=False)
val_df.to_csv(out_str_val, index=False)
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crops/migrations/0004_crop_gardens.py | LukasBaecker/be-stadtlabor | 1 | 164728 | <filename>crops/migrations/0004_crop_gardens.py
# Generated by Django 3.1 on 2022-01-18 20:41
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('gardens', '0007_auto_20211231_2258'),
('crops', '0003_auto_20211205_1004'),
]
operations = [
migrations.AddField(
model_name='crop',
name='gardens',
field=models.ManyToManyField(to='gardens.Garden'),
),
]
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tests/tensor/sum_test.py | kbrodt/tor4 | 0 | 29496 | from tor4 import tensor
def test_tensor_sum():
a = tensor(data=[-1, 1, 2])
a_sum = a.sum()
assert a_sum.tolist() == 2
assert not a_sum.requires_grad
def test_tensor_sum_backward():
a = tensor(data=[-1, 1, 2.0], requires_grad=True)
a_sum = a.sum()
a_sum.backward()
assert a_sum.tolist() == 2
assert a_sum.requires_grad
assert a.grad.tolist() == [1, 1, 1]
def test_tensor_sum_backward2():
a = tensor(data=[-1, 1, 2.0], requires_grad=True)
a_sum = a.sum()
a_sum.backward(tensor(3))
assert a_sum.tolist() == 2
assert a_sum.requires_grad
assert a.grad.tolist() == [3, 3, 3]
def test_tensor_sum1_backward():
a = tensor(data=[[-1, 1, 2], [1, 2, 3.0]], requires_grad=True)
a_sum = a.sum(dim=1)
a_sum.backward(tensor(data=[2, 3]))
assert a_sum.tolist() == [2, 6]
assert a_sum.requires_grad
assert a.grad.tolist() == [[2, 2, 2], [3, 3, 3]]
def test_tensor_sum2_backward():
a = tensor(data=[[[-1], [1], [2]], [[1], [2], [3.0]]], requires_grad=True)
a_sum = a.sum(dim=1)
a_sum.backward(tensor(data=[[2], [3]]))
assert a_sum.tolist() == [[2], [6]]
assert a_sum.requires_grad
assert a.grad.tolist() == [[[2], [2], [2]], [[3], [3], [3]]]
def test_tensor_sum3_backward():
a = tensor(data=[[[-1], [1], [2]], [[1], [2], [3.0]]], requires_grad=True)
a_sum = a.sum()
a_sum.backward()
assert a_sum.tolist() == 8
assert a_sum.requires_grad
assert a.grad.tolist() == [[[1], [1], [1]], [[1], [1], [1]]]
def test_tensor_sum4_backward():
a = tensor(data=[[[-1], [1], [2]], [[1], [2], [3.0]]], requires_grad=True)
a_sum = a.sum(dim=(1, 0))
a_sum.backward()
assert a_sum.tolist() == [8]
assert a_sum.requires_grad
assert a.grad.tolist() == [[[1], [1], [1]], [[1], [1], [1]]]
def test_tensor_sum_keepdim1_backward():
a = tensor(data=[[-1, 1, 2], [1, 2, 3.0]], requires_grad=True)
a_sum = a.sum(dim=1, keepdim=True)
a_sum.backward(tensor(data=[[2], [3]]))
assert a_sum.tolist() == [[2], [6]]
assert a_sum.requires_grad
assert a.grad.tolist() == [[2, 2, 2], [3, 3, 3]]
def test_tensor_sum_keepdim2_backward():
a = tensor(data=[[[-1], [1], [2]], [[1], [2], [3.0]]], requires_grad=True)
a_sum = a.sum(dim=1, keepdim=True)
a_sum.backward(tensor(data=[[[2]], [[3]]]))
assert a_sum.tolist() == [[[2]], [[6]]]
assert a_sum.requires_grad
assert a.grad.tolist() == [[[2], [2], [2]], [[3], [3], [3]]]
def test_tensor_sum_keepdim3_backward():
a = tensor(data=[[[-1], [1], [2]], [[1], [2], [3.0]]], requires_grad=True)
a_sum = a.sum()
a_sum.backward()
assert a_sum.tolist() == 8
assert a_sum.requires_grad
assert a.grad.tolist() == [[[1], [1], [1]], [[1], [1], [1]]]
def test_tensor_sum_keepdim4_backward():
a = tensor(data=[[[-1], [1], [2]], [[1], [2], [3.0]]], requires_grad=True)
a_sum = a.sum(dim=(1, 0), keepdim=True)
a_sum.backward()
assert a_sum.tolist() == [[[8]]]
assert a_sum.requires_grad
assert a.grad.tolist() == [[[1], [1], [1]], [[1], [1], [1]]]
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] |
zapi/views.py | zyn777/7pi | 0 | 56981 | import logging
from django.contrib import auth
from django.contrib.auth.decorators import login_required
from django.http import HttpResponseRedirect
from django.shortcuts import render
from zapi.forms import LoginForm
logger = logging.getLogger(__name__)
def index(request):
return render(request, "index.html")
def login(request):
if request.method == 'GET':
form = LoginForm()
return render(request, 'login.html', {'form': form})
else:
form = LoginForm(request.POST)
if form.is_valid():
username = request.POST.get('username', '')
password = request.POST.get('password', '')
user = auth.authenticate(username=username, password=password)
if user and user.is_active:
auth.login(request, user)
logger.info("+" * 100)
logger.info(f"({username}) 登陆了")
logger.info("+" * 100)
return HttpResponseRedirect('/')
else:
logger.error("x" * 100)
logger.error(f"({username}) 尝试登录,输入了错误的密码({password})")
logger.error("x" * 100)
return render(request, 'login.html', {'form': form, 'error_msg': "用户名或密码错误"})
else:
return render(request, 'login.html', {'form': form})
@login_required
def logout(request):
logger.info("-" * 100)
logger.info(f"({request.user.username}) 登出了")
logger.info("-" * 100)
auth.logout(request)
return HttpResponseRedirect("login")
| [
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Plugins/Aspose.Email Java for Python/tests/ProgrammingEmail/ManageAttachments/ManageAttachments.py | aspose-email/Aspose.Email-for-Java | 24 | 3464 | <gh_stars>10-100
# To change this license header, choose License Headers in Project Properties.
# To change this template file, choose Tools | Templates
# and open the template in the editor.
#if __name__ == "__main__":
# print "Hello World"
from ProgrammingEmail import ManageAttachments
import jpype
import os.path
asposeapispath = os.path.join(os.path.abspath("./../../../"), "lib/")
dataDir = os.path.join(os.path.abspath("./"), "data/")
print "You need to put your Aspose.Email for Java APIs .jars in this folder:\n"+asposeapispath
#print dataDir
jpype.startJVM(jpype.getDefaultJVMPath(), "-Djava.ext.dirs=%s" % asposeapispath)
hw = ManageAttachments(dataDir)
hw.main() | [
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] |
example/train.py | prodmodel/prodmodel | 53 | 135154 | from sklearn import tree
def train(X, y):
clf = tree.DecisionTreeClassifier(max_depth=10, random_state=0)
clf = clf.fit(X, y)
return clf
| [
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sarcopenia_ai/apps/slice_detection/predict.py | notmatthancock/sarcopenia-ai | 9 | 102791 | <filename>sarcopenia_ai/apps/slice_detection/predict.py<gh_stars>1-10
import SimpleITK as sitk
import cv2
from sarcopenia_ai.apps.slice_detection.utils import place_line_on_img, decode_slice_detection_prediction, \
preprocess_sitk_image_for_slice_detection, adjust_detected_position_spacing
from sarcopenia_ai.core.input_parser import InputParser
from sarcopenia_ai.core.model_wrapper import BaseModelWrapper, allocate_tf_gpu_devices
from sarcopenia_ai.io import load_image
from sarcopenia_ai.preprocessing.preprocessing import to256
def parse_inputs():
parser = InputParser()
parser.add_argument('--batch_size', type=int, default=3
, help='number of distinct images to samples from in a given batch')
parser.add_argument('--ds_factor', type=int, default=2, help='output downsampling factor')
parser.add_argument('--input_spacing', type=int, default=1, help='spacing of input image')
parser.add_argument('--cuda_devices', type=str, default='0,1')
parser.add_argument('--model_path', type=str, default='/data/slice_detection/')
parser.add_argument('--output_path', type=str, default='.')
parser.add_argument('--image', type=str, default=[], nargs='+')
parser.add_argument('--workers', type=int, default=2)
parser.add_argument('--prob_threshold', type=float, default=0.1)
args = parser.parse()
return args
def load_model(model_path):
# Setup model
model_wrapper = BaseModelWrapper(model_path,
name=None,
config=None,
data_loader=None,
is_multi_gpu=False
)
model_wrapper.setup_model()
print(model_wrapper.model.summary())
return model_wrapper.model
def main():
args = parse_inputs()
# GPU allocation options
args.num_gpus, args.cuda_devices = allocate_tf_gpu_devices(args.cuda_devices)
args.is_multi_gpu = args.num_gpus > 1
print(args)
# Setup model
model_wrapper = BaseModelWrapper(args.model_path)
model_wrapper.setup_model()
for image_path in args.image:
print(image_path)
sitk_image, image_name = load_image(image_path)
image2d = preprocess_sitk_image_for_slice_detection(sitk_image)
spacing = sitk_image.GetSpacing()
print('direction', sitk_image.GetDirection())
print('spacing', spacing)
print('image shape', image2d.shape)
preds = model_wrapper.model.predict(image2d)
pred_z, prob = decode_slice_detection_prediction(preds)
slice_z = adjust_detected_position_spacing(pred_z, spacing)
if prob > args.prob_threshold:
print('Slice detected at position {} with confidence {}'.format(slice_z, prob))
image = sitk.GetArrayFromImage(sitk_image)
print(image.shape)
slice_image = image[slice_z, :, :]
image2d = place_line_on_img(image2d[0], pred_z, pred_z, r=1)
cv2.imwrite(f'/{args.output_path}/{image_name}_slice.jpg', to256(slice_image))
cv2.imwrite(f'/{args.output_path}/{image_name}_frontal.jpg', to256(image2d))
else:
print('slice not detected')
if __name__ == '__main__':
main()
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scrape.py | shuaibi27/uiuc-course-scraper | 1 | 94106 | <filename>scrape.py
import argparse, requests, json
from bs4 import BeautifulSoup
parser = argparse.ArgumentParser()
parser.add_argument("--subject")
args = parser.parse_args()
data = requests.get('http://catalog.illinois.edu/courses-of-instruction/' + str(args.subject))
if data.status_code >= 400:
print('Status Code: ' + str(data.status_code))
exit()
html = BeautifulSoup(data.text, 'html.parser')
container = html.find('div', {'class': 'courses'})
courses = {}
for courseblock in container.find_all('div', {'class': 'courseblock'}):
title = courseblock.find('p', {'class': 'courseblocktitle'}).text
desc = courseblock.find('p', {'class': 'courseblockdesc'}).text.replace('\xa0', ' ').replace('\n', '')
name = title[:len(str(args.subject)) + 4].replace('\xa0', ' ')
label = title[len(str(args.subject)) + 7 : title.find('credit:') - 3]
hours = title[title.find('credit:') + 8 : -2]
key = name.replace(' ', '').lower()
courses[key] = {
'name': name,
'label': label,
'hours': hours,
'description': desc
}
# print(name + ' | ' + label + ' | ' + hours)
# print(desc + '\n')
with open(args.subject + '.json', 'w') as outfile:
json.dump(courses, outfile) | [
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{{cookiecutter.directory_name}}/apps/core/querysets/soft_delete.py | zurek11/django-project-template | 0 | 90801 | from django.db.models import QuerySet
from django.utils import timezone
class SoftDeleteQuerySet(QuerySet):
def delete(self):
return super(SoftDeleteQuerySet, self).update(deleted_at=timezone.now(), is_deleted=True)
def hard_delete(self):
return super(SoftDeleteQuerySet, self).delete()
def alive(self):
return self.filter(is_deleted=False)
def dead(self):
return self.exclude(is_deleted=True)
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code/tokenization.py | kcarnold/counterfactual-lm | 2 | 1610577 | import re
import string
from nltk.tokenize import RegexpTokenizer, PunktSentenceTokenizer
WORD_RE = re.compile(r'\w+(?:[\',:]\w+)*')
END_PUNCT = set('.,?!:')
def token_spans(text):
for match in re.finditer(r'[^-/\s]+', text):
start, end = match.span()
token_match = WORD_RE.search(text, start, end)
if token_match is not None:
span = token_match.span()
yield span
tok_end = span[1]
if tok_end < end and text[tok_end] in END_PUNCT:
yield tok_end, tok_end + 1
START_DOC = '<D>'
START_PARA = '<P>'
START_SENT = '<S>'
END_SENT = '</S>'
paragraph_re = re.compile(r'(?:[ ]*[^\s][^\n]*[\n]?)+')
paragraph_tokenizer = RegexpTokenizer(paragraph_re)
sentence_tokenizer = PunktSentenceTokenizer()
def tokenize(doc):
res = [START_DOC]
afters = []
end_of_prev_para = 0
for para_start, para_end in paragraph_tokenizer.span_tokenize(doc):
afters.append(doc[end_of_prev_para:para_start])
para = doc[para_start:para_end]
end_of_prev_para = para_end
end_of_prev_sentence = 0
res.append(START_PARA)
for sent_start, sent_end in sentence_tokenizer.span_tokenize(para):
sent = para[sent_start:sent_end]
tspans = list(token_spans(sent))
if not tspans:
continue
afters.append(para[end_of_prev_sentence:sent_start])
end_of_prev_sentence = sent_end
res.append(START_SENT)
end_of_prev_token = 0
for tok_start, tok_end in tspans:
afters.append(sent[end_of_prev_token:tok_start])
res.append(sent[tok_start:tok_end])
end_of_prev_token = tok_end
res.append(END_SENT)
afters.append(sent[end_of_prev_token:])
end_of_prev_para -= len(para) - end_of_prev_sentence
afters.append(doc[end_of_prev_para:])
return res, afters
def tokenize_mid_document(doc_so_far):
if len(doc_so_far.strip()) == 0:
return [START_DOC, START_PARA, START_SENT, ''], ['', '', '', '']
tok_list, afters = tokenize(doc_so_far)
if doc_so_far.endswith('\n\n'):
# starting a new paragraph
if tok_list[-1] in [START_PARA, START_SENT]:
print("Huh? Ended with double-newlines but also with start-of-para?", repr(tok_list[-5:]))
tok_list += [START_PARA, START_SENT, '']
afters += ['', '', '']
else:
assert tok_list[-1] == END_SENT
if tok_list[-2] in '.?!':
# Real EOS
tok_list += [START_SENT, '']
afters += ['', '']
elif doc_so_far[-1] in string.whitespace:
# The last EOS was spurious, but we're not mid-word.
tok_list[-1] = ""
else:
# The last EOS was spurious, but we ARE mid-word.
tok_list.pop(-1)
after = afters.pop(-1)
afters[-1] += after
return tok_list, afters
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] |
mars/core/entity/core.py | chineking/mars | 1 | 196835 | # Copyright 1999-2021 Alibaba Group Holding Ltd.
#
# 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.
from ...serialization.serializables import (
Serializable,
FieldTypes,
DictField,
ReferenceField,
)
from ...utils import AttributeDict
from ..base import Base
class EntityData(Base):
__slots__ = ("_siblings",)
type_name = None
# required fields
_op = ReferenceField("op", "mars.core.operand.base.Operand")
# optional fields
_extra_params = DictField("extra_params", key_type=FieldTypes.string)
def __init__(self, *args, **kwargs):
extras = AttributeDict(
(k, kwargs.pop(k)) for k in set(kwargs) - set(self._FIELDS)
)
kwargs["_extra_params"] = kwargs.pop("_extra_params", extras)
super().__init__(*args, **kwargs)
@property
def op(self):
return self._op
@property
def inputs(self):
return self.op.inputs
@inputs.setter
def inputs(self, new_inputs):
self.op.inputs = new_inputs
def is_sparse(self):
return self.op.is_sparse()
issparse = is_sparse
@property
def extra_params(self):
return self._extra_params
def build_graph(self, **kw):
from ..graph.builder.utils import build_graph
return build_graph([self], **kw)
def visualize(self, graph_attrs=None, node_attrs=None, **kw):
from graphviz import Source
g = self.build_graph(**kw)
dot = g.to_dot(
graph_attrs=graph_attrs,
node_attrs=node_attrs,
result_chunk_keys={c.key for c in self.chunks},
)
return Source(dot)
def _need_execution(self): # pylint: disable=no-self-use
# some tileable may generate unknown meta,
# they need to be executed first
return False
class Entity(Serializable):
_allow_data_type_ = ()
type_name = None
_data = ReferenceField("data", EntityData)
def __init__(self, data=None, **kw):
super().__init__(_data=data, **kw)
def __dir__(self):
obj_dir = object.__dir__(self)
if self._data is not None:
obj_dir = sorted(set(dir(self._data) + obj_dir))
return obj_dir
def __str__(self):
return self._data.__str__()
def __repr__(self):
return self._data.__repr__()
def _check_data(self, data):
if data is not None and not isinstance(data, self._allow_data_type_):
raise TypeError(f"Expect {self._allow_data_type_}, got {type(data)}")
@property
def data(self):
return self._data
@data.setter
def data(self, new_data):
self._check_data(new_data)
self._data = new_data
def __copy__(self):
return self.copy()
def copy(self):
return self.copy_to(type(self)(None))
def copy_to(self, target):
target.data = self._data
return target
def copy_from(self, obj):
self.data = obj.data
def tiles(self):
from .tileables import handler
new_entity = self.copy()
new_entity.data = handler.tiles(self.data)
return new_entity
def __getattr__(self, attr):
return getattr(self._data, attr)
def __setattr__(self, key, value):
try:
object.__setattr__(self, key, value)
except AttributeError:
return setattr(self._data, key, value)
def _need_execution(self):
return self._data._need_execution()
ENTITY_TYPE = (Entity, EntityData)
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home/admin.py | abdulshak1999/notes | 2 | 155122 | <filename>home/admin.py
from django.contrib import admin
from home.models import Note
class NoteAdmin(admin.ModelAdmin):
prepopulated_fields = {
'slug': ('title', )
}
admin.site.register(Note, NoteAdmin)
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qiskit/chemistry/drivers/fcidumpd/dumper.py | sorin-bolos/qiskit-aqua | 2 | 65742 | # -*- coding: utf-8 -*-
# This code is part of Qiskit.
#
# (C) Copyright IBM 2020.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modifications or derivative works of this code must retain this
# copyright notice, and modified files need to carry a notice indicating
# that they have been altered from the originals.
"""FCIDump dumper."""
from typing import List, Optional
from io import TextIOWrapper
import itertools
import numpy as np
def dump(outpath: str, norb: int, nelec: int, hijs: List[float], hijkls: List[float], einact: float,
ms2: int = 0, orbsym: Optional[List[int]] = None, isym: int = 1
) -> None:
# pylint: disable=wrong-spelling-in-docstring
"""Generates a FCIDump output.
Args:
outpath: Path to the output file.
norb: The number of orbitals.
nelec: The number of electrons.
hijs: The pair of alpha and beta 1-electron integrals. The latter may be None.
hijkls: The triplet of alpha/alpha, beta/alpha and beta/beta 2-electron integrals. The
latter two may be None.
einact: The inactive energy.
ms2: 2*S, where S is the spin quantum number.
orbsym: A list of spatial symmetries of the orbitals.
isym: The spatial symmetry of the wave function.
"""
hij, hij_b = hijs
hijkl, hijkl_ba, hijkl_bb = hijkls
# assert that either all beta variables are None or all of them are not
assert all([h is None for h in [hij_b, hijkl_ba, hijkl_bb]]) \
or all([h is not None for h in [hij_b, hijkl_ba, hijkl_bb]])
assert norb == hij.shape[0] == hijkl.shape[0]
mos = range(norb)
with open(outpath, 'w') as outfile:
# print header
outfile.write('&FCI NORB={:4d},NELEC={:4d},MS2={:4d}\n'.format(norb, nelec, ms2))
if orbsym is None:
outfile.write(' ORBSYM=' + '1,'*norb + '\n')
else:
assert len(orbsym) == norb
outfile.write(' ORBSYM=' + ','.join(orbsym) + '\n')
outfile.write(' ISYM={:d},\n/&END\n'.format(isym))
# append 2e integrals
_dump_2e_ints(hijkl, mos, outfile)
if hijkl_ba is not None:
_dump_2e_ints(hijkl_ba.transpose(), mos, outfile, beta=1)
if hijkl_bb is not None:
_dump_2e_ints(hijkl_bb, mos, outfile, beta=2)
# append 1e integrals
_dump_1e_ints(hij, mos, outfile)
if hij_b is not None:
_dump_1e_ints(hij_b, mos, outfile, beta=True)
# TODO append MO energies (last three indices are 0)
# append inactive energy
_write_to_outfile(outfile, einact, (0, 0, 0, 0))
def _dump_1e_ints(hij: List[float], mos: List[int], outfile: TextIOWrapper,
beta: bool = False) -> None:
idx_offset = 1 if not beta else 1+len(mos)
hij_elements = set()
for i, j in itertools.product(mos, repeat=2):
if i == j:
_write_to_outfile(outfile, hij[i][j], (i+idx_offset, j+idx_offset, 0, 0))
continue
if (j, i) in hij_elements and np.isclose(hij[i][j], hij[j][i]):
continue
_write_to_outfile(outfile, hij[i][j], (i+idx_offset, j+idx_offset, 0, 0))
hij_elements.add((i, j))
def _dump_2e_ints(hijkl: List[float], mos: List[int], outfile: TextIOWrapper,
beta: int = 0) -> None:
idx_offsets = [1, 1]
for b in range(beta):
idx_offsets[1-b] += len(mos)
hijkl_elements = set()
# pylint: disable=invalid-name
for elem in itertools.product(mos, repeat=4):
if np.isclose(hijkl[elem], 0.0, atol=1e-14):
continue
if len(set(elem)) == 1:
_write_to_outfile(outfile, hijkl[elem], (*[e+idx_offsets[0] for e in elem[:2]],
*[e+idx_offsets[1] for e in elem[2:]]))
continue
if beta != 1 and elem[::-1] in hijkl_elements and \
np.isclose(hijkl[elem], hijkl[elem[::-1]]):
continue
bra_perms = set(itertools.permutations(elem[:2]))
ket_perms = set(itertools.permutations(elem[2:]))
if beta == 1:
permutations = itertools.product(bra_perms, ket_perms)
else:
permutations = itertools.chain(
itertools.product(bra_perms, ket_perms),
itertools.product(ket_perms, bra_perms)
)
for perm in {e1 + e2 for e1, e2 in permutations}:
if perm in hijkl_elements and np.isclose(hijkl[elem], hijkl[perm]):
break
else:
_write_to_outfile(outfile, hijkl[elem], (*[e+idx_offsets[0] for e in elem[:2]],
*[e+idx_offsets[1] for e in elem[2:]]))
hijkl_elements.add(elem)
def _write_to_outfile(outfile: str, value: float, indices: List[int]):
outfile.write('{:23.16E}{:4d}{:4d}{:4d}{:4d}\n'.format(value, *indices))
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] |
super_laser_gui.py | hemmerlinglab/Prehistoric-Data-Acquisition | 0 | 93855 | <filename>super_laser_gui.py
import sys, os, serial, datetime, time
import numpy as np
from configparser import ConfigParser
import scipy
from scipy.interpolate import interp1d
import fileinput
from simple_pid import PID
from wlm import *
# shouldn't need this -> from Fiber import *
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5.QtCore import *
from matplotlib.backends.qt_compat import QtCore, QtWidgets, is_pyqt5
if is_pyqt5():
from matplotlib.backends.backend_qt5agg import (
FigureCanvas, NavigationToolbar2QT as NavigationToolbar)
else:
from matplotlib.backends.backend_qt4agg import (
FigureCanvas, NavigationToolbar2QT as NavigationToolbar)
from matplotlib.figure import Figure
class App(QWidget):
def __init__(self):
super().__init__()
self.title = 'Super Laser Locker'
self.left = 0
self.top = 0
self.width = 1500
self.height = 400
self.set_point = 0 # THz
self.update_interval = 1 # ms
self.no_of_points = 100
self.no_of_arduinos = 1
self.wlm = WavelengthMeter()
self.initUI()
self.timer = QTimer()
self.timer.timeout.connect(self.tick)
self.timer.start(self.update_interval)
def tick(self):
all_freq_reads = self.wlm.frequencies
for laser in self.laser_objs.keys():
freq_read = all_freq_reads[int(self.laser_objs[laser].chan) - 1]
if freq_read >= 0:
freq_mess = freq_read
if self.laser_objs[laser].lockable and self.laser_objs[laser].lock_check.isChecked():
control = self.laser_objs[laser].my_pid(freq_mess)
ard_num = int(4095.0/20 * control + 4095.0/2.0)
mystr = '{:04d}'.format(ard_num).encode('utf-8')
self.laser_objs[laser].my_ard.ser.write(mystr)
elif freq_read == -3.0:
freq_mess = 'UNDER'
elif freq_read == -4.0:
freq_mess = 'OVER'
else:
freq_mess = 'ERROR'
self.laser_objs[laser].update_frequency(freq_mess)
def initUI(self):
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
self.main_layout = QHBoxLayout()
self.laser_objs = {}
self.lasers = read_config()
for las in self.lasers.keys():
newlas = Laser()
newlas.update_name(las)
newlas.update_lockable(self.lasers[las]['lockable'])
newlas.update_channel(self.lasers[las]['chan'])
newlas.filename = self.lasers[las]['setfile']
# if newlas.lockable:
# newlas.my_ard = Arduino(self.lasers[las]['com_port'])
# else:
# print('arduino not created')
newlas.get_setpoint()
self.main_layout.addWidget(newlas)
self.laser_objs[las] = newlas
self.setLayout(self.main_layout)
self.show()
class Laser(QWidget):
def __init__(self):
super().__init__()
self.name = ''
self.type = ''
self.chan = 0
self.lockable = True
self.locking = False
self.frequency = 0
self.setpoint = 0
self.p = 100
self.i = 1000
self.d = 0
self.ard_mess = 2048
self.offset = 0
self.fstep = 50
self.filename = ''
self.basefolder = 'z:\\'
self.my_pid = PID(self.p,self.i,self.d,self.setpoint,sample_time = 0.01, output_limits = [-10,10])
self.my_ard = ''
self.layout = QGridLayout()
self.name_label = QLabel(self.name)
name_font = QFont("Times",30,QFont.Bold)
self.name_label.setFont(name_font)
self.set_label = QLabel('Setpoint (THz):')
self.ard_label = QLabel('Control Value:')
self.off_label = QLabel('Set Offset (THz):')
self.step_label = QLabel('Step Size (MHz):')
self.p_label = QLabel('P:')
self.i_label = QLabel('I:')
self.d_label = QLabel('D:')
self.freq_value = QLabel("{0:.6f}".format(self.frequency))
self.set_value = QLineEdit("{0:.6f}".format(self.setpoint))
self.ard_value = QLabel(str(self.ard_mess))
self.off_value = QLineEdit("{0:.6f}".format(self.offset))
self.step_value = QLineEdit(str(self.fstep))
self.p_value = QLineEdit(str(self.p))
self.i_value = QLineEdit(str(self.i))
self.d_value = QLineEdit(str(self.d))
self.scan_label = QLabel('Frequency Shift (MHz):')
self.laser_scan = QSpinBox()
self.laser_scan.setMinimum(-5000)
self.laser_scan.setMaximum(5000)
self.laser_scan.setSingleStep(np.int(self.fstep))
self.laser_scan.valueChanged.connect(self.set_setpoint)
self.laser_scan.valueChanged.connect(self.set_fstep)
self.p_value.returnPressed.connect(self.update_p)
self.i_value.returnPressed.connect(self.update_i)
self.d_value.returnPressed.connect(self.update_d)
self.pid_label = QLabel('PID Values')
self.lock_check = QCheckBox('Lock')
self.layout.addWidget(self.name_label,0,0)
self.layout.addWidget(QLabel('THz'),0,2)
self.layout.addWidget(self.freq_value,0,1)
self.layout.addWidget(self.lock_check,1,0)
self.layout.addWidget(self.ard_label,2,0)
self.layout.addWidget(self.ard_value,2,1)
self.layout.addWidget(self.set_label,3,0)
self.layout.addWidget(self.set_value,3,1)
self.layout.addWidget(self.scan_label,4,0)
self.layout.addWidget(self.laser_scan,4,1)
self.layout.addWidget(self.off_label,5,0)
self.layout.addWidget(self.off_value,5,1)
self.layout.addWidget(self.step_label,6,0)
self.layout.addWidget(self.step_value,6,1)
self.layout.addWidget(self.pid_label,7,0)
self.layout.addWidget(self.p_label,8,0)
self.layout.addWidget(self.p_value,8,1)
self.layout.addWidget(self.i_label,9,0)
self.layout.addWidget(self.i_value,9,1)
self.layout.addWidget(self.d_label,10,0)
self.layout.addWidget(self.d_value,10,1)
self.setLayout(self.layout)
def update_frequency(self,new_freq):
nf = new_freq
self.frequency = nf
try:
self.freq_value.setText("{0:.6f}".format(nf))
except:
self.freq_value.setText(nf)
def update_name(self,new_name):
nn = str(new_name)
self.name = nn
self.name_label.setText(nn)
def update_channel(self,new_chan):
nc = int(new_chan)
self.chan = new_chan
def update_p(self):
self.p = np.float(self.p_value.text())
self.my_pid.Kp = self.p
def update_i(self):
self.i = np.float(self.i_value.text())
self.my_pid.Ki = self.i
def update_d(self):
self.d = np.float(self.d_value.text())
self.my_pid.Kd = self.d
# def update_type(self,new_type):
# nt = str(new_type)
# self.type = nt
# self.type_label.setText(nt)
def update_lockable(self,new_lockable):
if new_lockable == 'True':
nl = True
else:
nl = False
self.lockable = nl
if not self.lockable:
self.ard_label.hide()
self.ard_value.hide()
self.scan_label.hide()
self.laser_scan.hide()
self.off_label.hide()
self.off_value.hide()
self.step_label.hide()
self.step_value.hide()
self.pid_label.hide()
self.p_label.hide()
self.p_value.hide()
self.i_label.hide()
self.i_value.hide()
self.d_value.hide()
self.d_label.hide()
self.lock_check.hide()
def set_fstep(self):
new_fstep = np.int(self.step_value.text())
self.laser_scan.setSingleStep(new_fstep)
self.fstep = new_fstep
def set_setpoint(self):
ns = np.float(self.offset) + np.float(self.fstep)*1e-6
filepath = self.basefolder + self.filename
file = open(filepath,'w')
file.write(str(ns))
file.close()
self.setpoint = ns
self.set_value.setText("{0:.6f}".format(ns))
self.my_pid.setpoint = self.setpoint
def get_setpoint(self):
filepath = self.basefolder + self.filename
file = open(filepath,'r')
new_set = np.float(file.readline())
file.close()
self.setpoint = new_set
self.set_value.setText("{0:.6f}".format(new_set))
self.off_value.setText("{0:.6f}".format(new_set))
def update_ardmess(self,new_mess):
nm = new_mess
self.ard_mess = new_mess
self.ard_label.setText(new_mess)
class Arduino():
def __init__(self,com_port):
serial_port = com_port
baud_rate = 9600;
try:
self.ser = serial.Serial(serial_port, baud_rate,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
stopbits=serial.STOPBITS_ONE,
timeout=1)
except:
try:
ser.close()
except:
print ("Serial port already closed" )
self.ser = serial.Serial(serial_port, baud_rate,
bytesize=serial.SEVENBITS,
parity=serial.PARITY_ODD,
stopbits=serial.STOPBITS_ONE,
timeout=1)
def read_config(filename = 'laser_config.ini'):
config = ConfigParser()
config.read(filename)
laser_ids = config.sections()
# make dictionary out of config
lasers = {}
for l in laser_ids:
opts = config.options(l)
lasers[l] = {}
for o in opts:
lasers[l][o] = config.get(l, o)
return lasers
def set_dark(app):
dark_palette = QPalette()
dark_palette.setColor(QPalette.Window, QColor(53, 53, 53))
dark_palette.setColor(QPalette.WindowText, Qt.white)
dark_palette.setColor(QPalette.Base, QColor(25, 25, 25))
dark_palette.setColor(QPalette.AlternateBase, QColor(53, 53, 53))
dark_palette.setColor(QPalette.ToolTipBase, Qt.white)
dark_palette.setColor(QPalette.ToolTipText, Qt.white)
dark_palette.setColor(QPalette.Text, Qt.white)
dark_palette.setColor(QPalette.Button, QColor(53, 53, 53))
dark_palette.setColor(QPalette.ButtonText, Qt.white)
dark_palette.setColor(QPalette.BrightText, Qt.red)
dark_palette.setColor(QPalette.Link, QColor(42, 130, 218))
dark_palette.setColor(QPalette.Highlight, QColor(42, 130, 218))
dark_palette.setColor(QPalette.HighlightedText, Qt.black)
app.setPalette(dark_palette)
app.setStyleSheet("QToolTip { color: #ffffff; background-color: #2a82da; border: 1px solid white; }")
if __name__ == '__main__':
app = QApplication(sys.argv)
app.setStyle('Fusion')
set_dark(app)
ex = App()
sys.exit(app.exec_()) | [
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] |
wwwdccn/proceedings/migrations/0001_initial.py | lfpratik/dccnsys | 16 | 191605 | # Generated by Django 2.2.4 on 2019-10-01 15:05
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
initial = True
dependencies = [
('submissions', '0006_auto_20190905_1746'),
('conferences', '0014_artifactdescriptor_mandatory'),
]
operations = [
migrations.CreateModel(
name='VolumeAssignment',
fields=[
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('active', models.BooleanField(default=False)),
('proc_type', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='conferences.ProceedingType')),
('submission', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='submissions.Submission')),
('volume', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='conferences.ProceedingVolume')),
],
),
]
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] |
visualize_code_vec.py | sonoisa/code2vec | 22 | 172361 | <filename>visualize_code_vec.py
import torch
from tensorboardX import SummaryWriter
vec_path = "./output/code.vec"
writer = SummaryWriter()
with open(vec_path, "r", encoding="utf-8") as f:
labels = []
vectors = []
first = True
for line in f.readlines():
if first:
first = False
continue
line = line.strip(' \r\n\t')
data = line.split("\t")
word = data[0]
vector = [float(x) for x in data[1].split(" ")]
labels.append(word)
vectors.append(vector)
writer.add_embedding(torch.FloatTensor(vectors), metadata=labels)
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] |
fastestimator/backend/cast.py | hanskrupakar/fastestimator | 57 | 68066 | # Copyright 2019 The FastEstimator Authors. 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.
# ==============================================================================
from typing import Collection, TypeVar, Union
import numpy as np
import tensorflow as tf
import torch
from fastestimator.util.util import STRING_TO_TF_DTYPE, STRING_TO_TORCH_DTYPE
Tensor = TypeVar('Tensor', tf.Tensor, torch.Tensor, np.ndarray)
def cast(data: Union[Collection, Tensor], dtype: str) -> Union[Collection, Tensor]:
"""Cast the data to a specific data type recursively.
This method can be used with Numpy data:
```python
data = {"x": np.ones((10,15)), "y":[np.ones((4)), np.ones((5, 3))], "z":{"key":np.ones((2,2))}}
fe.backend.to_type(data)
# {'x': dtype('float64'), 'y': [dtype('float64'), dtype('float64')], 'z': {'key': dtype('float64')}}
data = fe.backend.cast(data, "float16")
fe.backend.to_type(data)
# {'x': dtype('float16'), 'y': [dtype('float16'), dtype('float16')], 'z': {'key': dtype('float16')}}
```
This method can be used with TensorFlow tensors:
```python
data = {"x": tf.ones((10,15)), "y":[tf.ones((4)), tf.ones((5, 3))], "z":{"key":tf.ones((2,2))}}
fe.backend.to_type(data) # {'x': tf.float32, 'y': [tf.float32, tf.float32], 'z': {'key': tf.float32}}
data = fe.backend.cast(data, "uint8")
fe.backend.to_type(data) # {'x': tf.uint8, 'y': [tf.uint8, tf.uint8], 'z': {'key': tf.uint8}}
```
This method can be used with PyTorch tensors:
```python
data = {"x": torch.ones((10,15)), "y":[torch.ones((4)), torch.ones((5, 3))], "z":{"key":torch.ones((2,2))}}
fe.backend.to_type(data) # {'x': torch.float32, 'y': [torch.float32, torch.float32], 'z': {'key': torch.float32}}
data = fe.backend.cast(data, "float64")
fe.backend.to_type(data) # {'x': torch.float64, 'y': [torch.float64, torch.float64], 'z': {'key': torch.float64}}
```
Args:
data: A tensor or possibly nested collection of tensors.
dtype: Target data type, can be one of following: uint8, int8, int16, int32, int64, float16, float32, float64.
Returns:
A collection with the same structure as `data` with target data type.
"""
if isinstance(data, dict):
return {key: cast(value, dtype) for (key, value) in data.items()}
elif isinstance(data, list):
return [cast(val, dtype) for val in data]
elif isinstance(data, tuple):
return tuple([cast(val, dtype) for val in data])
elif isinstance(data, set):
return set([cast(val, dtype) for val in data])
elif tf.is_tensor(data):
return tf.cast(data, STRING_TO_TF_DTYPE[dtype])
elif isinstance(data, torch.Tensor):
return data.type(STRING_TO_TORCH_DTYPE[dtype])
else:
return np.array(data, dtype=dtype)
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] |
amp_reconstruct_betterRes.py | kseetharam/genPolaron | 0 | 100273 | <filename>amp_reconstruct_betterRes.py<gh_stars>0
import numpy as np
import xarray as xr
import pf_dynamic_sph as pfs
from timeit import default_timer as timer
import time
import os
# import matplotlib
# import matplotlib.pyplot as plt
if __name__ == "__main__":
# ---- INITIALIZE GRIDS ----
(Lx, Ly, Lz) = (60, 60, 60)
(dx, dy, dz) = (0.25, 0.25, 0.25)
higherCutoff = False; cutoffRat = 1.0
betterResolution = True; resRat = 0.5
# (Lx, Ly, Lz) = (21, 21, 21)
# (dx, dy, dz) = (0.375, 0.375, 0.375)
# higherCutoff = False; cutoffRat = 1.0
# betterResolution = False; resRat = 1.0
NGridPoints_cart = (1 + 2 * Lx / dx) * (1 + 2 * Ly / dy) * (1 + 2 * Lz / dz)
print(NGridPoints_cart)
# Toggle parameters
toggleDict = {'Dynamics': 'real'}
# ---- SET OUTPUT DATA FOLDER ----
mRat = 1.0
datapath = '/Users/kis/Dropbox/VariationalResearch/HarvardOdyssey/genPol_data/NGridPoints_{:.2E}'.format(NGridPoints_cart)
if higherCutoff is True:
datapath = datapath + '_cutoffRat_{:.2f}'.format(cutoffRat)
if betterResolution is True:
datapath = datapath + '_resRat_{:.2f}'.format(resRat)
datapath = datapath + '/massRatio={:.1f}'.format(mRat)
if toggleDict['Dynamics'] == 'real':
innerdatapath = datapath + '/redyn'
elif toggleDict['Dynamics'] == 'imaginary':
innerdatapath = datapath + '/imdyn'
innerdatapath = innerdatapath + '_spherical'
interpdatapath = innerdatapath + '/interp'
if os.path.isdir(interpdatapath) is False:
os.mkdir(interpdatapath)
# # Analysis of Total Dataset
aIBi = -5
Pnorm_des = 4.0
# Pnorm_des = 3.0
# Pnorm_des = 2.067
# Pnorm_des = 1.8
# Pnorm_des = 1.4
# Pnorm_des = 1.34
# Pnorm_des = 1.28
# Pnorm_des = 1.04
# Pnorm_des = 1.22
# Pnorm_des = 1.1
# Pnorm_des = 0.8
# Pnorm_des = 0.52
qds = xr.open_dataset(innerdatapath + '/P_{:.3f}_aIBi_{:.2f}.nc'.format(Pnorm_des * 0.7926654595212022, aIBi))
n0 = qds.attrs['n0']; gBB = qds.attrs['gBB']; mI = qds.attrs['mI']; mB = qds.attrs['mB']
nu = np.sqrt(n0 * gBB / mB)
mc = mI * nu
P = qds.attrs['P']
qds_P = qds
qds_P.coords['P'] = np.array(P)
tVals = qds['tc'].values
# print(tVals.size)
# tVals = tVals[np.array([-1])]
print(P, P / mc, mRat, aIBi)
# print(tVals)
# tind = 5
# t = tVals[tind]
# import matplotlib.pyplot as plt
# tVals_full = qds['t'].values
# vImp_Vals = (P - qds['Pph'].values) / mc
# fig, ax = plt.subplots()
# ax.plot(tVals_full, vImp_Vals, 'b-')
# ax.plot(tVals_full, np.ones(tVals_full.size), 'k--')
# plt.show()
for tind, t in enumerate(tVals):
print(tind, t)
# # FULL RECONSTRUCTION OF 3D CARTESIAN BETA_K FROM 2D SPHERICAL BETA_K (doing actual interpolation in 2D spherical instead of 3D nonlinear cartesian)
CSAmp_ds = (qds_P['Real_CSAmp'] + 1j * qds_P['Imag_CSAmp']).sel(tc=t); CSAmp_ds.attrs = qds.attrs; CSAmp_ds.attrs['Nph'] = qds_P['Nph'].sel(t=t).values
# Generate data
# dkxL = 1e-2; dkyL = 1e-2; dkzL = 1e-2
# linDimList = [(2, 2)]
dkxL = 5e-2; dkyL = 5e-2; dkzL = 5e-2
linDimList = [(10, 10)]
for ldtup in linDimList:
tupstart = timer()
linDimMajor, linDimMinor = ldtup
print('lDM: {0}, lDm: {1}'.format(linDimMajor, linDimMinor))
interp_ds = pfs.reconstructMomDists(CSAmp_ds, linDimMajor, linDimMinor, dkxL, dkyL, dkzL)
interp_ds.to_netcdf(interpdatapath + '/InterpDat_P_{:.2f}_aIBi_{:.2f}_t_{:.2f}_lDM_{:.2f}_lDm_{:.2f}.nc'.format(P, aIBi, t, linDimMajor, linDimMinor))
tupend = timer()
print('Total Time: {0}'.format(tupend - tupstart))
time.sleep(2)
print('\n')
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] |
algorithms/maths/chinese_remainder_theorem.py | hbqdev/algorithms | 22,426 | 7072 | <reponame>hbqdev/algorithms<filename>algorithms/maths/chinese_remainder_theorem.py
from algorithms.maths.gcd import gcd
from typing import List
def solve_chinese_remainder(num : List[int], rem : List[int]):
"""
Computes the smallest x that satisfies the chinese remainder theorem
for a system of equations.
The system of equations has the form:
x % num[0] = rem[0]
x % num[1] = rem[1]
...
x % num[k - 1] = rem[k - 1]
Where k is the number of elements in num and rem, k > 0.
All numbers in num needs to be pariwise coprime otherwise an exception is raised
returns x: the smallest value for x that satisfies the system of equations
"""
if not len(num) == len(rem):
raise Exception("num and rem should have equal length")
if not len(num) > 0:
raise Exception("Lists num and rem need to contain at least one element")
for n in num:
if not n > 1:
raise Exception("All numbers in num needs to be > 1")
if not _check_coprime(num):
raise Exception("All pairs of numbers in num are not coprime")
k = len(num)
x = 1
while True:
i = 0
while i < k:
if x % num[i] != rem[i]:
break
i += 1
if i == k:
return x
else:
x += 1
def _check_coprime(l : List[int]):
for i in range(len(l)):
for j in range(len(l)):
if i == j:
continue
if gcd(l[i], l[j]) != 1:
return False
return True
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subcommands/play_category.py | brunomateus/open_source_android_apps | 2 | 93199 | """Scrape Google Play category data from Google Play."""
import argparse
import json
import logging
import os
from lxml.html import html5parser
import requests
from util.parse import parse_package_details
__log__ = logging.getLogger(__name__)
PLAY_STORE_LINK = 'https://play.google.com/store/apps/details?id={}'
CATEGORY_DIR = 'categories'
HEADERS = {
'Accept-Language': 'en,en-GB;q=0.8,en-US;q=0.7,de;q=0.5,de-DE;q=0.3,nl;q=0.2'
}
def get_play_page(package_name):
url = PLAY_STORE_LINK.format(package_name)
__log__.info('Request %s', url)
return requests.get(url, headers=HEADERS)
def find_category_string(html_text):
parser = html5parser.fromstring(html_text)
try:
category_link = parser.cssselect('.category')[0]
category_span = category_link.cssselect('[itemprop=genre]')[0]
return category_span.text
except IndexError as e:
__log__.exception('Cannot match category in HTML')
return None
def write_category_file(package_name, category, details_dir):
category_path = os.path.join(details_dir, CATEGORY_DIR)
os.makedirs(category_path, exist_ok=True)
file_name = '{}.json'.format(package_name)
file_path = os.path.join(category_path, file_name)
with open(file_path, 'w') as json_file:
json.dump({
'packageName': package_name,
'appCategory': category
}, json_file)
__log__.info('Wrote %s', file_path)
def define_cmdline_arguments(parser: argparse.ArgumentParser):
"""Add arguments to parser."""
parser.add_argument(
'PLAY_STORE_DETAILS_DIR', type=str,
help='Directory containing JSON files with details from Google Play.')
parser.set_defaults(func=_main)
def _main(args):
"""Pass arguments to respective function."""
__log__.info('------- Arguments: -------')
__log__.info('PLAY_STORE_DETAILS_DIR: %s', args.PLAY_STORE_DETAILS_DIR)
for package_name, _ in parse_package_details(args.PLAY_STORE_DETAILS_DIR):
response = get_play_page(package_name)
category = find_category_string(response.text)
if not category:
continue
__log__.info('Found category "%s" for %s', category, package_name)
write_category_file(package_name, category, args.PLAY_STORE_DETAILS_DIR)
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Freshmen.bundle/Contents/Code/__init__.py | OmicronTheta/pgma | 0 | 76223 | <reponame>OmicronTheta/pgma
# Freshmen.net Plex Agent
import re, os, platform, urllib
from difflib import SequenceMatcher
#Fix HTTPS errors when connecting to Facebox (neural.vigue.me) and Thumbor CDN (cdn.vigue.me)
import certifi
import requests
PLUGIN_LOG_TITLE = 'Freshmen' # Log Title
VERSION_NO = '2019.03.11.1'
# Delay used when requesting HTML, may be good to have to prevent being
# banned from the site
REQUEST_DELAY = 0
# URLS
BASE_URL = 'https://www.freshmen.net%s'
# Example Video Details URL
# https://www.helixstudios.net/video/3437/hosing-him-down.html
BASE_VIDEO_DETAILS_URL = 'https://www.freshmen.net/content/%s'
# Example Search URL:
# https://www.helixstudios.net/videos/?q=Hosing+Him+Down
BASE_SEARCH_URL = 'https://www.freshmen.net/search?q=%s'
# File names to match for this agent
file_name_pattern = re.compile(Prefs['regex'])
# Example File Name:
# https://media.helixstudios.com/scenes/hx111_scene2/hx111_scene2_member_1080p.mp4
# FILENAME_PATTERN = re.compile("")
# TITLE_PATTERN = re.compile("")
def Start():
HTTP.CacheTime = CACHE_1WEEK
HTTP.Headers['User-agent'] = 'Mozilla/4.0 (compatible; MSIE 8.0; ' \
'Windows NT 6.2; Trident/4.0; SLCC2; .NET CLR 2.0.50727; ' \
'.NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC 6.0)'
class Freshmen(Agent.Movies):
name = 'Freshmen'
languages = [Locale.Language.NoLanguage, Locale.Language.English]
primary_provider = False
fallback_agent = ['com.plexapp.agents.gayporncollector']
contributes_to = ['com.plexapp.agents.cockporn']
def Log(self, message, *args):
if Prefs['debug']:
Log(PLUGIN_LOG_TITLE + ' - ' + message, *args)
def intTest(self, s):
try:
int(s)
return int(s)
except ValueError:
return False
def similar(self, a, b):
return SequenceMatcher(None, a, b).ratio()
def search(self, results, media, lang, manual):
self.Log('-----------------------------------------------------------------------')
self.Log('SEARCH CALLED v.%s', VERSION_NO)
self.Log('SEARCH - Platform: %s %s', platform.system(), platform.release())
self.Log('SEARCH - media.title - %s', media.title)
self.Log('SEARCH - media.items[0].parts[0].file - %s', media.items[0].parts[0].file)
self.Log('SEARCH - media.primary_metadata.title - %s', media.primary_metadata.title)
self.Log('SEARCH - media.items - %s', media.items)
self.Log('SEARCH - media.filename - %s', media.filename)
self.Log('SEARCH - lang - %s', lang)
self.Log('SEARCH - manual - %s', manual)
self.Log('SEARCH - Prefs->cover - %s', Prefs['cover'])
self.Log('SEARCH - Prefs->folders - %s', Prefs['folders'])
self.Log('SEARCH - Prefs->regex - %s', Prefs['regex'])
if not media.items[0].parts[0].file:
return
path_and_file = media.items[0].parts[0].file.lower()
self.Log('SEARCH - File Path: %s', path_and_file)
(file_dir, basename) = os.path.split(os.path.splitext(path_and_file)[0])
final_dir = os.path.split(file_dir)[1]
self.Log('SEARCH - Enclosing Folder: %s', final_dir)
if Prefs['folders'] != "*":
folder_list = re.split(',\s*', Prefs['folders'].lower())
if final_dir not in folder_list:
self.Log('SEARCH - Skipping %s because the folder %s is not in the acceptable folders list: %s', basename, final_dir, ','.join(folder_list))
return
m = file_name_pattern.search(basename)
if not m:
self.Log('SEARCH - Skipping %s because the file name is not in the expected format.', basename)
return
self.Log('SEARCH - File Name: %s', basename)
groups = m.groupdict()
clip_name = groups['clip_name']
movie_url_name = re.sub('\s+', '+', clip_name)
movie_url = BASE_VIDEO_DETAILS_URL % movie_url_name
search_query_raw = list()
for piece in clip_name.split(' '):
if re.search('^[0-9A-Za-z]*$', piece.replace('!', '')) is not None:
search_query_raw.append(piece)
self.Log('SEARCH - Video URL: %s', movie_url)
html = HTML.ElementFromURL(movie_url, sleep=REQUEST_DELAY)
video_title = html.xpath('//*[@id="top"]/main/div/div/div[2]/div[2]/div[1]/div[1]/div/h1')
results.Append(MetadataSearchResult(id = movie_url, name = video_title, score = 100, lang = lang))
def update(self, metadata, media, lang, force=False):
self.Log('UPDATE CALLED')
if not media.items[0].parts[0].file:
return
file_path = media.items[0].parts[0].file
self.Log('UPDATE - File Path: %s', file_path)
self.Log('UPDATE - Video URL: %s', metadata.id)
url = metadata.id
# Fetch HTML
html = HTML.ElementFromURL(url, sleep=REQUEST_DELAY)
# Set tagline to URL
metadata.tagline = url
titlelist = html.xpath('//div[@class="left"]/div/h1/span/text()')
video_title = ''
for titlepart in titlelist:
video_title += str(titlepart)
self.Log('UPDATE - video_title: "%s"', video_title)
valid_image_names = list()
i = 0
video_image_list = html.xpath('//*[@class="gallery article"]/a/img')
try:
coverPrefs = Prefs['cover']
for image in video_image_list:
if i <= (self.intTest(coverPrefs)-1) or coverPrefs == "all available":
i = i + 1
poster_url = image.get('src')
valid_image_names.append(poster_url)
#self.Log(poster_url)
metadata.posters[poster_url]=Proxy.Media(HTTP.Request(poster_url), sort_order = i)
except Exception as e:
self.Log('UPDATE - Error getting posters: %s', e)
pass
# Try to get description text
try:
raw_about_text = html.xpath("//div[@class='left']/div[@class='more always-visible']/text()[2]")[0]
if "a" not in raw_about_text:
raw_about_text = html.xpath("//div[@class='left']/div[@class='more always-visible']/p/text()")[0]
self.Log('UPDATE - Description: %s', raw_about_text)
metadata.summary=raw_about_text
except Exception as e:
self.Log('UPDATE - Error getting description text: %s', e)
pass
# Try to get release date
try:
release_date=html.xpath('//*[@id="tab_comment"]/div[last()]/div[1]/text()')[1].split()[1];
self.Log('UPDATE - Release Date - New: %s', release_date)
metadata.originally_available_at = Datetime.ParseDate(release_date).date()
metadata.year = metadata.originally_available_at.year
except Exception as e:
self.Log('UPDATE - Error getting release date: %s', e)
pass
# Try to get and process the video cast
try:
metadata.roles.clear()
rolethumbs = list();
actor_image_list = html.xpath('//div[@class="actor"]/*[@class="photo"]/img')
for actor_image in actor_image_list:
headshot_url_hi_res = actor_image.get('src');
rolethumbs.append(headshot_url_hi_res)
htmlcast = html.xpath("//div[@class='actor']/div[@class='name']/text()")
self.Log('UPDATE - cast: "%s"', htmlcast)
index = 0
for cast in htmlcast:
cname = cast.strip()
if (len(cname) > 0):
role = metadata.roles.new()
role.name = cname
role.photo = rolethumbs[index]
index += 1
except Exception as e:
self.Log('UPDATE - Error getting video cast: %s', e)
pass
# Try to get and process the video genres
metadata.genres.add("Freshmen")
metadata.collections.add("Freshmen")
metadata.posters.validate_keys(valid_image_names)
metadata.content_rating = 'X'
metadata.title = video_title
metadata.studio = "Freshmen"
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GEOS_Util/coupled_diagnostics/verification/HadCRUT3/__init__.py | GEOS-ESM/GMAO_Shared | 1 | 49882 | <reponame>GEOS-ESM/GMAO_Shared
import os
import netCDF4 as nc
import scipy as sp
from g5lib import dset
__all__=['ctl']
class Ctl(dset.NCDset):
def __init__(self):
name='HadCRUT3'
flist=['/discover/nobackup/projects/gmao/oceanval/verification/HadCRUT3/HadCRUT3.nc']
f=nc.Dataset(flist[0])
tt=f.variables['t']
time=nc.num2date(tt[:],tt.units)
undef=f.variables['temp'].missing_value
f.close()
super(Ctl,self).__init__(flist,time=time,undef=undef,name=name,
lonname='longitude',
latname='latitude',
levname='unspecified',
timename='t')
def get_hadcrut3gl(self,annual=False):
'''
Gets HadCRUT3 globaly averaged T anomalies
'''
if not annual:
# Return monthly data
return sp.loadtxt('/discover/nobackup/projects/gmao/oceanval/verification/HadCRUT3/hadcrut3gl.txt', usecols=range(1,13))[0::2].flatten()
else:
# Return annual means
return sp.loadtxt('/discover/nobackup/projects/gmao/oceanval/verification/HadCRUT3/hadcrut3gl.txt', usecols=range(1,13))[0::2].mean(1)
ctl=Ctl()
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.venv/Lib/site-packages/pdoc/cli.py | JohanK91/MethodDice | 0 | 22707 | #!/usr/bin/env python3
"""pdoc's CLI interface and helper functions."""
import argparse
import ast
import importlib
import inspect
import os
import os.path as path
import json
import re
import sys
import warnings
from contextlib import contextmanager
from functools import lru_cache
from http.server import BaseHTTPRequestHandler, HTTPServer
from typing import Dict, List, Sequence
from warnings import warn
import pdoc
parser = argparse.ArgumentParser(
description="Automatically generate API docs for Python modules.",
epilog="Further documentation is available at <https://pdoc3.github.io/pdoc/doc>.",
)
aa = parser.add_argument
mode_aa = parser.add_mutually_exclusive_group().add_argument
aa(
'--version', action='version', version='%(prog)s ' + pdoc.__version__)
aa(
"modules",
type=str,
metavar='MODULE',
nargs="+",
help="The Python module name. This may be an import path resolvable in "
"the current environment, or a file path to a Python module or "
"package.",
)
aa(
"-c", "--config",
type=str,
metavar='OPTION=VALUE',
action='append',
default=[],
help="Override template options. This is an alternative to using "
"a custom config.mako file in --template-dir. This option "
"can be specified multiple times.",
)
aa(
"--filter",
type=str,
metavar='STRING',
default=None,
help="Comma-separated list of filters. When specified, "
"only identifiers containing the specified string "
"will be shown in the output. Search is case sensitive. "
"Has no effect when --http is set.",
)
aa(
"-f", "--force",
action="store_true",
help="Overwrite any existing generated (--output-dir) files.",
)
mode_aa(
"--html",
action="store_true",
help="When set, the output will be HTML formatted.",
)
mode_aa(
"--pdf",
action="store_true",
help="When set, the specified modules will be printed to standard output, "
"formatted in Markdown-Extra, compatible with most "
"Markdown-(to-HTML-)to-PDF converters.",
)
aa(
"--html-dir",
type=str,
help=argparse.SUPPRESS,
)
aa(
"-o", "--output-dir",
type=str,
metavar='DIR',
help="The directory to output generated HTML/markdown files to "
"(default: ./html for --html).",
)
aa(
"--html-no-source",
action="store_true",
help=argparse.SUPPRESS,
)
aa(
"--overwrite",
action="store_true",
help=argparse.SUPPRESS,
)
aa(
"--external-links",
action="store_true",
help=argparse.SUPPRESS,
)
aa(
"--template-dir",
type=str,
metavar='DIR',
default=None,
help="Specify a directory containing Mako templates "
"(html.mako, text.mako, config.mako and/or any templates they include). "
"Alternatively, put your templates in $XDG_CONFIG_HOME/pdoc and "
"pdoc will automatically find them.",
)
aa(
"--link-prefix",
type=str,
help=argparse.SUPPRESS,
)
aa(
"--close-stdin",
action="store_true",
help="When set, stdin will be closed before importing, to account for "
"ill-behaved modules that block on stdin."
)
DEFAULT_HOST, DEFAULT_PORT = 'localhost', 8080
def _check_host_port(s):
if s and ':' not in s:
raise argparse.ArgumentTypeError(
"'{}' doesn't match '[HOST]:[PORT]'. "
"Specify `--http :` to use default hostname and port.".format(s))
return s
aa(
"--http",
default='',
type=_check_host_port,
metavar='HOST:PORT',
help="When set, pdoc will run as an HTTP server providing documentation "
"for specified modules. If you just want to use the default hostname "
"and port ({}:{}), set the parameter to :.".format(DEFAULT_HOST, DEFAULT_PORT),
)
aa(
"--skip-errors",
action="store_true",
help="Upon unimportable modules, warn instead of raising."
)
args = argparse.Namespace()
class _WebDoc(BaseHTTPRequestHandler):
args = None # Set before server instantiated
template_config = None
def do_HEAD(self):
status = 200
if self.path != "/":
status = self.check_modified()
self.send_response(status)
self.send_header("Content-type", "text/html; charset=utf-8")
self.end_headers()
def check_modified(self):
try:
module = pdoc.import_module(self.import_path_from_req_url)
new_etag = str(os.stat(module.__file__).st_mtime)
except ImportError:
return 404
old_etag = self.headers.get('If-None-Match', new_etag)
if old_etag == new_etag:
# Don't log repeating checks
self.log_request = lambda *args, **kwargs: None
return 304
return 205
def do_GET(self):
# Deny favicon shortcut early.
if self.path == "/favicon.ico":
return None
importlib.invalidate_caches()
code = 200
if self.path == "/":
modules = [pdoc.import_module(module, reload=True)
for module in self.args.modules]
modules = sorted((module.__name__, inspect.getdoc(module))
for module in modules)
out = pdoc._render_template('/html.mako',
modules=modules,
**self.template_config)
elif self.path.endswith(".ext"):
# External links are a bit weird. You should view them as a giant
# hack. Basically, the idea is to "guess" where something lives
# when documenting another module and hope that guess can actually
# track something down in a more global context.
#
# The idea here is to start specific by looking for HTML that
# exists that matches the full external path given. Then trim off
# one component at the end and try again.
#
# If no HTML is found, then we ask `pdoc` to do its thang on the
# parent module in the external path. If all goes well, that
# module will then be able to find the external identifier.
import_path = self.path[:-4].lstrip("/")
resolved = self.resolve_ext(import_path)
if resolved is None: # Try to generate the HTML...
print("Generating HTML for %s on the fly..." % import_path, file=sys.stderr)
try:
out = pdoc.html(import_path.split(".")[0], **self.template_config)
except Exception as e:
print('Error generating docs: {}'.format(e), file=sys.stderr)
# All hope is lost.
code = 404
out = "External identifier <code>%s</code> not found." % import_path
else:
return self.redirect(resolved)
# Redirect '/pdoc' to '/pdoc/' so that relative links work
# (results in '/pdoc/cli.html' instead of 'cli.html')
elif not self.path.endswith(('/', '.html')):
return self.redirect(self.path + '/')
# Redirect '/pdoc/index.html' to '/pdoc/' so it's more pretty
elif self.path.endswith(pdoc._URL_PACKAGE_SUFFIX):
return self.redirect(self.path[:-len(pdoc._URL_PACKAGE_SUFFIX)] + '/')
else:
try:
out = self.html()
except Exception:
import traceback
from html import escape
code = 404
out = "Error importing module <code>{}</code>:\n\n<pre>{}</pre>".format(
self.import_path_from_req_url, escape(traceback.format_exc()))
out = out.replace('\n', '<br>')
self.send_response(code)
self.send_header("Content-type", "text/html; charset=utf-8")
self.end_headers()
self.echo(out)
def redirect(self, location):
self.send_response(302)
self.send_header("Location", location)
self.end_headers()
def echo(self, s):
self.wfile.write(s.encode("utf-8"))
def html(self):
"""
Retrieves and sends the HTML belonging to the path given in
URL. This method is smart and will look for HTML files already
generated and account for whether they are stale compared to
the source code.
"""
return pdoc.html(self.import_path_from_req_url,
reload=True, http_server=True, external_links=True,
skip_errors=args.skip_errors,
**self.template_config)
def resolve_ext(self, import_path):
def exists(p):
p = path.join(args.output_dir, p)
pkg = path.join(p, pdoc._URL_PACKAGE_SUFFIX.lstrip('/'))
mod = p + pdoc._URL_MODULE_SUFFIX
if path.isfile(pkg):
return pkg[len(args.output_dir):]
elif path.isfile(mod):
return mod[len(args.output_dir):]
return None
parts = import_path.split(".")
for i in range(len(parts), 0, -1):
p = path.join(*parts[0:i])
realp = exists(p)
if realp is not None:
return "/%s#%s" % (realp.lstrip("/"), import_path)
return None
@property
def import_path_from_req_url(self):
pth = self.path.split('#')[0].lstrip('/')
for suffix in ('/',
pdoc._URL_PACKAGE_SUFFIX,
pdoc._URL_INDEX_MODULE_SUFFIX,
pdoc._URL_MODULE_SUFFIX):
if pth.endswith(suffix):
pth = pth[:-len(suffix)]
break
return pth.replace('/', '.')
def module_path(m: pdoc.Module, ext: str):
return path.join(args.output_dir, *re.sub(r'\.html$', ext, m.url()).split('/'))
def _quit_if_exists(m: pdoc.Module, ext: str):
if args.force:
return
paths = [module_path(m, ext)]
if m.is_package: # If package, make sure the dir doesn't exist either
paths.append(path.dirname(paths[0]))
for pth in paths:
if path.lexists(pth):
print("File '%s' already exists. Delete it, or run with --force" % pth,
file=sys.stderr)
sys.exit(1)
@contextmanager
def _open_write_file(filename):
try:
with open(filename, 'w', encoding='utf-8') as f:
yield f
print(filename) # print created file path to stdout
except Exception:
try:
os.unlink(filename)
except Exception:
pass
raise
def recursive_write_files(m: pdoc.Module, ext: str, **kwargs):
assert ext in ('.html', '.md')
filepath = module_path(m, ext=ext)
dirpath = path.dirname(filepath)
if not os.access(dirpath, os.R_OK):
os.makedirs(dirpath)
with _open_write_file(filepath) as f:
if ext == '.html':
f.write(m.html(**kwargs))
elif ext == '.md':
f.write(m.text(**kwargs))
for submodule in m.submodules():
recursive_write_files(submodule, ext=ext, **kwargs)
def _flatten_submodules(modules: Sequence[pdoc.Module]):
for module in modules:
yield module
for submodule in module.submodules():
yield from _flatten_submodules((submodule,))
def _print_pdf(modules, **kwargs):
modules = list(_flatten_submodules(modules))
print(pdoc._render_template('/pdf.mako', modules=modules, **kwargs))
def _warn_deprecated(option, alternative='', use_config_mako=False):
msg = 'Program option `{}` is deprecated.'.format(option)
if alternative:
msg += ' Use `' + alternative + '`'
if use_config_mako:
msg += ' or override config.mako template'
msg += '.'
warn(msg, DeprecationWarning, stacklevel=2)
def _generate_lunr_search(modules: List[pdoc.Module],
index_docstrings: bool,
template_config: dict):
"""Generate index.js for search"""
def trim_docstring(docstring):
return re.sub(r'''
\s+| # whitespace sequences
\s+[-=~]{3,}\s+| # title underlines
^[ \t]*[`~]{3,}\w*$| # code blocks
\s*[`#*]+\s*| # common markdown chars
\s*([^\w\d_>])\1\s*| # sequences of punct of the same kind
\s*</?\w*[^>]*>\s* # simple HTML tags
''', ' ', docstring, flags=re.VERBOSE | re.MULTILINE)
def recursive_add_to_index(dobj):
info = {
'ref': dobj.refname,
'url': to_url_id(dobj.module),
}
if index_docstrings:
info['doc'] = trim_docstring(dobj.docstring)
if isinstance(dobj, pdoc.Function):
info['func'] = 1
index.append(info)
for member_dobj in getattr(dobj, 'doc', {}).values():
recursive_add_to_index(member_dobj)
@lru_cache()
def to_url_id(module):
url = module.url()
if url not in url_cache:
url_cache[url] = len(url_cache)
return url_cache[url]
index = [] # type: List[Dict]
url_cache = {} # type: Dict[str, int]
for top_module in modules:
recursive_add_to_index(top_module)
urls = sorted(url_cache.keys(), key=url_cache.__getitem__)
main_path = args.output_dir
with _open_write_file(path.join(main_path, 'index.js')) as f:
f.write("URLS=")
json.dump(urls, f, indent=0, separators=(',', ':'))
f.write(";\nINDEX=")
json.dump(index, f, indent=0, separators=(',', ':'))
# Generate search.html
with _open_write_file(path.join(main_path, 'doc-search.html')) as f:
rendered_template = pdoc._render_template('/search.mako', **template_config)
f.write(rendered_template)
def main(_args=None):
""" Command-line entry point """
global args
args = _args or parser.parse_args()
warnings.simplefilter("once", DeprecationWarning)
if args.close_stdin:
sys.stdin.close()
if (args.html or args.http) and not args.output_dir:
args.output_dir = 'html'
if args.html_dir:
_warn_deprecated('--html-dir', '--output-dir')
args.output_dir = args.html_dir
if args.overwrite:
_warn_deprecated('--overwrite', '--force')
args.force = args.overwrite
template_config = {}
for config_str in args.config:
try:
key, value = config_str.split('=', 1)
value = ast.literal_eval(value)
template_config[key] = value
except Exception:
raise ValueError(
'Error evaluating --config statement "{}". '
'Make sure string values are quoted?'
.format(config_str)
)
if args.html_no_source:
_warn_deprecated('--html-no-source', '-c show_source_code=False', True)
template_config['show_source_code'] = False
if args.link_prefix:
_warn_deprecated('--link-prefix', '-c link_prefix="foo"', True)
template_config['link_prefix'] = args.link_prefix
if args.external_links:
_warn_deprecated('--external-links')
template_config['external_links'] = True
if args.template_dir is not None:
if not path.isdir(args.template_dir):
print('Error: Template dir {!r} is not a directory'.format(args.template_dir),
file=sys.stderr)
sys.exit(1)
pdoc.tpl_lookup.directories.insert(0, args.template_dir)
# Support loading modules specified as python paths relative to cwd
sys.path.append(os.getcwd())
# Virtual environment handling for pdoc script run from system site
try:
venv_dir = os.environ['VIRTUAL_ENV']
except KeyError:
pass # pdoc was not invoked while in a virtual environment
else:
from glob import glob
from distutils.sysconfig import get_python_lib
libdir = get_python_lib(prefix=venv_dir)
sys.path.append(libdir)
# Resolve egg-links from `setup.py develop` or `pip install -e`
# XXX: Welcome a more canonical approach
for pth in glob(path.join(libdir, '*.egg-link')):
try:
with open(pth) as f:
sys.path.append(path.join(libdir, f.readline().rstrip()))
except IOError:
warn('Invalid egg-link in venv: {!r}'.format(pth))
if args.http:
template_config['link_prefix'] = "/"
# Run the HTTP server.
_WebDoc.args = args # Pass params to HTTPServer xP
_WebDoc.template_config = template_config
host, _, port = args.http.partition(':')
host = host or DEFAULT_HOST
port = int(port or DEFAULT_PORT)
print('Starting pdoc server on {}:{}'.format(host, port), file=sys.stderr)
httpd = HTTPServer((host, port), _WebDoc)
print("pdoc server ready at http://%s:%d" % (host, port), file=sys.stderr)
# Allow tests to perform `pdoc.cli._httpd.shutdown()`
global _httpd
_httpd = httpd
try:
httpd.serve_forever()
finally:
httpd.server_close()
sys.exit(0)
docfilter = None
if args.filter and args.filter.strip():
def docfilter(obj, _filters=args.filter.strip().split(',')):
return any(f in obj.refname or
isinstance(obj, pdoc.Class) and f in obj.doc
for f in _filters)
modules = [pdoc.Module(module, docfilter=docfilter,
skip_errors=args.skip_errors)
for module in args.modules]
pdoc.link_inheritance()
if args.pdf:
_print_pdf(modules, **template_config)
import textwrap
print("""
PDF-ready markdown written to standard output.
^^^^^^^^^^^^^^^
Convert this file to PDF using e.g. Pandoc:
{PANDOC_CMD}
or using Python-Markdown and Chrome/Chromium/WkHtmlToPDF:
markdown_py --extension=meta \\
--extension=abbr \\
--extension=attr_list \\
--extension=def_list \\
--extension=fenced_code \\
--extension=footnotes \\
--extension=tables \\
--extension=admonition \\
--extension=smarty \\
--extension=toc \\
pdf.md > pdf.html
chromium --headless --disable-gpu --print-to-pdf=pdf.pdf pdf.html
wkhtmltopdf --encoding utf8 -s A4 --print-media-type pdf.html pdf.pdf
or similar, at your own discretion.""".format(PANDOC_CMD=textwrap.indent(_PANDOC_COMMAND, ' ')),
file=sys.stderr)
sys.exit(0)
for module in modules:
if args.html:
_quit_if_exists(module, ext='.html')
recursive_write_files(module, ext='.html', **template_config)
elif args.output_dir: # Generate text files
_quit_if_exists(module, ext='.md')
recursive_write_files(module, ext='.md', **template_config)
else:
sys.stdout.write(module.text(**template_config))
# Two blank lines between two modules' texts
sys.stdout.write(os.linesep * (1 + 2 * int(module != modules[-1])))
lunr_config = pdoc._get_config(**template_config).get('lunr_search')
if lunr_config is not None:
_generate_lunr_search(
modules, lunr_config.get("index_docstrings", True), template_config)
_PANDOC_COMMAND = '''\
pandoc --metadata=title:"MyProject Documentation" \\
--from=markdown+abbreviations+tex_math_single_backslash \\
--pdf-engine=xelatex --variable=mainfont:"DejaVu Sans" \\
--toc --toc-depth=4 --output=pdf.pdf pdf.md\
'''
if __name__ == "__main__":
main(parser.parse_args())
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application/model/_base.py | keysona/blog | 0 | 5785 | <gh_stars>0
from flask_sqlalchemy import SQLAlchemy, Model
# class BaseModel(Model):
# def save(self):
# db.session.add(self)
# db.session.commit(self)
# def delete(self):
# db.session.
db = SQLAlchemy()
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Project-2/Ishan Pandey/main_gui.py | Mercury1508/IEEE-LEAD-2.0 | 1 | 180159 | <filename>Project-2/Ishan Pandey/main_gui.py
from tkinter import *
from PIL import ImageTk
import PIL.Image
import os
root = Tk()
root.title("Main GUI")
root.geometry("800x550")
root.configure(background='white')
def google_search():
os.system('python google_search.py')
def job_search():
os.system("python job_scrapper_gui.py")
def job_compare():
os.system("python job_compare.py")
option_frame = LabelFrame(root,bg="white",borderwidth=0,highlightthickness=0)
google_frame = LabelFrame(option_frame,bg="white",borderwidth=0,highlightthickness=0)
google_img = ImageTk.PhotoImage(PIL.Image.open("./Images\google.png"))
google_img_label = Label(google_frame,image = google_img,bg='white')
google_button = Button(google_frame,text="Google search",bg="white",fg="#135EC2",font=('Bahnschrift Light', 13, 'bold'),command=google_search)
job_search_frame = LabelFrame(option_frame,bg="white",borderwidth=0,highlightthickness=0)
job_search_img = ImageTk.PhotoImage(PIL.Image.open("./Images\logo.png"))
job_search_img_label = Label(job_search_frame,image = job_search_img,bg='white')
job_search_button = Button(job_search_frame,text="Job Search",bg="white",fg="#135EC2",font=('Bahnschrift Light', 13, 'bold'),command=job_search)
job_compare_frame = LabelFrame(option_frame,bg="white",borderwidth=0,highlightthickness=0)
job_compare_img = ImageTk.PhotoImage(PIL.Image.open("./Images\compare1.png"))
job_compare_img_label=Label(job_compare_frame,image = job_compare_img,bg='white')
job_compare_button = Button(job_compare_frame,text="Compare",bg="white",fg="#135EC2",font=('Bahnschrift Light', 13, 'bold'),command=job_compare)
option_frame.pack(pady=50,padx=50)
google_frame.pack(pady=10,padx=10)
google_img_label.pack(side=LEFT,padx=10)
google_button.pack(pady=25)
job_search_frame.pack(pady=25,padx=5)
job_search_img_label.pack(side=LEFT,padx=10)
job_search_button.pack(padx=5,pady=10)
job_compare_frame.pack(pady=30,padx=2)
job_compare_img_label.pack(side=LEFT,padx=10)
job_compare_button.pack(padx=5,pady=5)
root.mainloop()
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InterpretationTechniques/featureExamination/iceForPredictor.py | HelenaMaria112/PredictionInterpreter | 1 | 24454 | <gh_stars>1-10
'''
Created on 04.10.2019
@author: areb
'''
import pycebox.ice as pIce
from Connections.predictor import *
import matplotlib.pyplot as plt
from InterpretationTechniques.PlotAndShow import *
# https://github.com/AustinRochford/PyCEbox/blob/master/pycebox/ice.py
def plotIce(data, pr):
'''
:param data: pandas dataframe with datasets where each row represents a dataset
:param resultColumnName: Name of column in data that contains actual results
:param pr: Predictor of ML-System
saves and plots ICE
'''
pr.setReturnDistanceOfClass(True)
resultColumnName = pr.resultColumn
for i in pr.listOfNumericalColumns:
data[i]= data[i].astype(float).round(2).astype(str)
data = pr.encode(data)
columnCombinations = pr.unsortedColumnCombinations(data, resultColumnName)
for columnCombination in columnCombinations:
if not isinstance(columnCombination, tuple):
iceResult = pIce.ice(data, columnCombination, pr.predict, num_grid_points=None)
ax = pIce.ice_plot(iceResult, frac_to_plot=1.,
plot_points=True, point_kwargs=None,
x_quantile=False, plot_pdp=True,
centered=False, centered_quantile=0.,
color_by=None, cmap=None,
ax=None, pdp_kwargs=None)
ax.set_ylabel("Distance to Hyperplane of true result")
ax.set_xlabel(columnCombination)
ax.set_title("ICE for " + columnCombination)
lines = ax.lines
for lineIndex in range(len(lines)):
lines[lineIndex].set_label("Dataset "+str(lineIndex))
lines[len(lines)-1].set_label("Pdp")
#ax.legend(loc='upper left', bbox_to_anchor=(1, 1))
for line in ax.lines:
line.set_color("k")
line._linewidth = 0.5
lines[-1].linewidth=1
lines[-1].set_color("r")
xValues = pr.encodingDictionary[columnCombination]
ax.set_xticks(np.arange(1, len(xValues), 1))
ax.set_xticklabels(xValues[1:])
ax.tick_params(axis='both', which='major', labelsize=6)
ax.tick_params(axis='both', which='minor', labelsize=6)
plt.xticks(rotation=90)
saveName="ice"+str(columnCombination)
save(saveName, plt=plt)
def bspSammlung(data):
import pandas as pd
pr= Predictor(returnDistanceOfClass=True)
d = data.sample(3)
y = pd.DataFrame(index=range(9), columns=d.columns)
for i in range(len(d)):
y.iloc[3 * i + 0] = d.iloc[i]
y.iloc[3 * i + 0].loc["brutto"] = d.iloc[0].loc["brutto"]
y.iloc[3 * i + 1] = d.iloc[i]
y.iloc[3 * i + 1].loc["brutto"] = d.iloc[1].loc["brutto"]
y.iloc[3 * i + 2] = d.iloc[i]
y.iloc[3 * i + 2].loc["brutto"] = d.iloc[2].loc["brutto"]
y.loc[:]["gknto"] = pr.predict(y).astype(str)
ystr = ""
for r in range(len(y)):
for c in range(len(y.columns)):
ystr = ystr + y.iloc[r, c][0:min(50, len(y.iloc[r, c]))] + " \n"
ystr = ystr + "\n"
f = open("bspDaten.txt", "w+")
f.write(ystr)
f.close()
import pandas as pd
d = data.sample(3)
y = pd.DataFrame(index=range(9), columns=d.columns)
for i in range(len(d)):
y.iloc[3 * i + 0] = d.iloc[i]
y.iloc[3 * i + 0].loc["text"] = d.iloc[0].loc["text"]
y.iloc[3 * i + 1] = d.iloc[i]
y.iloc[3 * i + 1].loc["text"] = d.iloc[1].loc["text"]
y.iloc[3 * i + 2] = d.iloc[i]
y.iloc[3 * i + 2].loc["text"] = d.iloc[2].loc["text"]
y.loc[:]["gknto"] = pr.predict(y).astype(str)
ystr = ""
for r in range(len(y)):
for c in range(len(y.columns)):
ystr = ystr + y.iloc[r, c][0:min(50, len(y.iloc[r, c]))] + " \n"
ystr = ystr + "\n"
f = open("bspDaten.txt", "w+")
f.write(ystr)
f.close()
def writedataToFileWPredictionhead3(data, pr):
d=data[:3]
y = pd.DataFrame(index=range(9), columns=(d.columns))
for i in range(len(d)):
y.iloc[3 * i + 0] = d.iloc[i]
y.iloc[3 * i + 0].loc["text"] = d.iloc[0].loc["text"]
y.iloc[3 * i + 1] = d.iloc[i]
y.iloc[3 * i + 1].loc["text"] = d.iloc[1].loc["text"]
y.iloc[3 * i + 2] = d.iloc[i]
y.iloc[3 * i + 2].loc["text"] = d.iloc[2].loc["text"]
y["Result"] = pr.predict(y).astype(str)
ystr = ""
for r in range(len(y)):
for c in range(len(y.columns)):
ystr = ystr + y.iloc[r, c][:min(10, len(y.iloc[r, c])-1)] + " \n"
ystr = ystr + "\n"
f = open("bspDaten.txt", "w+")
f.write(ystr)
f.close() | [
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examples/exp_neurips19_MRM.py | xyguo/trimmedEM | 0 | 105911 | <reponame>xyguo/trimmedEM<gh_stars>0
import sys
import numpy as np
from trimmedEM import TrimmedEM
from utils.grader import MRMGrader
from utils.data_gen import regression_mixture, add_outliers
# Experiment for Mixture of Regression Model
epsilons = [0, 0.05, 0.1, 0.15, 0.2]
# epsilons = [0]
n_samples = 2000
mrm_sigma = 0.2
dim = 100
# sparsities = np.array([0.4, 0.2, 0.1, 0.05]) * dim
# sparsities = np.array([32, 24, 16, 12, 8, 4, 2])
sparsities = np.array([15, 13, 11, 9, 7, 5, 3])
sparsities = sparsities.astype(np.int)
mrm_g = MRMGrader(sigma=mrm_sigma)
results_MRM = {
'eps-1': np.array(epsilons),
'err-1': [],
'sparsity-1': np.array(sparsities),
'n_samples-1': n_samples,
'dim-1': dim,
'true-beta-1': [],
}
n_iters = 101
n_repeats = 20
## type 1: error v.s. n_samples / (sparsity * log(dim)), for different epsilon
print("==================\ntype 1: error v.s. n_samples / (sparsity * log(dim)), for different epsilon")
for r in range(n_repeats):
print("===\nRepeat {}".format(r))
err_rates = [[] for _ in range(len(epsilons))]
for i, eps in enumerate(results_MRM['eps-1']):
n_outliers = np.int(results_MRM['n_samples-1'] * eps)
results_MRM['true-beta-1'].append([])
for s in results_MRM['sparsity-1']:
# re-generate data with different sparsity
effective_idxs = np.random.choice(dim, size=s, replace=False)
true_beta = np.zeros(dim)
true_beta[effective_idxs] = 5
results_MRM['true-beta-1'][i].append(true_beta)
# generate data
X, Y = regression_mixture(n_samples=n_samples, n_features=dim,
mean=true_beta, sigma=mrm_sigma,
subspace=effective_idxs)
# corrupt data arbitrarily
XY = add_outliers(np.hstack((X, Y[:, np.newaxis])),
n_outliers=n_outliers,
dist_factor=50)
X_corrupted, Y_corrupted = XY[:, :-1], XY[:, -1].ravel()
# set initial point for gradient descent
init_distortion = np.linalg.norm(true_beta) * \
np.random.randn(results_MRM['dim-1']) / \
(4 * np.sqrt(dim))
beta0 = true_beta + init_distortion
model = TrimmedEM(n_iters=n_iters,
eta=0.1, sparsity=s,
alpha=0.0, grader=mrm_g,
init_val=beta0)
model.fit(X_corrupted, Y_corrupted)
err_rates[i].append(model.loss(groundtruth=true_beta))
# print("eps={}, sparsity={}, loss={}, loss / true_beta={}"
# .format(eps, s, err_rates[i][-1], err_rates[i][-1] / np.linalg.norm(true_beta)))
results_MRM['err-1'].append(np.array(err_rates))
results_MRM['err-1'] = np.array(results_MRM['err-1'])
results_MRM['true-beta-1'] = results_MRM['true-beta-1']
true_beta_norms = np.zeros(shape=(len(epsilons), len(sparsities)))
for e in range(len(epsilons)):
for s in range(len(sparsities)):
true_beta_norms[e,s] = np.linalg.norm(results_MRM['true-beta-1'][e][s])
print("err-1:")
print(np.mean(results_MRM['err-1'], axis=0) / true_beta_norms)
## type 2: error v.s. n_iterations, for different epsilon
print("===============\nType 2: error v.s. n_iterations, for different eps\n")
true_sparsity = 7
dim = 100
epsilons = [0, 0.05, 0.1, 0.15, 0.2]
results_MRM['eps-2'] = np.array(epsilons)
results_MRM['err-2'] = []
results_MRM['sparsity-2'] = true_sparsity
results_MRM['n_samples-2'] = n_samples
results_MRM['dim-2'] = dim
results_MRM['true-beta-2'] = []
for r in range(n_repeats):
print("===\nRepeat {}".format(r))
effective_idxs = np.random.choice(dim, size=true_sparsity, replace=False)
true_beta = np.zeros(dim)
true_beta[effective_idxs] = 50
results_MRM['true-beta-2'].append(true_beta)
X, Y = regression_mixture(n_samples=results_MRM['n_samples-2'],
n_features=results_MRM['dim-2'],
mean=true_beta, sigma=mrm_sigma,
subspace=effective_idxs)
err_rates = []
for i, eps in enumerate(results_MRM['eps-2']):
init_distortion = np.linalg.norm(results_MRM['true-beta-2'][-1]) * \
np.random.randn(results_MRM['dim-2']) / \
(4 * np.sqrt(results_MRM['dim-2']))
beta0 = results_MRM['true-beta-2'][-1] + init_distortion
n_outliers = np.int(results_MRM['n_samples-2'] * eps)
# corrupt data arbitrarily
XY = add_outliers(np.hstack((X, Y[:, np.newaxis])),
n_outliers=n_outliers,
dist_factor=50)
X_corrupted, Y_corrupted = XY[:, :-1], XY[:, -1].ravel()
model = TrimmedEM(n_iters=n_iters, eta=0.1,
sparsity=results_MRM['sparsity-2'],
alpha=0.0, grader=mrm_g,
init_val=beta0,
groundtruth=results_MRM['true-beta-2'][-1],
record_all_loss=True)
model.fit(X_corrupted, Y_corrupted)
err_rates.append(model.iteration_losses)
# print("eps={}, final_loss={}".format(eps, err_rates[-1][-1]))
results_MRM['err-2'].append(np.array(err_rates))
results_MRM['err-2'] = np.array(results_MRM['err-2'])
results_MRM['true-beta-2'] = np.array(results_MRM['true-beta-2'])
print("err-2:")
# print(np.min(np.mean(results_MRM['err-2'] /
# np.linalg.norm(results_MRM['true-beta-2'], axis=1)[:, np.newaxis, np.newaxis],
# axis=0),
# axis=1))
print(np.mean(results_MRM['err-2'] /
np.linalg.norm(results_MRM['true-beta-2'], axis=1)[:, np.newaxis, np.newaxis],
axis=0)[:, -1])
## type III: error v.s. n_iterations, for different dim
print("=================\ntype III: error v.s. n_iterations, for different dim")
results_MRM['eps-3'] = 0.2
results_MRM['err-3'] = []
results_MRM['n_samples-3'] = n_samples
results_MRM['dim-3'] = np.array([i * 40 for i in range(2, 7)])
# results_MRM['sparsity-3'] = (results_MRM['dim-3'] * 0.05).astype(np.int)
results_MRM['sparsity-3'] = 7
results_MRM['true-beta-3'] = []
n_outliers = np.int(results_MRM['n_samples-3'] * results_MRM['eps-3'])
for r in range(n_repeats):
print("===\nRepeat {}".format(r))
err_rates = []
for i, d in enumerate(results_MRM['dim-3']):
effective_idxs = np.random.choice(d, size=results_MRM['sparsity-3'],
replace=False)
true_beta = np.zeros(d)
true_beta[effective_idxs] = 10
init_distortion = np.linalg.norm(true_beta) * \
np.random.randn(d) / \
(4 * np.sqrt(d))
beta0 = true_beta + init_distortion
if r == 0:
results_MRM['true-beta-3'].append(true_beta)
X, Y = regression_mixture(n_samples=results_MRM['n_samples-3'],
n_features=d,
mean=true_beta,
sigma=mrm_sigma,
subspace=effective_idxs)
# corrupt data arbitrarily
XY = add_outliers(np.hstack((X, Y[:, np.newaxis])),
n_outliers=n_outliers,
dist_factor=50)
X_corrupted, Y_corrupted = XY[:, :-1], XY[:, -1].ravel()
model = TrimmedEM(n_iters=n_iters, eta=0.1,
sparsity=results_MRM['sparsity-3'],
alpha=0.0, grader=mrm_g,
init_val=beta0,
groundtruth=true_beta, record_all_loss=True)
model.fit(X_corrupted, Y_corrupted)
err_rates.append(model.iteration_losses)
# print("dim={}, final_loss={}".format(d, err_rates[-1][-1]))
results_MRM['err-3'].append(np.array(err_rates))
results_MRM['err-3'] = np.array(results_MRM['err-3'])
true_beta_norm = np.array([np.linalg.norm(x) for x in results_MRM['true-beta-3']])
print("err-3:")
# print(np.min(np.mean(results_MRM['err-3'], axis=0), axis=1) / true_beta_norm)
print(np.mean(results_MRM['err-3'], axis=0)[:, -1] / true_beta_norm)
filename_MRM = "../results_for_MRM_20190830"
np.savez(filename_MRM, **results_MRM)
sys.exit(0)
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datahub_core/printable.py | grovesy/datahub | 67 | 40886 | <reponame>grovesy/datahub<filename>datahub_core/printable.py
from pprint import pformat
class Printable:
def __repr__(self):
return "<" + type(self).__name__ + "> " + pformat(vars(self), indent=4, width=1)
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src/zope/app/content/__init__.py | zopefoundation/zope.app.content | 0 | 8270 | <reponame>zopefoundation/zope.app.content<filename>src/zope/app/content/__init__.py
##############################################################################
#
# Copyright (c) 2002 Zope Foundation and Contributors.
# All Rights Reserved.
#
# This software is subject to the provisions of the Zope Public License,
# Version 2.1 (ZPL). A copy of the ZPL should accompany this distribution.
# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
# FOR A PARTICULAR PURPOSE.
#
##############################################################################
"""Content Type convenience lookup functions."""
from zope.interface import provider
from zope.interface import providedBy
from zope.schema.interfaces import IVocabularyFactory
from zope.app.content.interfaces import IContentType
from zope.componentvocabulary.vocabulary import UtilityVocabulary
from zope.security.proxy import removeSecurityProxy
def queryType(object, interface):
"""Returns the object's interface which implements interface.
>>> from zope.interface import Interface
>>> class IContentType(Interface):
... pass
>>> from zope.interface import Interface, implementer, directlyProvides
>>> class I(Interface):
... pass
>>> class J(Interface):
... pass
>>> directlyProvides(I, IContentType)
>>> @implementer(I)
... class C(object):
... pass
>>> @implementer(J, I)
... class D(object):
... pass
>>> obj = C()
>>> c1_ctype = queryType(obj, IContentType)
>>> c1_ctype.__name__
'I'
>>> class I1(I):
... pass
>>> class I2(I1):
... pass
>>> class I3(Interface):
... pass
>>> @implementer(I1)
... class C1(object):
... pass
>>> obj1 = C1()
>>> c1_ctype = queryType(obj1, IContentType)
>>> c1_ctype.__name__
'I'
>>> @implementer(I2)
... class C2(object):
... pass
>>> obj2 = C2()
>>> c2_ctype = queryType(obj2, IContentType)
>>> c2_ctype.__name__
'I'
>>> @implementer(I3)
... class C3(object):
... pass
>>> obj3 = C3()
If Interface doesn't provide `IContentType`, `queryType` returns ``None``.
>>> c3_ctype = queryType(obj3, IContentType)
>>> c3_ctype
>>> c3_ctype is None
True
>>> class I4(I):
... pass
>>> directlyProvides(I4, IContentType)
>>> @implementer(I4)
... class C4(object):
... pass
>>> obj4 = C4()
>>> c4_ctype = queryType(obj4, IContentType)
>>> c4_ctype.__name__
'I4'
"""
# Remove the security proxy, so that we can introspect the type of the
# object's interfaces.
naked = removeSecurityProxy(object)
object_iro = providedBy(naked).__iro__
for iface in object_iro:
if interface.providedBy(iface):
return iface
return None
def queryContentType(object):
"""Returns the interface implemented by object which implements
:class:`zope.app.content.interfaces.IContentType`.
>>> from zope.interface import Interface, implementer, directlyProvides
>>> class I(Interface):
... pass
>>> directlyProvides(I, IContentType)
>>> @implementer(I)
... class C(object):
... pass
>>> obj = C()
>>> c1_ctype = queryContentType(obj)
>>> c1_ctype.__name__
'I'
"""
return queryType(object, IContentType)
@provider(IVocabularyFactory)
class ContentTypesVocabulary(UtilityVocabulary):
interface = IContentType
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serial_for_humans/utils.py | PeterMitrano/SerialForHumans | 0 | 182525 | <reponame>PeterMitrano/SerialForHumans<gh_stars>0
from asciimatics.event import KeyboardEvent
from asciimatics.widgets import Frame, TextBox, Text
class MyTextBox(TextBox):
def __init__(self, height, label=None, name=None, as_string=False,
on_change=None):
super(TextBox, self).__init__(height, label, name, as_string, on_change)
self.disabled = True
class MyFrame(Frame):
def __init__(self, screen, model, data=None):
super(MyFrame, self).__init__(screen, screen.height, screen.width, hover_focus=True,
has_border=False, reduce_cpu=True, data=data)
self._model = model
self.screen = screen
# Set up color scheme
self.palette['background'] = (0, 0, 0)
self.palette['borders'] = (7, 0, 0)
self.palette['title'] = (7, 0, 0)
self.palette['label'] = (2, 0, 0)
self.palette['disabled'] = (7, 0, 0)
self.palette['edit_text'] = (7, 0, 0)
self.palette['focus_edit_text'] = (7, 0, 0)
self.palette['button'] = (2, 0, 0)
self.palette['focus_button'] = (2, 1, 0)
self.palette['control'] = (7, 0, 0)
self.palette['focus_control'] = (7, 0, 0)
self.palette['selected_control'] = (7, 0, 0)
self.palette['selected_focus_control'] = (7, 1, 0)
self.palette['field'] = (7, 0, 0)
self.palette['focus_field'] = (7, 0, 0)
self.palette['selected_field'] = (0, 0, 7)
self.palette['selected_focus_field'] = (0, 0, 7)
class InputText(Text):
KEY_ENTER = 10
def __init__(self, writer, label=None, name=None, on_change=None):
super(InputText, self).__init__(label, name, on_change)
self.writer = writer
def process_event(self, event):
if isinstance(event, KeyboardEvent):
if event.key_code == InputText.KEY_ENTER:
message_to_write = self.value
self.value = ""
self.reset()
self.writer(message_to_write)
else:
return super().process_event(event)
else:
return super().process_event(event) | [
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] |
migrations/versions/dd503a5987b5_.py | atwh0405/miniblog | 0 | 40362 | <reponame>atwh0405/miniblog
"""empty message
Revision ID: dd503a5987b5
Revises: <KEY>
Create Date: 2016-08-30 16:48:54.954000
"""
# revision identifiers, used by Alembic.
revision = 'dd503a5987b5'
down_revision = '<KEY>'
from alembic import op
import sqlalchemy as sa
def upgrade():
### commands auto generated by Alembic - please adjust! ###
op.add_column('users', sa.Column('name', sa.String(length=64), nullable=True))
### end Alembic commands ###
def downgrade():
### commands auto generated by Alembic - please adjust! ###
op.drop_column('users', 'name')
### end Alembic commands ###
| [
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src/payu_payment/serializers.py | wilantury/payu_integration_backend | 0 | 60895 | <filename>src/payu_payment/serializers.py
from rest_framework import serializers
from .models import LogPurchase
class LogPurchaseSerializer(serializers.ModelSerializer):
class Meta:
model = LogPurchase
fields = '__all__' | [
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product/views/classy_views.py | bootandy/flask-sample | 2 | 157199 | <gh_stars>1-10
from flask import Flask, render_template
from flask.ext.classy import FlaskView
from product import app
from product.models import *
class UserView(FlaskView):
def index(self):
users = User.objects()
return render_template('users/index.html', users=users)
def get(self, id):
user = User.objects.get(id=id)
return render_template('users/single.html', user=user)
UserView.register(app)
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FortressOfSolitude/_FortressOfSolitude/NeutrinoKey/models.py | BDD16/FortressOfSolitude | 0 | 27852 | """
DBA 1337_TECH, AUSTIN TEXAS © MAY 2020
Proof of Concept code, No liabilities or warranties expressed or implied.
"""
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models
from datetime import datetime
from .cryptoutils import CryptoTools
from base64 import b64encode, b64decode
from django.contrib.auth import get_user_model
from random import random
# Create your models here.
# Constants
LENGTH_OF_KEK = 32 # 256 bits or 32 bytes
LENGTH_OF_DEK = 32 # 256 bits or 32 bytes
LENGTH_OF_SALT = 32 # 256 bits or 32 bytes
'''
KeyMold is a models.Manager clas extension that includes creating a Kek and retrieving a kek
no inputs
'''
class KeyMold(models.Manager):
def _create_kek(request, **kwargs):
pwd = <PASSWORD>.user.password
# print("deriving kek")
self.kek = DeriveKek_default(pwd)
return self.kek
def get_queryset(self):
qs = models.QuerySet(self.model)
if self._db is not None:
qs = qs.using('default')
return qs
'''
TelescopeCoord is a models.Manager that allows to find the neutron star that will be used for the keyMold to make a Key Encryption Key [kek].
no inputs
'''
class TelescopeCoord(models.Manager):
def get_queryset(self):
qs = models.QuerySet(self.model)
if self._db is not None:
qs = qs.using('default')
return qs
'''
QuasiPlasma is a models.Manager that allows for deriving Data Encryption Keys [DEKs] and retrieving deks from the neutron stars plasma.
no inputs
'''
class QuasiPlasma(models.Manager):
def _create_dek(request, **kwargs):
pwd = request.user.password
self.dek = DeriveDek_default(pwd)
return self.dek
def get_queryset(self):
qs = models.QuerySet(self.model)
if self._db is not None:
qs = qs.using('default')
return qs
'''
KEK is the Key encryption Key [KEK] model.Model class extension that has the ability to derive a new KEK as well as wrap the KEK.
no inputs
'''
class KEK(models.Model):
# Never should the key be passed as clear text always use the wrap or unwrap functions
crypto = CryptoTools()
kek = None
wrappedKek = None
result_wrapped_nonce = models.CharField(max_length=128, default=b64encode(int(55).to_bytes(4, 'big')))
result_wrapped_kek = models.CharField(max_length=128, default=None)
objects = TelescopeCoord()
class Meta:
verbose_name = 'KEK'
def unwrap_key(self, password):
if isinstance(password, str) and self.kek == None and self.wrappedKek == None:
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
self.kek = self.crypto.AesDecryptEAX(b64decode(self.result_wrapped_kek),
self.crypto.Sha256(password.encode()))
if isinstance(password, bytes) and self.kek == None and self.wrappedKek == None:
if isinstance(self.result_wrapped_nonce, str):
result_wrapped_nonce = (self.result_wrapped_nonce.encode()).replace(b"b'", b'')
result_wrapped_nonce = result_wrapped_nonce[:-1]
result_wrapped_nonce = result_wrapped_nonce + b'=' * (len(self.result_wrapped_nonce) % 4)
self.crypto.nonce = b64decode(result_wrapped_nonce)
else:
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
# print("wrappedKek: " + self.result_wrapped_kek)
if isinstance(self.result_wrapped_kek, str):
result_wrapped_kek = (self.result_wrapped_kek.encode()).replace(b"b'", b'')
result_wrapped_kek = result_wrapped_kek[:-1]
result_wrapped_kek = result_wrapped_kek + b'=' * (len(result_wrapped_kek) % 4)
elif isinstance(self.result_wrapped_kek, bytes):
result_wrapped_kek = self.result_wrapped_kek
self.kek = self.crypto.AesDecryptEAX(b64decode(result_wrapped_kek), CryptoTools().Sha256(password))
else:
try:
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
if not isinstance(password, bytes):
password = password.encode()
self.kek = self.crypto.AesDecryptEAX(b64decode(self.result_wrapped_kek), self.crypto.Sha256(password))
self.wrappedKek = None
except:
print('someone has attempted to spoof the KEK (key encryption key)')
return self.kek
def wrap_key(self, password):
if isinstance(password, str) and self.kek == None:
self.kek = self.crypto.AesEncryptEAX(data, self.crypto.Sha256(password.encode()))
self.wrappedKek = self.kek
self.kek = None
elif isinstance(password, bytes) and self.kek == None:
self.kek = self.crypto.AesEncryptEAX(data, self.crypto.Sha256(password))
self.wrappedKek = b64encode(self.kek)
self.kek = None
elif self.kek != None:
try:
# print("ATTEMPTING WRAPPING KEK")
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
# print("set nonce")
if isinstance(password, bytes):
self.wrappedKek = b64encode(self.crypto.AesEncryptEAX(self.kek, self.crypto.Sha256(password)))
else:
self.wrappedKek = b64encode(
self.crypto.AesEncryptEAX(self.kek, self.crypto.Sha256(password.encode())))
self.kek = None
except OSError as ERROR:
print(ERROR)
print('Wrapping KEK (key encryption key) was unsuccessful')
return self.wrappedKek
'''
using the model of KEK unwrap and wrap the kek then unwrap the dek then pass the dek to a more useable object
perhaps this will also fetch the dek that is associated with that data model, so needs to be a manytomany relation.
DEK is a models.Model or Data Encryption Key class that allows to store, derive, and wrap Data Encryption Keys from a KEK and Salt
'''
class DEK(models.Model):
crypto = CryptoTools()
dek = None
wrappedDek = None
SALT = None
result_wrapped_nonce = models.CharField(max_length=128, default=b64encode(int(55).to_bytes(4, 'big')))
result_wrappedDek = models.CharField(max_length=128)
result_SALT = models.CharField(max_length=45)
kek_to_retrieve = models.ManyToManyField(KEK)
objects = KeyMold()
class Meta:
verbose_name = 'DEK'
def wrap_key(self, kek, password):
if isinstance(kek, KEK) and isinstance(password, str):
kek.unwrap_key(password)
self.crypto.nonce = b64decode(kek.result_wrapped_nonce)
# print(self.result_wrappedDek)
self.dek = self.crypto.AesEncryptEAX(b64decode(self.result_wrappedDek), kek.kek)
kek.wrap_key(password)
return self.dek
elif isinstance(kek, KEK) and isinstance(password, bytes):
kek.unwrap_key(password)
self.crypto.nonce = b64decode(kek.result_wrapped_nonce)
self.dek = self.crypto.AesEncryptEAX(self.result_wrappedDek, kek.kek)
kek.wrap_key(password)
return self.dek
else:
try:
kek.unwrap_key(password)
self.crypto.nonce = b64decode(kek.result_wrapped_nonce)
self.dek = self.crypto.AesEncryptEAX(self.result_wrappedDek, self.crypto.Sha256(kek.kek))
kek.wrap_key(password)
return self.dek
except:
print('someone has attempted to spoof the DEK (data encryption key)')
def unwrap_key(self, kek, password):
if isinstance(kek, KEK) and isinstance(password, str):
master = kek.unwrap_key(password.encode())
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
self.dek = self.crypto.AesDecryptEAX(b64decode(self.result_wrappedDek), self.crypto.Sha256(master))
kek.wrap_key(password)
return self.dek
elif isinstance(kek, KEK) and isinstance(password, bytes):
kek.unwrap_key(password)
if isinstance(self.result_wrapped_nonce, str):
print("NONCEDEK_STR:" + self.result_wrapped_nonce)
result_wrapped_nonce = (self.result_wrapped_nonce.encode()).replace(b"b'", b'')
result_wrapped_nonce = result_wrapped_nonce[:-1]
result_wrapped_nonce = result_wrapped_nonce + b'=' * (len(result_wrapped_nonce) % 4)
self.crypto.nonce = b64decode(result_wrapped_nonce)
print(b'NONCEDEK>' + result_wrapped_nonce)
elif isinstance(self.result_wrapped_nonce, bytes):
print("YOLO")
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
if (not isinstance(self.result_wrappedDek, bytes)):
print("did we make it here" + str(self.result_wrappedDek))
result_wrappedDek = (self.result_wrappedDek.encode()).replace(b"b'", b'')
result_wrappedDek = result_wrappedDek[:-1]
print("did we make it here" + str(result_wrappedDek))
wrapper = result_wrappedDek + b'=' * (len(result_wrappedDek) % 4)
print("wrapper" + str(wrapper))
else:
print(self.result_wrappedDek)
result_wrappedDek = self.result_wrappedDek.replace(b"b'", b'')
result_wrappedDek = result_wrappedDek
wrapper = result_wrappedDek + b'=' * (len(result_wrappedDek) % 4)
cryptoObj = CryptoTools()
print(wrapper)
self.dek = self.crypto.AesDecryptEAX(b64decode(wrapper), cryptoObj.Sha256(kek.kek))
kek.wrap_key(password)
return self.dek
else:
try:
if not isinstance(password, bytes):
password = password.encode()
else:
password = password
kek.unwrap_key(password)
self.crypto.nonce = b64decode(self.result_wrapped_nonce)
# print("about to decrypt dek")
self.dek = self.crypto.AesDecryptEAX(b64decode(self.result_wrappedDek), self.crypto.Sha256(kek.kek))
kek.wrap_key(password)
return self.dek
except:
print('someone has attempted to spoof the KEK2 (key encryption key)')
'''
function to DeriveKek_default from an arbitrary password
'''
def DeriveKek_default(password):
crypto = CryptoTools()
if len(crypto.Sha256(password.encode())) != LENGTH_OF_KEK:
print('ERROR> NOT ENOUGH BYTES IN PASSWORD FOR DEK, NEED 32')
if isinstance(password, str):
somekek = crypto.Sha256(bytes(password.encode()))
somekek = crypto.AesEncryptEAX(password.encode(), somekek)
k = KEK(result_wrapped_kek=b64encode(somekek))
k.save()
return k
elif isinstance(password, bytes):
somekek = crypto.Sha256(bytes(password.encode()))
somekek = crypto.AesEncryptEAX(password.encode(), somekek)
k = KEK(result_wrapped_kek=b64encode(somekek), result_wrapped_nonce=crypto.nonce)
k.save()
return k
else:
print("ERROR>UNABLE TO GENERATE WRAPPED KEK, USE A CORRECT KEY FORMAT FOR WRAPPING")
'''
NeutronCore is a models.Model type class that allow for KEKs to be generated through a kek generator, time_generated, and of course the kek object
this is the model for when you need access to multiple KEKS for a single user
USE CASE: is old data relies on older KEKs but that older KEK is still active
but the user happened to change their password which would entail creating a new password and from that time the DEK chain would change to the newly
created KEK wrapped using the newly changed password.
'''
class NeutronCore(models.Model):
kek = models.ForeignKey(
get_user_model(), related_name='KEK',
on_delete=models.CASCADE,
default=1)
kekgenerator = models.ManyToManyField(KEK, related_name='KEK')
time_generated = models.DateTimeField('date star collapsed', auto_now_add=True)
objects = KeyMold()
class Meta:
verbose_name = 'neutron core'
ordering = ['-time_generated']
get_latest_by = 'time_generated'
def DeriveKek(self, password):
crypto = CryptoTools()
if len(crypto.Sha256(password.encode())) != LENGTH_OF_KEK:
print('ERROR> NOT ENOUGH BYTES IN PASSWORD FOR DEK, NEED 32')
if isinstance(password, str):
somekek = crypto.Sha256(bytes(password.encode()))
somekek = crypto.AesEncryptEAX(password.encode(), somekek)
k = KEK(result_wrapped_kek=b64encode(somekek), result_wrapped_nonce=b64encode(crypto.nonce))
k.save()
return k
elif isinstance(password, bytes):
somekek = crypto.Sha256(bytes(password.encode()))
somekek = crypto.AesEncryptEAX(password.encode(), somekek)
k = KEK(result_wrapped_kek=b64encode(somekek), result_wrapped_nonce=b64encode(crypto.nonce))
k.save()
return k
else:
print("ERROR>UNABLE TO GENERATE WRAPPED KEK, USE A CORRECT KEY FORMAT FOR WRAPPING")
def DeriveDek_default(password):
crypto = CryptoTools()
kekForDek = NeutronCore(get_user_model()).DeriveKek(password)
if isinstance(kekForDek, KEK):
if password != None and isinstance(password, str):
# Generate DEK based off this formula sha256(256 bit SALT + KEK)
self.SALT = crypto.RandomNumber(32)
crypto.nonce = b64decode(kekForDek.result_wrapped_nonce)
DerivedDek = crypto.Sha256(bytes(kekForDek.result_SALT) + crypto.AesDecryptEAX(
bytes(b64decode(str(kekForDek.result_wrapped_kek).encode())),
crypto.Sha256(bytes(password.encode()))))
dekgenerator = DerivedDek
dek = DerivedDek
dek = DEK.wrap_key(dek, password)
newDek = DEK(result_wrappedDek=b64encode(dek), result_SALT=kekForDek.result_SALT,
kek_to_retrieve=kekForDek, result_wrapped_nonce=b64encode(crypto.nonce))
newDek.save()
return newDek
'''
NeutronMatterCollector is for generating a Data Encryption Key [DEK]
no inputs
'''
class NeutronMatterCollector(models.Model):
dekgenerator = models.ManyToManyField(DEK,
related_name='kek_for_dek_generator') # length of 32 bytes (256bits) in base64 is 44, but will need to include an = ending and null so extending to 45.
try:
# print(get_user_model().user)
kekForDek = models.ForeignKey(
KEK, related_name='KEK_obj',
on_delete=models.CASCADE, default=1)
dek = models.ForeignKey(
DEK, related_name='DEK_obj',
on_delete=models.CASCADE,
default=1)
except:
try:
print("unable to locate KEK for username creating new one, this could be due to a new user")
kekForDek = models.ForeignKey(KEK, related_name='KEK_obj',
on_delete=models.CASCADE, default=1)
dek = models.ForeignKey(DEK, related_name='DEK_obj', on_delete=models.CASCADE, default=1)
print("successfully made a KEK and DEK")
except:
print("unable to create KEK")
print(get_user_model().natural_key(get_user_model()))
time_generated = models.DateTimeField('date integrated', auto_now_add=datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
objects = QuasiPlasma()
class Meta:
verbose_name = 'neutron matter collector'
ordering = ['-time_generated']
get_latest_by = 'time_generated'
def DeriveDek(self, password):
crypto = CryptoTools()
if isinstance(NeutronMatterCollector.kekForDek, KEK):
if password != None and isinstance(password, str):
# Generate DEK based off this formula sha256(256 bit SALT + KEK)
self.SALT = crypto.RandomNumber(32)
crypto.nonce = b64decode(NeutronMatterCollector.kekForDek.result_wrapped_nonce)
DerivedDek = crypto.Sha256(bytes(self.SALT) + crypto.AesDecryptEAX(
bytes(b64decode(str(self.kekForDek.result_wrapped_kek).encode())),
crypto.Sha256(bytes(password.encode()))))
self.dekgenerator = DerivedDek
dek = DerivedDek
dek = DEK.wrap_key(dek, password)
newDek = DEK(result_wrappedDek=b64encode(dek), result_SALT=b64encode(self.SALT),
kek_to_retrieve=self.dekgenerator)
newDek.save()
return newDek
else:
self.kekForDek = NeutronCore(get_user_model()).DeriveKek(password)
if isinstance(self.kekForDek, KEK):
if password != None and isinstance(password, str):
# Generate DEK based off this formula sha256(256 bit SALT + KEK)
self.SALT = crypto.RandomNumber(32)
crypto.nonce = b64decode(self.kekForDek.result_wrapped_nonce)
# print(self.kekForDek.result_wrapped_nonce)
# print(self.kekForDek.result_wrapped_kek)
# print(password)
DerivedDek = crypto.Sha256(
bytes(self.SALT) + crypto.AesDecryptEAX(b64decode(self.kekForDek.result_wrapped_kek),
crypto.Sha256(bytes(password.encode()))))
# self.dekgenerator.id.set(self.request.user)
dek = DerivedDek
# newkey = DEK()
# newkey.dek = dek
# dek = DEK.wrap_key(newkey, kek=self.kekForDek, password=password.encode())
dek = crypto.AesEncryptEAX(dek, crypto.Sha256(
crypto.AesDecryptEAX(b64decode(self.kekForDek.result_wrapped_kek),
crypto.Sha256(bytes(password.encode())))))
newDek = DEK(result_wrappedDek=b64encode(dek), result_SALT=b64encode(self.SALT),
result_wrapped_nonce=b64encode(crypto.nonce), id=self.id)
# newDek.kek_to_retrieve.set(self.dekgenerator)
# self.time_generated = models.DateTimeField('date integrated', auto_now_add=datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
self.save()
newDek.save()
self.dekgenerator.add(newDek)
self.save()
return newDek
class KryptonianSpeak:
def db_for_read(self, model, **hints):
return 'default'
def db_for_write(self, model, **hints):
return 'default'
def allow_relation(self, obj1, obj2, **hints):
return True
'''
db_list = ('default', 'superHeros', 'icePick', 'neutronStarMatter', 'neutronStarMold')
if obj1._state.db in db_list and obj2._state.db in db_list:
return True
return None
'''
def allow_migrate(self, db, app_label, model_name=None, **hints):
return True
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29923,
29968,
322,
27903,
13,
12008,
13,
13,
13,
1990,
5012,
29968,
29898,
9794,
29889,
3195,
1125,
13,
1678,
274,
17929,
353,
315,
17929,
24183,
580,
13,
1678,
316,
29895,
353,
6213,
13,
1678,
21021,
29928,
1416,
353,
6213,
13,
1678,
317,
1964,
29911,
353,
6213,
13,
1678,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
353,
4733,
29889,
27890,
29898,
3317,
29918,
2848,
29922,
29896,
29906,
29947,
29892,
2322,
29922,
29890,
29953,
29946,
12508,
29898,
524,
29898,
29945,
29945,
467,
517,
29918,
13193,
29898,
29946,
29892,
525,
3752,
29915,
4961,
13,
1678,
1121,
29918,
29893,
336,
2986,
29928,
1416,
353,
4733,
29889,
27890,
29898,
3317,
29918,
2848,
29922,
29896,
29906,
29947,
29897,
13,
13,
1678,
1121,
29918,
29903,
1964,
29911,
353,
4733,
29889,
27890,
29898,
3317,
29918,
2848,
29922,
29946,
29945,
29897,
13,
1678,
413,
1416,
29918,
517,
29918,
276,
509,
2418,
353,
4733,
29889,
14804,
1762,
14804,
3073,
29898,
6059,
29968,
29897,
13,
13,
1678,
3618,
353,
7670,
29924,
1025,
580,
13,
13,
1678,
770,
20553,
29901,
13,
4706,
26952,
29918,
978,
353,
525,
2287,
29968,
29915,
13,
13,
1678,
822,
12244,
29918,
1989,
29898,
1311,
29892,
413,
1416,
29892,
4800,
1125,
13,
4706,
565,
338,
8758,
29898,
446,
29895,
29892,
476,
29923,
29968,
29897,
322,
338,
8758,
29898,
5630,
29892,
851,
1125,
13,
9651,
413,
1416,
29889,
26238,
29918,
1989,
29898,
5630,
29897,
13,
9651,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
446,
29895,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
9651,
396,
1596,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29897,
13,
9651,
1583,
29889,
25950,
353,
1583,
29889,
29883,
17929,
29889,
29909,
267,
8566,
4641,
29923,
6604,
29898,
29890,
29953,
29946,
13808,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
511,
413,
1416,
29889,
446,
29895,
29897,
13,
9651,
413,
1416,
29889,
6312,
29918,
1989,
29898,
5630,
29897,
13,
9651,
736,
1583,
29889,
25950,
13,
13,
4706,
25342,
338,
8758,
29898,
446,
29895,
29892,
476,
29923,
29968,
29897,
322,
338,
8758,
29898,
5630,
29892,
6262,
1125,
13,
9651,
413,
1416,
29889,
26238,
29918,
1989,
29898,
5630,
29897,
13,
13,
9651,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
446,
29895,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
13,
9651,
1583,
29889,
25950,
353,
1583,
29889,
29883,
17929,
29889,
29909,
267,
8566,
4641,
29923,
6604,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29892,
413,
1416,
29889,
446,
29895,
29897,
13,
9651,
413,
1416,
29889,
6312,
29918,
1989,
29898,
5630,
29897,
13,
9651,
736,
1583,
29889,
25950,
13,
13,
4706,
1683,
29901,
13,
9651,
1018,
29901,
13,
18884,
413,
1416,
29889,
26238,
29918,
1989,
29898,
5630,
29897,
13,
18884,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
446,
29895,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
13,
18884,
1583,
29889,
25950,
353,
1583,
29889,
29883,
17929,
29889,
29909,
267,
8566,
4641,
29923,
6604,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29892,
1583,
29889,
29883,
17929,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
446,
29895,
29889,
446,
29895,
876,
13,
18884,
413,
1416,
29889,
6312,
29918,
1989,
29898,
5630,
29897,
13,
18884,
736,
1583,
29889,
25950,
13,
13,
9651,
5174,
29901,
13,
18884,
1596,
877,
5372,
650,
756,
16388,
304,
13345,
974,
278,
5012,
29968,
313,
1272,
20956,
1820,
29897,
1495,
13,
13,
1678,
822,
443,
6312,
29918,
1989,
29898,
1311,
29892,
413,
1416,
29892,
4800,
1125,
13,
4706,
565,
338,
8758,
29898,
446,
29895,
29892,
476,
29923,
29968,
29897,
322,
338,
8758,
29898,
5630,
29892,
851,
1125,
13,
9651,
5835,
353,
413,
1416,
29889,
26238,
29918,
1989,
29898,
5630,
29889,
12508,
3101,
13,
13,
9651,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
9651,
1583,
29889,
25950,
353,
1583,
29889,
29883,
17929,
29889,
29909,
267,
6185,
4641,
29923,
6604,
29898,
29890,
29953,
29946,
13808,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
511,
1583,
29889,
29883,
17929,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
6207,
876,
13,
13,
9651,
413,
1416,
29889,
6312,
29918,
1989,
29898,
5630,
29897,
13,
9651,
736,
1583,
29889,
25950,
13,
13,
4706,
25342,
338,
8758,
29898,
446,
29895,
29892,
476,
29923,
29968,
29897,
322,
338,
8758,
29898,
5630,
29892,
6262,
1125,
13,
9651,
413,
1416,
29889,
26238,
29918,
1989,
29898,
5630,
29897,
13,
13,
9651,
565,
338,
8758,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29892,
851,
1125,
13,
18884,
1596,
703,
29940,
1164,
4741,
2287,
29968,
29918,
10810,
6160,
718,
1583,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
18884,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
353,
313,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29889,
12508,
16655,
6506,
29898,
29890,
29908,
29890,
29915,
613,
289,
29915,
1495,
13,
18884,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
353,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
7503,
29899,
29896,
29962,
13,
18884,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
353,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
718,
289,
29915,
2433,
334,
313,
2435,
29898,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
1273,
29871,
29946,
29897,
13,
18884,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
18884,
1596,
29898,
29890,
29915,
29940,
1164,
4741,
2287,
29968,
16299,
718,
1121,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
13,
9651,
25342,
338,
8758,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29892,
6262,
1125,
13,
18884,
1596,
703,
29979,
29949,
3927,
1159,
13,
18884,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
13,
9651,
565,
313,
1333,
338,
8758,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29892,
6262,
22164,
13,
18884,
1596,
703,
18361,
591,
1207,
372,
1244,
29908,
718,
851,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
876,
13,
18884,
1121,
29918,
29893,
336,
2986,
29928,
1416,
353,
313,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29889,
12508,
16655,
6506,
29898,
29890,
29908,
29890,
29915,
613,
289,
29915,
1495,
13,
18884,
1121,
29918,
29893,
336,
2986,
29928,
1416,
353,
1121,
29918,
29893,
336,
2986,
29928,
1416,
7503,
29899,
29896,
29962,
13,
18884,
1596,
703,
18361,
591,
1207,
372,
1244,
29908,
718,
851,
29898,
2914,
29918,
29893,
336,
2986,
29928,
1416,
876,
13,
18884,
14476,
353,
1121,
29918,
29893,
336,
2986,
29928,
1416,
718,
289,
29915,
2433,
334,
313,
2435,
29898,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29897,
1273,
29871,
29946,
29897,
13,
18884,
1596,
703,
17699,
29908,
718,
851,
29898,
17699,
876,
13,
13,
9651,
1683,
29901,
13,
18884,
1596,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29897,
13,
18884,
1121,
29918,
29893,
336,
2986,
29928,
1416,
353,
1583,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29889,
6506,
29898,
29890,
29908,
29890,
29915,
613,
289,
29915,
1495,
13,
18884,
1121,
29918,
29893,
336,
2986,
29928,
1416,
353,
1121,
29918,
29893,
336,
2986,
29928,
1416,
13,
18884,
14476,
353,
1121,
29918,
29893,
336,
2986,
29928,
1416,
718,
289,
29915,
2433,
334,
313,
2435,
29898,
2914,
29918,
29893,
336,
2986,
29928,
1416,
29897,
1273,
29871,
29946,
29897,
13,
13,
9651,
274,
17929,
9930,
353,
315,
17929,
24183,
580,
13,
9651,
1596,
29898,
17699,
29897,
13,
9651,
1583,
29889,
25950,
353,
1583,
29889,
29883,
17929,
29889,
29909,
267,
6185,
4641,
29923,
6604,
29898,
29890,
29953,
29946,
13808,
29898,
17699,
511,
274,
17929,
9930,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
446,
29895,
29889,
446,
29895,
876,
13,
9651,
413,
1416,
29889,
6312,
29918,
1989,
29898,
5630,
29897,
13,
13,
9651,
736,
1583,
29889,
25950,
13,
13,
4706,
1683,
29901,
13,
9651,
1018,
29901,
13,
18884,
565,
451,
338,
8758,
29898,
5630,
29892,
6262,
1125,
13,
462,
1678,
4800,
353,
4800,
29889,
12508,
580,
13,
18884,
1683,
29901,
13,
462,
1678,
4800,
353,
4800,
13,
13,
18884,
413,
1416,
29889,
26238,
29918,
1989,
29898,
5630,
29897,
13,
18884,
1583,
29889,
29883,
17929,
29889,
5464,
346,
353,
289,
29953,
29946,
13808,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29918,
5464,
346,
29897,
13,
18884,
396,
1596,
703,
12717,
304,
1602,
4641,
316,
29895,
1159,
13,
18884,
1583,
29889,
25950,
353,
1583,
29889,
29883,
17929,
29889,
29909,
267,
6185,
4641,
29923,
6604,
29898,
29890,
29953,
29946,
13808,
29898,
1311,
29889,
2914,
29918,
29893,
336,
2986,
29928,
1416,
511,
1583,
29889,
29883,
17929,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
446,
29895,
29889,
446,
29895,
876,
13,
13,
18884,
413,
1416,
29889,
6312,
29918,
1989,
29898,
5630,
29897,
13,
18884,
736,
1583,
29889,
25950,
13,
9651,
5174,
29901,
13,
18884,
1596,
877,
5372,
650,
756,
16388,
304,
13345,
974,
278,
476,
29923,
29968,
29906,
313,
1989,
20956,
1820,
29897,
1495,
13,
13,
13,
12008,
13,
2220,
304,
2452,
573,
29968,
1416,
29918,
4381,
515,
385,
11472,
4800,
13,
12008,
13,
13,
13,
1753,
2452,
573,
29968,
1416,
29918,
4381,
29898,
5630,
1125,
13,
1678,
274,
17929,
353,
315,
17929,
24183,
580,
13,
1678,
565,
7431,
29898,
29883,
17929,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
5630,
29889,
12508,
22130,
2804,
365,
1430,
29954,
4690,
29918,
9800,
29918,
6059,
29968,
29901,
13,
4706,
1596,
877,
11432,
29958,
6058,
382,
6632,
23338,
29950,
6770,
29911,
2890,
2672,
17687,
1799,
17013,
15842,
5012,
29968,
29892,
14693,
3352,
29871,
29941,
29906,
1495,
13,
1678,
565,
338,
8758,
29898,
5630,
29892,
851,
1125,
13,
4706,
777,
446,
29895,
353,
274,
17929,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
13193,
29898,
5630,
29889,
12508,
22130,
13,
4706,
777,
446,
29895,
353,
274,
17929,
29889,
29909,
267,
8566,
4641,
29923,
6604,
29898,
5630,
29889,
12508,
3285,
777,
446,
29895,
29897,
13,
4706,
413,
353,
476,
29923,
29968,
29898,
2914,
29918,
29893,
336,
2986,
29918,
446,
29895,
29922,
29890,
29953,
29946,
12508,
29898,
5372,
446,
29895,
876,
13,
4706,
413,
29889,
7620,
580,
13,
4706,
736,
413,
13,
13,
1678,
25342,
338,
8758,
29898,
5630,
29892,
6262,
1125,
13,
4706,
777,
446,
29895,
353,
274,
17929,
29889,
29903,
2350,
29906,
29945,
29953,
29898,
13193,
29898,
5630,
29889,
12508,
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] |
tests/test_json_to_mako.py | melexis/json-to-mako | 0 | 186121 | <filename>tests/test_json_to_mako.py
from unittest import TestCase
from mlx.json_to_mako import json_to_mako_wrapper
class TestJsonToMako(TestCase):
def test_help(self):
with self.assertRaises(SystemExit) as ex:
json_to_mako_wrapper(['--help'])
self.assertEqual(0, ex.exception.code)
def test_version(self):
with self.assertRaises(SystemExit) as ex:
json_to_mako_wrapper(['--version'])
self.assertEqual(0, ex.exception.code)
def test_example_single_input(self):
json_to_mako_wrapper(['--input', 'example/family.json',
'--input', 'example/work.json',
'--template', 'example/address-book.mako',
'--output', 'tests/address-book.html'])
def test_example_dual_input(self):
json_to_mako_wrapper(['--input', 'example/family.json',
'--template', 'example/address-book.mako',
'--output', 'tests/address-book.html'])
def test_example_no_input(self):
with self.assertRaises(SystemExit) as ex:
json_to_mako_wrapper(['--template', 'example/address-book.mako',
'--output', 'tests/address-book.html'])
self.assertEqual(2, ex.exception.code)
def test_example_no_template(self):
with self.assertRaises(SystemExit) as ex:
json_to_mako_wrapper(['--input', 'example/family.json',
'--input', 'example/work.json',
'--output', 'tests/address-book.html'])
self.assertEqual(2, ex.exception.code)
def test_example_no_output(self):
with self.assertRaises(SystemExit) as ex:
json_to_mako_wrapper(['--input', 'example/family.json',
'--input', 'example/work.json',
'--template', 'example/address-book.mako'])
self.assertEqual(2, ex.exception.code)
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429,
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11739,
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401,
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13,
2
] |
setup.py | goude/thxtime | 0 | 149857 | <filename>setup.py
from setuptools import setup, find_packages
setup(
name="thxtime",
version="2.0.0",
packages=find_packages(),
)
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mcml_convolution.py | harveyiliu/mcml-photon-scattering-python | 3 | 79345 | <filename>mcml_convolution.py
import numpy as np
from scipy import integrate
import mcml_photon_scattering
class Beam:
"""Beam class - incident light beam class
Parameters to describe a photon beam.
Pencil: infinitely narrow beam. This is default for the
beam from the mcml output.
Flat: Flat beam with radius R.
Gaussian: Gaussian with 1/e2 radius R.
Others: general beam described by points with interpolation.
Class instance variables:
type - incident beam type, FLAT or GAUSSIAN
P - total beam power/energy [W or J]
R - beam radius, defined as 1/e^2 for Gaussian beam [cm]
Methods:
"""
def __init__(self):
self.type = None
self.P = 0
self.R = 0
class Node:
"""Node class - node link list binary tree class
Data structures for the binary tree used to store part of
the integrand evaluation.
Class instance variables:
x - x grid node position
y - y grid node position
left - left node pointer
right - right node pointer
Methods:
"""
def __init__(self):
self.x = None
self.y = None
self.left = None
self.right = None
def fill_node(x, y):
l = Node()
l.x = x
l.y = y
return l
def search_node(tree, x):
l = tree
found = False
while (l != None and found == False):
if x < l.x:
l = l.left
elif x > l.x:
l = l.right
else:
found = True
return l
def insert_node(tree, x, y):
l1 = None
l2 = tree
while l2 != None:
l1 = l2
if x < l2.x:
l2 = l2.left
else:
l2 = l2.right
if l1 == None: # Empty tree.
tree = fill_node(x, y)
elif x < l1.x:
l1.left = fill_node(x, y)
else:
l1.right = fill_node(x, y)
class ConvVar:
"""ConvVar class - convoluation variables class
A global structure to pass the current coordinate of the
physical quantities being evaluated and the pointers of the
input and output parameters to the integration function.
Class instance variables:
r - r position
iz - iz index
ia - ia index
tree - A tree to store ITheta() & ExpBessI0().
Methods:
"""
def __init__(self):
self.r = 0
self.iz = 0
self.ia = 0
self.tree = None # A tree to store ITheta() & ExpBessI0().
class ConvInput:
"""ConvInput class - beam convolution input class
Input parameters for each independent run.
z and r are for the cylindrical coordinate system. [cm]
a is for the angle alpha between the photon exiting
direction and the surface normal. [radian]
The grid line separations in z, r, and alpha
directions are dz, dr, and da respectively. The numbers
of grid lines in z, r, and alpha directions are
nz, nr, and na respectively.
The member layerspecs will point to an array of
structures which store parameters of each layer.
This array has (number_layers + 2) elements. One
element is for a layer.
The layers 0 and (num_layers + 1) are for top ambient
medium and the bottom ambient medium respectively.
For convolution, the grid line separations in z, and alpha
directions are still dz, and da respectively. The numbers
of grid lines in z, and alpha directions are still
nz, and na respectively. However, the grid line separation
and the number of grid lines in r direction are drc and
nrc respectively.
Class instance variables:
beam - incident beam class instance object
drc - convolution r grid separation.[cm]
nrc - convolution array range 0..nrc-1.
eps - relative error in convolution
Methods:
"""
def __init__(self, mcmlModel, beamType = 'FLAT', P = 1, R = 0):
self.beam = Beam()
if beamType.lower() == 'FLAT'.lower():
self.beam.type = 'FLAT' # incident beam of finite size
elif beamType.lower() == 'GAUSSIAN'.lower():
self.beam.type = 'GAUSSIAN'
else:
self.beam.type = 'FLAT'
self.mcmlModel = mcmlModel
self.convVar = ConvVar()
self.beam.P = P
self.beam.R = np.maximum(R, 1e-5) # minimum radius required
minR = 1.2*(R + mcmlModel.nr*mcmlModel.dr)
self.drc = np.maximum(mcmlModel.dr, minR/200)
self.nrc = int(minR/self.drc)
class MCMLConv(ConvInput):
"""MCMLConv class - multi-layered photon scattering model beam convolution
inherits from ConvInput beam setup
Structures for scored physical quantities
from mcml and to be convolved for photon
beams of finite size. Therefore, "Out"
here means the output of both mcml and conv.
The member allocated is used to keep the status
of the arrays. It is set to 1 if all the arrays
are allocated and assigned values. It is set to
0 otherwise.
z and r represent z and r coordinates of the
cylindrical coordinate system. [cm]
a is the angle alpha between the photon exiting
direction and the normal to the surfaces. [radian]
See comments of the InputStruct.
See manual for the physcial quantities.
Class instance variables:
Rd_rac - convolved data. [J/(cm2 sr)]
Rd_rc - 1D radial distribution of diffuse reflectance [J/cm2]
A_rzc - 2D probability density in turbid media over r & z [J/cm3]
Tt_rac - 2D distribution of total transmittance [J/(cm2 sr)]
Tt_rc - 1D radial distribution of transmittance [J/cm2]
Methods:
"""
def __init__(self, mcmlModel, beamType = 'FLAT', P = 1, R = 0):
# extend the ConvInput base class instance variables
ConvInput.__init__(self, mcmlModel, beamType, P, R)
# initialize the model grid arrays
self.Rd_rac = np.matrix(np.zeros((self.nrc, self.mcmlModel.na)))
self.Rd_rc = np.zeros(self.nrc)
self.A_rzc = np.matrix(np.zeros((self.nrc, self.mcmlModel.nz)))
self.Tt_rac = np.matrix(np.zeros((self.nrc, self.mcmlModel.na)))
self.Tt_rc = np.zeros(self.nrc)
self.F_rzc = np.matrix(np.zeros((self.nrc, self.mcmlModel.nz)))
def run_conv(self):
self.conv_Rd_ra()
self.conv_Rd_r()
self.conv_A_rz()
self.conv_Tt_ra()
self.conv_Tt_r()
self.conv_A2F()
def conv_Rd_ra(self):
P = self.beam.P
R = self.beam.R
for irc in range(self.nrc):
rc = (irc + 0.5)*self.drc
self.convVar.r = rc
self.convVar.tree = None # init the tree
for ia in range(self.mcmlModel.na):
self.convVar.ia = ia
if self.beam.type.lower() == 'FLAT'.lower():
self.Rd_rac[irc, ia] = 2*P/(R*R) \
*flat_integration(Rd_ra_FG_integrand, self)
else : # Gaussian
self.Rd_rac[irc, ia] = 4*P/(R*R) \
*Gauss_integration(Rd_ra_FG_integrand, self)
def conv_Rd_r(self):
P = self.beam.P
R = self.beam.R
for irc in range(self.nrc):
rc = (irc + 0.5)*self.drc
self.convVar.r = rc
if self.beam.type.lower() == 'FLAT'.lower():
self.Rd_rc[irc] = 2*P/(R*R) \
*flat_integration(Rd_r_FG_integrand, self)
else : # Gaussian
self.Rd_rc[irc] = 4*P/(R*R) \
*Gauss_integration(Rd_r_FG_integrand, self)
def conv_A_rz(self):
P = self.beam.P
R = self.beam.R
for irc in range(self.nrc):
rc = (irc + 0.5)*self.drc
self.convVar.r = rc
self.convVar.tree = None # init the tree
for iz in range(self.mcmlModel.nz):
self.convVar.iz = iz
if self.beam.type.lower() == 'FLAT'.lower():
self.A_rzc[irc, iz] = 2*P/(R*R) \
*flat_integration(A_rz_FG_integrand, self)
else: # Gaussian
self.A_rzc[irc, iz] = 4*P/(R*R) \
*Gauss_integration(A_rz_FG_integrand, self)
def conv_Tt_ra(self):
P = self.beam.P
R = self.beam.R
for irc in range(self.nrc):
rc = (irc + 0.5)*self.drc
self.convVar.r = rc
self.convVar.tree = None # init the tree
for ia in range(self.mcmlModel.na):
self.convVar.ia = ia
if self.beam.type.lower() == 'FLAT'.lower():
self.Tt_rac[irc, ia] = 2*P/(R*R) \
*flat_integration(Tt_ra_FG_integrand, self)
else: # Gaussian
self.Tt_rac[irc, ia] = 4*P/(R*R) \
*Gauss_integration(Tt_ra_FG_integrand, self)
def conv_Tt_r(self):
P = self.beam.P
R = self.beam.R
for irc in range(self.nrc):
rc = (irc + 0.5)*self.drc
self.convVar.r = rc
if self.beam.type.lower() == 'FLAT'.lower():
self.Tt_rc[irc] = 2*P/(R*R) \
*flat_integration(Tt_r_FG_integrand, self)
else : # Gaussian
self.Tt_rc[irc] = 4*P/(R*R) \
*Gauss_integration(Tt_r_FG_integrand, self)
def conv_A2F(self):
nz = self.mcmlModel.nz
for irc in range(self.nrc):
for iz in range(nz):
mua = self.mcmlModel.get_mua_at_iz(iz)
if (mua > 0.0):
self.F_rzc[irc, iz] = self.A_rzc[irc, iz]/mua # F in J/cm2
def center_half_max_depth(self):
nz = self.mcmlModel.nz
dz = self.mcmlModel.dz
depth = 0
for iz in range(nz):
if self.F_rzc[0, iz] <= 0.5*self.F_rzc[0, 0]:
depth = (iz + 0.5)*dz
break
return depth
def surface_half_max_width(self):
width = 0
for irc in range(self.nrc):
if self.F_rzc[irc, 0] <= 0.5*self.F_rzc[0, 0]:
width = 2*(irc + 0.5)*self.drc
break
return width
def I_theta(r, r2, R):
if R >= (r + r2):
temp = 1
elif np.fabs(r - r2) <= R:
temp = (r*r + r2*r2 - R*R)/(2*r*r2)
if np.fabs(temp) > 1:
temp = np.sign(temp)
temp = np.arccos(temp)/np.pi
else : # R < fabs(r-r2)
temp = 0
return temp
def modified_Bess_I0(x):
# Modified Bessel function exp(-x) I0(x), for x >=0.
# We modified from the original bessi0(). Instead of
# I0(x) itself, it returns I0(x) exp(-x).
ax = np.fabs(x)
if ax < 3.75:
y = x/3.75
y *= y
ans = np.exp(-ax)*(1.0 + y*(3.5156229 + y*(3.0899424 + y*(1.2067492 \
+ y*(0.2659732 + y*(0.360768e-1 + y*0.45813e-2))))))
else:
y = 3.75/ax
ans = (1/(ax**0.5))*(0.39894228 + y*(0.1328592e-1 \
+ y*(0.225319e-2 + y*(-0.157565e-2 + y*(0.916281e-2 \
+ y*(-0.2057706e-1 + y*(0.2635537e-1 + y*(-0.1647633e-1 \
+ y * 0.392377e-2))))))))
return ans
def exp_Bess_I0(r, r2, R):
_RR = 1/(R*R)
x = 4*r*r2*_RR
y = 2*(r2*r2 + r*r)*_RR
expbess = np.exp(-y + x)*modified_Bess_I0(x)
return expbess
def RT_ra_interp(r2, RT_ra, mcmlConv):
# Interpolate for the arrays Rd_ra[] or Tt_ra[].
nr = mcmlConv.mcmlModel.nr
ir2 = r2/mcmlConv.mcmlModel.dr
ia = mcmlConv.convVar.ia
if nr < 3:
RT_at_r2 = RT_ra[0, ia]
elif ir2 < (nr - 1.5): # interpolation
ir2lo = np.maximum(0, int(ir2 - 0.5)) # truncation
RT_lo = RT_ra[ir2lo, ia]
RT_hi = RT_ra[ir2lo + 1, ia]
RT_at_r2 = RT_lo + (RT_hi - RT_lo)*(ir2 - ir2lo - 0.5)
else: # extrapolation
ir2lo = nr - 3
RT_lo = RT_ra[ir2lo, ia]
RT_hi = RT_ra[ir2lo + 1, ia]
if RT_lo >= RT_hi: # Noise test
RT_at_r2 = RT_lo + (RT_hi - RT_lo)*(ir2 - ir2lo - 0.5)
else:
RT_at_r2 = 0.0
return np.maximum(0, RT_at_r2)
def RT_r_interp(r2, RT_r, mcmlConv):
# Interpolate for the arrays Rd_r[] or Tt_r[].
nr = mcmlConv.mcmlModel.nr
ir2 = r2/mcmlConv.mcmlModel.dr
if nr < 3:
RT_at_r2 = RT_r[0]
elif ir2 < (nr - 1.5): # interpolation
ir2lo = np.maximum(0, int(ir2 - 0.5)) # truncation
RT_lo = RT_r[ir2lo]
RT_hi = RT_r[ir2lo + 1]
RT_at_r2 = RT_lo + (RT_hi - RT_lo)*(ir2 - ir2lo - 0.5)
else: # extrapolation
ir2lo = nr - 3
RT_lo = RT_r[ir2lo]
RT_hi = RT_r[ir2lo + 1]
if RT_lo >= RT_hi: # Noise test
RT_at_r2 = RT_lo + (RT_hi - RT_lo)*(ir2 - ir2lo - 0.5)
else:
RT_at_r2 = 0.0
return np.maximum(0, RT_at_r2)
def A_rz_interp(r2, mcmlConv):
# Interpolate for the arrays A_rz[]
A_rz = mcmlConv.mcmlModel.A_rz
nr = mcmlConv.mcmlModel.nr
ir2 = r2/mcmlConv.mcmlModel.dr
iz = mcmlConv.convVar.iz
if nr < 3:
A_at_r2 = A_rz[0, iz]
elif ir2 < (nr - 1.5): # interpolation
ir2lo = np.maximum(0, int(ir2 - 0.5)) # truncation
A_lo = A_rz[ir2lo, iz]
A_hi = A_rz[ir2lo + 1, iz]
A_at_r2 = A_lo + (A_hi - A_lo)*(ir2 - ir2lo - 0.5)
else: # extrapolation
ir2lo = nr - 3
A_lo = A_rz[ir2lo, iz]
A_hi = A_rz[ir2lo + 1, iz]
if A_lo >= A_hi: # Noise test
A_at_r2 = A_lo + (A_hi - A_lo)*(ir2 - ir2lo - 0.5)
else:
A_at_r2 = 0.0
return np.maximum(0, A_at_r2)
def Rd_ra_FG_integrand(r2, mcmlConv):
# Convolution integrand for either flat or gaussian beams.
# See comments for A_rzFGIntegrand().
# r" in the integration.
RT_ra = mcmlConv.mcmlModel.Rd_ra
Rd_at_r2 = RT_ra_interp(r2, RT_ra, mcmlConv)
R = mcmlConv.beam.R
r = mcmlConv.convVar.r
tree = mcmlConv.convVar.tree
link = search_node(tree, r2)
if link != None: # f in tree.
f = link.y
else:
if mcmlConv.beam.type.lower() == 'FLAT'.lower():
f = I_theta(r, r2, R)
else: # Gaussian
f = exp_Bess_I0(r, r2, R)
insert_node(tree, r2, f)
f *= Rd_at_r2*r2
return f
def Rd_r_FG_integrand(r2, mcmlConv):
# Convolution integrand for either flat or gaussian beams.
# See comments for A_rzFGIntegrand().
# r" in the integration
RT_r = mcmlConv.mcmlModel.Rd_r
Rd_at_r2 = RT_r_interp(r2, RT_r, mcmlConv)
R = mcmlConv.beam.R
r = mcmlConv.convVar.r
if mcmlConv.beam.type.lower() == 'FLAT'.lower():
f = Rd_at_r2*I_theta(r, r2, R)*r2
else : # Gaussian
f = Rd_at_r2*exp_Bess_I0(r, r2, R)*r2
return f
def A_rz_FG_integrand(r2, mcmlConv):
# Convolution integrand for either flat or gaussian beams.
# Return the integrand for the convolution integral.
# r2 is the r" in the formula shown in the manual.
# When r2 is in the range of recorded array, interpolation
# is used to evaluate the diffuse reflectance at r2.
# Note that since the last grid elements collect all the
# photon weight that falls beyond the grid system, we should
# avoid using them in the convolution.
# r" in the integration
A_at_r2 = A_rz_interp(r2, mcmlConv)
R = mcmlConv.beam.R
r = mcmlConv.convVar.r
tree = mcmlConv.convVar.tree
link = search_node(tree, r2)
if link != None: # f in tree
f = link.y
else:
if mcmlConv.beam.type.lower() == 'FLAT'.lower():
f = I_theta(r, r2, R)
else: # Gaussian
f = exp_Bess_I0(r, r2, R)
insert_node(tree, r2, f)
f *= A_at_r2*r2
return f
def Tt_ra_FG_integrand(r2, mcmlConv):
# Convolution integrand for either flat or gaussian beams.
# See comments for A_rzFGIntegrand().
# r" in the integration.
TT_ra = mcmlConv.mcmlModel.Tt_ra
Tt_at_r2 = RT_ra_interp(r2, TT_ra, mcmlConv)
R = mcmlConv.beam.R
r = mcmlConv.convVar.r
tree = mcmlConv.convVar.tree
link = search_node(tree, r2)
if link != None: # f in tree
f = link.y
else:
if mcmlConv.beam.type.lower() == 'FLAT'.lower():
f = I_theta(r, r2, R)
else : # Gaussian
f = exp_Bess_I0(r, r2, R)
insert_node(tree, r2, f)
f *= Tt_at_r2*r2
return f
def Tt_r_FG_integrand(r2, mcmlConv):
# Convolution integrand for either flat or gaussian beams.
# See comments for A_rzFGIntegrand().
# r" in the integration
TT_r = mcmlConv.mcmlModel.Tt_r
Tt_at_r2 = RT_r_interp(r2, TT_r, mcmlConv)
R = mcmlConv.beam.R
r = mcmlConv.convVar.r
if mcmlConv.beam.type.lower() == 'FLAT'.lower():
f = Tt_at_r2*I_theta(r, r2, R)*r2
else : # Gaussian
f = Tt_at_r2*exp_Bess_I0(r, r2, R)*r2
return f
def flat_integration(func, mcmlConv):
rc = mcmlConv.convVar.r
R = mcmlConv.beam.R
b_max = (mcmlConv.mcmlModel.nr - 0.5)*mcmlConv.mcmlModel.dr
a = np.maximum(0, rc - R)
b = np.minimum(b_max, rc + R)
if (a >= b):
return 0
else:
return integrate.quad(func, a, b, args=(mcmlConv,), \
epsabs=1.0e-4, epsrel=1.0e-5, limit=500)[0]
def Gauss_integration(func, mcmlConv):
# Used by convolution over Gaussian beam. Ignore the value
# beyond GAUSSLIMIT radius.
GAUSSLIMIT = 4
rc = mcmlConv.convVar.r
R = mcmlConv.beam.R
b_max = (mcmlConv.mcmlModel.nr - 0.5)*mcmlConv.mcmlModel.dr
a = np.maximum(0, (rc - GAUSSLIMIT * R))
b = np.minimum(b_max, (rc + GAUSSLIMIT * R))
if (a >= b):
return 0
else:
return integrate.quad(func, a, b, args=(mcmlConv,), \
epsabs=1.0e-4, epsrel=1.0e-5, limit=500)[0]
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data/studio21_generated/introductory/3172/starter_code.py | vijaykumawat256/Prompt-Summarization | 0 | 75442 | <filename>data/studio21_generated/introductory/3172/starter_code.py
def parse_fen(string):
| [
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] |
tests/rest_t/app_t/test_security.py | maxfischer2781/tardis | 4 | 104728 | from tardis.exceptions.tardisexceptions import TardisError
from tardis.rest.app.security import (
create_access_token,
check_authorization,
check_authentication,
get_algorithm,
get_secret_key,
get_user,
hash_password,
TokenData,
)
from tardis.utilities.attributedict import AttributeDict
from fastapi import HTTPException, status
from fastapi.security import SecurityScopes
from jose import JWTError
from datetime import datetime, timedelta
from unittest import TestCase
from unittest.mock import patch
class TestSecurity(TestCase):
mock_config_patcher = None
@classmethod
def setUpClass(cls) -> None:
cls.mock_config_patcher = patch("tardis.rest.app.security.Configuration")
cls.mock_config = cls.mock_config_patcher.start()
@classmethod
def tearDownClass(cls) -> None:
cls.mock_config_patcher.stop()
def setUp(self) -> None:
self.secret_key = (
"689e7af69a70ad0d97f771371738be00452e81e128a876491c1d373dfbcca949"
)
self.algorithm = "HS256"
self.infinite_resources_get_token = "<KEY>" # noqa B950
self.limited_resources_get_token = "<KEY>" # noqa B950
self.infinite_resources_get_update_token = "<KEY>" # noqa B950
def mocked_get_user(user_name):
if user_name == "test":
return AttributeDict(
user_name="test",
hashed_password="<PASSWORD>", # noqa B509
scopes=["resources:get"],
)
return None
config = self.mock_config.return_value
config.Services.restapi.secret_key = self.secret_key
config.Services.restapi.algorithm = self.algorithm
config.Services.restapi.get_user.side_effect = mocked_get_user
@staticmethod
def clear_lru_cache():
get_algorithm.cache_clear()
get_secret_key.cache_clear()
get_user.cache_clear()
@patch("tardis.rest.app.security.datetime")
def test_create_access_token(self, mocked_datetime):
self.clear_lru_cache()
token = create_access_token(user_name="test", scopes=["resources:get"])
self.assertEqual(token, self.infinite_resources_get_token)
self.clear_lru_cache()
token = create_access_token(
user_name="test",
scopes=["resources:get"],
secret_key="c2ac5e498f6287c58fa941d0d2cfaf2dc271762a7ba03dcfc3ceb91bb1895d05", # noqa B950
algorithm=self.algorithm,
)
self.assertEqual(
token,
"<KEY>", # noqa B950
)
self.clear_lru_cache()
mocked_datetime.utcnow.return_value = datetime.utcfromtimestamp(0)
token = create_access_token(
user_name="test",
scopes=["resources:get"],
expires_delta=timedelta(minutes=15),
)
self.assertEqual(token, self.limited_resources_get_token)
self.clear_lru_cache()
token = create_access_token(
user_name="test", scopes=["resources:get", "resources:put"]
)
self.assertEqual(token, self.infinite_resources_get_update_token)
def test_check_authorization(self):
self.clear_lru_cache()
security_scopes = SecurityScopes(["resources:get"])
token_data = check_authorization(
security_scopes, self.infinite_resources_get_token
)
self.assertEqual(
token_data, TokenData(scopes=security_scopes.scopes, user_name="test")
)
security_scopes = SecurityScopes(["resources:put"])
with self.assertRaises(HTTPException) as he:
check_authorization(security_scopes, self.infinite_resources_get_token)
self.assertEqual(he.exception.status_code, status.HTTP_401_UNAUTHORIZED)
self.assertEqual(he.exception.detail, "Not enough permissions")
token_data = check_authorization(
security_scopes, self.infinite_resources_get_update_token
)
self.assertEqual(
token_data,
TokenData(scopes=["resources:get", "resources:put"], user_name="test"),
)
security_scopes = SecurityScopes()
check_authorization(security_scopes, self.infinite_resources_get_token)
with self.assertRaises(HTTPException) as he:
check_authorization(security_scopes, "1234567890abdcef")
self.assertEqual(he.exception.status_code, status.HTTP_401_UNAUTHORIZED)
self.assertEqual(he.exception.detail, "Could not validate credentials")
@patch("tardis.rest.app.security.jwt")
def test_check_authorization_jwt_error(self, mocked_jwt):
mocked_jwt.decode.side_effect = JWTError
with self.assertRaises(HTTPException) as he:
check_authorization(SecurityScopes(), self.infinite_resources_get_token)
self.assertEqual(he.exception.status_code, status.HTTP_401_UNAUTHORIZED)
self.assertEqual(he.exception.detail, "Could not validate credentials")
mocked_jwt.decode.side_effect = None
def test_check_authentication(self):
self.clear_lru_cache()
with self.assertRaises(HTTPException) as he:
check_authentication(user_name="fails", password="<PASSWORD>")
self.assertEqual(he.exception.status_code, status.HTTP_400_BAD_REQUEST)
self.assertEqual(he.exception.detail, "Incorrect username or password")
self.clear_lru_cache()
with self.assertRaises(HTTPException) as he:
check_authentication(user_name="test", password="<PASSWORD>")
self.assertEqual(he.exception.status_code, status.HTTP_400_BAD_REQUEST)
self.assertEqual(he.exception.detail, "Incorrect username or password")
self.clear_lru_cache()
self.assertEqual(
check_authentication(user_name="test", password="<PASSWORD>"),
{
"hashed_password": <PASSWORD>", # noqa B509
"scopes": ["resources:get"],
"user_name": "test",
},
)
def test_get_algorithm(self):
self.clear_lru_cache()
self.assertEqual(get_algorithm(), self.algorithm)
self.clear_lru_cache()
self.mock_config.side_effect = AttributeError
with self.assertRaises(TardisError):
get_algorithm()
self.mock_config.side_effect = None
def test_get_secret_key(self):
self.clear_lru_cache()
self.assertEqual(get_secret_key(), self.secret_key)
self.clear_lru_cache()
self.mock_config.side_effect = AttributeError
with self.assertRaises(TardisError):
get_secret_key()
self.mock_config.side_effect = None
def test_get_user(self):
self.clear_lru_cache()
self.assertEqual(
get_user("test"),
{
"hashed_password": <PASSWORD>", # noqa B509
"scopes": ["resources:get"],
"user_name": "test",
},
)
self.clear_lru_cache()
self.mock_config.side_effect = AttributeError
with self.assertRaises(TardisError):
get_user("test")
self.mock_config.side_effect = None
@patch("tardis.rest.app.security.gensalt")
def test_hash_password(self, mocked_gensalt):
mocked_gensalt.return_value = b"$2b$12$aQ1hv6.1AJSfLL/u4ttm7u"
self.assertEqual(
hash_password("<PASSWORD>"),
b"$2b$12$aQ1hv6.1AJSfLL/u4ttm7uyhV2r1fDdzUw2719FE7Fznq9w6EK1xe",
)
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29918,
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13,
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29893,
29953,
29923,
29968,
29896,
17115,
613,
13,
4706,
1723,
13,
2
] |
Codeup/6068.py | lkc263/Algorithm_Study_Python | 0 | 171366 |
score = int(input())
if score >= 90:
print("A")
elif score >= 70:
print("B")
elif score >= 40:
print("C")
else:
print("D") | [
1,
29871,
13,
13628,
353,
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13,
13,
361,
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13,
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13,
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13,
23681,
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29900,
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13,
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703,
29907,
1159,
13,
2870,
29901,
13,
1678,
1596,
703,
29928,
1159,
2
] |
ambari-server/src/test/python/stacks/test_ambari_configuration.py | thaibui/ambari | 0 | 1616463 | """
Licensed to the Apache Software Foundation (ASF) under one
or more contributor license agreements. See the NOTICE file
distributed with this work for additional information
regarding copyright ownership. The ASF licenses this file
to you 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 os
from mock.mock import MagicMock, patch
from unittest import TestCase
# Mock classes for reading from a file
class MagicFile(object):
def __init__(self, data):
self.data = data
def read(self):
return self.data
def __exit__(self, exc_type, exc_val, exc_tb):
pass
def __enter__(self):
return self
pass
class TestAmbariConfiguration(TestCase):
def setUp(self):
import imp
self.test_directory = os.path.dirname(os.path.abspath(__file__))
relative_path = '../../../main/resources/stacks/ambari_configuration.py'
ambari_configuration_path = os.path.abspath(os.path.join(self.test_directory, relative_path))
class_name = 'AmbariConfiguration'
with open(ambari_configuration_path, 'rb') as fp:
ambari_configuration_impl = imp.load_module('ambari_configuration', fp,
ambari_configuration_path,
('.py', 'rb', imp.PY_SOURCE))
self.ambari_configuration_class = getattr(ambari_configuration_impl, class_name)
def testMissingData(self):
ambari_configuration = self.ambari_configuration_class('{}')
self.assertIsNone(ambari_configuration.get_ambari_server_configuration())
self.assertIsNone(ambari_configuration.get_ambari_server_properties())
def testMissingSSOConfiguration(self):
services_json = {
"ambari-server-configuration": {
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNone(ambari_configuration.get_ambari_sso_configuration())
self.assertIsNone(ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.property"))
self.assertFalse(ambari_configuration.should_enable_sso("AMBARI"))
def testMissingAmbariProperties(self):
services_json = {
"ambari-server-configuration": {
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
ambari_sso_details = ambari_configuration.get_ambari_sso_details()
self.assertFalse(ambari_sso_details.is_jwt_enabled())
self.assertIsNone(ambari_sso_details.get_jwt_audiences())
self.assertIsNone(ambari_sso_details.get_jwt_cookie_name())
self.assertIsNone(ambari_sso_details.get_jwt_provider_url())
self.assertIsNone(ambari_sso_details.get_jwt_public_key_file())
self.assertIsNone(ambari_sso_details.get_jwt_public_key())
def testAmbariSSOConfigurationNotManagingServices(self):
services_json = {
"ambari-server-configuration": {
"sso-configuration": {
"ambari.sso.enabled_services": "AMBARI"
}
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNotNone(ambari_configuration.get_ambari_sso_configuration())
self.assertEquals("AMBARI", ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.enabled_services"))
self.assertFalse(ambari_configuration.is_managing_services())
self.assertFalse(ambari_configuration.should_enable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_disable_sso("AMBARI"))
services_json = {
"ambari-server-configuration": {
"sso-configuration": {
"ambari.sso.manage_services" : "false",
"ambari.sso.enabled_services" : "AMBARI, RANGER"
}
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNotNone(ambari_configuration.get_ambari_sso_configuration())
self.assertEquals("AMBARI, RANGER", ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.enabled_services"))
self.assertFalse(ambari_configuration.is_managing_services())
self.assertFalse(ambari_configuration.should_enable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_disable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_enable_sso("RANGER"))
self.assertFalse(ambari_configuration.should_disable_sso("RANGER"))
services_json = {
"ambari-server-configuration": {
"sso-configuration": {
"ambari.sso.manage_services" : "false",
"ambari.sso.enabled_services" : "*"
}
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNotNone(ambari_configuration.get_ambari_sso_configuration())
self.assertEquals("*", ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.enabled_services"))
self.assertFalse(ambari_configuration.is_managing_services())
self.assertFalse(ambari_configuration.should_enable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_disable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_enable_sso("RANGER"))
self.assertFalse(ambari_configuration.should_disable_sso("RANGER"))
def testAmbariSSOConfigurationManagingServices(self):
services_json = {
"ambari-server-configuration": {
"sso-configuration": {
"ambari.sso.manage_services" : "true",
"ambari.sso.enabled_services": "AMBARI"
}
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNotNone(ambari_configuration.get_ambari_sso_configuration())
self.assertEquals("AMBARI", ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.enabled_services"))
self.assertTrue(ambari_configuration.is_managing_services())
self.assertTrue(ambari_configuration.should_enable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_disable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_enable_sso("RANGER"))
self.assertTrue(ambari_configuration.should_disable_sso("RANGER"))
services_json = {
"ambari-server-configuration": {
"sso-configuration": {
"ambari.sso.manage_services" : "true",
"ambari.sso.enabled_services" : "AMBARI, RANGER"
}
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNotNone(ambari_configuration.get_ambari_sso_configuration())
self.assertEquals("AMBARI, RANGER", ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.enabled_services"))
self.assertTrue(ambari_configuration.is_managing_services())
self.assertTrue(ambari_configuration.should_enable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_disable_sso("AMBARI"))
self.assertTrue(ambari_configuration.should_enable_sso("RANGER"))
self.assertFalse(ambari_configuration.should_disable_sso("RANGER"))
services_json = {
"ambari-server-configuration": {
"sso-configuration": {
"ambari.sso.manage_services" : "true",
"ambari.sso.enabled_services" : "*"
}
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
self.assertIsNotNone(ambari_configuration.get_ambari_sso_configuration())
self.assertEquals("*", ambari_configuration.get_ambari_sso_configuration_value("ambari.sso.enabled_services"))
self.assertTrue(ambari_configuration.is_managing_services())
self.assertTrue(ambari_configuration.should_enable_sso("AMBARI"))
self.assertFalse(ambari_configuration.should_disable_sso("AMBARI"))
self.assertTrue(ambari_configuration.should_enable_sso("RANGER"))
self.assertFalse(ambari_configuration.should_disable_sso("RANGER"))
def testAmbariJWTProperties(self):
services_json = {
"ambari-server-properties": {
"authentication.jwt.publicKey": "/etc/ambari-server/conf/jwt-cert.pem",
"authentication.jwt.enabled": "true",
"authentication.jwt.providerUrl": "https://knox.ambari.apache.org",
"authentication.jwt.cookieName": "hadoop-jwt",
"authentication.jwt.audiences": ""
},
"ambari-server-configuration": {
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
ambari_sso_details = ambari_configuration.get_ambari_sso_details()
self.assertTrue(ambari_sso_details.is_jwt_enabled())
self.assertEquals('', ambari_sso_details.get_jwt_audiences())
self.assertEquals('hadoop-jwt', ambari_sso_details.get_jwt_cookie_name())
self.assertEquals('https://knox.ambari.apache.org', ambari_sso_details.get_jwt_provider_url())
self.assertEquals('/etc/ambari-server/conf/jwt-cert.pem', ambari_sso_details.get_jwt_public_key_file())
self.assertIsNone(ambari_sso_details.get_jwt_public_key()) # This is none since the file does not exist for unit tests.
@patch("os.path.isfile", new=MagicMock(return_value=True))
@patch('__builtin__.open')
def testReadCertFileWithHeaderAndFooter(self, open_mock):
mock_file = MagicFile(
'-----BEGIN CERTIFICATE-----\n'
'MIIE3DCCA8SgAwIBAgIJAKfbOMmFyOlNMA0GCSqGSIb3DQEBBQUAMIGkMQswCQYD\n'
'................................................................\n'
'dXRpbmcxFzAVBgNVBAMTDmNsb3VkYnJlYWstcmdsMSUwIwYJKoZIhvcNAQkBFhZy\n'
'-----END CERTIFICATE-----\n')
open_mock.side_effect = [mock_file, mock_file, mock_file, mock_file]
services_json = {
"ambari-server-properties": {
"authentication.jwt.publicKey": "/etc/ambari-server/conf/jwt-cert.pem",
"authentication.jwt.enabled": "true",
"authentication.jwt.providerUrl": "https://knox.ambari.apache.org",
"authentication.jwt.cookieName": "hadoop-jwt",
"authentication.jwt.audiences": ""
},
"ambari-server-configuration": {
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
ambari_sso_details = ambari_configuration.get_ambari_sso_details()
self.assertEquals('-----BEGIN CERTIFICATE-----\n'
'MIIE3DCCA8SgAwIBAgIJAKfbOMmFyOlNMA0GCSqGSIb3DQEBBQUAMIGkMQswCQYD\n'
'................................................................\n'
'dXRpbmcxFzAVBgNVBAMTDmNsb3VkYnJlYWstcmdsMSUwIwYJKoZIhvcNAQkBFhZy\n'
'-----END CERTIFICATE-----',
ambari_sso_details.get_jwt_public_key(True, False))
self.assertEquals('-----BEGIN CERTIFICATE-----'
'MIIE3DCCA8SgAwIBAgIJAKfbOMmFyOlNMA0GCSqGSIb3DQEBBQUAMIGkMQswCQYD'
'................................................................'
'<KEY>'
'-----END CERTIFICATE-----',
ambari_sso_details.get_jwt_public_key(True, True))
self.assertEquals('<KEY>'
'................................................................\n'
'<KEY>',
ambari_sso_details.get_jwt_public_key(False, False))
self.assertEquals('<KEY>'
'................................................................'
'<KEY>',
ambari_sso_details.get_jwt_public_key(False, True))
@patch("os.path.isfile", new=MagicMock(return_value=True))
@patch('__builtin__.open')
def testReadCertFileWithoutHeaderAndFooter(self, open_mock):
mock_file = MagicFile(
'<KEY>'
'................................................................\n'
'dXRpbmcxFzAVBgNVBAMTDmNsb3VkYnJlYWstcmdsMSUwIwYJKoZIhvcNAQkBFhZy\n')
open_mock.side_effect = [mock_file, mock_file, mock_file, mock_file]
services_json = {
"ambari-server-properties": {
"authentication.jwt.publicKey": "/etc/ambari-server/conf/jwt-cert.pem",
"authentication.jwt.enabled": "true",
"authentication.jwt.providerUrl": "https://knox.ambari.apache.org",
"authentication.jwt.cookieName": "hadoop-jwt",
"authentication.jwt.audiences": ""
},
"ambari-server-configuration": {
}
}
ambari_configuration = self.ambari_configuration_class(services_json)
ambari_sso_details = ambari_configuration.get_ambari_sso_details()
self.assertEquals('-----BEGIN CERTIFICATE-----\n'
'<KEY>'
'................................................................\n'
'<KEY>'
'-----END CERTIFICATE-----',
ambari_sso_details.get_jwt_public_key(True, False))
self.assertEquals('-----BEGIN CERTIFICATE-----'
'<KEY>'
'................................................................'
'<KEY>'
'-----END CERTIFICATE-----',
ambari_sso_details.get_jwt_public_key(True, True))
self.assertEquals('<KEY>'
'................................................................\n'
'<KEY>',
ambari_sso_details.get_jwt_public_key(False, False))
self.assertEquals('<KEY>'
'................................................................'
'<KEY>',
ambari_sso_details.get_jwt_public_key(False, True))
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] |
eclcli/network/v2/fic_service.py | hanasuke/eclcli | 32 | 1605159 | <reponame>hanasuke/eclcli
from eclcli.common import command
from eclcli.common import utils
from ..networkclient.common import utils as to_obj
class ListFICService(command.Lister):
def get_parser(self, prog_name):
parser = super(ListFICService, self).get_parser(prog_name)
return parser
def take_action(self, parsed_args):
network_client = self.app.client_manager.network
columns = (
'id',
'name',
'zone',
)
column_headers = (
'ID',
'Name',
'Zone',
)
data = [to_obj.FICService(ficsv) for ficsv in
network_client.list_fic_services().get('fic_services')]
return (column_headers,
(utils.get_item_properties(
s, columns,
) for s in data))
class ShowFICService(command.ShowOne):
def get_parser(self, prog_name):
parser = super(ShowFICService, self).get_parser(prog_name)
parser.add_argument(
'fic_service_id',
metavar="FIC_SERVICE_ID",
help="ID of FIC Service to show."
)
return parser
def take_action(self, parsed_args):
network_client = self.app.client_manager.network
ficsv_id = parsed_args.fic_service_id
dic = network_client.show_fic_service(ficsv_id).get('fic_service')
columns = utils.get_columns(dic)
obj = to_obj.FICService(dic)
data = utils.get_item_properties(
obj, columns, )
return columns, data
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] |
tools/debug/run_role.py | cheretbe/ansible-playbooks | 0 | 62777 | #!/usr/bin/env python3
import sys
import os
import types
import subprocess
import json
import yaml
import shutil
def run_dialog(parameters):
dialog_cmd = ["dialog"] + parameters
dialog_env = os.environ.copy()
# By default dialog returns 255 on ESC. It gets mixed up with error code -1
# converted to unsigned 8-bit. We set DIALOG_ESC variable to use the same
# code as Cancel since we don't need to distinguish ESC and Cancel.
dialog_env["DIALOG_ESC"] = "1"
proc = subprocess.Popen(dialog_cmd, stderr = subprocess.PIPE, env=dialog_env)
stderr = proc.communicate()[1]
if proc.returncode == 1:
sys.exit("Cancelled by user")
elif proc.returncode != 0:
print(stderr.decode("utf-8"))
raise subprocess.CalledProcessError(proc.returncode, dialog_cmd, output=stderr)
else:
return stderr.decode("utf-8")
def load_roles():
roles = []
for dir_entry in os.listdir("/opt/ansible-playbooks"):
full_path = os.path.join("/opt/ansible-playbooks", dir_entry)
if os.path.isdir(full_path):
role_info = read_role_info(dir_entry, full_path)
if not role_info is None:
roles.append(role_info)
return roles
def read_role_info(role_name, role_path):
role_info = None
if os.path.isfile(os.path.join(role_path, "tasks", "main.yml")):
role_info = types.SimpleNamespace()
role_info.name = role_name
vars_file = os.path.join(role_path, "defaults", "main.yml")
if os.path.isfile(vars_file):
with open(vars_file, "r") as f:
role_info.default_vars = yaml.safe_load(f)
else:
role_info.default_vars = None
return role_info
def save_config():
os.makedirs(os.path.dirname(config_file_name), exist_ok=True)
with open(config_file_name, "w", encoding="utf-8") as f:
json.dump(config, f, ensure_ascii=False, indent=4)
if shutil.which("dialog") is None:
sys.exit("ERROR: Command 'dialog' is not found. Please install corresponding package")
config_file_name = os.path.expanduser("~/.cache/cheretbe/ansible-playbooks/run_role_cfg.json")
if os.path.isfile(config_file_name):
with open(config_file_name) as f:
config = json.load(f)
else:
config = {}
roles = load_roles()
roles.sort(key=lambda x: x.name)
last_used_role = config.get("last_used_role", None)
last_used_role_idx = None
dialog_list = []
for idx, i in enumerate(roles):
dialog_list += [str(idx), i.name]
if last_used_role and (i.name == last_used_role):
last_used_role_idx = idx
dialog_params = ["--keep-tite", "--no-tags", "--menu", "Select a role:",
"0", "0", "0"] + dialog_list
if not last_used_role_idx is None:
dialog_params = ["--default-item", str(last_used_role_idx)] + dialog_params
selection = run_dialog(dialog_params)
current_role = roles[int(selection)].name
config["last_used_role"] = current_role
save_config()
print(f"Using role '{current_role}'")
role_default_vars = roles[int(selection)].default_vars
last_used_custom_vars = None
if config.get("custom_vars", None):
last_used_custom_vars = config["custom_vars"].get(current_role, None)
current_role_vars = {}
if not role_default_vars is None:
caption_length = 0
for var_name in role_default_vars:
if len(var_name) > caption_length:
caption_length = len(var_name)
dialog_list = []
for idx, key in enumerate(role_default_vars):
var_value = ""
if last_used_custom_vars:
if key in last_used_custom_vars:
var_value = last_used_custom_vars[key]
dialog_list += [key + ":", str(idx + 1), "2", var_value, str(idx + 1),
str(caption_length + 4), "100", "0"]
selection = run_dialog(["--keep-tite", "--no-tags",
"--form", f"Override variable values for role '{current_role}':", "0", "0", "0"] +
dialog_list)
dialog_vars = selection.split("\n")
for idx, key in enumerate(role_default_vars):
if dialog_vars[idx]:
current_role_vars[key] = dialog_vars[idx]
if not config.get("custom_vars", None):
config["custom_vars"] = {}
config["custom_vars"][current_role] = current_role_vars
save_config()
inventory = json.loads(subprocess.check_output(["ansible-inventory",
"--list", "--export"]))
inventory_groups = []
for group in inventory["all"]["children"]:
if group in inventory:
inventory_groups.append(group)
if len(inventory_groups) == 0:
subprocess.run(["ansible-inventory", "--list"])
sys.exit("ERROR: No groups were found in the inventory. Check inventory configuration")
last_used_group = config.get("last_used_group", None)
if last_used_group == "all":
last_used_group_idx = "all"
else:
last_used_group_idx = None
dialog_list = ["all", "All hosts"]
for idx, i in enumerate(inventory_groups):
dialog_list += [str(idx), i]
if last_used_group and i == last_used_group:
last_used_group_idx = idx
# --menu <text> <height> <width> <menu height> <tag1> <item1> ...
dialog_params = ["--keep-tite", "--no-tags", "--menu", "Select a group:",
"0", "0", "0"] + dialog_list
if not last_used_group_idx is None:
dialog_params = ["--default-item", str(last_used_group_idx)] + dialog_params
selection = run_dialog(dialog_params)
if selection == "all":
print("Using all hosts")
current_group = None
config["last_used_group"] = "all"
else:
current_group = inventory_groups[int(selection)]
print(f"Using group '{current_group}'")
config["last_used_group"] = current_group
save_config()
hosts_subset = []
if current_group:
inventory_hosts = []
for host in inventory[current_group]["hosts"]:
inventory_hosts.append(host)
last_used_hosts = inventory_hosts
if not config.get("hosts", None) is None:
last_used_hosts = config["hosts"].get(current_group, inventory_hosts)
dialog_list = []
for idx, i in enumerate(inventory_hosts):
item_state = "on" if i in last_used_hosts else "off"
dialog_list += [str(idx), i, item_state]
selection = run_dialog(["--keep-tite", "--no-tags",
"--checklist", f"Select hosts ({current_group}):", "0", "0", "0"] +
dialog_list)
current_hosts = []
for host_idx in selection.split():
current_hosts.append(inventory_hosts[int(host_idx)])
if len(current_hosts) == 0:
sys.exit("No hosts were selected. Exiting")
print("Using hosts", current_hosts)
hosts_subset = ["-l", ",".join(current_hosts)]
if not config.get("hosts", None):
config["hosts"] = {}
config["hosts"][current_group] = current_hosts
save_config()
ansible_playbook_cmd = ["ansible-playbook", "/opt/ansible-playbooks/run_role.yml",
"--extra-vars", f"role_name={current_role}"] + hosts_subset
if len(current_role_vars) != 0:
ansible_playbook_cmd += ["--extra-vars", json.dumps(current_role_vars)]
subprocess.check_call(ansible_playbook_cmd) | [
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] |
Flo et toto/Exercices/Commande.py | geverartsdev/TechnofuturTIC | 0 | 1609242 | <gh_stars>0
print---- imprimmer
int---- entier
float---- décimal
str---- texte
bool---- booléen
if...(true/false):----Si
elif...():----Si autres
else :----Autres
input()----Entre
while()----Tant que
len()----Longueur
upper()----Minuscules -> Majuscules
lower()----Majuscules -> Minuscules
dict----Dictionnaire
import----importer (import random)
for...in----Pour chauqe ... dans/du...
range----portée
split()---- séparation des caractère
class---- classe
__init__()---- initialisation
self----moi
| [
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azure/functions/_abc.py | DalavanCloud/azure-functions-python-worker | 1 | 181437 | import abc
import typing
T = typing.TypeVar('T')
class Out(abc.ABC, typing.Generic[T]):
@abc.abstractmethod
def set(self, val: T) -> None:
pass
@abc.abstractmethod
def get(self) -> T:
pass
class Context(abc.ABC):
@property
@abc.abstractmethod
def invocation_id(self) -> str:
pass
@property
@abc.abstractmethod
def function_name(self) -> str:
pass
@property
@abc.abstractmethod
def function_directory(self) -> str:
pass
class HttpRequest(abc.ABC):
@property
@abc.abstractmethod
def method(self) -> str:
pass
@property
@abc.abstractmethod
def url(self) -> str:
pass
@property
@abc.abstractmethod
def headers(self) -> typing.Mapping[str, str]:
pass
@property
@abc.abstractmethod
def params(self) -> typing.Mapping[str, str]:
pass
def get_body(self) -> bytes:
pass
class HttpResponse(abc.ABC):
@property
@abc.abstractmethod
def status_code(self) -> int:
pass
@property
@abc.abstractmethod
def headers(self) -> typing.MutableMapping[str, str]:
pass
@abc.abstractmethod
def get_body(self) -> bytes:
pass
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] |
scvelo/logging.py | saksham219/scvelo | 0 | 1611908 | """Logging and Profiling
"""
from . import settings
from datetime import datetime
from time import time as get_time
from platform import python_version
_VERBOSITY_LEVELS_FROM_STRINGS = {'error': 0, 'warn': 1, 'info': 2, 'hint': 3}
def info(*args, **kwargs):
return msg(*args, v='info', **kwargs)
def error(*args, **kwargs):
args = ('Error:',) + args
return msg(*args, v='error', **kwargs)
def warn(*args, **kwargs):
args = ('WARNING:',) + args
return msg(*args, v='warn', **kwargs)
def hint(*args, **kwargs):
return msg(*args, v='hint', **kwargs)
def _settings_verbosity_greater_or_equal_than(v):
if isinstance(settings.verbosity, str):
settings_v = _VERBOSITY_LEVELS_FROM_STRINGS[settings.verbosity]
else:
settings_v = settings.verbosity
return settings_v >= v
def msg(*msg, v=4, time=False, memory=False, reset=False, end='\n',
no_indent=False, t=None, m=None, r=None):
"""Write message to logging output.
Log output defaults to standard output but can be set to a file
by setting `sc.settings.log_file = 'mylogfile.txt'`.
v : {'error', 'warn', 'info', 'hint'} or int, (default: 4)
0/'error', 1/'warn', 2/'info', 3/'hint', 4, 5, 6...
time, t : bool, optional (default: False)
Print timing information; restart the clock.
memory, m : bool, optional (default: Faulse)
Print memory information.
reset, r : bool, optional (default: False)
Reset timing and memory measurement. Is automatically reset
when passing one of ``time`` or ``memory``.
end : str (default: '\n')
Same meaning as in builtin ``print()`` function.
no_indent : bool (default: False)
Do not indent for ``v >= 4``.
"""
# variable shortcuts
if t is not None: time = t
if m is not None: memory = m
if r is not None: reset = r
if isinstance(v, str):
v = _VERBOSITY_LEVELS_FROM_STRINGS[v]
if v == 3: # insert "--> " before hints
msg = ('-->',) + msg
if v >= 4 and not no_indent:
msg = (' ',) + msg
if _settings_verbosity_greater_or_equal_than(v):
if not time and not memory and len(msg) > 0:
_write_log(*msg, end=end)
if reset:
try:
settings._previous_memory_usage, _ = get_memory_usage()
except:
pass
settings._previous_time = get_time()
if time:
elapsed = get_passed_time()
msg = msg + ('({})'.format(_sec_to_str(elapsed)),)
_write_log(*msg, end=end)
if memory:
_write_log(get_memory_usage(), end=end)
m = msg
def _write_log(*msg, end='\n'):
"""Write message to log output, ignoring the verbosity level.
This is the most basic function.
Parameters
----------
*msg :
One or more arguments to be formatted as string. Same behavior as print
function.
"""
from .settings import logfile
if logfile == '':
print(*msg, end=end)
else:
out = ''
for s in msg:
out += str(s) + ' '
with open(logfile, 'a') as f:
f.write(out + end)
def _sec_to_str(t):
"""Format time in seconds.
Parameters
----------
t : int
Time in seconds.
"""
from functools import reduce
return "%d:%02d:%02d.%02d" % \
reduce(lambda ll, b: divmod(ll[0], b) + ll[1:],
[(t*100,), 100, 60, 60])
def get_passed_time():
now = get_time()
elapsed = now - settings._previous_time
settings._previous_time = now
return elapsed
def print_passed_time():
now = get_time()
elapsed = now - settings._previous_time
settings._previous_time = now
from functools import reduce
elapsed = "%d:%02d:%02d.%02d" % reduce(lambda ll, b: divmod(ll[0], b) + ll[1:], [(elapsed*100,), 100, 60, 60])
return elapsed
def print_version():
from . import __version__
_write_log('Running scvelo', __version__, '(python ' + python_version() + ')', 'on {}.'.format(get_date_string()))
def print_versions():
for mod in ['scvelo', 'scanpy', 'anndata', 'loompy', 'numpy', 'scipy', 'matplotlib', 'sklearn', 'pandas']:
mod_name = mod[0] if isinstance(mod, tuple) else mod
mod_install = mod[1] if isinstance(mod, tuple) else mod
try: print('{}=={}'.format(mod_install, __import__(mod_name).__version__), end=' ')
except (ImportError, AttributeError): pass
print()
def get_date_string():
return datetime.now().strftime("%Y-%m-%d %H:%M")
from anndata.logging import print_memory_usage
from anndata.logging import get_memory_usage
from sys import stdout
class ProgressReporter:
def __init__(self, total, interval=3):
self.count = 0
self.total = total
self.timestamp = get_time()
self.interval = interval
def update(self):
self.count += 1
if settings.verbosity > 1 and (get_time() - self.timestamp > self.interval or self.count == self.total):
self.timestamp = get_time()
percent = int(self.count * 100 / self.total)
stdout.write('\r' + '... %d%%' % percent)
stdout.flush()
def finish(self):
if settings.verbosity > 1:
stdout.write('\r')
stdout.flush()
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] |
spider/bookinfo/items.py | leitelyaya/Broadview-analysing-sales-figures | 5 | 65250 | # -*- coding: utf-8 -*-
# Define here the models for your scraped items
#
# See documentation in:
# http://doc.scrapy.org/en/latest/topics/items.html
import scrapy
class BookinfoItem(scrapy.Item):
# define the fields for your item here like:
# name = scrapy.Field()
coverImage = scrapy.Field() #"cover.jpg",
classify = scrapy.Field() #"分类",
index = scrapy.Field() #"列表页中的排名",
pageNo = scrapy.Field() #"列表中的第几页",
content = scrapy.Field() #"html内容"
| [
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2
] |
search_engine/worker.py | Dhruvacube/search-engine | 0 | 29121 | import importlib
from uvicorn.workers import UvicornWorker
class DynamicUvicornWorker(UvicornWorker):
"""
This class is called `DynamicUvicornWorker` because it assigns values
according to the module available Union['asyncio', 'uvloop']
It also set `lifespan` to `off` :)
"""
spam_spec = importlib.util.find_spec("uvloop")
found = spam_spec is not None
if found:
CONFIG_KWARGS = {"loop": "uvloop", "http": "auto", "lifespan": "off"}
else:
CONFIG_KWARGS = {"loop": "auto", "http": "auto", "lifespan": "off"}
| [
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] |
randstrip.py | itec78/fumcaso | 0 | 74929 | <reponame>itec78/fumcaso<filename>randstrip.py
#!/usr/bin/python3
from PIL import Image
from PIL import ImageFont
from PIL import ImageDraw
import csv
import random
import os
import json
fileDir = os.path.dirname(os.path.abspath(__file__))
def replaceText(text,config):
"""This function replace $WILDCARD with a word found in subs.csv
subs.csv definition is 1st colum $WILDCARD, subsequent columns, possible values (chosen at random), delimiter is ;"""
with open(config["csvLocation"]+"/"+config["csvSubs"]) as subs:
csvReader = csv.reader(subs,delimiter=";")
for row in csvReader:
if text.find(row[0]) != -1:
text = text.replace(row[0],row[random.randint(1,len(row)-1)],1)
return text
print("Parsing error \""+text+"\" not found")
quit()
def fetchText(indText,config):
"""This function fetch the text for the image with two characters
rtext.csv definition is: 1st column the name of the file (i.e. B001.png), 2nd number of actors (at the moment
they are limited to two; then a couple of columns or each actor with x and y coord of the strings; after the coords the outcomes,
one column for each actor
Delimiter is ; and line feeds @, if there aren't any options, it returns 0 (no text)
It returns two arrays, coords is a tuple (x,y) and result is the outcome"""
with open(config["csvLocation"]+"/"+config["csvSpeech"]) as rtext:
csvReader = csv.reader(rtext,delimiter=';')
for row in csvReader:
if row[0]==indText:
noActors = int(row[1])
if noActors == 0:
return 0
else:
firstElement = 2+(noActors*2)
lastElement = len(row)-(noActors-1)
randQuote = random.randrange(firstElement,lastElement,noActors)
coords = []
result = []
for x in range(0,noActors):
coords.append((row[2+x*2],row[3+x*2]))
result.append(row[randQuote+x])
return coords,result
def fetchVign(config):
"""This functions fetch an image, randomly, chosen from a markov tree defined in ram.csv
ram.csv definition is: 1st column the name of the image (without extension), subsequent columns, possible outcomes chosen randomly
It returns an array with the file names"""
starts = []
startdest = []
nvign = 0
currVign = "000"
story = []
with open(config["csvLocation"]+"/"+config["csvTree"]) as ram:
csvReader = csv.reader(ram)
for row in csvReader:
starts.append(row[0])
startdest.append(row)
while nvign <100:
story.append(startdest[starts.index(currVign)][random.randint(1,len(startdest[starts.index(currVign)])-1)])
currVign = story[nvign]
if currVign == "END":
return story
story[nvign]+=".png"
nvign +=1
print("tree with no END")
quit()
def addThing(indVign,config):
"""This function adds a small image (object) to a larger image
obj.csv definition is: name of the image (i.e. A001.png), x-coord, y-coord, subsequent columns possible outcomes
It returns a tuple (object file name, x, y)"""
with open(config["csvLocation"]+"/"+config["csvObj"]) as obj:
csvReader = csv.reader(obj)
for row in csvReader:
if row[0] == indVign:
return row[random.randint(3,len(row)-1)],row[1],row[2]
return 0
def writeStrip(story,config):
"""This function creates the strip returning an image object that could be saved or viewed. It takes an array with filenames as parameter
The first image is always 000, then appends to strip the files, then decorates it fetching text and adding objects. If the object is an R, then
repeats the last object."""
strip = []
for indVign in story:
try:
vign = Image.open(config["imagesLocation"]+"/"+indVign).convert('RGBA')
addtext = ImageDraw.Draw(vign)
fnt = ImageFont.truetype(config["font"],config["fontSize"])
textVign = fetchText(indVign,config)
if textVign!=0:
try:
for x in range(len(textVign[0])):
text_vign = textVign[1][x]
try:
while text_vign.find('$') != -1:
text_vign = replaceText(text_vign,config)
except AttributeError as err:
print("Problem parsing:")
print(textVign)
print(err)
quit()
text_vign = text_vign.replace('@','\n')
addtext.multiline_text((int(textVign[0][x][0]),int(textVign[0][x][1])),text_vign,fill="#000000",font=fnt,align="center")
except TypeError:
print("Problem finding text for:")
print(indVign)
quit()
obj = addThing(indVign,config)
if obj!=0:
if obj[0] == 'R':
objImg = Image.open(config["imagesLocation"]+"/"+prevObj[0])
else:
prevObj = obj
objImg = Image.open(config["imagesLocation"]+"/"+obj[0])
vign.paste(objImg,(int(obj[1]),int(obj[2])))
strip.append(vign)
except FileNotFoundError:
pass
image = Image.new('RGBA',(config["xSize"],config["ySize"]))
xshift=0
for vign in strip:
image.paste(vign,(xshift,0))
xshift += config["panelLength"]
ImageDraw.Draw(image).rectangle([0,0,config["xSize"]-1,config["ySize"]-1], fill=None, outline="black", width=1)
return image
def createStrip(config,specialPlatform=""):
"""Create strip and save it
createStrip(str path/filename)"""
try:
story = fetchVign(config)
finalStrip = writeStrip(story,config)
if specialPlatform == "android":
return finalStrip
else:
finalStrip.save(config["saveLocation"]+config["filename"])
return 0
except Exception as err:
return err
def readConfig(profile=False,platform=False):
"""Read configuration file"""
try:
with open(fileDir+"/config.json") as f:
config = json.load(f)
except IOError:
print("config.json not found")
return False
if not(profile):
profile = config["defaultProfile"]
else:
profile = profile[0]
try:
checkProfile = config[profile]
except KeyError:
print("Profile "+profile+" not found")
quit()
saveLocation = checkLocal(config[profile]["saveLocation"])
imagesLocation = checkLocal(config[profile]["imagesLocation"])
csvLocation = checkLocal(config[profile]["csvLocation"])
csvTree = config[profile]["csvTree"]
csvSpeech = config[profile]["csvSpeech"]
csvSubs = config[profile]["csvSubs"]
csvObj = config[profile]["csvObj"]
font = checkLocal(config[profile]["font"])
fontSize = int((config[profile]["fontSize"]))
xSize = config[profile]["xSize"]
ySize = config[profile]["ySize"]
panelLength = config[profile]["panelLength"]
if platform:
token = checkLocal(config[profile][platform]["token"])
filename = checkLocal(config[profile][platform]["filename"])
try:
text = config[profile][platform]["text"]
except KeyError:
text = False
return {"saveLocation":saveLocation,"imagesLocation":imagesLocation,"csvLocation":csvLocation,"fontSize":fontSize,"font":font,"token":token,"filename":filename,"xSize":xSize,"ySize":ySize,"panelLength":panelLength,"csvTree":csvTree,"csvSpeech":csvSpeech,"csvSubs":csvSubs,"csvObj":csvObj,"text":text}
filename = config[profile]["filename"]
return {"saveLocation":saveLocation,"imagesLocation":imagesLocation,"csvLocation":csvLocation,"fontSize":fontSize,"font":font,"filename":filename,"xSize":xSize,"ySize":ySize,"panelLength":panelLength,"csvTree":csvTree,"csvSpeech":csvSpeech,"csvSubs":csvSubs,"csvObj":csvObj}
def checkLocal(directory):
"""Checks if it's a relative or absolute path"""
if directory[0] == ".":
return fileDir + directory[1:]
else:
return directory
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-s','--story',metavar='story',default='',nargs=4,help='name of the images')
parser.add_argument('-a','--a4',default=False,action='store_true',help='print on an A4 in PDF, needs -o output, disables -x xsize')
parser.add_argument('-m','--multiple',metavar='multiple',default=[1],nargs=1,type=int,help='multiple output (int >0), if no output -o specified, it just tests the stories')
parser.add_argument('-x','--xsize',metavar='xsize',default=0,type=int,nargs=1,help='resize image x')
parser.add_argument('-p','--profile',metavar='profile',default="",type=str,nargs=1,help='profile')
parser.add_argument('-o','--output',metavar='output',const=True,default=False,nargs="?",help='output file, if name not specified, default path will be used')
args = parser.parse_args()
if args.multiple[0] <= 0: #Wrong multiple choice
quit()
config = readConfig(profile=args.profile)
if args.output == True: #Output on but no filename specified
fileName = config["saveLocation"]+config["filename"]
elif type(args.output) == str: #Output specified
fileName = args.output
pdfs = list() #Prepare a list for the PDF
for ist in range(0,args.multiple[0]):
if (args.story == ''): #No story specified
story = fetchVign(config)
else:
story = [] #Story specified
for x in args.story:
story.append(x)
finalStrip = writeStrip(story,config)
if args.a4: #Prints a PDF
finalStrip = finalStrip.resize((2249,516))
pdfs.append(finalStrip)
else:
if args.xsize != 0: #Resize specified
finalStrip = finalStrip.resize((args.xsize[0],int(args.xsize[0]/2400*500)))
if args.multiple[0] == 1: #No multiple selected
if args.output == False:
finalStrip.show()
else:
finalStrip.save(fileName)
else: #Multiple selected
if args.output == False:
print(story)
else:
finalStrip.save(fileName + str(ist).zfill(3) + ".png")
if args.a4:
ypos = 100
nopage = 0
if args.output == False:
print("Output not specified")
quit()
pagePdf = list()
for pag in range(0,int((args.multiple[0]-1)/6+1)):
image = Image.new('RGB',(2479,3508),(255,255,255))
fnt = ImageFont.truetype(config["font"],config["fontSize"])
ImageDraw.Draw(image).text((2479 - 500, 3508 - 200),"https://github.com/oloturia/fumcaso",fill="black",font=fnt)
pagePdf.append(image)
for ist,strip_num in enumerate(range(0,args.multiple[0])):
pagePdf[nopage].paste(pdfs[strip_num],box=(110,ypos))
ypos += 516 + 20
if ypos > 3508-569:
ypos = 100
nopage += 1
if fileName[len(fileName)-4:] != ".pdf":
fileName += ".pdf"
pagePdf[0].save(fileName, resolution=300, save_all=True, append_images=pagePdf[1:])
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mass/tensorflow_nets/naive-fusion/naive_fusion_net.py | pquochuy/xsleepnet | 15 | 129514 | import tensorflow as tf
from nn_basic_layers import *
from filterbank_shape import FilterbankShape
from ops import *
class Naive_Fusion_Net(object):
def __init__(self, config):
# Placeholders for input, output and dropout
self.config = config
self.input_x1 = tf.placeholder(tf.float32,shape=[None, self.config.epoch_seq_len, self.config.deep_ntime, self.config.nchannel],name='input_x1')
self.input_x2 = tf.placeholder(tf.float32, [None, self.config.epoch_seq_len, self.config.seq_frame_seq_len, self.config.seq_ndim, self.config.nchannel], name="input_x2")
self.input_y = tf.placeholder(tf.float32, [None, self.config.epoch_seq_len, self.config.nclass], name="input_y")
self.dropout_rnn = tf.placeholder(tf.float32, name="dropout_rnn")
self.dropout_cnn = tf.placeholder(tf.float32, name="dropout_cnn")
self.istraining = tf.placeholder(tf.bool, name='istraining') # idicate training for batch normmalization
self.seq_frame_seq_len = tf.placeholder(tf.int32, [None]) # for the dynamic RNN
self.epoch_seq_len = tf.placeholder(tf.int32, [None]) # for the dynamic RNN
self.construct_fcnnrnn_net()
self.construct_seqsleepnet()
self.score = []
self.prediction = []
with tf.variable_scope("output_layer"):
for i in range(self.config.epoch_seq_len):
score_i = fc(tf.concat([tf.squeeze(self.deep_rnn_out[:,i,:]), tf.squeeze(self.seq_rnn_out2[:,i,:])], 1),
self.config.seq_nhidden2 * 2 + self.config.deep_nhidden * 2,
self.config.nclass,
name="joint_output",
relu=False)
pred_i = tf.argmax(score_i, 1, name="pred-%s" % i)
self.score.append(score_i)
self.prediction.append(pred_i)
self.output_loss = 0
with tf.name_scope("output-loss"):
for i in range(self.config.epoch_seq_len):
loss_i = tf.nn.softmax_cross_entropy_with_logits(labels=tf.squeeze(self.input_y[:,i,:]), logits=self.score[i])
loss_i = tf.reduce_sum(loss_i, axis=[0])
self.output_loss += loss_i
self.output_loss = self.output_loss/self.config.epoch_seq_len # average over sequence length
self.accuracy = []
with tf.name_scope("accuracy"):
for i in range(self.config.epoch_seq_len):
correct_prediction_i = tf.equal(self.prediction[i], tf.argmax(tf.squeeze(self.input_y[:,i,:]), 1))
accuracy_i = tf.reduce_mean(tf.cast(correct_prediction_i, "float"), name="accuracy-%s" % i)
self.accuracy.append(accuracy_i)
# add on regularization except for the filter bank layers
with tf.name_scope("l2_loss"):
vars = tf.trainable_variables()
except_vars_eeg = tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES, scope='seq_filterbank-layer-eeg')
except_vars_eog = tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES, scope='seq_filterbank-layer-eog')
except_vars_emg = tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES, scope='seq_filterbank-layer-emg')
l2_loss = tf.add_n([ tf.nn.l2_loss(v) for v in vars
if v not in except_vars_eeg and v not in except_vars_eog and v not in except_vars_emg])
self.loss = self.output_loss + self.config.l2_reg_lambda*l2_loss
#############################################################
# Construct fcnnrnn here
#############################################################
def construct_fcnnrnn_net(self):
self.g_enc_depths = [16, 16, 32, 32, 64, 64, 128, 128, 256]
deep_X = tf.reshape(self.input_x1, [-1, self.config.deep_ntime, self.config.nchannel])
with tf.device('/gpu:0'), tf.variable_scope("deep_all_cnn_layer") as scope:
deep_cnn_feat = self.all_convolution_block(deep_X,"all_conv_block")
deep_num_cnn_feat = 6*self.g_enc_depths[-1]
deep_cnn_feat = tf.reshape(deep_cnn_feat, [-1, deep_num_cnn_feat])
print("deep_cnn_feat")
print(deep_cnn_feat.get_shape())
deep_rnn_input = tf.reshape(deep_cnn_feat, [-1, self.config.epoch_seq_len, deep_num_cnn_feat])
# bidirectional sequence-level recurrent layer
with tf.device('/gpu:0'), tf.variable_scope("deep_epoch_rnn_layer") as scope:
deep_fw_cell, deep_bw_cell = bidirectional_recurrent_layer(self.config.deep_nhidden,
self.config.deep_nlayer,
input_keep_prob=self.dropout_rnn,
output_keep_prob=self.dropout_rnn)
self.deep_rnn_out, self.deep_rnn_state = bidirectional_recurrent_layer_output(deep_fw_cell,
deep_bw_cell,
deep_rnn_input,
self.epoch_seq_len,
scope=scope)
print(self.deep_rnn_out.get_shape())
#############################################################
# End deepsleepnet here
#############################################################
#############################################################
# Construct seqsleepnet here
#############################################################
def construct_seqsleepnet(self):
filtershape = FilterbankShape()
#triangular filterbank
self.Wbl = tf.constant(filtershape.lin_tri_filter_shape(nfilt=self.config.seq_nfilter,
nfft=self.config.seq_nfft,
samplerate=self.config.seq_samplerate,
lowfreq=self.config.seq_lowfreq,
highfreq=self.config.seq_highfreq),
dtype=tf.float32,
name="W-filter-shape-eeg")
with tf.device('/gpu:0'), tf.variable_scope("seq_filterbank-layer-eeg"):
# Temporarily crush the feature_mat's dimensions
Xeeg = tf.reshape(tf.squeeze(self.input_x2[:,:,:,:,0]), [-1, self.config.seq_ndim])
# first filter bank layer
self.Weeg = tf.Variable(tf.random_normal([self.config.seq_ndim, self.config.seq_nfilter],dtype=tf.float32))
# non-negative constraints
self.Weeg = tf.sigmoid(self.Weeg)
# mask matrix should be replaced by shape-specific filter bank, e.g. triangular,rectangle.
self.Wfb = tf.multiply(self.Weeg,self.Wbl)
HWeeg = tf.matmul(Xeeg, self.Wfb) # filtering
HWeeg = tf.reshape(HWeeg, [-1, self.config.epoch_seq_len, self.config.seq_frame_seq_len, self.config.seq_nfilter])
if(self.config.nchannel > 1):
with tf.device('/gpu:0'), tf.variable_scope("seq_filterbank-layer-eog"):
# Temporarily crush the feature_mat's dimensions
Xeog = tf.reshape(tf.squeeze(self.input_x2[:,:,:,:,1]), [-1, self.config.seq_ndim])
# first filter bank layer
self.Weog = tf.Variable(tf.random_normal([self.config.seq_ndim, self.config.seq_nfilter],dtype=tf.float32))
# non-negative constraints
self.Weog = tf.sigmoid(self.Weog)
# mask matrix should be replaced by shape-specific filter bank, e.g. triangular,rectangle.
self.Wfb = tf.multiply(self.Weog,self.Wbl)
HWeog = tf.matmul(Xeog, self.Wfb) # filtering
HWeog = tf.reshape(HWeog, [-1, self.config.epoch_seq_len, self.config.seq_frame_seq_len, self.config.seq_nfilter])
if(self.config.nchannel > 2):
with tf.device('/gpu:0'), tf.variable_scope("seq_filterbank-layer-emg"):
# Temporarily crush the feature_mat's dimensions
Xemg = tf.reshape(tf.squeeze(self.input_x2[:,:,:,:,2]), [-1, self.config.seq_ndim])
# first filter bank layer
self.Wemg = tf.Variable(tf.random_normal([self.config.seq_ndim, self.config.seq_nfilter],dtype=tf.float32))
# non-negative constraints
self.Wemg = tf.sigmoid(self.Wemg)
# mask matrix should be replaced by shape-specific filter bank, e.g. triangular,rectangle.
self.Wfb = tf.multiply(self.Wemg,self.Wbl)
HWemg = tf.matmul(Xemg, self.Wfb) # filtering
HWemg = tf.reshape(HWemg, [-1, self.config.epoch_seq_len, self.config.seq_frame_seq_len, self.config.seq_nfilter])
if(self.config.nchannel > 2):
X2 = tf.concat([HWeeg, HWeog, HWemg], axis = 3)
elif(self.config.nchannel > 1):
X2 = tf.concat([HWeeg, HWeog], axis = 3)
else:
X2 = HWeeg
X2 = tf.reshape(X2, [-1, self.config.seq_frame_seq_len, self.config.seq_nfilter*self.config.nchannel])
# bidirectional epoch-level recurrent layer
with tf.variable_scope("seq_frame_rnn_layer") as scope:
seq_fw_cell1, seq_bw_cell1 = bidirectional_recurrent_layer_bn(self.config.seq_nhidden1,
self.config.seq_nlayer1,
seq_len=self.config.seq_frame_seq_len,
is_training=self.istraining,
input_keep_prob=self.dropout_rnn, # we have dropouted in the convolutional layer
output_keep_prob=self.dropout_rnn)
seq_rnn_out1, seq_rnn_state1 = bidirectional_recurrent_layer_output(seq_fw_cell1,
seq_bw_cell1,
X2,
self.seq_frame_seq_len,
scope=scope)
print(seq_rnn_out1.get_shape())
with tf.variable_scope("seq_frame_attention_layer"):
self.seq_attention_out1, _ = attention(seq_rnn_out1, self.config.seq_attention_size1)
print(self.seq_attention_out1.get_shape())
seq_e_rnn_input = tf.reshape(self.seq_attention_out1, [-1, self.config.epoch_seq_len, self.config.seq_nhidden1*2])
# bidirectional seq-level recurrent layer
with tf.variable_scope("seq_epoch_rnn_layer") as scope:
seq_fw_cell2, seq_bw_cell2 = bidirectional_recurrent_layer_bn(self.config.seq_nhidden2,
self.config.seq_nlayer2,
seq_len=self.config.epoch_seq_len,
is_training=self.istraining,
input_keep_prob=self.dropout_rnn, # we have dropouted the output of frame-wise rnn
output_keep_prob=self.dropout_rnn)
self.seq_rnn_out2, self.seq_rnn_state2 = bidirectional_recurrent_layer_output(seq_fw_cell2,
seq_bw_cell2,
seq_e_rnn_input,
self.epoch_seq_len,
scope=scope)
print(self.seq_rnn_out2.get_shape())
#############################################################
# End seqsleepnet
############################################################
def all_convolution_block(self, input, name):
in_dims = input.get_shape().as_list()
print(in_dims)
h_i = input
if len(in_dims) == 2:
h_i = tf.expand_dims(input, -1)
elif len(in_dims) < 2 or len(in_dims) > 3:
raise ValueError('Generator input must be 2-D or 3-D')
kwidth = 31
with tf.variable_scope(name, reuse=tf.AUTO_REUSE) as scope:
for layer_idx, layer_depth in enumerate(self.g_enc_depths):
bias_init = tf.constant_initializer(0.)
h_i_dwn = downconv(h_i, layer_depth, kwidth=kwidth,
init=tf.truncated_normal_initializer(stddev=0.02),
bias_init=bias_init,
name='enc_{}'.format(layer_idx))
print("h_i_dwn")
print(h_i_dwn.get_shape())
print('Downconv {} -> {}'.format(h_i.get_shape(),h_i_dwn.get_shape()))
h_i = h_i_dwn
print('-- Enc: leakyrelu activation --')
h_i = leakyrelu(h_i)
if(layer_idx < len(self.g_enc_depths) - 1):
h_i = dropout(h_i, self.dropout_cnn)
return h_i
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] |
support.py | Soarxyn/PEF-Structural-Analysis | 4 | 38358 | <reponame>Soarxyn/PEF-Structural-Analysis
from typing import Tuple
from enum import Enum
from auxiliary.algebra import Vector3, psin, pcos
# this is an auxiliary class used for initializing the Support class's members' values
class SupportType(Enum):
SIMPLE: Tuple = (1, 0) # tuple values are the number
PINNED: Tuple = (2, 0) # of forces and the number
FIXED: Tuple = (2, 1) # of moments, in that order
# this is a class that defines one of three support types: simple, pinned or fixed
class Support:
def __init__(self, name: str, angle: float = 0):
# this member is the reaction vector from the support
# its values are used for solving the system
self.reaction: Vector3 = Vector3(0, 0, 0)
if SupportType[name].value[0] > 1:
self.reaction.x = 1
self.reaction.y = 1
else:
self.reaction.x = pcos(angle)
self.reaction.y = psin(angle)
if SupportType[name].value[1] == 1:
self.reaction.z = 1
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] |
tests/conftest.py | starlinglab/integrity-backend | 1 | 125048 | import pytest
@pytest.fixture
def reverse_geocode_mocker(mocker):
def patch(return_value):
mocker.patch(
"integritybackend.geocoder.Geocoder.reverse_geocode",
lambda *_: return_value,
)
return patch
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] |
stocks/helper.py | arminbhy/stock-market-analysis | 1 | 190933 | <reponame>arminbhy/stock-market-analysis
#!/usr/bin/env python
import numpy
import pystache
def _direction_to_str(direction):
if direction == 1:
return "Positive"
if direction == -1:
return "Negative"
return "None"
def _direction(a,b):
if a > b:
return 1
if a == b:
return 0
return -1
def _rsi(v):
if v > 70:
return 'Over-Bought'
if v < 30:
return 'Over-Sold'
if v > 60:
return 'Almost-Over-Bought'
if v < 40:
return 'Almost-Over-Sold'
return 'Avearge'
class Helper:
'Class for everything related to ticker'
def __init__(self, data):
self.data = data
def len(self):
return len(self.data)
def last_value(self):
return self.data[len(self.data) - 1]
def min(self, n=14):
return min(self.data[len(self.data) - n:])
def max(self, n=14):
return max(self.data[len(self.data) - n:])
def days_since_min(self, n=14):
group = self.data[len(self.data) - n:]
group.reverse()
return group.index(self.min(n))
def days_since_max(self, n=14):
group = self.data[len(self.data) - n:]
group.reverse()
return group.index(self.max(n))
def direction(self):
return _direction(
self.data[len(self.data) - 1],
self.data[len(self.data) - 2] )
def direction_str(self):
return _direction_to_str(self.direction())
def direction_compareto_average(self, n=14):
return _direction(
self.data[len(self.data) - 1],
numpy.mean(self.data[len(self.data) - n:]))
def direction_since_max_or_min(self, n=14):
return self.direction_compareto_average(
min(self.days_since_max(n),
self.days_since_min(n)) + 1)
def report(self, n=14):
return pystache.render('Direction {{direction}}, Value {{value}}, {{n}}D Min {{min}}, Max {{max}}, Days Since Min {{since_min}}, Max {{since_max}}', {
'n' : n,
'direction' : _direction_to_str(self.direction()),
'value' : round(self.data[len(self.data) - 1],2),
'min' : round(self.min(n),2),
'max' : round(self.max(n),2),
'since_min' : self.days_since_min(n),
'since_max' : self.days_since_max(n)
})
class RSIHelper(Helper):
def status(self):
return _rsi(self.data[len(self.data) - 1])
def min_status(self, n=14):
return _rsi(self.min(n))
def max_status(self, n=14):
return _rsi(self.max(n))
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src/discriminator_cnn_ver.py | samirsahoo007/Conditional-SeqGAN-Tensorflow | 51 | 46765 | # -*- coding: utf-8 -*- #
"""*********************************************************************************************"""
# FileName [ discriminator.py ]
# Synopsis [ Discriminator model ]
# Author [ <NAME> (Andi611) ]
# Copyright [ Copyleft(c), NTUEE, NTU, Taiwan ]
"""*********************************************************************************************"""
###############
# IMPORTATION #
###############
import math
import tensorflow as tf
from configuration import config, BUCKETS
#######################
# CLASS DISCRIMINATOR #
#######################
"""
A CNN Discriminator model for text classification:
Uses an embedding layer, followed by a convolutional, max-pooling and softmax layer.
"""
class Discriminator(object):
##################
# INITIALIZATION #
##################
"""
Loads Discriminator parameters and construct model.
"""
def __init__(self, config, vocab_size):
#--general settings--#
self.vocab_size = vocab_size
self.max_seq_len = BUCKETS[-1][0] + BUCKETS[-1][1]
self.batch_size = config.batch_size
#--discriminator hyper-parameters--#
self.lr = config.d_lr
self.embedding_dim = config.d_embedding_dim
self.num_class = config.d_num_class
self.l2_reg_lambda = config.d_l2_reg_lambda
self.dropout_keep_prob = tf.get_variable(name='dropout_keep_prob', shape=[], initializer=tf.constant_initializer(config.d_dropout_keep_prob))
#--discriminator constant-parameters--#
self.filter_sizes = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20]
self.num_filters = [100, 200, 200, 200, 200, 100, 100, 100, 100, 100, 160, 160]
#--placeholders--#
self.input_x = tf.placeholder('int32', [None, self.max_seq_len], name='input_x')
self.input_y = tf.placeholder('float32', [None, self.num_class], name='input_y')
#--construct model--#
self.build_model()
###############
# BUILD MODEL #
###############
"""
Construct tensorflow model.
"""
def build_model(self):
with tf.variable_scope('discriminator'):
#--embedding layer--#
with tf.device('/cpu:0'), tf.variable_scope('word_embedding'):
self.W = tf.get_variable(name='W',
shape=[self.vocab_size, self.embedding_dim],
initializer=tf.truncated_normal_initializer(stddev=6/math.sqrt(self.embedding_dim)))
self.word_embedding = tf.nn.embedding_lookup(params=self.W, ids=self.input_x)
self.word_embedding_expanded = tf.expand_dims(input=self.word_embedding, axis=-1)
#--convolution+maxpool layer for each filter size--#
pooled_outputs = []
for filter_size, num_filter in zip(self.filter_sizes, self.num_filters):
with tf.variable_scope('conv_maxpool_%s' % filter_size):
#--convolution layer--#
filter_shape = [filter_size, self.embedding_dim, 1, num_filter]
W = tf.get_variable(name='W', shape=filter_shape, initializer=tf.truncated_normal_initializer(stddev=0.1))
b = tf.get_variable(name='b', shape=[num_filter], initializer=tf.constant_initializer(0.1))
conv = tf.nn.conv2d(input=self.word_embedding_expanded,
filter=W,
strides=[1, 1, 1, 1],
padding='VALID',
name='conv')
#--add bias and nonlinearity--#
conv_b = tf.nn.bias_add(value=conv, bias=b, name='conv_b')
h = tf.nn.relu(conv_b, name='relu')
#--maxpooling--#
pooled = tf.nn.max_pool(value=h,
ksize=[1, self.max_seq_len - filter_size + 1, 1, 1],
strides=[1, 1, 1, 1],
padding='VALID',
name='max_pooling')
pooled_outputs.append(pooled)
#--combine all the pooled features--#
total_num_filters = sum(self.num_filters)
self.h_pool = tf.concat(values=pooled_outputs, axis=3)
self.h_pool_flat = tf.reshape(self.h_pool, [-1, total_num_filters])
#--add highway--#
with tf.name_scope('highway'):
self.h_highway = self._highway(input_=self.h_pool_flat, size=self.h_pool_flat.get_shape()[1], num_layers=1, bias=0)
#--add dropout--#
with tf.name_scope('dropout'):
self.h_drop = tf.nn.dropout(x=self.h_highway, keep_prob=self.dropout_keep_prob)
#--l2 regularization loss--#
l2_loss = tf.constant(0.0)
#--final (unnormalized) scores and predictions--#
with tf.name_scope('output'):
W = tf.get_variable(name='W', shape=[total_num_filters, self.num_class], initializer=tf.truncated_normal_initializer(stddev=0.1))
b = tf.get_variable(name='b', shape=[self.num_class], initializer=tf.constant_initializer(0.1))
l2_loss += tf.nn.l2_loss(W)
l2_loss += tf.nn.l2_loss(b)
self.scores = tf.nn.xw_plus_b(self.h_drop, W, b, name="scores")
self.ypred_for_auc = tf.nn.softmax(self.scores)
self.predictions = tf.argmax(self.scores, 1, name="predictions")
#--calculat mean cross-entropy loss--#
with tf.name_scope("loss"):
losses = tf.nn.softmax_cross_entropy_with_logits_v2(logits=self.scores, labels=self.input_y)
self.loss = tf.reduce_mean(losses) + self.l2_reg_lambda * l2_loss
#--train_op--#
self.optimizer = tf.train.AdamOptimizer(self.lr)
self.params = [param for param in tf.trainable_variables() if 'discriminator' in param.name]
gradients = self.optimizer.compute_gradients(loss=self.loss, var_list=self.params, aggregation_method=2)
self.train_op = self.optimizer.apply_gradients(gradients)
#****************************************************#
#***************** HELPER FUNCTIONS *****************#
#****************************************************#
############
# _HIGHWAY #
############
"""
Called by build_model(). Highway Network (cf. http://arxiv.org/abs/1505.00387).
t = sigmoid(Wy + b)
z = t * g(Wy + b) + (1 - t) * y
where g is nonlinearity, t is transform gate, and (1 - t) is carry gate.
borrowed from https://github.com/mkroutikov/tf-lstm-char-cnn.
"""
def _highway(self, input_, size, num_layers=1, bias=-2.0, f=tf.nn.relu, scope='Highway'):
with tf.variable_scope(scope):
for idx in range(num_layers):
g = f(self._linear(input_, size, scope='highway_lin_%d' % idx))
t = tf.sigmoid(self._linear(input_, size, scope='highway_gate_%d' % idx) + bias)
output = t * g + (1. - t) * input_
input_ = output
return output
###########
# _LINEAR #
###########
"""
Called by _highway().
An alternative to tf.nn.rnn_cell._linear function, which has been removed in Tensorfow 1.0.1
Linear map: output[k] = sum_i(Matrix[k, i] * input_[i] ) + Bias[k]
Args:
input_: a tensor or a list of 2D, batch x n, Tensors.
output_size: int, second dimension of W[i].
scope: VariableScope for the created subgraph; defaults to "Linear".
Returns:
A 2D Tensor with shape [batch x output_size] equal to
sum_i(input_[i] * W[i]), where W[i]s are newly created matrices.
Raises:
ValueError: if some of the arguments has unspecified or wrong shape.
"""
def _linear(self, input_, output_size, scope=None):
shape = input_.get_shape().as_list()
if len(shape) != 2:
raise ValueError("Linear is expecting 2D arguments: %s" % str(shape))
if not shape[1]:
raise ValueError("Linear expects shape[1] of arguments: %s" % str(shape))
input_size = shape[1]
with tf.variable_scope(scope or "SimpleLinear"):
matrix = tf.get_variable("Matrix", [output_size, input_size], dtype=input_.dtype)
bias_term = tf.get_variable("Bias", [output_size], dtype=input_.dtype)
return tf.matmul(input_, tf.transpose(matrix)) + bias_term
########
# MAIN #
########
"""
For testing and debug purpose
"""
if __name__ == '__main__':
discriminator = Discriminator(config)
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template/__init__.py | khanhcsc/tts-bot | 0 | 172512 | <gh_stars>0
from template.bot import Bot
from template.context import Context
from template.handle import handle
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statuspage_io.py | spyder007/pi-monitoring | 0 | 20606 | <reponame>spyder007/pi-monitoring
import logging
import statuspage_io_client
import configuration
from enums import OpLevel
logger = logging.getLogger(__name__)
class Incident:
"""Incident Class
This class represents the details about a Statuspage.io incident
Attributes:
name: The incident name.
description: The incident description.
"""
name: str = "Incident Name"
description: str = "Incident Description"
class IncidentResult:
"""IncidentResult Class
This class represents information about incidents created or resolved as part of a status change
Attributes:
incidentCreated: True if an incident was created, false otherwise.
incidentResolved: True if an incident was created, false otherwise.
"""
incidentCreated: bool = False
incidentResolved: bool = False
incident: Incident
def __init__(self):
self.incidentCreated = False
self.incidentResolved = False
self.incident = Incident()
class StatusResult:
"""StatusResult Class
This class represents information about actions taken during a check and update.
Attributes:
statusChanged: True if the status has changed from the previous check, false otherwise.
incidentResult: An instance of [IncidentResult][statuspage_io.IncidentResult].
"""
statusChanged: bool = False
incidentResult: IncidentResult = IncidentResult()
def __init__(self):
self.incidentResult = IncidentResult()
class StatusPageOperator:
"""StatusResult Class
This class represents information about actions taken during a check and update.
Attributes:
config: An instance of [StatusPageSettings][configuration.StatusPageSettings] which contains settings for Statuspage.io communication
client: An instance of [StatusPageClient][statuspage_io_client.StatusPageClient], built from the configuration values provided.
"""
config: configuration.StatusPageSettings = configuration.StatusPageSettings()
client: statuspage_io_client.StatusPageClient
def __init__(self, statusPageConfig: configuration.StatusPageSettings):
""" Constructor
Initialize the instance using the provided [StatusPageSettings][configuration.StatusPageSettings].
"""
self.config = statusPageConfig
self.client = statuspage_io_client.StatusPageClient(
self.config.apiKey, self.config.pageId)
def IsConfigured(self) -> bool:
""" Validate configuration data
Returns:
True if the operator has a valid configuration, False otherwise.
"""
return self.config.apiKey != ""
def UpdateComponentStatus(self, componentId: str, opLevel: OpLevel, incidentDetails: Incident = {}) -> StatusResult:
""" Update Component Status
Using the provided OpLevel, determine the component's statuspage.io status.
If the incoming `opLevel` is [Operational][enums.OpLevel] and the statuspage.io status is not, the component's status will be changed to `operational`, and any open incidents for that component will be resolved.
If the incoming `opLevel` is any other value and the statuspage.io status is operational, the component's status will be changed to `major_outage` and an incident will be created using the provided `incidentDetails`
Args:
componentId: The component ID to check
opLevel: The current OpLevel for the provided component
incidentDetails: An instance of [Incident][statuspage_io.Incident] which has the details of the incident to be created, if necessary.
Returns:
An instance of [StatusResult][statuspage_io.StatusResult]
"""
if opLevel == OpLevel.Operational:
componentStatus = "operational"
else:
componentStatus = "major_outage"
if (componentStatus not in self.client.component_status_list):
raise ValueError(str.format(
"Invalid status '{0}'. Valid values are {1}", componentStatus, self.client.component_status_list))
result = StatusResult()
component = self.client.getComponent(componentId)
if (component.status != componentStatus):
result.statusChanged = True
logger.info("Changing status from %s to %s",
component.status, componentStatus)
self._updateComponentStatus(componentId, componentStatus)
result.incidentResult = self._processIncidentOnStatusChange(
componentId, componentStatus, incidentDetails)
return result
def _updateComponentStatus(self, componentId, newComponentStatus):
if (newComponentStatus not in self.client.component_status_list):
raise ValueError(str.format(
"Invalid status '{0}'. Valid values are {1}", newComponentStatus, self.client.component_status_list))
logger.debug("Setting component status to %s: %s",
newComponentStatus, componentId)
payload = {"component": {"status": newComponentStatus}}
self.client.updateComponent(componentId, payload)
def _filter_set(self, incidents, componentId):
def iterator_func(incident):
for comp in incident.components:
if comp.id == componentId:
return True
return False
return filter(iterator_func, incidents)
def _getAssociatedIncident(self, componentId):
result = self.client.getUnresolvedIncidents()
return list(self._filter_set(result, componentId))
def _processIncidentOnStatusChange(self, componentId: str, newComponentStatus: str, incidentDetails: Incident) -> IncidentResult:
''' Create or Close incidents based on the incoming component status
For now, if it's operational, close open incidents, and if it's not operational, create a new
ticket if one isn't already open for this component. Future state will involve more detail around outage and maintenance
'''
incidentResult = IncidentResult()
incidentResult.incident = incidentDetails
associatedIncidents = self._getAssociatedIncident(componentId)
asscIncidentCount = len(associatedIncidents)
logger.info("Associated Incidents for %s: %d",
componentId, asscIncidentCount)
if (newComponentStatus == "operational" and asscIncidentCount > 0):
for incident in associatedIncidents:
self._closeIncident(incident.id)
incidentResult.incidentResolved = True
elif (newComponentStatus == "major_outage" and asscIncidentCount == 0):
self._createIncident(
componentId, newComponentStatus, incidentDetails)
incidentResult.incidentCreated = True
return incidentResult
def _closeIncident(self, incidentId):
logger.info("Closing incident %s", incidentId)
payload = {"incident": {"status": "resolved"}}
self.client.updateIncident(incidentId, payload)
def _createIncident(self, componentId, newComponentStatus: str, incidentDetails: Incident):
logger.info("Creating incident: Component %s - New Component Status %s",
componentId, newComponentStatus)
payload = {"incident":
{
"name": incidentDetails.name,
"status": "investigating",
"body": incidentDetails.description,
"component_ids": [componentId],
"components": {componentId: newComponentStatus}
}
}
self.client.createIncident(payload)
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AR_Proxies.py | maquinolopez/ProxyUQ | 0 | 114906 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jan 12 11:00:26 2022
@author: jac
"""
from numpy import array
from pandas import read_csv, unique
from ProxyUQ import ProxyUQ
from pyplotfuncmc import PlotSolnsMC
cat = read_csv("AtmosphericRivers/AR_Cat.csv")
ARivers = []
for y in unique(cat['Year']):
tmp = cat.loc[cat['Year'] == y]
intensity = 0
for index, row in tmp.iterrows():
#intensity += row['Hours']*row['Category']
intensity += row['IWV max']
#print("%d - %f" % (y,intensity))
ARivers += [[y,intensity]]
ARivers = array(ARivers)
#rt = ProxyUQ( "AtmosphericRivers/LL14", p_list=[1,2,3,4,5,6], y_by=1)
ax, quan = PlotSolnsMC( rt[0], rt[4])
ax.plot( 1950-ARivers[:,0], ARivers[:,1]/5000+0.1, '-')
ax.set_ylabel("Al/Si")
ax.set_xlabel("y BP")
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flask_sspi/_common.py | ceprio/flask-sspi | 0 | 122944 | import sspi, sspicon
import win32api
import base64
import logging
logger = logging.getLogger(__name__)
from flask import Response
from flask import _request_ctx_stack as stack
from flask import make_response
from flask import request, session, g
import threading
from functools import wraps
from socket import gethostname
import os
import datetime
from uuid import uuid4
_PKG_NAME = 'NTLM' # OR 'Negotiate' in future implementations (for kerberos)
_sessions = {} # There is going to be one _sessions per process
_sessions_lock = threading.Lock() # each process may have threads
# time before a user needs to be re-authenticated
_session_duration = 30 # in minutes, don't change dynamically
def _user_context_processor():
if hasattr(g, "current_user") and g.current_user is not None:
return dict(current_user=g.current_user)
else:
return {}
def init_sspi(app, service='HTTP', hostname=gethostname(), package='NTLM', add_context_processor=True, session_duration=None):
'''
Configure the SSPI service, and validate the presence of the
appropriate informations if necessary.
:param app: a flask application
:type app: flask.Flask
:param service: GSSAPI service name
:type service: str
:param hostname: hostname the service runs under
:type hostname: str
:param package: package the service runs under ('NTLM') ('Negotiate' is not yet implemented)
:type package: str
:param add_context_processor: Adds a context processor that find the current_user name from flask g variable content
:type add_context_processor: bool
:param session_duration: in minutes, time before a user needs to be re-authenticated
:type session_duration: int
'''
global _SERVICE_NAME
_SERVICE_NAME = "%s@%s" % (service, hostname)
_PKG_NAME = package
if session_duration:
_session_duration = session_duration
if add_context_processor:
app.context_processor(_user_context_processor)
def _unauthorized(token):
'''
Indicate that authentication is required
:param token: token for the next negotiation or None for the first try
:type token: str
'''
if not token:
return Response('Unauthorized', 401, {'WWW-Authenticate': 'NTLM', 'server':'Microsoft-IIS/8.5'}, mimetype='text/html') # this can also be Negotiate but does not work on my server
else:
return Response('Unauthorized', 401, {'WWW-Authenticate': token, 'server':'Microsoft-HTTPAPI/2.0'}, mimetype='text/html') # this can also be Negotiate but does not work on my server
def _forbidden():
'''
Indicate a complete authentication failure
'''
return Response('Forbidden', 403)
def _get_user_name():
try:
return win32api.GetUserName()
except win32api.error as details:
# Seeing 'access denied' errors here for non-local users (presumably
# without permission to login locally). Get the fully-qualified
# username, although a side-effect of these permission-denied errors
# is a lack of Python codecs - so printing the Unicode value fails.
# So just return the repr(), and avoid codecs completely.
return repr(win32api.GetUserNameEx(win32api.NameSamCompatible))
def _sspi_authenticate(token):
'''
Performs GSSAPI Negotiate Authentication
On success also stashes the server response token for mutual authentication
at the top of request context with the name sspi_token, along with the
authenticated user principal with the name sspi_user.
@param token: Authentication Token
@type token: str
@returns sspi return code or None on failure and token
@rtype: str or None
'''
global _sessions, _sessions_lock
uuid = session['uuid']
if token.startswith(_PKG_NAME):
recv_token_encoded = ''.join(token.split()[1:])
recv_token = base64.b64decode(recv_token_encoded)
with _sessions_lock:
_sa = _sessions[uuid]['sa']
lock = _sessions[uuid]['lock']
lock.acquire()
try:
error_code, token = _sa.authorize(recv_token)
except sspi.error as details:
logger.debug(f"sspi.error: {details}")
# TODO: Close _sa?
with _sessions_lock:
del _sessions[uuid]
return None, None
finally:
lock.release()
token = token[0].Buffer
if token:
token = f"{_PKG_NAME} {base64.b64encode(token).decode('utf-8')}"
return error_code, token # standard exit; different error codes for different stages
raise Exception("Wrong authentication mode")
def cleanup_sessions():
# cleanup other entries according to 'last_access'
global _sessions, _sessions_lock
with _sessions_lock:
del_sessions = []
for key, d in _sessions.items():
if d['lock'].locked():
continue
if _session_duration * 60 < (datetime.datetime.now() - d['last_access']).seconds:
del_sessions.append(key)
for key in del_sessions:
del _sessions[key]
def _init_session():
global _sessions, _sessions_lock
logger.debug("Init session")
if 'uuid' not in session:
session['uuid'] = uuid = uuid4().bytes # init uuid on client
else:
uuid = session['uuid']
with _sessions_lock:
if uuid not in _sessions: # make sure
_sessions[uuid] = {
'sa': sspi.ServerAuth(_PKG_NAME),
'lock': threading.Lock(),
'last_access': datetime.datetime.now(),
}
cleanup_sessions()
def _sspi_handler(session):
global _sessions, _sessions_lock
if 'uuid' not in session or session['uuid'] not in _sessions:
_init_session()
uuid = session['uuid']
if 'username' in _sessions[uuid]: # 'username' is used to know if sspi authorized
if _session_duration * 60 < (datetime.datetime.now() - _sessions[uuid]['last_access']).seconds:
logger.debug('timed out.')
with _sessions_lock:
if uuid in _sessions: # make sure
del _sessions[uuid]
_init_session()
else:
logger.debug('Already authenticated')
with _sessions[uuid]['lock']:
_sessions[uuid]['last_access'] = datetime.datetime.now()
return None
token_encoded = None
recv_token_encoded = request.headers.get("Authorization")
if recv_token_encoded:
logger.debug(f"recv:{recv_token_encoded}")
rc, token_encoded = _sspi_authenticate(recv_token_encoded)
if rc == sspicon.SECPKG_NEGOTIATION_COMPLETE:
logger.debug("Negotiation complete")
return None
elif rc not in (sspicon.SEC_I_CONTINUE_NEEDED, sspicon.SEC_I_COMPLETE_NEEDED, sspicon.SEC_I_COMPLETE_AND_CONTINUE):
logger.debug(f"Forbiden rc={rc}")
return _forbidden()
logger.debug(f"Unauthorized yet, continue: {token_encoded}")
return _unauthorized(token_encoded) # token is None on fist pass
class Impersonate():
'''
Class that creates a context for the impersonalisation of the client user.
May be used to get his name or group appartenance. Could also be used
to make trusted connections with databases (not tested).
Preferred usage:
with Impersonate():
...
'''
def __init__(self, _session=None):
""" If _session is passed as argument IT MUST BE LOCKED.
This allows the use of Impersonate within a locked session context.
"""
self._session = _session
def open(self):
'''
Start of the impersonalisation
'''
global _sessions, _sessions_lock
if not self._session:
uuid = session['uuid']
with _sessions_lock:
_sessions[uuid]['lock'].acquire() # make sure to unlock
self.lock = _sessions[uuid]['lock']
self._sa = _sessions[uuid]['sa']
else:
self._sa = self._session['sa']
self._sa.ctxt.ImpersonateSecurityContext()
def close(self):
'''
End of the impersonalisation
'''
if self._sa:
self._sa.ctxt.RevertSecurityContext()
self._sa = None
if not self._session:
self.lock.release()
def __del__(self):
if self._sa:
self.close()
def __enter__(self):
self.open()
return self
def __exit__(self, type, value, tb):
self.close()
def requires_authentication(function):
'''
Require that the wrapped view function only be called by users
authenticated with SSPI. The view function will have the authenticated
users principal passed to it as its first argument.
:param function: flask view function
:type function: function
:returns: decorated function
:rtype: function
'''
global _sessions, _sessions_lock
@wraps(function)
def decorated(*args, **kwargs):
ret = _sspi_handler(session)
if ret is not None:
return ret
else:
uuid = session['uuid']
with _sessions_lock:
_session = _sessions[uuid]
lock = _session['lock']
lock.acquire()
try:
if 'username' not in _session:
# get username through impersonalisation
with Impersonate(_session):
current_user = _get_user_name()
g.current_user = current_user
_session['username'] = current_user
_session['last_access'] = datetime.datetime.now()
else:
g.current_user = _session['username']
finally:
lock.release()
# call route function
response = function(g.current_user, *args, **kwargs)
response = make_response(response)
return response
return decorated
def authenticate(function):
'''
Require that the wrapped view function only be called by users
authenticated with SSPI.
:param function: flask view function
:type function: function
:returns: decorated function
:rtype: function
'''
global _sessions, _sessions_lock
@wraps(function)
def decorated(*args, **kwargs):
ret = _sspi_handler(session)
if ret is not None:
return ret
else:
uuid = session['uuid']
with _sessions_lock:
_session = _sessions[uuid]
lock = _session['lock']
lock.acquire()
try:
if 'username' not in _session:
# get username through impersonalisation
with Impersonate(_session):
current_user = _get_user_name()
g.current_user = current_user
_session['username'] = current_user
_session['last_access'] = datetime.datetime.now()
else:
g.current_user = _session['username']
finally:
lock.release()
# call route function
response = function(*args, **kwargs)
if response:
response = make_response(response)
return response
return decorated
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] |
app/improving_agent/src/template_queries/drug_may_treat_disease.py | suihuanglab/evidARA | 0 | 69481 | <reponame>suihuanglab/evidARA<filename>app/improving_agent/src/template_queries/drug_may_treat_disease.py
from improving_agent.models import Edge, EdgeBinding, NodeBinding, Result
from improving_agent.src.biolink.spoke_biolink_constants import SPOKE_LABEL_COMPOUND
from improving_agent.exceptions import TemplateQuerySpecError, UnmatchedIdentifierError
from improving_agent.src.basic_query import BasicQuery
from improving_agent.src.normalization.edge_normalization import (
BIOLINK_TREATS,
BIOLINK_DISEASE,
KNOWLEDGE_TYPE_INFERRED,
SUPPORTED_INFERRED_DRUG_SUBJ
)
from improving_agent.src.provenance import IMPROVING_AGENT_PROVENANCE_ATTR
from improving_agent.src.psev import get_psev_scores
from improving_agent.util import get_evidara_logger
logger = get_evidara_logger(__name__)
CYPHER_COMPOUND_SEARCH = """
MATCH (c:Compound)
WHERE c.identifier in $identifiers
RETURN c
"""
def extract_compound_result(record, querier):
node_info = record['c']
identifier = node_info['identifier']
result_node = querier.make_result_node(node_info, identifier)
return identifier, result_node
def compound_search(tx, identifiers, querier):
records = tx.run(CYPHER_COMPOUND_SEARCH, identifiers=identifiers)
result_nodes = {}
for record in records:
identifier, result_node = extract_compound_result(record, querier)
result_nodes[identifier] = result_node
return result_nodes
class DrugMayTreatDisease:
template_query_name = 'Drug -- may treat -- Disease'
# TODO: abstract if possible once other templates are known
def __init__(self, qnodes, qedges, query_options, max_results):
# query config
self.qnodes = qnodes
self.qedges = qedges
self.query_options = query_options
self.max_results = max_results
# convenience references
self.edge_id_treats = list(self.qedges.keys())[0]
self.node_id_compound = self.qedges[self.edge_id_treats].subject
self.node_id_disease = self.qedges[self.edge_id_treats].object
# results
self.knowledge_graph = None
@staticmethod
def matches_template(qedges, qnodes):
if len(qedges) > 1:
return False
for qedge in qedges.values():
if (
qedge.knowledge_type != KNOWLEDGE_TYPE_INFERRED
or qedge.predicates != [BIOLINK_TREATS]
):
return False
if len(qnodes) != 2:
return False
if not all(cat in SUPPORTED_INFERRED_DRUG_SUBJ
for cat
in qnodes[qedge.subject].categories):
return False
if qnodes[qedge.object].categories != [BIOLINK_DISEASE]:
return False
return True
def make_result_edge(self, subj_id, obj_id):
return Edge(
predicate='biolink:treats',
subject=subj_id,
object=obj_id,
attributes=[IMPROVING_AGENT_PROVENANCE_ATTR]
)
def do_query(self, session):
logger.info(f'Doing template query: {self.template_query_name}')
# first get psev scores for concept; if we don't have it there's
# no point continuing
if len(self.query_options['psev_context']) > 1:
raise TemplateQuerySpecError(
f'For template query={self.template_query_name} imProving Agent '
'expects exactly one disease specified on the object node. Disease '
'identifier must map to Disease Ontology via the Node Normalizer.'
)
disease_concept = self.query_options['psev_context'][0]
compound_psev_scores = get_psev_scores([disease_concept], node_type=SPOKE_LABEL_COMPOUND)[disease_concept]
if not compound_psev_scores:
raise UnmatchedIdentifierError(
f'No ML predictions available for disease equivalent to {disease_concept}'
)
# do lookup
basic_query = BasicQuery(
self.qnodes,
self.qedges,
self.query_options,
self.max_results
)
results, knowledge_graph = basic_query.do_query(session)
# sort compound_psev_scores
count_to_get = self.max_results - len(results)
sorted_compound_scores = {
k: v
for k, v
in sorted(compound_psev_scores.items(), key=lambda item: item[1])[:count_to_get]
}
# remove the known to treat compounds from the top scored
for node in knowledge_graph['nodes'].values():
for attribute in node.attributes:
if attribute.original_attribute_name == 'identifier':
try:
sorted_compound_scores.pop(attribute.value)
except KeyError:
continue
if not sorted_compound_scores:
return results, knowledge_graph
# now we can add the remaining highly scored results
self.knowledge_graph = knowledge_graph
new_results = []
node_ids = list(sorted_compound_scores.keys())
result_nodes = session.read_transaction(compound_search, node_ids, basic_query)
for i, id_ in enumerate(result_nodes):
result_edge = self.make_result_edge(id_, disease_concept)
self.knowledge_graph['edges'][f'inferred_{i}'] = result_edge
self.knowledge_graph['nodes'][id_] = result_nodes[id_]
new_results.append(Result(
node_bindings={self.node_id_disease: NodeBinding(disease_concept),
self.node_id_compound: NodeBinding(id_)},
edge_bindings={self.edge_id_treats: EdgeBinding(f'inferred_{i}')},
score=sorted_compound_scores[id_]
))
results = sorted(results + new_results, key=lambda x: x.score, reverse=True)
return results, self.knowledge_graph
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] |
src/sellers/migrations/0002_rename_description_seller_descr.py | evis-market/web-interface-backend | 2 | 61431 | # Generated by Django 3.2.7 on 2021-10-03 15:09
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
('sellers', '0001_initial'),
]
operations = [
migrations.RenameField(
model_name='seller',
old_name='description',
new_name='descr',
),
]
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] |
src/utils/auto_node_create.py | MoD-i/data-exchange-backend | 0 | 95033 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
# created_on: 2018-07-27 21:37
"""
auto_node_create.py
AIM: Automatically:
1. Install Multichain
2. Check/Use or Create new Node
3. Connect Node with MoD-i Blockchain
Pre-requisites:
1. OS: Linux(Debian) or Windows
2. `sudo` password in Linux
3. Python >= 3.6
"""
import os
import subprocess
import requests
import socket
import getpass
from pathlib import Path
import re
import sys
import logging
__version__ = '1.0.0'
__author__ = '<NAME> <<EMAIL>>'
__copyright__ = 'Copyright (C) 2018 MoD-i. All rights reserved.'
__license__ = 'Distributed under terms of the MIT license.'
logger = logging.getLogger(__name__)
HOSTNAME = socket.gethostname()
USER = getpass.getuser()
COUNT = 0
SUFFIX = 'node'
HOME_DIR = str(Path.home())
BASE_NAME = f'{HOSTNAME}-{USER}-{SUFFIX}'
NODE_NAME = f'{BASE_NAME}{COUNT}'
NODE_DIR = os.path.join(HOME_DIR, NODE_NAME)
REGEX = re.escape(BASE_NAME) + r'[0-9]+'
RE_OBJ = re.compile(REGEX, re.IGNORECASE)
EXISTING_NODES = []
##
# check if all-ready a MoD-i created default node present
# default node name: {hostname}-{count}-node
##
def check_node():
found = 0
for dirs in os.listdir(HOME_DIR):
if RE_OBJ.match(dirs):
found += 1
EXISTING_NODES.append(dirs)
return found
def create_node():
global NODE_DIR
if len(EXISTING_NODES) > 0:
logger.warning('Creating another node.')
last_node_no = max(map(lambda node: int(node[-1]), EXISTING_NODES))
new_node_no = last_node_no + 1
os.mkdir(os.path.join(HOME_DIR, BASE_NAME + str(new_node_no)))
NODE_DIR = str(os.path.join(HOME_DIR, BASE_NAME + str(new_node_no)))
else:
logger.warning('Creating new node.')
os.mkdir(NODE_DIR)
def connect_node():
global NODE_DIR
print('command\n:', NODE_DIR)
# p = subprocess.run(['multichaind', f'-datadir={NODE_DIR}', '[email protected]:2657'], shell=True,
# p = subprocess.run(['multichaind -datadir=/home/toran/mint-ThinkPad-L440-root-node0 [email protected]:2657'], shell=True,
p = subprocess.run([f'multichaind -datadir={NODE_DIR} [email protected]:2657'], shell=True,
stdout=subprocess.PIPE)
res = p.stdout.decode()
print(res)
def install_multichain():
# TODO: check if already installed and skip
os.chdir('/tmp/')
subprocess.run(['wget', 'https://www.multichain.com/download/multichain-1.0.5.tar.gz'])
subprocess.run(['tar', '-xvzf', 'multichain-1.0.5.tar.gz'])
os.chdir('multichain-1.0.5')
subprocess.run(['sudo', 'mv', 'multichaind', 'multichain-cli', 'multichain-util', '/usr/local/bin'])
if __name__ == '__main__':
found = check_node()
if found==1:
print(f'There is already {found} nodes linked to the MoD-i blockchain')
elif found>1:
print(f'There are already {found} nodes linked to the MoD-i blockchain')
while True:
if found == 0:
user_inp = input("Do you want to create a node [y/n] : ")
else:
user_inp = input("Do you still want to create a new node [y/n] : ")
if user_inp.lower() in ('n', 'no'):
logger.info('Aborted. Exiting.')
sys.exit()
elif user_inp.lower() in ('y', 'yes'):
install_multichain()
logger.info('multichain installed')
create_node()
logger.info('One node created.')
connect_node()
logger.info('Node connected.')
# TODO: Tell datadir, chain name etc
sys.exit()
else:
print('Please enter a valid option')
logger.info('Invaid option entered.')
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] |
src/terial/web/views/classifier_views.py | keunhong/photoshape | 81 | 69563 | <reponame>keunhong/photoshape
import logging
import math
import subprocess
import json
from collections import defaultdict
from pathlib import Path
import aiohttp_jinja2
import uuid
from aiohttp import web
import numpy as np
from multidict import MultiDict
import toolbox.web
from terial import config, models, controllers
from terial.classifier.inference.utils import compute_weighted_scores
from terial.database import session_scope
logger = logging.getLogger(__name__)
def get_model_inference_dir(snapshot_name, model_name):
snapshot_dir = config.BRDF_CLASSIFIER_SNAPSHOTS_DIR / snapshot_name
return snapshot_dir / 'inference' / model_name
@aiohttp_jinja2.template('classifier/list_models.html')
async def list_models(request: web.Request):
models_by_snapshot = defaultdict(list)
snapshot_paths = list(reversed(sorted(
(config.BRDF_CLASSIFIER_DIR_REMOTE / 'lmdb').iterdir())))
snapshot_paths.extend(reversed(sorted(
config.BRDF_CLASSIFIER_SNAPSHOTS_DIR.iterdir())))
for snapshot_path in snapshot_paths:
snapshot_name = snapshot_path.name
checkpoint_dir = Path(config.BRDF_CLASSIFIER_DIR_REMOTE,
'checkpoints', snapshot_name)
if not checkpoint_dir.exists():
continue
model_json_paths = reversed(sorted(
checkpoint_dir.glob('*/model_params.json')))
for model_json_path in model_json_paths:
model_name = model_json_path.parent.name
with model_json_path.open('r') as f:
model_params = json.load(f)
best_stats_path = model_json_path.parent / 'model_best_stats.json'
if best_stats_path.exists():
with best_stats_path.open('r') as f:
best_stats = json.load(f)
else:
best_stats = None
snapshot_name = snapshot_path.name
model_inference_dir = (config.BRDF_CLASSIFIER_DIR_REMOTE / 'inference'
/ snapshot_name / model_name)
if model_inference_dir.exists():
inference_epochs = [p.name for p in model_inference_dir.iterdir()]
else:
inference_epochs = []
models_by_snapshot[snapshot_name].append({
'params': model_params,
'best_stats': best_stats,
'snapshot_name': snapshot_path.name,
'model_name': model_json_path.parent.name,
'model_path': str(model_json_path),
'inference_epochs': inference_epochs,
})
return {
'models_by_snapshot': models_by_snapshot,
}
@aiohttp_jinja2.template('classifier/list_models_ablation.html')
async def list_models_ablation(request: web.Request):
models_by_snapshot = defaultdict(list)
snapshot_paths = list(reversed(sorted(
(config.BRDF_CLASSIFIER_DIR_REMOTE / 'lmdb').iterdir())))
snapshot_paths.extend(reversed(sorted(
config.BRDF_CLASSIFIER_SNAPSHOTS_DIR.iterdir())))
for snapshot_path in snapshot_paths:
snapshot_name = snapshot_path.name
checkpoint_dir = Path(config.BRDF_CLASSIFIER_DIR_REMOTE, 'checkpoints',
snapshot_name)
if not checkpoint_dir.exists():
continue
model_json_paths = reversed(sorted(
checkpoint_dir.glob('*/model_params.json')))
for model_json_path in model_json_paths:
model_name = model_json_path.parent.name
with model_json_path.open('r') as f:
model_params = json.load(f)
best_stats_path = model_json_path.parent / 'model_best_stats.json'
if best_stats_path.exists():
with best_stats_path.open('r') as f:
best_stats = json.load(f)
else:
best_stats = None
train_stats_path = model_json_path.parent / 'model_train_stats.json'
if train_stats_path.exists():
try:
with train_stats_path.open('r') as f:
train_stats = json.load(f)
except json.JSONDecodeError:
train_stats = None
else:
train_stats = None
snapshot_name = snapshot_path.name
model_inference_dir = (config.BRDF_CLASSIFIER_DIR_REMOTE / 'inference'
/ snapshot_name / model_name)
if model_inference_dir.exists():
inference_epochs = [p.name for p in model_inference_dir.iterdir()]
else:
inference_epochs = []
models_by_snapshot[snapshot_name].append({
'params': model_params,
'best_stats': best_stats,
'train_stats': train_stats,
'snapshot_name': snapshot_path.name,
'model_name': model_json_path.parent.name,
'model_path': str(model_json_path),
'inference_epochs': inference_epochs,
})
return {
'models_by_snapshot': models_by_snapshot,
}
async def download_blend_file(request: web.Request):
inference_path = request.query.get('inference_path', None)
if not inference_path:
raise web.HTTPNotFound()
inference_path = Path(inference_path)
if not inference_path.exists():
raise web.HTTPNotFound()
animate = request.query.get('animate', 'false') == 'true'
no_floor = request.query.get('no_floor', 'false') == 'true'
scene_type = request.query.get('type', 'inferred')
if scene_type not in {'inferred', 'mtl'}:
raise web.HTTPBadRequest(text="Invalid scene type.")
filename = Path('/tmp', f'{uuid.uuid4()}.blend')
command = [
'python', '-m', 'terial.classifier.rendering.create_blend_file',
str(inference_path), filename,
'--pack-assets',
'--type', scene_type,
'--use-weighted-scores',
# '--use-minc-substances',
]
if animate:
command.append('--animate')
if no_floor:
command.append('--no-floor')
logger.info('Launching command %s', str(command))
subprocess.call(command)
if animate:
out_name = f'{inference_path.stem}.{scene_type}.anim.blend'
else:
out_name = f'{inference_path.stem}.{scene_type}.blend'
response = web.StreamResponse(
status=200,
headers=MultiDict({
'Content-Disposition': f'attachment; filename={out_name}'
}),
)
await response.prepare(request)
with filename.open('rb') as f:
await response.write(f.read())
await response.write_eof()
return response
@aiohttp_jinja2.template('classifier/inference_results_detailed.html')
async def show_inference_results_detailed(request):
return await show_inference_results(request)
@aiohttp_jinja2.template('classifier/inference_results_simple.html')
async def show_inference_results_simple(request):
return await show_inference_results(request)
async def show_inference_results(request: web.Request):
snapshot_name = request.match_info.get('snapshot')
model_name = request.match_info.get('model')
epoch = request.match_info.get('epoch')
page = int(request.query.get('page', 0))
page_size = int(request.query.get('page_size', 12))
topk = int(request.query.get('topk', 3))
shape_ids = request.query.get('shape_ids', None)
pair_ids = request.query.get('pair_ids', None)
shape_source = request.query.get('shape_source', None)
shape_category = request.query.get('shape_category', None)
max_dist = float(request.query.get('max_dist', config.INFERENCE_MAX_DIST))
if shape_ids is not None:
shape_ids = shape_ids.replace(' ', '').strip(', ')
shape_ids = [int(i) for i in shape_ids.split(',')]
if pair_ids is not None:
pair_ids = pair_ids.replace(' ', '').strip(', ')
pair_ids = [int(i) for i in pair_ids.split(',')]
if model_name is None:
raise web.HTTPBadRequest()
if snapshot_name is None:
raise web.HTTPBadRequest()
snapshot_dir = config.BRDF_CLASSIFIER_DIR_REMOTE / 'snapshots' / snapshot_name
if not snapshot_dir.exists():
snapshot_dir = config.BRDF_CLASSIFIER_DIR_REMOTE / 'lmdb' / snapshot_name
if not snapshot_dir.exists():
raise web.HTTPNotFound()
inference_dir = (config.BRDF_CLASSIFIER_DIR_REMOTE / 'inference'
/ snapshot_name / model_name / epoch)
if not inference_dir.exists():
raise web.HTTPNotFound()
if (snapshot_dir / 'snapshot.json').exists():
with (snapshot_dir / 'snapshot.json').open('r') as f:
snapshot_dict = json.load(f)
else:
with (snapshot_dir / 'meta.json').open('r') as f:
snapshot_dict = json.load(f)
filters = []
if shape_ids:
filters.append(models.Shape.id.in_(shape_ids))
if pair_ids:
filters.append(models.ExemplarShapePair.id.in_(pair_ids))
if shape_source:
filters.append(models.Shape.source == shape_source)
if shape_category:
filters.append(models.Shape.category == shape_category)
if topk:
filters.append(models.ExemplarShapePair.rank <= topk)
with session_scope() as sess:
materials, _ = controllers.fetch_materials(sess)
mat_by_id = {
m.id: m for m in materials
}
shapes, count, pair_count = controllers.fetch_shapes_with_pairs(
sess, page=page,
page_size=page_size,
filters=filters,
max_dist=max_dist)
results_by_shape = _aggregate_shape_inferences(
inference_dir,
mat_by_id,
shapes, topk=topk, max_dist=max_dist)
n_pages = int(math.ceil(count / page_size))
return {
'snapshot_name': snapshot_name,
'dataset_name': snapshot_dict.get(
'dataset_name', snapshot_dict.get('dataset', '<unknown dataset>')),
'model_name': model_name,
'epoch': epoch,
'cur_page': page,
'page_size': page_size,
'n_total': count,
'n_pairs': pair_count,
'n_pages': n_pages,
'results_by_shape': results_by_shape,
'mat_by_id': mat_by_id,
}
def _aggregate_shape_inferences(inference_dir,
mat_by_id, shapes,
topk, max_dist):
results_by_shape = defaultdict(list)
for shape in shapes:
pairs = shape.get_topk_pairs(topk, max_dist)
for pair in pairs:
pair_inference = compute_pair_inference(
inference_dir, mat_by_id, pair)
if pair_inference is None:
continue
results_by_shape[pair.shape].append(pair_inference)
return results_by_shape
def compute_pair_inference(inference_dir, mat_by_id, pair):
# seg_substances = compute_segment_substances(pair, return_ids=True)
seg_substances = None
json_path = Path(inference_dir, f'{pair.id}.json')
if not json_path.exists():
logger.info('JSON path %s does not exist', json_path)
return None
with json_path.open('r') as f:
inference_dict = json.load(f)
try:
seg_map = pair.load_data(config.PAIR_SHAPE_CLEAN_SEGMENT_MAP_NAME) - 1
except FileNotFoundError:
seg_map = pair.load_data(config.PAIR_SHAPE_CLEAN_SEGMENT_MAP_NAME_OLD) - 1
seg_mask_by_seg_id = {}
for seg_id in np.unique(seg_map):
if seg_id == -1:
continue
seg_mask_by_seg_id[str(seg_id)] = toolbox.web.image_to_base64(
(seg_map == seg_id).astype(np.uint8) * 255)
# _remove_disabled_materials(inference_dict, mat_by_id)
compute_weighted_scores(inference_dict, mat_by_id, sort=True,
force_substances=True)
rend_baseline_path = (config.BRDF_CLASSIFIER_DIR_REMOTE
/ 'inference' / 'random' / 'renderings-cropped'
/ f'{pair.id}.inferred.0000.jpg')
rend_minc_inferred_path = (inference_dir.parent / '45-minc-subst'
/ 'renderings-cropped'
/ f'{pair.id}.inferred.0000.jpg')
rend_inferred_path = (inference_dir / 'renderings-cropped'
/ f'{pair.id}.inferred.0000.jpg')
# if not rend_inferred_path.exists():
# rend_inferred_path = (inference_dir / 'renderings-aligned-cropped'
# / f'{pair.id}.inferred.0000.jpg')
# if not rend_inferred_path.exists():
# rend_inferred_path = (inference_dir / 'renderings-cropped'
# / f'{pair.id}.inferred.0000.jpg')
rend_inferred_frontal_path = (inference_dir / 'renderings-frontal'
/ f'{pair.id}.inferred.0000.jpg')
rend_mtl_path = (config.BRDF_CLASSIFIER_DIR_REMOTE
/ 'inference' / 'default' / 'renderings-cropped'
/ f'{pair.id}.mtl.0000.jpg')
# rend_mtl_path = (inference_dir / 'renderings'
# / f'{pair.id}.mtl.0000.png')
rendering_path = inference_dir / 'renderings' / f'{pair.id}.png'
return {
'pair': pair,
'shape': pair.shape,
'exemplar': pair.exemplar,
'seg_mask_by_seg_id': seg_mask_by_seg_id,
'rend_inferred_path': rend_inferred_path,
'rend_inferred_frontal_path': rend_inferred_frontal_path,
'rend_minc_inferred_path': rend_minc_inferred_path,
'rend_mtl_path': rend_mtl_path,
'rend_baseline_path': rend_baseline_path,
'rendering_path': rendering_path,
'inference_path': json_path,
**inference_dict,
}
def _remove_disabled_materials(inference_dict, mat_by_id):
for seg_id, seg_topk in inference_dict['segments'].items():
seg_new_topk = []
for match in seg_topk['material']:
mat = mat_by_id[match['id']]
if mat.enabled:
seg_new_topk.append(match)
seg_topk['material'] = seg_new_topk | [
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1482,
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3332,
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] |
stve/application/__init__.py | TE-ToshiakiTanaka/stve | 0 | 182245 | from stve.application.stvetestrunner import StveTestRunner
| [
1,
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345,
29889,
6214,
29889,
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342,
27492,
1053,
624,
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2
] |
meiduo_mall/apps/carts/views.py | wuhaogithub/wuhao_project_2019_10 | 0 | 168457 | import json
from django.http import JsonResponse
from django.shortcuts import render
# Create your views here.
from django.views import View
from django_redis import get_redis_connection
from apps.goods.models import SKU
from utils.response_code import RETCODE
"""
1. 如果用户未登录,可以实现添加购物车的功能.
如果用户登录,也可以实现添加购物车的功能.
2.如果用户未登录, 我们要保存 商品id,商品数量,商品的选中状态
如果用户登录, 我们要保存 用户id, 商品id,商品数量,商品的选中状态
3.如果用户未登录, 保存在 浏览器中 cookie中
如果用户登录, 保存在数据库中 (为了让大家更好的学习redis)我们把数据保存到redis中
4. 如果用户未登录, cookie的数据格式
{
sku_id:{count:5,selected:True},
sku_id:{count:2,selected:False},
sku_id:{count:7,selected:True},
}
如果用户登录, Redis .Redis的数据是保存在内存中,
我们要尽量少的占用内存空间
user_id ,sku_id,count,selected
1, 100,2,True
101,5,False
102,10,True
103,10,False
key 100:2
selected_100:True
101:5
selected_101:False
102:10
selected_102:True
103:10
selected_103:False
hash
user_id 100:2
101:5
102:10
103:10
set 选中的在集合中
selected_user_id [100,102]
hash
user_id 100:2
101:-5
102:10
103:-10
5.
{
sku_id:{count:5,selected:True},
sku_id:{count:2,selected:False},
sku_id:{count:7,selected:True},
}
base64
1G = 1024MB
1M=1024KB
1KB=1024B
1B=8bite 比特位 0 1
A 0100 0001
0100 0001 0100 0001 0100 0001
A A A
010000 010100 000101 000001
x y z a
5.1 将字典转换为二进制
5.2 再进行base64编码
http://doc.redisfans.com/
"""
from django.contrib.auth.mixins import LoginRequiredMixin
class CartsView(View):
"""
1.功能分析
用户行为:
前端行为: 当用户点击加入购物车的时候,前端要收集用户信息,sku_id,count,默认是选中
后端行为:
2. 分析后端实现的大体步骤
1.接收数据,判断商品信息
2.先获取用户信息
3.根据用户是否登陆来判断
4.登陆用户操作数据(redis)
4.1 连接数据库
4.2 操作数据库
4.3 返回相应
5.未登录用户操作cookie
5.1 组织数据
5.2 对数据进行编码
5.3 设置cookie
5.4 返回相应
6.返回相应
3.确定请求方式和路由
POST carts
"""
def post(self,request):
# 1.接收数据,判断商品信息
data=json.loads(request.body.decode())
sku_id=data.get('sku_id')
count=data.get('count')
if not all([sku_id,count]):
return JsonResponse({'code':RETCODE.PARAMERR,'errmsg':'参数不全'})
try:
sku=SKU.objects.get(id=sku_id)
except SKU.DoesNotExist:
return JsonResponse({'code':RETCODE.NODATAERR,'errmsg':'没有此商品'})
try:
count=int(count)
except Exception:
return JsonResponse({'code':RETCODE.PARAMERR,'errmsg':"参数错误"})
#添加购物车默认就是选中
selected=True
# 2.先获取用户信息
user=request.user
# 3.根据用户是否登陆来判断
# is_authenticated 是认证用户(注册用户)
if user.is_authenticated:
# 4.登陆用户操作数据(redis)
# 4.1 连接数据库
redis_conn = get_redis_connection('carts')
# 4.2 操作数据库
# hash key:
# sku_id:count
# field:value
# field:value
# 需要累加数据
# redis_conn.hset('carts_%s'%user.id,sku_id,count)
# 一 创建管道
pl=redis_conn.pipeline()
# 二 将指令收集到管道中
pl.hincrby('carts_%s' % user.id, sku_id, count)
# set
pl.sadd('selected_%s' % user.id, sku_id)
# 三 执行管道
pl.execute()
# redis_conn.hincrby('carts_%s'%user.id,sku_id,count)
# # set
#
# redis_conn.sadd('selected_%s'%user.id,sku_id)
# 4.3 返回相应
return JsonResponse({'code':RETCODE.OK,'errmsg':'ok'})
else:
# 5.未登录用户操作cookie
# 5.0 先获取cookie中 可能存在的数据
carts_str=request.COOKIES.get('carts')
if carts_str is None:
#说明没有购物车数据
cookie_data = {
sku_id: {'count': count, 'selected': True}
}
else:
#说明有购物车数据
# 先base64解码
decode_data=base64.b64decode(carts_str)
# 再bytes转字典
cookie_data=pickle.loads(decode_data)
# 再需要进行判断
# {1:{count:5,selected:True}}
# 商品id是否在字典中
# 1
if sku_id in cookie_data:
#累加数量
origin_count=cookie_data[sku_id]['count']
# count=origin_count+count
count+=origin_count
#更新字典数据
cookie_data[sku_id]={'count':count,'selected':True}
else:
cookie_data[sku_id]={'count':count,'selected':True}
# 5.1 组织数据
"""
{
sku_id:{count:5,selected:True},
sku_id:{count:2,selected:False},
sku_id:{count:7,selected:True},
}
"""
# 5.2 对数据进行编码
# 字典转bytes
cookie_bytes=pickle.dumps(cookie_data)
# base64编码
cookie_str=base64.b64encode(cookie_bytes)
# 5.3 设置cookie
response=JsonResponse({'code':RETCODE.OK,'errmsg':'ok'})
response.set_cookie('carts',cookie_str,max_age=7*24*3600)
# 5.4 返回相应
return response
"""
1.功能分析
用户行为:
前端行为:
后端行为:
2. 分析后端实现的大体步骤
1.先获取用户信息
2.如果用户为登陆,则从cookie中获取信息
{
sku_id:{count:5,selected:True},
sku_id:{count:2,selected:False},
sku_id:{count:7,selected:True},
}
2.1 获取商品id
2.2 根据商品id进行商品信息的查询
2.3 将对象转换为字典
2.4 返回相应
3.如果用户登陆,则从redis中获取信息
3.1 连接redis
3.2 获取redis数据
hash sku_id:count
set [sku_id,sku_id]
3.3 获取商品id
3.4 根据商品id进行商品信息的查询
3.5 将对象转换为字典
3.6 返回相应
1.先获取用户信息
2.如果用户为登陆,则从cookie中获取信息
{
sku_id:{count:5,selected:True},
sku_id:{count:2,selected:False},
sku_id:{count:7,selected:True},
}
3.如果用户登陆,则从redis中获取信息
3.1 连接redis
3.2 获取redis数据
hash sku_id:count
set [sku_id,sku_id]
4 获取商品id
5 根据商品id进行商品信息的查询
6 将对象转换为字典
7 返回相应
3.确定请求方式和路由
"""
def get(self,request):
#
# 1.先获取用户信息
user=request.user
if user.is_authenticated:
# 3.如果用户登陆,则从redis中获取信息
# 3.1 连接redis
redis_conn = get_redis_connection('carts')
# 3.2 获取redis数据
# hash sku_id:count
# {sku_id:count,sku_id:count,....}
# {1:10,2:20}
id_counts=redis_conn.hgetall('carts_%s'%user.id)
# set [sku_id,sku_id]
# [sku_id,sku_id]
# [1]
selected_ids=redis_conn.smembers('selected_%s'%user.id)
#将redis数据转换为cookie格式
# cookie_str = {sku_id:{count:5,selected:True}}
cookie_dict = {}
for sku_id,count in id_counts.items():
# if sku_id in selected_ids:
# selected=True
# else:
# selected=False
cookie_dict[int(sku_id)]={
'count':int(count),
'selected':sku_id in selected_ids
}
else:
# 2.如果用户为登陆,则从cookie中获取信息
# {
# sku_id:{count:5,selected:True},
# sku_id:{count:2,selected:False},
# sku_id:{count:7,selected:True},
# }
#
cookie_data=request.COOKIES.get('carts')
if cookie_data is not None:
#先进行base64解码
cookie_dict=pickle.loads(base64.b64decode(cookie_data))
else:
cookie_dict={}
# 4 获取商品id -- 因为redis的数据结构和cookie的数据结构不一致
# 我们应该让他们的数据一致
# cookie_dict = {
# sku_id:{count:5,selected:True},
# sku_id:{count:2,selected:False},
# sku_id:{count:7,selected:True},
# }
ids=cookie_dict.keys() #[1,2,3,4,5,6]
# 5 根据商品id进行商品信息的查询
carts_list=[]
for id in ids:
sku=SKU.objects.get(id=id)
# 6 将对象转换为字典
carts_list.append({
'id':sku.id,
'name':sku.name,
'count': cookie_dict.get(sku.id).get('count'),
'selected': str(cookie_dict.get(sku.id).get('selected')), # 将True,转'True',方便json解析
'default_image_url':sku.default_image.url,
'price':str(sku.price), # 从Decimal('10.2')中取出'10.2',方便json解析
'amount':str(sku.price * cookie_dict.get(sku.id).get('count')),
})
# 7 返回相应
return render(request,'cart.html',context={'cart_skus':carts_list})
"""
1.功能分析
用户行为: 用户可能会点击某一个商品的数量/选中状态
前端行为: 前端需要收集 点击的 sku_id,count,selected 以及用户信息
后端行为: 实现更新
2. 分析后端实现的大体步骤
1.接收数据
2.验证数据
3.获取用户信息
4.登陆用户更新redis
4.1 连接redis
4.2 更新数据
4.3 返回相应
5.未登录用户更新cookie
5.1 获取cookie中的数据,并进行判断
如果有数据则需要进行解码
5.2 更新数据 cart={}
5.3 将字典进行编码
5.4 设置cookie
5.5 返回相应
3.确定请求方式和路由
"""
def put(self,request):
# 1.接收数据
data=json.loads(request.body.decode())
sku_id=data.get('sku_id')
count=data.get('count')
selected=data.get('selected')
# 2.验证数据(省略)
try:
sku=SKU.objects.get(id=sku_id)
except SKU.DoesNotExist:
return JsonResponse({'code':RETCODE.NODATAERR,'errmsg':'没有此信息'})
# 3.获取用户信息
user=request.user
if user.is_authenticated:
# 4.登陆用户更新redis
# 4.1 连接redis
redis_conn = get_redis_connection('carts')
# 4.2 更新数据
#hash
redis_conn.hset('carts_%s'%user.id,sku_id,count)
# set
if selected:
redis_conn.sadd('selected_%s'%user.id,sku_id)
else:
redis_conn.srem('selected_%s'%user.id,sku_id)
# 4.3 返回相应
data={
'count':count,
'id':sku_id,
'selected':selected,
'name': sku.name,
'default_image_url': sku.default_image.url,
'price': sku.price,
'amount': sku.price * count,
}
return JsonResponse({'code':RETCODE.OK,'errmsg':'ok','cart_sku':data})
else:
# 5.未登录用户更新cookie
# 5.1 获取cookie中的数据,并进行判断
cookie_str=request.COOKIES.get('carts')
if cookie_str is not None:
# 如果有数据则需要进行解码
cookie_dict=pickle.loads(base64.b64decode(cookie_str))
else:
cookie_dict={}
# 5.2 更新数据 cart={}
# sku_id 是否在字典列表中
# carts = {sku_id:{count:5,selected:True}}
if sku_id in cookie_dict:
cookie_dict[sku_id]={
'count':count,
'selected':selected
}
# 5.3 将字典进行编码
cookie_data=base64.b64encode(pickle.dumps(cookie_dict))
# 5.4 设置cookie
data = {
'count': count,
'id': sku_id,
'selected': selected,
'name': sku.name,
'default_image_url': sku.default_image.url,
'price': sku.price,
'amount': sku.price * count,
}
response = JsonResponse({'code': RETCODE.OK, 'errmsg': 'ok', 'cart_sku': data})
response.set_cookie('carts',cookie_data,max_age=7*24*3600)
# 5.5 返回相应
return response
"""
1.功能分析
用户行为:
前端行为:
后端行为:
2. 分析后端实现的大体步骤
1.接收数据
2.验证数据
3.获取用户信息,并进行判断
4.登陆则操作redis
4.1 连接redis
4.2 hash
set
4.3 返回相应
5.未登录则操作cookie
5.1 先获取cookie数据,并进行判断
如果有数据,则进行解码
5.2 删除数据 {}
5.3 对数据进行编码
5.4 设置cookie数据
5.5 返回相应
3.确定请求方式和路由
"""
def delete(self,request):
# 1.接收数据
data=json.loads(request.body.decode())
sku_id=data.get('sku_id')
# 2.验证数据
try:
# sku=SKU.objects.get(id=sku_id)
# pk primary key 主键
sku=SKU.objects.get(pk=sku_id)
except SKU.DoesNotExist:
return JsonResponse({'code':RETCODE.NODATAERR,'errmsg':'没有此数据'})
# 3.获取用户信息,并进行判断
user = request.user
if user.is_authenticated:
# 4.登陆则操作redis
# 4.1 连接redis
redis_conn = get_redis_connection('carts')
# 4.2 hash
redis_conn.hdel('carts_%s'%user.id,sku_id)
# set
redis_conn.srem('selected_%s'%user.id,sku_id)
# 4.3 返回相应
return JsonResponse({'code':RETCODE.OK,'errmsg':'ok'})
else:
# 5.未登录则操作cookie
# 5.1 先获取cookie数据,并进行判断
cookie_str=request.COOKIES.get('carts')
if cookie_str is not None:
# 如果有数据,则进行解码
cookie_dict=pickle.loads(base64.b64decode(cookie_str))
else:
cookie_dict={}
# 5.2 删除数据 {}
if sku_id in cookie_dict:
del cookie_dict[sku_id]
# 5.3 对数据进行编码
cookie_data=base64.b64encode(pickle.dumps(cookie_dict))
# 5.4 设置cookie数据
response= JsonResponse({'code': RETCODE.OK, 'errmsg': 'ok'})
response.set_cookie('carts',cookie_data,max_age=7*24*3600)
# 5.5 返回相应
return response
"""
1.功能分析
用户行为: 当用户在未登录的情况下,添加了几样商品到购物车中
当用户登陆的时候,实现了购物车数据添加到redis中
前端行为:
登陆的时候,把cookie数据给后端
后端行为: 登陆的时候,将cookie数据合并到redis中
2. 分析后端实现的大体步骤
登陆的时候,将cookie数据合并到redis中
1.获取cookie数据,用户信息
2.删除cookie信息
3.把cookie数据加入到redis中
3.确定请求方式和路由
抽象的事务具体化
1.获取cookie数据
cookie
{
1:{count:5,selected:False},
3:{count:5,selected:True},
}
2.把redis数据读取下来
redis
hash {1:100,2:100}
set {1,2}
初始化一个字典
一个列表用于记录选中的id
一个列表用于记录未选中的id
3. 对cookie数据进行遍历
合并
new_update_hash {1:5,3:5} 更新到redis中
new_update_selected_set {3} 更新到reids中
new_update_unselected_set {1} 更新到reids中
4.将合并的数据更新到redis中
1.当cookie中和redis中都有相同的商品时,数量怎么办?
产品1: 以cookie为主, v
产品2: 以Redis为主,
产品3: 以Redis+cookie为主,
2.cookie中有数据,redis中没有
将cookie中的数据,添加到redis中
3.redis中已有的数据,不动
"""
######################以下代码为编码################################
import pickle
import base64
# 组织数据
carts={
'1':{'count':5,'selected':True}
}
# 5.1 将字典转换为二进制
bytes_data=pickle.dumps(carts)
# 5.2 再进行base64编码
encode_data=base64.b64encode(bytes_data)
encode_data
#####################以下代码为解码#####################################
# 5.3 先将base64解码
decode_data=base64.b64decode(encode_data)
# 5.4 将bytes类型转换为字典
pickle.loads(decode_data)
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mlsriracha/deploy.py | awcchungster/mlsriracha | 0 | 49078 | <filename>mlsriracha/deploy.py<gh_stars>0
from mlsriracha.plugins.azureml.deploy import AzureMlDeploy
from mlsriracha.plugins.gcpvertex.deploy import GcpVertexDeploy
from mlsriracha.plugins.awssagemaker.deploy import AwsSageMakerDeploy
class DeployAdapter:
def __init__(self, provider: str):
self.provider_name = provider.lower()
print('This is a prediction job')
try: provider
except NameError:
raise RuntimeError(f'{str} is not a valid provider')
if provider.lower() == 'azureml':
print('Using Azure ML as a provider')
self.provider_obj = AzureMlDeploy()
elif provider.lower() == 'gcpvertex':
print('Using GCP Vertex as a provider')
self.provider_obj = GcpVertexDeploy()
elif provider.lower() == 'awssagemaker':
print('Using AWS SageMaker as a provider')
self.provider_obj = AwsSageMakerDeploy()
else:
raise RuntimeError(f'{str} is not a valid provider')
def model_artifact(self, filename: str):
return self.provider_obj.model_artifact(filename)
def endpoint_metadata(self):
return self.provider_obj.endpoint_metadata() | [
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kcsd/utility_functions.py | mczerwinski/kCSD-python | 0 | 151846 | <gh_stars>0
# -*- coding: utf-8 -*-
"""
These are some useful functions used in CSD methods,
They include CSD source profiles to be used as ground truths,
placement of electrodes in 1D, 2D and 3D., etc
These scripts are based on Grzegorz Parka's,
Google Summer of Code 2014, INFC/pykCSD
This was written by :
<NAME>, <NAME>, <NAME>
Laboratory of Neuroinformatics,
Nencki Institute of Experimental Biology, Warsaw.
N-D Bresenham line algo Copyright 2012 <NAME>
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 __future__ import print_function, division, absolute_import
import numpy as np
import os
import pickle
from scipy import interpolate
import json
import sys
import kcsd
try:
from joblib.parallel import Parallel, delayed
PARALLEL_AVAILABLE = True
except ImportError:
PARALLEL_AVAILABLE = False
raise_errror = """Unknown electrode position file format.
Load either one column file (or a one row file) with x positions,
y positions, z positions, or a 3 column file with x and y and z positions.
"""
def load_swc(path):
"""Load swc morphology from file
Used for sKCSD
Parameters
----------
path : str
Returns
-------
morphology : np.array
"""
morphology = np.loadtxt(path)
return morphology
def save_sim(path,k):
"""
Save estimated CSD, potential and cell morphology to file.
Used for saving sKCSD results
Parameters:
-----------
path : str
k : sKCSD object
"""
est_csd = k.values('CSD', transformation=None)
est_pot = k.values("POT", transformation=None)
np.save(os.path.join(path, "csd.npy"), est_csd)
print("Save csd, ", os.path.join(path, "csd.npy"))
np.save(os.path.join(path, "pot.npy"), est_pot)
print("Save pot, ", os.path.join(path, "pot.npy"))
cell_data = {'morphology':k.cell.morphology.tolist(),
'ele_pos':k.cell.ele_pos.tolist(),
'n_src':k.cell.n_src}
with open(os.path.join(path, "cell_data"), 'w') as handle:
json.dump(cell_data, handle)
def load_sim(path):
"""
Load sKCSD estimation results (CSD, potential and cell specifics).
Parameters
----------
path: str
Returns
-------
est_csd : np.array
est_pot : np.array
cell_obj : sKCSDcell object
"""
est_csd = np.load(os.path.join(path, "csd.npy"))
est_pot = np.load(os.path.join(path, "pot.npy"))
try:
with open(os.path.join(path, "cell_data"), 'r') as handle:
cell_data = json.load(handle)
except Exception as error:
print('Could not load', os.path.join(path, "cell_data"))
return est_csd, est_pot, None
morphology = np.array(cell_data['morphology'])
ele_pos = np.array(cell_data['ele_pos'])
cell_obj = kcsd.sKCSDcell(morphology, ele_pos, cell_data['n_src'])
return est_csd, est_pot, cell_obj
def load_elpos(path):
"""Load electrode postions.
File format: text file, one column, x of all the electrodes, y of
all the electrodes, z of all the electrodes
Parameters
----------
path : str
Returns
-------
ele_pos : np.array
"""
raw_ele_pos = np.loadtxt(path)
if len(raw_ele_pos.shape) == 1:
if raw_ele_pos.shape[0]%3:
raise Exception('Unknown electrode position file format.')
else:
n_el = raw_ele_pos.shape[0]//3
ele_pos = np.zeros(shape=(n_el, 3))
ele_pos[:, 0] = raw_ele_pos[:n_el]
ele_pos[:, 1] = raw_ele_pos[n_el:2 * n_el]
ele_pos[:, 2] = raw_ele_pos[2 * n_el:]
elif len(raw_ele_pos.shape) == 2:
if raw_ele_pos.shape[1] == 1:
if raw_ele_pos.shape[0]%3:
raise Exception('Unknown electrode position file format.')
else:
n_el = raw_ele_pos.shape[0]/3
ele_pos = np.zeros(shape=(n_el, 3))
ele_pos[:, 0] = raw_ele_pos[:n_el]
ele_pos[:, 1] = raw_ele_pos[n_el:2 * n_el]
ele_pos[:, 2] = raw_ele_pos[2 * n_el:]
elif raw_ele_pos.shape[0] == 1:
if raw_ele_pos.shape[1]%3:
raise Exception('Unknown electrode position file format.')
else:
n_el = raw_ele_pos.shape[1]/3
ele_pos = np.zeros(shape=(n_el,3))
ele_pos[:, 0] = raw_ele_pos[:n_el]
ele_pos[:, 1] = raw_ele_pos[n_el:2 * n_el]
ele_pos[:, 2] = raw_ele_pos[2 * n_el:]
elif raw_ele_pos.shape[1] == 3:
ele_pos = raw_ele_pos
else:
raise Exception('Unknown electrode position file format.')
else:
raise Exception('Unknown electrode position file format.')
return ele_pos
def check_for_duplicated_electrodes(elec_pos):
"""Checks for duplicate electrodes
Parameters
----------
elec_pos : np.array
Returns
-------
has_duplicated_elec : Boolean
"""
unique_elec_pos = np.vstack({tuple(row) for row in elec_pos})
has_duplicated_elec = unique_elec_pos.shape == elec_pos.shape
return has_duplicated_elec
def distribute_srcs_1D(X, n_src, ext_x, R_init):
"""Distribute sources in 1D equally spaced
Parameters
----------
X : np.arrays
points at which CSD will be estimated
n_src : int
number of sources to be included in the model
ext_x : floats
how much should the sources extend the area X
R_init : float
Same as R in 1D case
Returns
-------
X_src : np.arrays
positions of the sources
R : float
effective radius of the basis element
"""
X_src = np.mgrid[(np.min(X) - ext_x):(np.max(X) + ext_x):
np.complex(0, n_src)]
R = R_init
return X_src, R
def distribute_srcs_2D(X, Y, n_src, ext_x, ext_y, R_init):
"""Distribute n_src's in the given area evenly
Parameters
----------
X, Y : np.arrays
points at which CSD will be estimated
n_src : int
demanded number of sources to be included in the model
ext_x, ext_y : floats
how should the sources extend the area X, Y
R_init : float
demanded radius of the basis element
Returns
-------
X_src, Y_src : np.arrays
positions of the sources
nx, ny : ints
number of sources in directions x,y
new n_src = nx * ny may not be equal to the demanded number of sources
R : float
effective radius of the basis element
"""
Lx = np.max(X) - np.min(X)
Ly = np.max(Y) - np.min(Y)
Lx_n = Lx + (2 * ext_x)
Ly_n = Ly + (2 * ext_y)
[nx, ny, Lx_nn, Ly_nn, ds] = get_src_params_2D(Lx_n, Ly_n, n_src)
ext_x_n = (Lx_nn - Lx) / 2
ext_y_n = (Ly_nn - Ly) / 2
X_src, Y_src = np.mgrid[(np.min(X) - ext_x_n):(np.max(X) + ext_x_n):
np.complex(0, nx),
(np.min(Y) - ext_y_n):(np.max(Y) + ext_y_n):
np.complex(0, ny)]
# d = round(R_init / ds)
R = R_init # R = d * ds
return X_src, Y_src, R
def get_src_params_2D(Lx, Ly, n_src):
"""Distribute n_src sources evenly in a rectangle of size Lx * Ly
Parameters
----------
Lx, Ly : floats
lengths in the directions x, y of the area,
the sources should be placed
n_src : int
demanded number of sources
Returns
-------
nx, ny : ints
number of sources in directions x, y
new n_src = nx * ny may not be equal to the demanded number of sources
Lx_n, Ly_n : floats
updated lengths in the directions x, y
ds : float
spacing between the sources
"""
coeff = [Ly, Lx - Ly, -Lx * n_src]
rts = np.roots(coeff)
r = [r for r in rts if type(r) is not complex and r > 0]
nx = r[0]
ny = n_src / nx
ds = Lx / (nx - 1)
nx = np.floor(nx) + 1
ny = np.floor(ny) + 1
Lx_n = (nx - 1) * ds
Ly_n = (ny - 1) * ds
return (nx, ny, Lx_n, Ly_n, ds)
def distribute_srcs_3D(X, Y, Z, n_src, ext_x, ext_y, ext_z, R_init):
"""Distribute n_src sources evenly in a rectangle of size Lx * Ly * Lz
Parameters
----------
X, Y, Z : np.arrays
points at which CSD will be estimated
n_src : int
desired number of sources we want to include in the model
ext_x, ext_y, ext_z : floats
how should the sources extend over the area X,Y,Z
R_init : float
demanded radius of the basis element
Returns
-------
X_src, Y_src, Z_src : np.arrays
positions of the sources in 3D space
nx, ny, nz : ints
number of sources in directions x,y,z
new n_src = nx * ny * nz may not be equal to the demanded number of
sources
R : float
updated radius of the basis element
"""
Lx = np.max(X) - np.min(X)
Ly = np.max(Y) - np.min(Y)
Lz = np.max(Z) - np.min(Z)
Lx_n = Lx + 2 * ext_x
Ly_n = Ly + 2 * ext_y
Lz_n = Lz + 2 * ext_z
(nx, ny, nz, Lx_nn, Ly_nn, Lz_nn, ds) = get_src_params_3D(Lx_n,
Ly_n,
Lz_n,
n_src)
ext_x_n = (Lx_nn - Lx) / 2
ext_y_n = (Ly_nn - Ly) / 2
ext_z_n = (Lz_nn - Lz) / 2
X_src, Y_src, Z_src = np.mgrid[(np.min(X) - ext_x_n):(np.max(X) + ext_x_n):
np.complex(0, nx),
(np.min(Y) - ext_y_n):(np.max(Y) + ext_y_n):
np.complex(0, ny),
(np.min(Z) - ext_z_n):(np.max(Z) + ext_z_n):
np.complex(0, nz)]
# d = np.round(R_init / ds)
R = R_init
return (X_src, Y_src, Z_src, R)
def get_src_params_3D(Lx, Ly, Lz, n_src):
"""Helps to evenly distribute n_src sources in a cuboid of size Lx * Ly * Lz
Parameters
----------
Lx, Ly, Lz : floats
lengths in the directions x, y, z of the area,
the sources should be placed
n_src : int
demanded number of sources to be included in the model
Returns
-------
nx, ny, nz : ints
number of sources in directions x, y, z
new n_src = nx * ny * nz may not be equal to the demanded number of
sources
Lx_n, Ly_n, Lz_n : floats
updated lengths in the directions x, y, z
ds : float
spacing between the sources (grid nodes)
"""
V = Lx * Ly * Lz
V_unit = V / n_src
L_unit = V_unit**(1. / 3.)
nx = np.ceil(Lx / L_unit)
ny = np.ceil(Ly / L_unit)
nz = np.ceil(Lz / L_unit)
ds = Lx / (nx - 1)
Lx_n = (nx - 1) * ds
Ly_n = (ny - 1) * ds
Lz_n = (nz - 1) * ds
return (nx, ny, nz, Lx_n, Ly_n, Lz_n, ds)
def L_model_fast(k_pot, pots, lamb, i):
"""Method for Fast L-curve computation
Parameters
----------
k_pot : np.array
pots : list
lambd : list
i : int
Returns
-------
modelnorm : float
residual : float
"""
k_inv = np.linalg.inv(k_pot + lamb*np.identity(k_pot.shape[0]))
beta_new = np.dot(k_inv, pots)
V_est = np.dot(k_pot, beta_new)
modelnorm = np.einsum('ij,ji->i', beta_new.T, V_est)
residual = np.linalg.norm(V_est - pots)
modelnorm = np.max(modelnorm)
return modelnorm, residual
def parallel_search(k_pot, pots, lambdas, n_jobs=4):
"""Method for Parallel L-curve computation
Parameters
----------
k_pot : np.array
pots : list
lambdas : list
Returns
-------
modelnormseq : list
residualseq : list
"""
if PARALLEL_AVAILABLE:
jobs = (delayed(L_model_fast)(k_pot, pots, lamb, i)
for i, lamb in enumerate(lambdas))
modelvsres = Parallel(n_jobs=n_jobs, backend='threading')(jobs)
else:
# Please verify this!
modelvsres = []
for i, lamb in enumerate(lambdas):
modelvsres.append(L_model_fast(k_pot, pots, lamb, i))
modelnormseq, residualseq = zip(*modelvsres)
return modelnormseq, residualseq
def _bresenhamline_nslope(slope):
"""
Normalize slope for Bresenham's line algorithm.
>>> s = np.array([[-2, -2, -2, 0]])
>>> _bresenhamline_nslope(s)
array([[-1., -1., -1., 0.]])
>>> s = np.array([[0, 0, 0, 0]])
>>> _bresenhamline_nslope(s)
array([[ 0., 0., 0., 0.]])
>>> s = np.array([[0, 0, 9, 0]])
>>> _bresenhamline_nslope(s)
array([[ 0., 0., 1., 0.]])
"""
scale = np.amax(np.abs(slope), axis=1).reshape(-1, 1)
zeroslope = (scale == 0).all(1)
scale[zeroslope] = np.ones(1)
normalizedslope = np.array(slope, dtype=np.double) / scale
normalizedslope[zeroslope] = np.zeros(slope[0].shape)
return normalizedslope
def _bresenhamlines(start, end, max_iter):
"""
Returns npts lines of length max_iter each. (npts x max_iter x dimension)
>>> s = np.array([[3, 1, 9, 0],[0, 0, 3, 0]])
>>> _bresenhamlines(s, np.zeros(s.shape[1]), max_iter=-1)
array([[[ 3, 1, 8, 0],
[ 2, 1, 7, 0],
[ 2, 1, 6, 0],
[ 2, 1, 5, 0],
[ 1, 0, 4, 0],
[ 1, 0, 3, 0],
[ 1, 0, 2, 0],
[ 0, 0, 1, 0],
[ 0, 0, 0, 0]],
<BLANKLINE>
[[ 0, 0, 2, 0],
[ 0, 0, 1, 0],
[ 0, 0, 0, 0],
[ 0, 0, -1, 0],
[ 0, 0, -2, 0],
[ 0, 0, -3, 0],
[ 0, 0, -4, 0],
[ 0, 0, -5, 0],
[ 0, 0, -6, 0]]])
"""
if max_iter == -1:
max_iter = np.amax(np.amax(np.abs(end - start), axis=1))
npts, dim = start.shape
nslope = _bresenhamline_nslope(end - start)
# steps to iterate on
stepseq = np.arange(1, max_iter + 1)
stepmat = np.tile(stepseq, (dim, 1)).T
# some hacks for broadcasting properly
bline = start[:, np.newaxis, :] + nslope[:, np.newaxis, :] * stepmat
# Approximate to nearest int
return np.array(np.rint(bline), dtype=start.dtype)
def bresenhamline(start, end, max_iter=5):
"""
Returns a list of points from (start, end] by ray tracing a line b/w the
points.
Parameters:
start: An array of start points (number of points x dimension)
end: An end points (1 x dimension)
or An array of end point corresponding to each start point
(number of points x dimension)
max_iter: Max points to traverse. if -1, maximum number of required
points are traversed
Returns:
linevox (n x dimension) A cumulative array of all points traversed by
all the lines so far.
>>> s = np.array([[3, 1, 9, 0],[0, 0, 3, 0]])
>>> bresenhamline(s, np.zeros(s.shape[1]), max_iter=-1)
array([[ 3, 1, 8, 0],
[ 2, 1, 7, 0],
[ 2, 1, 6, 0],
[ 2, 1, 5, 0],
[ 1, 0, 4, 0],
[ 1, 0, 3, 0],
[ 1, 0, 2, 0],
[ 0, 0, 1, 0],
[ 0, 0, 0, 0],
[ 0, 0, 2, 0],
[ 0, 0, 1, 0],
[ 0, 0, 0, 0],
[ 0, 0, -1, 0],
[ 0, 0, -2, 0],
[ 0, 0, -3, 0],
[ 0, 0, -4, 0],
[ 0, 0, -5, 0],
[ 0, 0, -6, 0]])
"""
# Return the points as a single array
return _bresenhamlines(start, end, max_iter).reshape(-1, start.shape[-1])
class LoadData(object):
def __init__(self,path):
self.Func = {}
self.Path = {}
self.path = path
self.get_paths()
self.load('morphology')
self.load('electrode_positions')
self.load('LFP')
def assign(self,what, value):
if what == 'morphology':
self.morphology = value
elif what == 'electrode_positions':
self.ele_pos = value
elif what == 'LFP':
self.LFP = value
def sub_dir_path(self,d):
return filter(os.path.isdir, [os.path.join(d,f) for f in os.listdir(d)])
def get_fname(self,d,fnames):
if len(fnames) == 1:
return os.path.join(d,fnames[0])
else:
paths = []
for fname in fnames:
paths.append(os.path.join(d,fname))
return paths
def get_paths(self):
dir_list = self.sub_dir_path(self.path)
for drc in dir_list:
files = os.listdir(drc)
if drc.endswith("morphology"):
self.path_morphology = self.get_fname(drc,files)
self.Path['morphology'] = self.path_morphology
self.Func['morphology'] = load_swc
if drc.endswith("positions"):
self.path_ele_pos = self.get_fname(drc,files)
self.Path["electrode_positions"] = self.path_ele_pos
self.Func["electrode_positions"] = load_elpos
if drc.endswith("LFP"):
self.path_LFP = self.get_fname(drc,files)
self.Path["LFP"] = self.path_LFP
self.Func["LFP"] = np.loadtxt
def load(self, what, func=None, path=None):
if not func:
func = self.Func[what]
if not path:
path = self.Path[what]
#print(what,'unknown file type. Currently recognized file types are morphology, electrode_positions, LFP')
#return
if isinstance(path,list):
for p in path:
if p.endswith('swc'):
path = p
break
try:
f = open(path)
except IOError:
print('Could not open file',path)
self.assign(what,None)
return
try:
data = func(f)
self.assign(what,data)
except ValueError:
print('Could not load file',path)
self.assign(what,None)
f.close()
return
print('Load',path)
f.close()
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Examples/AdvancedUsage/LoadingOptions/ViewProtectedDocument.py | groupdocs-viewer-cloud/groupdocs-viewer-cloud-python-samples | 0 | 84375 | <filename>Examples/AdvancedUsage/LoadingOptions/ViewProtectedDocument.py
# Import modules
import groupdocs_viewer_cloud
from Common import Common
# This example demonstrates how to render password-protected documents
class ViewProtectedDocument:
@classmethod
def Run(cls):
apiInstance = groupdocs_viewer_cloud.ViewApi.from_config(Common.GetConfig())
view_options = groupdocs_viewer_cloud.ViewOptions()
view_options.file_info = groupdocs_viewer_cloud.FileInfo()
view_options.file_info.file_path = "SampleFiles/password_protected.docx"
view_options.file_info.password = "<PASSWORD>"
view_options.view_format = "HTML"
request = groupdocs_viewer_cloud.CreateViewRequest(view_options)
response = apiInstance.create_view(request)
print("ViewProtectedDocument completed: " + str(len(response.pages)))
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tests/init.py | Animenosekai/yuno | 1 | 19482 | <filename>tests/init.py
import inspect
import pathlib
import sys
import yuno
# CONSTANTS
TEST_OBJECT = {
"a": 1,
"b": 2,
"c": 3,
"test_dict": {
"a": 1,
"b": 2,
"c": 3
},
"float": 1.1,
"int": 1,
"test_list": [1, 2, 3],
"null": None,
"string": "test",
"boolean": True
}
TEST_LIST = [
"string",
1,
1.1,
None,
[1, 2, 3],
TEST_OBJECT,
True
]
TEST_DOCUMENT = {"_id": "test_document", "hello": "world", "test_list": TEST_LIST, "test_dict": TEST_OBJECT,
"boolean": True, "float": 1.1, "int": 1, "null": None, "string": "test"}
KEPT_DATABASES = {'admin', 'local', 'config'}
REALTIME_TIMEOUT = 5
# UTILITY FUNCTIONS
def get_args(func):
return inspect.signature(func).parameters.keys()
STEP = f"CI/Testing - v{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}"
def log(message):
try:
yuno.utils.logging.log(message, yuno.utils.logging.LogLevels.INFO, step=STEP)
except Exception:
pass
def close(mongo: yuno.MongoDB, client: yuno.YunoClient):
log("Closing the client connection")
client.close()
if mongo.__process__ is not None:
log("Stopping MongoDB")
mongo.close()
# INITIALIZATION FUNCTIONS
f = pathlib.Path("./MONGO_PORT")
if f.is_file():
MONGO_PORT = int(f.read_text().replace(" ", ""))
else:
MONGO_PORT = 27017
def init_mongo():
log("Initializing MongoDB with port: " + str(MONGO_PORT))
mongo = yuno.MongoDB(port=MONGO_PORT, db_path="./test", log_config={"path": "./test.log"})
try:
log("Starting MongoDB")
mongo.start()
except RuntimeError:
log("MongoDB seems to be already running?")
return mongo
def init_client():
mongo = init_mongo()
client = yuno.YunoClient(mongo)
for database in set(client.database_names()).difference({'admin', 'local', 'config'}):
log(f"Dropping database: {database}")
del client[database]
return mongo, client
def init_database():
mongo, client = init_client()
log("Initializing Database")
database = yuno.YunoDatabase(client, "test")
log("Cleaning up the database")
for collection in database.list_collection_names():
log(f"Dropping collection: {collection}")
del database[collection]
return mongo, client, database
def init_collection():
mongo, client, database = init_database()
log("Initializing collection")
collection = yuno.YunoCollection(database, "test")
log("Cleaning up the collection")
for document in collection.find(include=["_id"]):
log(f"Deleting document: {document.__id__}")
del collection[document.__id__]
return mongo, client, database, collection
def init_document():
mongo, client, database, collection = init_collection()
log("Initializing Document")
collection.test_document = TEST_DOCUMENT
return mongo, client, database, collection, collection.test_document
# DECORATORS
def use_mongo(func):
def wrapper(*args, **kwargs):
mongo = init_mongo()
avail = get_args(func)
if "mongo" in avail:
kwargs["mongo"] = mongo
result = func(*args, **kwargs)
if mongo.__process__ is not None:
log("Stopping MongoDB")
mongo.close()
return result
return wrapper
def use_client(func):
def wrapper(*args, **kwargs):
mongo, client = init_client()
avail = get_args(func)
for arg, value in [("mongo", mongo), ("client", client)]:
if arg in avail:
kwargs[arg] = value
result = func(*args, **kwargs)
close(mongo, client)
return result
return wrapper
def use_database(func):
def wrapper(*args, **kwargs):
mongo, client, database = init_database()
avail = get_args(func)
for arg, value in [("mongo", mongo), ("client", client), ("database", database)]:
if arg in avail:
kwargs[arg] = value
result = func(*args, **kwargs)
close(mongo, client)
return result
return wrapper
def use_collection(func):
def wrapper(*args, **kwargs):
mongo, client, database, collection = init_collection()
avail = get_args(func)
for arg, value in [("mongo", mongo), ("client", client), ("database", database), ("collection", collection)]:
if arg in avail:
kwargs[arg] = value
result = func(*args, **kwargs)
close(mongo, client)
return result
return wrapper
def verification_callback(obj):
log(f"cursor ~ Verifying object {obj}")
return obj
def use_cursor(func):
def wrapper(*args, **kwargs):
mongo, client, database, collection = init_collection()
collection.hello = {'_id': "hello", 'hello': "world"}
cursor = yuno.cursor.Cursor(collection.__collection__.find({"_id": "hello"}), verification=verification_callback)
avail = get_args(func)
for arg, value in [("mongo", mongo), ("client", client), ("database", database), ("collection", collection), ("cursor", cursor)]:
if arg in avail:
kwargs[arg] = value
result = func(*args, **kwargs)
close(mongo, client)
return result
return wrapper
def use_document(func):
def wrapper(*args, **kwargs):
mongo, client, database, collection, document = init_document()
avail = get_args(func)
for arg, value in [("mongo", mongo), ("client", client), ("database", database), ("collection", collection), ("document", document)]:
if arg in avail:
kwargs[arg] = value
result = func(*args, **kwargs)
close(mongo, client)
return result
return wrapper
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] |
picosb/soc/cpu.py | mwbrown/picorv-sandbox | 0 | 114017 |
from amaranth import *
from .bus import NativeBusMaster
class PicoRV32(NativeBusMaster):
def __init__(self) -> None:
super().__init__()
self.rv_trap = Signal()
def elaborate(self, platform):
m = super().elaborate(platform)
m.submodules += Instance("picorv32",
p_PROGADDR_RESET = C(0x10000000, Shape(32)), # 32'h 1000_0000,
p_PROGADDR_IRQ = C(0x10000010, Shape(32)), # 32'h 1000_0010,
p_COMPRESSED_ISA = C(1),
i_clk = ClockSignal(),
i_resetn = ~ResetSignal(),
o_trap = self.rv_trap,
# Native memory interface
o_mem_valid = self.mem_valid_o,
o_mem_addr = self.mem_addr_o,
o_mem_wdata = self.mem_wdata_o,
o_mem_wstrb = self.mem_byte_wr_ena_o,
o_mem_instr = self.mem_instr_o,
i_mem_ready = self.mem_ready_i,
i_mem_rdata = self.mem_rdata_i,
# Memory lookahead interface (ignored)
o_mem_la_read = Signal(),
o_mem_la_write = Signal(),
o_mem_la_addr = Signal(32),
o_mem_la_wdata = Signal(32),
o_mem_la_wstrb = Signal(4),
# Coprocessor interface (not implemented)
o_pcpi_valid = Signal(),
o_pcpi_insn = Signal(32),
o_pcpi_rs1 = Signal(32),
o_pcpi_rs2 = Signal(32),
i_pcpi_wr = C(0), #(1'b0),
i_pcpi_rd = C(0, Shape(32)), #(32'b0),
i_pcpi_wait = C(0), #(1'b0),
i_pcpi_ready = C(0), #(1'b0),
# IRQ interface (not implemented)
i_irq = C(0, Shape(32)), #(32'b0),
o_eoi = Signal(32),
# Trace interface (ignored)
o_trace_valid = Signal(),
o_trace_data = Signal(36)
)
return m
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mjt/mjt/report/lot_wise_production_summary/lot_wise_production_summary.py | hamzaali15/mjt | 0 | 188291 | # Copyright (c) 2013, earthians and contributors
# For license information, please see license.txt
from __future__ import unicode_literals
import frappe
def execute(filters=None):
columns = get_columns()
data = get_data(filters)
return columns, data
def get_columns():
columns = [
{
"fieldname": "lot_no",
"fieldtype": "Link",
"label": "Lot No",
"options": "Batch",
"width": 150
},
{
"fieldname": "department",
"fieldtype": "Link",
"label": "Department",
"options": "Manufacturing Department",
"width": 150
},
{
"fieldname": "quality_name",
"fieldtype": "Data",
"label": "Quality Name",
"width": 150
},
{
"fieldname": "party_code",
"fieldtype": "Link",
"label": "Party Code",
"options": "Supplier",
"width": 150
},
{
"fieldname": "supplier_name",
"fieldtype": "Data",
"label": "Party Name",
"width": 200,
'fetch_from': 'party_code.supplier_name'
},
{
"fieldname": "design_no",
"fieldtype": "Link",
"label": "Design No",
"options": "Design",
"width": 150
},
{
"fieldname": "design_name",
"fieldtype": "Data",
"label": "Design Name",
"width": 150
},
{
"fieldname": "in_qty",
"fieldtype": "Float",
"label": "In Qty",
"width": 100
},
{
"fieldname": "out_qty",
"fieldtype": "Float",
"label": "Out Qty",
"width": 100
},
{
"fieldname": "shortage",
"fieldtype": "Float",
"label": "Over / Shortage",
"width": 120
},
{
"fieldname": "shortage_per",
"fieldtype": "Float",
"label": "Over / Shortage (%)",
"width": 140
}
]
return columns
def get_data(filters):
lst = []
query = """select
tpi.lot_no as lot_no
from `tabProcess Order` as tp
inner join `tabProcess Order Item` as tpi on tp.name = tpi.parent
where tpi.lot_no is not null and tp.docstatus = 1"""
if filters.get('from_date'):
query += " and tp.date >= '{0}'".format(filters.get('from_date'))
if filters.get('to_date'):
query += " and tp.date <= '{0}'".format(filters.get('to_date'))
if filters.get('company'):
query += " and tp.company = '{0}'".format(filters.get('company'))
if filters.get('lot'):
query += " and tpi.lot_no like '{0}'".format(filters.get('lot'))
if filters.get('department'):
query += " and tp.department = '{0}'".format(filters.get('department'))
if filters.get('quality_code'):
query += " and tpi.quality_code = '{0}'".format(filters.get('quality_code'))
# query += """ group by tp.department,tpi.party_name,tpi.quality_name,tpi.design_no
# order by tpi.lot_no,tp.department"""
result = frappe.db.sql(query, as_dict=True)
lot_lst = []
for r in result:
if r['lot_no']:
lot_no = str(r['lot_no'].split("-")[0])
lot_lst.append(lot_no)
if lot_lst:
for r in set(lot_lst):
lot_like = "%" + r + "%"
query = """select
tpi.lot_no as lot_no,
tp.department as department,
tpi.party_name as party_code,
ts.supplier_name as supplier_name,
tpi.quality_name as quality_name,
tpi.quality_code as quality_code,
tp.process_name as process_name,
tpi.design_no as design,
d.design as design_name,
sum(tpi.quantity) as in_qty,
0 as out_qty
from `tabProcess Order` as tp
left join `tabProcess Order Item` as tpi on tp.name = tpi.parent
left join `tabSupplier` as ts on ts.name = tpi.party_name
left join `tabDesign` as d on d.name = tpi.design_no
where tpi.lot_no like '{0}' and tpi.lot_no is not null and tpi.party_name is not null and tp.docstatus = 1""".format(lot_like)
if filters.get('from_date'):
query += " and tp.date >= '{0}'".format(filters.get('from_date'))
if filters.get('to_date'):
query += " and tp.date <= '{0}'".format(filters.get('to_date'))
if filters.get('company'):
query += " and tp.company = '{0}'".format(filters.get('company'))
if filters.get('lot'):
query += " and tpi.lot_no like '{0}'".format(filters.get('lot'))
if filters.get('department'):
query += " and tp.department = '{0}'".format(filters.get('department'))
if filters.get('quality_code'):
query += " and tpi.quality_code = '{0}'".format(filters.get('quality_code'))
query += """ group by tp.department,tpi.party_name,tpi.quality_name,tpi.design_no
order by tpi.lot_no,tp.department"""
result2 = frappe.db.sql(query, as_dict=True)
for res in result2:
query2 = """select
sum(tpfi.quantity) as out_qty
from `tabProcess Order` as tp
left join `tabProcess Order Finish Item` as tpfi on tp.name = tpfi.parent
where tpfi.lot_no like '{0}'
and tp.department = '{1}'
and tpfi.quality_code = '{2}'
and tpfi.party_name = '{3}'
and tp.docstatus = 1""".format(lot_like, res.department, res.quality_code, res.party_code)
if filters.get('from_date'):
query2 += " and tp.date >= '{0}'".format(filters.get('from_date'))
if filters.get('to_date'):
query2 += " and tp.date <= '{0}'".format(filters.get('to_date'))
if filters.get('company'):
query2 += " and tp.company = '{0}'".format(filters.get('company'))
if res.design:
query2 += " and tpfi.design_no = '{0}' ".format(res.design)
else:
query2 += " and tpfi.design_no is null"
result3 = frappe.db.sql(query2, as_dict=True)
if result3:
if result3[0].out_qty:
res['out_qty'] = result3[0].out_qty
lst.append({
"lot_no": r,
"department": res.department,
"party_code": res.party_code,
"supplier_name": res.supplier_name,
"quality_name": res.quality_name,
"process_name": res.process_name,
"design_no": res.design,
"design_name": res.design_name,
"in_qty": res.in_qty,
"out_qty": res.out_qty,
"shortage": res.out_qty - res.in_qty,
"shortage_per": ((res.out_qty - res.in_qty) * 100) / res.in_qty if res.in_qty else 0
})
return lst | [
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check_data_integrity/__init__.py | mpmuc84/helper-scripts | 4 | 79200 | """
This package contains the modules for both the script checking for data inconsistencies in an opencast
instance as well as for the script for fixing some of those inconsistencies and modules shared by both scripts.
""" | [
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relancer-exp/original_notebooks/wenruliu_adult-income-dataset/decision-tree-f1-98-acc-99-auc-99.py | Chenguang-Zhu/relancer | 1 | 91073 | #!/usr/bin/env python
# coding: utf-8
# # Import Base Packages
# In[ ]:
import pandas as pd
import numpy as np
import warnings
warnings.filterwarnings('ignore')
# # Interface function to feature engineering data
# In[ ]:
from sklearn.preprocessing import LabelEncoder
from sklearn.preprocessing import StandardScaler
from sklearn.preprocessing import PolynomialFeatures
column_names = [ 'age', 'workclass', 'fnlwgt', 'education', 'educational-num', 'marital-status', 'occupation', 'relationship', 'race', 'gender', 'capital-gain', 'capital-loss', 'hours-per-week', 'native-country', 'income' ]
columns_to_encoding = [ 'workclass', 'marital-status', 'occupation', 'relationship', 'race', 'gender' ]
columns_to_normalize = [ 'age', 'educational-num', 'hours-per-week', 'capital-gain', 'capital-loss' ]
le = LabelEncoder()
scaler = StandardScaler()
pl = PolynomialFeatures(2, include_bias=False)
def feature_engineering(filename, train=True):
df = pd.read_csv(filename, index_col=False)
df.drop(['fnlwgt', 'education', 'native-country'], axis=1, inplace=True)
df = pd.get_dummies(df, columns=columns_to_encoding)
df["income"] = le.fit_transform(df['income'])
if train:
X_temp = pl.fit_transform(df[columns_to_normalize])
X_temp = scaler.fit_transform(X_temp)
df.drop(columns_to_normalize, axis=1, inplace=True)
X_train = np.hstack((df.values, X_temp))
y_train = df['income']
columns_names = pl.get_feature_names(df.columns)
return np.hstack((df.columns.values, columns_names)), X_train, y_train
else:
X_temp = pl.transform(df[columns_to_normalize])
X_temp = scaler.transform(X_temp)
df.drop(columns_to_normalize, axis=1, inplace=True)
X_test = np.hstack((df.values, X_temp))
y_test = df['income']
columns_names = pl.get_feature_names(df.columns)
return np.hstack((df.columns.values, columns_names)), X_test, y_test
# # Load Data
# In[ ]:
columns_names, X, y = feature_engineering("../../../input/wenruliu_adult-income-dataset/adult.csv", train=True)
# In[ ]:
from sklearn.model_selection import train_test_split
def rmnan(X, y):
X_, y_ = [], []
for x, yt in zip(X, y):
if np.isnan(x).any() or np.isnan(yt).any():
continue
X_.append(x)
y_.append(yt)
return np.array(X_), np.array(y_)
X, y = rmnan(X, y)
# In[ ]:
X, X_test, y, y_test = train_test_split(X, y, test_size=0.30, random_state=42)
y.shape, y_test.shape
# # Find Best number of components to PCA
# In[ ]:
from sklearn.tree import DecisionTreeClassifier
from sklearn.decomposition import PCA
from sklearn.model_selection import RandomizedSearchCV
from sklearn.metrics import make_scorer
from sklearn.metrics import fbeta_score
from sklearn.metrics import accuracy_score
from sklearn.model_selection import RepeatedStratifiedKFold
param_distribution = { 'max_depth': np.arange(1, 15), }
scoring = { 'Accuracy': make_scorer(accuracy_score), 'F1_Score': make_scorer(fbeta_score, beta=1, average='micro'), }
# In[ ]:
result = []
kf = RepeatedStratifiedKFold(n_splits=2, n_repeats=2)
for fold, (train_index, test_index) in enumerate(kf.split(X, y)):
X_tr, X_tst = X[train_index], X[test_index]
y_tr, y_tst = y[train_index], y[test_index]
for i in range(1, 20):
# train
pca = PCA(i)
X_t = pca.fit_transform(X_tr)
search_cv = RandomizedSearchCV(DecisionTreeClassifier(), param_distribution, scoring=scoring, n_jobs=-1, cv=RepeatedStratifiedKFold(n_splits=2, n_repeats=2), refit='F1_Score')
search_cv.fit(X_t, y_tr)
model = search_cv.best_estimator_
# test
X_t = pca.transform(X_tst)
y_pred = model.predict(X_t)
# model evaluation
f1 = fbeta_score(y_tst, y_pred, beta=1)
acc = accuracy_score(y_tst, y_pred)
print(f"fold: {fold} - cp:{i} train: {search_cv.best_score_} test: f1={f1}, acc={acc}")
result.append((fold, i, acc, f1, pca, model))
# In[ ]:
best_f1 = 0
best_model = None
for fold, n, acc, f1, pca, model in result:
if best_f1 < f1:
best_f1 = f1
best_model=(fold, n, acc, f1, pca, model)
pca_components = best_model[1]
pca_components
# # Get best model with best pca_components number
# In[ ]:
result, metrics_ = [], []
kf = RepeatedStratifiedKFold(n_splits=10, n_repeats=1)
for fold, (train_index, test_index) in enumerate(kf.split(X, y)):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
# train
pca = PCA(pca_components)
X_t = pca.fit_transform(X_train)
search_cv = RandomizedSearchCV(DecisionTreeClassifier(), param_distribution, scoring=scoring, n_jobs=-1, cv=RepeatedStratifiedKFold(n_splits=10, n_repeats=1), refit='F1_Score')
search_cv.fit(X_t, y_train)
model = search_cv.best_estimator_
# test
X_t = pca.transform(X_test)
y_pred = model.predict(X_t)
# model evaluation
f1 = fbeta_score(y_test, y_pred, beta=1)
acc = accuracy_score(y_test, y_pred)
print(f"fold: {fold} - cp:{pca_components} train: {search_cv.best_score_} test: f1={f1}, acc={acc}")
result.append((X_train, y_train, X_test, y_test, fold, i, acc, f1, pca, model))
metrics_.append((f1, acc))
# In[ ]:
best_f1 = 0
best_model = None
for X_train, y_train, X_test, y_test, fold, n, acc, f1, pca, model in result:
if best_f1 < f1:
best_f1 = f1
best_model=(X_train, y_train, X_test, y_test, fold, n, acc, f1, pca, model)
X_train, y_train, X_test, y_test = X, y, X_test, y_test #best_model[:4]
# # Analyse Model Result
# In[ ]:
from sklearn import metrics
pca, model = best_model[-2], best_model[-1]
probs = model.predict_proba(pca.transform(X_test))
preds = probs[:,1]
fpr, tpr, threshold = metrics.roc_curve(y_test, preds)
roc_auc = metrics.auc(fpr, tpr)
# method I: plt
import matplotlib.pyplot as plt
plt.title('Receiver Operating Characteristic')
plt.plot(fpr, tpr, 'b', label = 'AUC = %0.2f' % roc_auc)
plt.legend(loc = 'lower right')
plt.plot([0, 1], [0, 1],'r--')
plt.xlim([0, 1])
plt.ylim([0, 1])
plt.ylabel('True Positive Rate')
plt.xlabel('False Positive Rate')
print()
# In[ ]:
f1_r, acc_r = [], []
for f1, acc in metrics_:
f1_r.append(f1)
acc_r.append(acc)
f1_r, acc_r = np.array(f1_r), np.array(acc_r)
l = f1_r.shape[0]
plt.title(f'F1 Score in Folds(PCA components = {pca_components})')
plt.plot(range(l), f1_r, 'r', label = 'F1 Score')
plt.plot(range(l), acc_r, 'b', label = 'Accuracy')
plt.legend(loc = 'lower right')
plt.xticks(range(l))
plt.xlim([0, l - 1])
plt.ylim([0.95, 1])
plt.ylabel('F1 Score')
plt.xlabel('Fold')
plt.grid()
print()
# ## Plot feature importances
# In[ ]:
def plot_feature_importances(clf, X_train, y_train=None, top_n=10, figsize=(8,8), print_table=False, title="Feature Importances"):
# https://www.kaggle.com/grfiv4/plotting-feature-importances
__name__ = "plot_feature_importances"
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
X_train = pd.DataFrame(data=X_train, columns=[f"PC{i}" for i in range(1, X_train.shape[1] + 1)])
feat_imp = pd.DataFrame({'importance':clf.feature_importances_})
feat_imp['feature'] = X_train.columns
feat_imp.sort_values(by='importance', ascending=False, inplace=True)
feat_imp = feat_imp.iloc[:top_n]
feat_imp.sort_values(by='importance', inplace=True)
feat_imp = feat_imp.set_index('feature', drop=True)
feat_imp.plot.barh(title=title, figsize=figsize)
plt.xlabel('Feature Importance Score')
print()
if print_table:
from IPython.display import display
print("Top {} features in descending order of importance".format(top_n))
print(feat_imp.sort_values(by='importance', ascending=False))
return feat_imp
pca, clf = best_model[-2], best_model[-1]
feature_importance = plot_feature_importances(clf, pca.transform(X_train), top_n=X_train.shape[1], title=clf.__class__.__name__)
# ## Get Features Used to Generate PCA Components
# In[ ]:
# https://stackoverflow.com/questions/22348668/pca-decomposition-with-python-features-relevances
pca, clf = best_model[-2], best_model[-1]
index_components = [int(x[2:]) for x in feature_importance.index.values]
def features_used_to_generate_pca_components(index_components, pca, clf, columns_names):
for i in index_components:
index_features = np.abs(pca.components_[i - 1]).argsort()[:4]
features = columns_names[index_features]
print(f'PC{i}')
print(f'Features:')
for f in features:
print("\t" + f)
print()
features_used_to_generate_pca_components(index_components, pca, clf, columns_names)
# ## Confusion Matrix
# In[ ]:
from sklearn.metrics import confusion_matrix
pca, clf = best_model[-2], best_model[-1]
y_pred = clf.predict(pca.transform(X_test))
cm = confusion_matrix(y_test, y_pred)
cm
# In[ ]:
import itertools
def plot_confusion_matrix(cm, classes, normalize=False, title='Confusion matrix', cmap=plt.cm.Blues):
""" This function prints and plots the confusion matrix. Normalization can be applied by setting `normalize=True`. """
if normalize:
cm = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
print("Normalized confusion matrix")
else:
print('Confusion matrix, without normalization')
print(cm)
plt.imshow(cm, interpolation='nearest', cmap=cmap)
plt.title(title)
print()
tick_marks = np.arange(len(classes))
plt.xticks(tick_marks, classes, rotation=45)
plt.yticks(tick_marks, classes)
fmt = '.2f' if normalize else 'd'
thresh = cm.max() / 2.
for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
plt.text(j, i, format(cm[i, j], fmt), horizontalalignment="center", color="white" if cm[i, j] > thresh else "black")
plt.ylabel('True label')
plt.xlabel('Predicted label')
plt.tight_layout()
plot_confusion_matrix(cm, [0, 1], True)
# ## Classification Report
# In[ ]:
from sklearn.metrics import classification_report
print(classification_report(y_test, y_pred))
# # Save Best Model
# In[ ]:
from sklearn.tree import export_graphviz
# Export as dot file
export_graphviz(best_model[-1], out_file='tree.dot', class_names = [">= 50K", "< 50K"], rounded = True, proportion = False, precision = 2, filled = True)
# Convert to png using system command (requires Graphviz)
from subprocess import call
call(['dot', '-Tpng', 'tree.dot', '-o', 'tree.png', '-Gdpi=600'])
# Display in jupyter notebook
from IPython.display import Image
Image(filename = 'tree.png')
# In[ ]:
from sklearn.externals import joblib
joblib.dump(best_model, 'lgr.joblib')
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sdk/python/pulumi_azure/core/get_resources.py | apollo2030/pulumi-azure | 0 | 137009 | # coding=utf-8
# *** WARNING: this file was generated by the Pulumi Terraform Bridge (tfgen) Tool. ***
# *** Do not edit by hand unless you're certain you know what you are doing! ***
import json
import warnings
import pulumi
import pulumi.runtime
from typing import Union
from .. import utilities, tables
class GetResourcesResult:
"""
A collection of values returned by getResources.
"""
def __init__(__self__, name=None, required_tags=None, resource_group_name=None, resources=None, type=None, id=None):
if name and not isinstance(name, str):
raise TypeError("Expected argument 'name' to be a str")
__self__.name = name
"""
The name of this Resource.
"""
if required_tags and not isinstance(required_tags, dict):
raise TypeError("Expected argument 'required_tags' to be a dict")
__self__.required_tags = required_tags
if resource_group_name and not isinstance(resource_group_name, str):
raise TypeError("Expected argument 'resource_group_name' to be a str")
__self__.resource_group_name = resource_group_name
if resources and not isinstance(resources, list):
raise TypeError("Expected argument 'resources' to be a list")
__self__.resources = resources
"""
One or more `resource` blocks as defined below.
"""
if type and not isinstance(type, str):
raise TypeError("Expected argument 'type' to be a str")
__self__.type = type
"""
The type of this Resource. (e.g. `Microsoft.Network/virtualNetworks`).
"""
if id and not isinstance(id, str):
raise TypeError("Expected argument 'id' to be a str")
__self__.id = id
"""
id is the provider-assigned unique ID for this managed resource.
"""
class AwaitableGetResourcesResult(GetResourcesResult):
# pylint: disable=using-constant-test
def __await__(self):
if False:
yield self
return GetResourcesResult(
name=self.name,
required_tags=self.required_tags,
resource_group_name=self.resource_group_name,
resources=self.resources,
type=self.type,
id=self.id)
def get_resources(name=None,required_tags=None,resource_group_name=None,type=None,opts=None):
"""
Use this data source to access information about existing resources.
:param str name: The name of the Resource.
:param dict required_tags: A mapping of tags which the resource has to have in order to be included in the result.
:param str resource_group_name: The name of the Resource group where the Resources are located.
:param str type: The Resource Type of the Resources you want to list (e.g. `Microsoft.Network/virtualNetworks`). A full list of available Resource Types can be found [here](https://docs.microsoft.com/en-us/azure/azure-resource-manager/azure-services-resource-providers).
> This content is derived from https://github.com/terraform-providers/terraform-provider-azurerm/blob/master/website/docs/d/resources.html.markdown.
"""
__args__ = dict()
__args__['name'] = name
__args__['requiredTags'] = required_tags
__args__['resourceGroupName'] = resource_group_name
__args__['type'] = type
if opts is None:
opts = pulumi.InvokeOptions()
if opts.version is None:
opts.version = utilities.get_version()
__ret__ = pulumi.runtime.invoke('azure:core/getResources:getResources', __args__, opts=opts).value
return AwaitableGetResourcesResult(
name=__ret__.get('name'),
required_tags=__ret__.get('requiredTags'),
resource_group_name=__ret__.get('resourceGroupName'),
resources=__ret__.get('resources'),
type=__ret__.get('type'),
id=__ret__.get('id'))
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LiveFeedPythonScripts/FeedFromOtherDevice/Share PC Screen With Android/screenshot.py | viveksb007/LiveFeed | 10 | 176527 | import time
import cv2
import pyscreenshot as ImageGrab
import numpy as np
class Screenshot(object):
def get_frame(self):
img = np.array(ImageGrab.grab().convert('RGB'), dtype=np.uint8)
img = cv2.cvtColor(img, cv2.COLOR_RGB2BGR)
ret2, jpeg = cv2.imencode('.jpg', img)
return jpeg.tostring()
def __del__(self):
self.cam.release()
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sdk/loganalytics/azure-mgmt-loganalytics/azure/mgmt/loganalytics/models/search_get_schema_response.py | tzhanl/azure-sdk-for-python | 1 | 7092 | # 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 msrest.serialization import Model
class SearchGetSchemaResponse(Model):
"""The get schema operation response.
:param metadata: The metadata from search results.
:type metadata: ~azure.mgmt.loganalytics.models.SearchMetadata
:param value: The array of result values.
:type value: list[~azure.mgmt.loganalytics.models.SearchSchemaValue]
"""
_attribute_map = {
'metadata': {'key': 'metadata', 'type': 'SearchMetadata'},
'value': {'key': 'value', 'type': '[SearchSchemaValue]'},
}
def __init__(self, **kwargs):
super(SearchGetSchemaResponse, self).__init__(**kwargs)
self.metadata = kwargs.get('metadata', None)
self.value = kwargs.get('value', None)
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