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249,100 | jmgilman/Neolib | neolib/pyamf/amf3.py | Decoder.readObject | def readObject(self):
"""
Reads an object from the stream.
"""
ref = self.readInteger(False)
if ref & REFERENCE_BIT == 0:
obj = self.context.getObject(ref >> 1)
if obj is None:
raise pyamf.ReferenceError('Unknown reference %d' % (ref >> 1,))
if self.use_proxies is True:
obj = self.readProxy(obj)
return obj
ref >>= 1
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obj.__readamf__(DataInput(self))
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self._readDynamic(class_def, obj_attrs)
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alias.applyAttributes(obj, obj_attrs, codec=self)
if self.use_proxies is True:
obj = self.readProxy(obj)
return obj | python | def readObject(self):
"""
Reads an object from the stream.
"""
ref = self.readInteger(False)
if ref & REFERENCE_BIT == 0:
obj = self.context.getObject(ref >> 1)
if obj is None:
raise pyamf.ReferenceError('Unknown reference %d' % (ref >> 1,))
if self.use_proxies is True:
obj = self.readProxy(obj)
return obj
ref >>= 1
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obj.__readamf__(DataInput(self))
if self.use_proxies is True:
obj = self.readProxy(obj)
return obj
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self._readStatic(class_def, obj_attrs)
self._readDynamic(class_def, obj_attrs)
elif class_def.encoding == ObjectEncoding.STATIC:
self._readStatic(class_def, obj_attrs)
else:
raise pyamf.DecodeError("Unknown object encoding")
alias.applyAttributes(obj, obj_attrs, codec=self)
if self.use_proxies is True:
obj = self.readProxy(obj)
return obj | [
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249,101 | jmgilman/Neolib | neolib/pyamf/amf3.py | Decoder.readXML | def readXML(self):
"""
Reads an xml object from the stream.
@return: An etree interface compatible object
@see: L{xml.set_default_interface}
"""
ref = self.readInteger(False)
if ref & REFERENCE_BIT == 0:
return self.context.getObject(ref >> 1)
xmlstring = self.stream.read(ref >> 1)
x = xml.fromstring(xmlstring)
self.context.addObject(x)
return x | python | def readXML(self):
"""
Reads an xml object from the stream.
@return: An etree interface compatible object
@see: L{xml.set_default_interface}
"""
ref = self.readInteger(False)
if ref & REFERENCE_BIT == 0:
return self.context.getObject(ref >> 1)
xmlstring = self.stream.read(ref >> 1)
x = xml.fromstring(xmlstring)
self.context.addObject(x)
return x | [
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249,102 | jmgilman/Neolib | neolib/pyamf/amf3.py | Decoder.readByteArray | def readByteArray(self):
"""
Reads a string of data from the stream.
Detects if the L{ByteArray} was compressed using C{zlib}.
@see: L{ByteArray}
@note: This is not supported in ActionScript 1.0 and 2.0.
"""
ref = self.readInteger(False)
if ref & REFERENCE_BIT == 0:
return self.context.getObject(ref >> 1)
buffer = self.stream.read(ref >> 1)
try:
buffer = zlib.decompress(buffer)
compressed = True
except zlib.error:
compressed = False
obj = ByteArray(buffer)
obj.compressed = compressed
self.context.addObject(obj)
return obj | python | def readByteArray(self):
"""
Reads a string of data from the stream.
Detects if the L{ByteArray} was compressed using C{zlib}.
@see: L{ByteArray}
@note: This is not supported in ActionScript 1.0 and 2.0.
"""
ref = self.readInteger(False)
if ref & REFERENCE_BIT == 0:
return self.context.getObject(ref >> 1)
buffer = self.stream.read(ref >> 1)
try:
buffer = zlib.decompress(buffer)
compressed = True
except zlib.error:
compressed = False
obj = ByteArray(buffer)
obj.compressed = compressed
self.context.addObject(obj)
return obj | [
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249,103 | jmgilman/Neolib | neolib/pyamf/amf3.py | Encoder.writeBoolean | def writeBoolean(self, n):
"""
Writes a Boolean to the stream.
"""
t = TYPE_BOOL_TRUE
if n is False:
t = TYPE_BOOL_FALSE
self.stream.write(t) | python | def writeBoolean(self, n):
"""
Writes a Boolean to the stream.
"""
t = TYPE_BOOL_TRUE
if n is False:
t = TYPE_BOOL_FALSE
self.stream.write(t) | [
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249,104 | jmgilman/Neolib | neolib/pyamf/amf3.py | Encoder.writeInteger | def writeInteger(self, n):
"""
Writes an integer to the stream.
@type n: integer data
@param n: The integer data to be encoded to the AMF3 data stream.
"""
if n < MIN_29B_INT or n > MAX_29B_INT:
self.writeNumber(float(n))
return
self.stream.write(TYPE_INTEGER)
self.stream.write(encode_int(n)) | python | def writeInteger(self, n):
"""
Writes an integer to the stream.
@type n: integer data
@param n: The integer data to be encoded to the AMF3 data stream.
"""
if n < MIN_29B_INT or n > MAX_29B_INT:
self.writeNumber(float(n))
return
self.stream.write(TYPE_INTEGER)
self.stream.write(encode_int(n)) | [
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249,105 | jmgilman/Neolib | neolib/pyamf/amf3.py | Encoder.writeNumber | def writeNumber(self, n):
"""
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@type n: C{float}
"""
self.stream.write(TYPE_NUMBER)
self.stream.write_double(n) | python | def writeNumber(self, n):
"""
Writes a float to the stream.
@type n: C{float}
"""
self.stream.write(TYPE_NUMBER)
self.stream.write_double(n) | [
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249,106 | jmgilman/Neolib | neolib/pyamf/amf3.py | Encoder.writeProxy | def writeProxy(self, obj):
"""
Encodes a proxied object to the stream.
@since: 0.6
"""
proxy = self.context.getProxyForObject(obj)
self.writeObject(proxy, is_proxy=True) | python | def writeProxy(self, obj):
"""
Encodes a proxied object to the stream.
@since: 0.6
"""
proxy = self.context.getProxyForObject(obj)
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249,107 | jmgilman/Neolib | neolib/pyamf/amf3.py | Encoder.writeObject | def writeObject(self, obj, is_proxy=False):
"""
Writes an object to the stream.
"""
if self.use_proxies and not is_proxy:
self.writeProxy(obj)
return
self.stream.write(TYPE_OBJECT)
ref = self.context.getObjectReference(obj)
if ref != -1:
self._writeInteger(ref << 1)
return
self.context.addObject(obj)
# object is not referenced, serialise it
kls = obj.__class__
definition = self.context.getClass(kls)
alias = None
class_ref = False # if the class definition is a reference
if definition:
class_ref = True
alias = definition.alias
else:
alias = self.context.getClassAlias(kls)
definition = ClassDefinition(alias)
self.context.addClass(definition, alias.klass)
if class_ref:
self.stream.write(definition.reference)
else:
ref = 0
if definition.encoding != ObjectEncoding.EXTERNAL:
ref += definition.attr_len << 4
final_reference = encode_int(ref | definition.encoding << 2 |
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self.stream.write(final_reference)
definition.reference = encode_int(
definition.reference << 2 | REFERENCE_BIT)
if alias.anonymous:
self.stream.write('\x01')
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self.serialiseString(alias.alias)
# work out what the final reference for the class will be.
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# again.
if alias.external:
obj.__writeamf__(DataOutput(self))
return
attrs = alias.getEncodableAttributes(obj, codec=self)
if alias.static_attrs:
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for attr in alias.static_attrs:
value = attrs.pop(attr)
self.writeElement(value)
if definition.encoding == ObjectEncoding.STATIC:
return
if definition.encoding == ObjectEncoding.DYNAMIC:
if attrs:
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if type(attr) in python.int_types:
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self.serialiseString(attr)
self.writeElement(value)
self.stream.write('\x01') | python | def writeObject(self, obj, is_proxy=False):
"""
Writes an object to the stream.
"""
if self.use_proxies and not is_proxy:
self.writeProxy(obj)
return
self.stream.write(TYPE_OBJECT)
ref = self.context.getObjectReference(obj)
if ref != -1:
self._writeInteger(ref << 1)
return
self.context.addObject(obj)
# object is not referenced, serialise it
kls = obj.__class__
definition = self.context.getClass(kls)
alias = None
class_ref = False # if the class definition is a reference
if definition:
class_ref = True
alias = definition.alias
else:
alias = self.context.getClassAlias(kls)
definition = ClassDefinition(alias)
self.context.addClass(definition, alias.klass)
if class_ref:
self.stream.write(definition.reference)
else:
ref = 0
if definition.encoding != ObjectEncoding.EXTERNAL:
ref += definition.attr_len << 4
final_reference = encode_int(ref | definition.encoding << 2 |
REFERENCE_BIT << 1 | REFERENCE_BIT)
self.stream.write(final_reference)
definition.reference = encode_int(
definition.reference << 2 | REFERENCE_BIT)
if alias.anonymous:
self.stream.write('\x01')
else:
self.serialiseString(alias.alias)
# work out what the final reference for the class will be.
# this is okay because the next time an object of the same
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# again.
if alias.external:
obj.__writeamf__(DataOutput(self))
return
attrs = alias.getEncodableAttributes(obj, codec=self)
if alias.static_attrs:
if not class_ref:
[self.serialiseString(attr) for attr in alias.static_attrs]
for attr in alias.static_attrs:
value = attrs.pop(attr)
self.writeElement(value)
if definition.encoding == ObjectEncoding.STATIC:
return
if definition.encoding == ObjectEncoding.DYNAMIC:
if attrs:
for attr, value in attrs.iteritems():
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self.serialiseString(attr)
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self.stream.write('\x01') | [
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249,108 | jmgilman/Neolib | neolib/pyamf/amf3.py | Encoder.writeXML | def writeXML(self, n):
"""
Writes a XML string to the data stream.
@type n: L{ET<xml.ET>}
@param n: The XML Document to be encoded to the AMF3 data stream.
"""
self.stream.write(TYPE_XMLSTRING)
ref = self.context.getObjectReference(n)
if ref != -1:
self._writeInteger(ref << 1)
return
self.context.addObject(n)
self.serialiseString(xml.tostring(n).encode('utf-8')) | python | def writeXML(self, n):
"""
Writes a XML string to the data stream.
@type n: L{ET<xml.ET>}
@param n: The XML Document to be encoded to the AMF3 data stream.
"""
self.stream.write(TYPE_XMLSTRING)
ref = self.context.getObjectReference(n)
if ref != -1:
self._writeInteger(ref << 1)
return
self.context.addObject(n)
self.serialiseString(xml.tostring(n).encode('utf-8')) | [
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249,109 | dossier/dossier.web | dossier/web/tags.py | v1_tag_associate | def v1_tag_associate(request, tags, tag):
'''Associate an HTML element with a tag.
The association should be a JSON serialized object on the
request body. Here is an example association that should
make the object's structure clear:
.. code-block:: python
{
"url": "http://example.com/abc/xyz?foo=bar",
"text": "The text the user highlighted.",
"stream_id": "{unix timestamp}-{md5 of url}",
"hash": "{nilsimsa hash of the HTML}",
"timestamp": {unix timestamp},
"xpath": {
"start_node": "/html/body/p[1]/text()[2]",
"start_idx": 3,
"end_node": "/html/body/p[1]/text()[3]",
"end_idx": 9
}
}
All fields are required and cannot be empty or ``null``.
The tag of the association should be specified in the URL
and is delimited by ``//``.
'''
tag = tag.decode('utf-8').strip()
assoc = dict(json.loads(request.body.read()), **{'tag': tag})
tags.add(assoc) | python | def v1_tag_associate(request, tags, tag):
'''Associate an HTML element with a tag.
The association should be a JSON serialized object on the
request body. Here is an example association that should
make the object's structure clear:
.. code-block:: python
{
"url": "http://example.com/abc/xyz?foo=bar",
"text": "The text the user highlighted.",
"stream_id": "{unix timestamp}-{md5 of url}",
"hash": "{nilsimsa hash of the HTML}",
"timestamp": {unix timestamp},
"xpath": {
"start_node": "/html/body/p[1]/text()[2]",
"start_idx": 3,
"end_node": "/html/body/p[1]/text()[3]",
"end_idx": 9
}
}
All fields are required and cannot be empty or ``null``.
The tag of the association should be specified in the URL
and is delimited by ``//``.
'''
tag = tag.decode('utf-8').strip()
assoc = dict(json.loads(request.body.read()), **{'tag': tag})
tags.add(assoc) | [
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249,110 | dossier/dossier.web | dossier/web/tags.py | v1_tag_list | def v1_tag_list(tags, tag=''):
'''List all direct children tags of the given parent.
If no parent is specified, then list all top-level tags.
The JSON returned for ``/dossier/v1/tags/list/foo/bar``
might look like this:
.. code-block:: python
{
'children': [
{'name': 'baz', 'parent': 'bar', 'tag': 'foo/bar/baz'},
]
}
'''
tag = tag.decode('utf-8').strip()
return {'children': tags.list(tag)} | python | def v1_tag_list(tags, tag=''):
'''List all direct children tags of the given parent.
If no parent is specified, then list all top-level tags.
The JSON returned for ``/dossier/v1/tags/list/foo/bar``
might look like this:
.. code-block:: python
{
'children': [
{'name': 'baz', 'parent': 'bar', 'tag': 'foo/bar/baz'},
]
}
'''
tag = tag.decode('utf-8').strip()
return {'children': tags.list(tag)} | [
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249,111 | dossier/dossier.web | dossier/web/tags.py | v1_tag_suggest | def v1_tag_suggest(request, tags, prefix, parent=''):
'''Provide fast suggestions for tag components.
This yields suggestions for *components* of a tag and a given
prefix. For example, given the tags ``foo/bar/baz`` and
``fob/bob``, here are some example completions (ordering may be
different):
.. code-block:: text
/dossier/v1/tags/suggest/prefix/f => ['foo', 'fob']
/dossier/v1/tags/suggest/prefix/foo => ['foo']
/dossier/v1/tags/suggest/prefix/b/parent/foo => ['bar']
/dossier/v1/tags/suggest/prefix/b/parent/fob => ['bob']
/dossier/v1/tags/suggest/prefix/b/parent/foo/bar => ['baz']
N.B. Each of the lists above are wrapped in the following
JSON envelope for the response:
.. code-block:: text
{'suggestions': ['foo', 'fob']}
An optional query parameter, ``limit``, may be passed to control
the number of suggestions returned.
'''
prefix = prefix.decode('utf-8').strip()
parent = parent.decode('utf-8').strip()
limit = min(10000, int(request.params.get('limit', 100)))
return {'suggestions': tags.suggest(parent, prefix, limit=limit)} | python | def v1_tag_suggest(request, tags, prefix, parent=''):
'''Provide fast suggestions for tag components.
This yields suggestions for *components* of a tag and a given
prefix. For example, given the tags ``foo/bar/baz`` and
``fob/bob``, here are some example completions (ordering may be
different):
.. code-block:: text
/dossier/v1/tags/suggest/prefix/f => ['foo', 'fob']
/dossier/v1/tags/suggest/prefix/foo => ['foo']
/dossier/v1/tags/suggest/prefix/b/parent/foo => ['bar']
/dossier/v1/tags/suggest/prefix/b/parent/fob => ['bob']
/dossier/v1/tags/suggest/prefix/b/parent/foo/bar => ['baz']
N.B. Each of the lists above are wrapped in the following
JSON envelope for the response:
.. code-block:: text
{'suggestions': ['foo', 'fob']}
An optional query parameter, ``limit``, may be passed to control
the number of suggestions returned.
'''
prefix = prefix.decode('utf-8').strip()
parent = parent.decode('utf-8').strip()
limit = min(10000, int(request.params.get('limit', 100)))
return {'suggestions': tags.suggest(parent, prefix, limit=limit)} | [
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249,112 | dossier/dossier.web | dossier/web/tags.py | v1_stream_id_associations | def v1_stream_id_associations(tags, stream_id):
'''Retrieve associations for a given stream_id.
The associations returned have the exact same structure as defined
in the ``v1_tag_associate`` route with one addition: a ``tag``
field contains the full tag name for the association.
'''
stream_id = stream_id.decode('utf-8').strip()
return {'associations': tags.assocs_by_stream_id(stream_id)} | python | def v1_stream_id_associations(tags, stream_id):
'''Retrieve associations for a given stream_id.
The associations returned have the exact same structure as defined
in the ``v1_tag_associate`` route with one addition: a ``tag``
field contains the full tag name for the association.
'''
stream_id = stream_id.decode('utf-8').strip()
return {'associations': tags.assocs_by_stream_id(stream_id)} | [
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249,113 | dossier/dossier.web | dossier/web/tags.py | v1_url_associations | def v1_url_associations(tags, url):
'''Retrieve associations for a given URL.
The associations returned have the exact same structure as defined
in the ``v1_tag_associate`` route with one addition: a ``tag``
field contains the full tag name for the association.
'''
url = urllib.unquote_plus(url.decode('utf-8')).strip()
return {'associations': tags.assocs_by_url(url)} | python | def v1_url_associations(tags, url):
'''Retrieve associations for a given URL.
The associations returned have the exact same structure as defined
in the ``v1_tag_associate`` route with one addition: a ``tag``
field contains the full tag name for the association.
'''
url = urllib.unquote_plus(url.decode('utf-8')).strip()
return {'associations': tags.assocs_by_url(url)} | [
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249,114 | dossier/dossier.web | dossier/web/tags.py | v1_tag_associations | def v1_tag_associations(tags, tag):
'''Retrieve associations for a given tag.
The associations returned have the exact same structure as defined
in the ``v1_tag_associate`` route with one addition: a ``tag``
field contains the full tag name for the association.
'''
tag = tag.decode('utf-8').strip()
return {'associations': tags.assocs_by_tag(tag)} | python | def v1_tag_associations(tags, tag):
'''Retrieve associations for a given tag.
The associations returned have the exact same structure as defined
in the ``v1_tag_associate`` route with one addition: a ``tag``
field contains the full tag name for the association.
'''
tag = tag.decode('utf-8').strip()
return {'associations': tags.assocs_by_tag(tag)} | [
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249,115 | dossier/dossier.web | dossier/web/tags.py | Tags.delete_all | def delete_all(self):
'''Deletes all tag data.
This does not destroy the ES index, but instead only
deletes all tags with the configured doc types.
'''
try:
self.conn.indices.delete_mapping(
index=self.index, doc_type=self.type_tag)
except TransportError:
logger.warn('type %r in index %r already deleted',
self.index, self.type_tag, exc_info=True)
try:
self.conn.indices.delete_mapping(
index=self.index, doc_type=self.type_assoc)
except TransportError:
logger.warn('type %r in index %r already deleted',
self.index, self.type_assoc, exc_info=True) | python | def delete_all(self):
'''Deletes all tag data.
This does not destroy the ES index, but instead only
deletes all tags with the configured doc types.
'''
try:
self.conn.indices.delete_mapping(
index=self.index, doc_type=self.type_tag)
except TransportError:
logger.warn('type %r in index %r already deleted',
self.index, self.type_tag, exc_info=True)
try:
self.conn.indices.delete_mapping(
index=self.index, doc_type=self.type_assoc)
except TransportError:
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] | Deletes all tag data.
This does not destroy the ES index, but instead only
deletes all tags with the configured doc types. | [
"Deletes",
"all",
"tag",
"data",
"."
] | 1cad1cce3c37d3a4e956abc710a2bc1afe16a092 | https://github.com/dossier/dossier.web/blob/1cad1cce3c37d3a4e956abc710a2bc1afe16a092/dossier/web/tags.py#L272-L289 |
249,116 | dossier/dossier.web | dossier/web/tags.py | Tags._create_mappings | def _create_mappings(self):
'Create the field type mapping.'
created1 = self._create_tag_mapping()
created2 = self._create_assoc_mapping()
return created1 or created2 | python | def _create_mappings(self):
'Create the field type mapping.'
created1 = self._create_tag_mapping()
created2 = self._create_assoc_mapping()
return created1 or created2 | [
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249,117 | cogniteev/docido-python-sdk | docido_sdk/toolbox/__init__.py | get_last_traceback | def get_last_traceback():
"""Retrieve the last traceback as an `unicode` string."""
import traceback
from StringIO import StringIO
tb = StringIO()
traceback.print_exc(file=tb)
return to_unicode(tb.getvalue()) | python | def get_last_traceback():
"""Retrieve the last traceback as an `unicode` string."""
import traceback
from StringIO import StringIO
tb = StringIO()
traceback.print_exc(file=tb)
return to_unicode(tb.getvalue()) | [
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249,118 | Sean1708/HipPy | hippy/__init__.py | write | def write(file_name, data):
"""Encode and write a Hip file."""
with open(file_name, 'w') as f:
f.write(encode(data)) | python | def write(file_name, data):
"""Encode and write a Hip file."""
with open(file_name, 'w') as f:
f.write(encode(data)) | [
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249,119 | fred49/linshare-api | linshareapi/user/threadmembers.py | ThreadsMembers2.get | def get(self, thread_uuid, uuid):
""" Get one thread member."""
members = (v for v in self.list(thread_uuid) if v.get('userUuid') == uuid)
for i in members:
self.log.debug(i)
return i
return None | python | def get(self, thread_uuid, uuid):
""" Get one thread member."""
members = (v for v in self.list(thread_uuid) if v.get('userUuid') == uuid)
for i in members:
self.log.debug(i)
return i
return None | [
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249,120 | fred49/linshare-api | linshareapi/user/threadmembers.py | WorkgroupMembers.delete | def delete(self, wg_uuid, uuid):
""" Delete one thread member."""
url = "%(base)s/%(wg_uuid)s/members/%(uuid)s" % {
'base': self.local_base_url,
'wg_uuid': wg_uuid,
'uuid': uuid
}
return self.core.delete(url) | python | def delete(self, wg_uuid, uuid):
""" Delete one thread member."""
url = "%(base)s/%(wg_uuid)s/members/%(uuid)s" % {
'base': self.local_base_url,
'wg_uuid': wg_uuid,
'uuid': uuid
}
return self.core.delete(url) | [
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249,121 | cariad/py-wpconfigr | wpconfigr/__main__.py | run_from_cli | def run_from_cli():
"""
Perform an update instigated from a CLI.
"""
arg_parser = argparse.ArgumentParser(
description='Read and write properties in a wp-config.php file. '
'Include a --value argument to set the value, omit it to '
'read the value of the specified key.',
prog='python -m wpconfigr')
arg_parser.add_argument('--filename',
help='wp-config.php filename',
required=True)
arg_parser.add_argument('--key',
help='Property key',
required=True)
arg_parser.add_argument('--value',
help='New property value',
required=False)
arg_parser.add_argument('--log-level',
default='CRITICAL',
help='Log level',
required=False)
arg_parser.add_argument('--set-true',
action='store_true',
help='Set the value as boolean true')
arg_parser.add_argument('--set-false',
action='store_true',
help='Set the value as boolean false')
args = arg_parser.parse_args()
if args.set_true and args.set_false:
arg_parser.error('Cannot set --set-true and --set-false.')
if args.value and args.set_true:
arg_parser.error('Cannot set --value and --set-true.')
if args.value and args.set_false:
arg_parser.error('Cannot set --value and --set-false.')
basicConfig(level=str(args.log_level).upper())
updater = WpConfigFile(filename=args.filename)
if args.set_true:
value = True
elif args.set_false:
value = False
else:
value = args.value
if value is not None:
updater.set(key=args.key, value=value)
else:
got = updater.get(key=args.key)
if got:
print(got) | python | def run_from_cli():
"""
Perform an update instigated from a CLI.
"""
arg_parser = argparse.ArgumentParser(
description='Read and write properties in a wp-config.php file. '
'Include a --value argument to set the value, omit it to '
'read the value of the specified key.',
prog='python -m wpconfigr')
arg_parser.add_argument('--filename',
help='wp-config.php filename',
required=True)
arg_parser.add_argument('--key',
help='Property key',
required=True)
arg_parser.add_argument('--value',
help='New property value',
required=False)
arg_parser.add_argument('--log-level',
default='CRITICAL',
help='Log level',
required=False)
arg_parser.add_argument('--set-true',
action='store_true',
help='Set the value as boolean true')
arg_parser.add_argument('--set-false',
action='store_true',
help='Set the value as boolean false')
args = arg_parser.parse_args()
if args.set_true and args.set_false:
arg_parser.error('Cannot set --set-true and --set-false.')
if args.value and args.set_true:
arg_parser.error('Cannot set --value and --set-true.')
if args.value and args.set_false:
arg_parser.error('Cannot set --value and --set-false.')
basicConfig(level=str(args.log_level).upper())
updater = WpConfigFile(filename=args.filename)
if args.set_true:
value = True
elif args.set_false:
value = False
else:
value = args.value
if value is not None:
updater.set(key=args.key, value=value)
else:
got = updater.get(key=args.key)
if got:
print(got) | [
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249,122 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | manage_file_analysis | def manage_file_analysis(args: argparse.Namespace, filename: str, data: object) -> None:
"""
Take care of the analysis of a datafile
"""
key = DataStore.hashfile(filename)
print('Analyzing {} --> {}'.format(filename, key))
if data.check_key(key): # if exists in database, prepopulate
fit = LineFit(filename, data=data.get_data(key))
else:
fit = LineFit(filename)
if args.time:
noise, curvature, rnge, domn = fit.analyze(time=args.time)
newrow = [args.time, noise, curvature,
rnge, domn, fit.accepts[args.time]]
data.update1(key, newrow, len(fit.noises))
else:
fit.analyze_full()
newrows = np.array([range(len(fit.noises)), fit.noises,
fit.curves, fit.ranges, fit.domains, fit.accepts])
data.update(key, newrows)
data.save() | python | def manage_file_analysis(args: argparse.Namespace, filename: str, data: object) -> None:
"""
Take care of the analysis of a datafile
"""
key = DataStore.hashfile(filename)
print('Analyzing {} --> {}'.format(filename, key))
if data.check_key(key): # if exists in database, prepopulate
fit = LineFit(filename, data=data.get_data(key))
else:
fit = LineFit(filename)
if args.time:
noise, curvature, rnge, domn = fit.analyze(time=args.time)
newrow = [args.time, noise, curvature,
rnge, domn, fit.accepts[args.time]]
data.update1(key, newrow, len(fit.noises))
else:
fit.analyze_full()
newrows = np.array([range(len(fit.noises)), fit.noises,
fit.curves, fit.ranges, fit.domains, fit.accepts])
data.update(key, newrows)
data.save() | [
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249,123 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | get_args | def get_args() -> argparse.Namespace:
"""
Get program arguments.
Just use --help....
"""
parser = argparse.ArgumentParser(prog='python3 linefit.py',
description=('Parameterize and analyze '
'usability of conduit edge data'))
parser.add_argument('files', metavar='F', type=str, nargs='*',
help=('File(s) for processing. '
'Each file has a specific format: '
'See README (or header) for specification.'))
parser.add_argument('-p', '--plot', action='store_true', default=False,
help=('Create Plot of file(s)? Note, unless --time flag used, '
'will plot middle time.'))
parser.add_argument('-pd', '--plotdata', action='store_true', default=False,
help='Create plot of current datastore.')
parser.add_argument('-a', '--analyze', action='store_true', default=False,
help=('Analyze the file and determine Curvature/Noise parameters. '
'If --time not specified, will examine entire file. '
'This will add results to datastore with false flags '
'in accept field if not provided.'))
parser.add_argument('-mt', '--machinetest', action='store_true', default=False,
help=('Determine if the times from the file are usable based on '
'supervised learning model. If --time not specified, '
'will examine entire file.'))
parser.add_argument('-m', '--model', type=str, default='nn',
help=('Learning Model to use. Options are ["nn", "svm", "forest", "sgd"]'))
parser.add_argument('-nnk', '--nnk', type=int, default=10,
help=('k-Parameter for k nearest neighbors. Google it.'))
parser.add_argument('-t', '--time', type=int, default=None,
help=('Time (column) of data to use for analysis OR plotting. '
'Zero-Indexed'))
parser.add_argument('-d', '--datastore', type=str, default=DATASTORE,
help=("Datastore filename override. "
"Don't do this unless you know what you're doing"))
parser.add_argument('-pds', '--printdata', action='store_true', default=False,
help=("Print data"))
parser.add_argument('-pdss', '--printdatashort', action='store_true', default=False,
help=("Print data short"))
args = parser.parse_args()
return args | python | def get_args() -> argparse.Namespace:
"""
Get program arguments.
Just use --help....
"""
parser = argparse.ArgumentParser(prog='python3 linefit.py',
description=('Parameterize and analyze '
'usability of conduit edge data'))
parser.add_argument('files', metavar='F', type=str, nargs='*',
help=('File(s) for processing. '
'Each file has a specific format: '
'See README (or header) for specification.'))
parser.add_argument('-p', '--plot', action='store_true', default=False,
help=('Create Plot of file(s)? Note, unless --time flag used, '
'will plot middle time.'))
parser.add_argument('-pd', '--plotdata', action='store_true', default=False,
help='Create plot of current datastore.')
parser.add_argument('-a', '--analyze', action='store_true', default=False,
help=('Analyze the file and determine Curvature/Noise parameters. '
'If --time not specified, will examine entire file. '
'This will add results to datastore with false flags '
'in accept field if not provided.'))
parser.add_argument('-mt', '--machinetest', action='store_true', default=False,
help=('Determine if the times from the file are usable based on '
'supervised learning model. If --time not specified, '
'will examine entire file.'))
parser.add_argument('-m', '--model', type=str, default='nn',
help=('Learning Model to use. Options are ["nn", "svm", "forest", "sgd"]'))
parser.add_argument('-nnk', '--nnk', type=int, default=10,
help=('k-Parameter for k nearest neighbors. Google it.'))
parser.add_argument('-t', '--time', type=int, default=None,
help=('Time (column) of data to use for analysis OR plotting. '
'Zero-Indexed'))
parser.add_argument('-d', '--datastore', type=str, default=DATASTORE,
help=("Datastore filename override. "
"Don't do this unless you know what you're doing"))
parser.add_argument('-pds', '--printdata', action='store_true', default=False,
help=("Print data"))
parser.add_argument('-pdss', '--printdatashort', action='store_true', default=False,
help=("Print data short"))
args = parser.parse_args()
return args | [
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249,124 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.get_keys | def get_keys(self) -> typing.List[str]:
"""
Return list of SHA512 hash keys that exist in datafile
:return: list of keys
"""
keys = []
for key in self.data.keys():
if key not in ['__header__', '__version__', '__globals__']:
keys.append(key)
return keys | python | def get_keys(self) -> typing.List[str]:
"""
Return list of SHA512 hash keys that exist in datafile
:return: list of keys
"""
keys = []
for key in self.data.keys():
if key not in ['__header__', '__version__', '__globals__']:
keys.append(key)
return keys | [
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249,125 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.check_key | def check_key(self, key: str) -> bool:
"""
Checks if key exists in datastore. True if yes, False if no.
:param: SHA512 hash key
:return: whether or key not exists in datastore
"""
keys = self.get_keys()
return key in keys | python | def check_key(self, key: str) -> bool:
"""
Checks if key exists in datastore. True if yes, False if no.
:param: SHA512 hash key
:return: whether or key not exists in datastore
"""
keys = self.get_keys()
return key in keys | [
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249,126 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.get_traindata | def get_traindata(self) -> np.ndarray:
"""
Pulls all available data and concatenates for model training
:return: 2d array of points
"""
traindata = None
for key, value in self.data.items():
if key not in ['__header__', '__version__', '__globals__']:
if traindata is None:
traindata = value[np.where(value[:, 4] != 0)]
else:
traindata = np.concatenate((traindata, value[np.where(value[:, 4] != 0)]))
return traindata | python | def get_traindata(self) -> np.ndarray:
"""
Pulls all available data and concatenates for model training
:return: 2d array of points
"""
traindata = None
for key, value in self.data.items():
if key not in ['__header__', '__version__', '__globals__']:
if traindata is None:
traindata = value[np.where(value[:, 4] != 0)]
else:
traindata = np.concatenate((traindata, value[np.where(value[:, 4] != 0)]))
return traindata | [
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249,127 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.printdata | def printdata(self) -> None:
""" Prints data to stdout """
np.set_printoptions(threshold=np.nan)
print(self.data)
np.set_printoptions(threshold=1000) | python | def printdata(self) -> None:
""" Prints data to stdout """
np.set_printoptions(threshold=np.nan)
print(self.data)
np.set_printoptions(threshold=1000) | [
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249,128 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.update | def update(self, key: str, data: np.ndarray) -> None:
""" Update entry in datastore """
self.data[key] = data | python | def update(self, key: str, data: np.ndarray) -> None:
""" Update entry in datastore """
self.data[key] = data | [
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249,129 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.update1 | def update1(self, key: str, data: np.ndarray, size: int) -> None:
""" Update one entry in specific record in datastore """
print(data)
if key in self.get_keys():
self.data[key][data[0]] = data
else:
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newdata[data[0]] = data
self.data[key] = newdata | python | def update1(self, key: str, data: np.ndarray, size: int) -> None:
""" Update one entry in specific record in datastore """
print(data)
if key in self.get_keys():
self.data[key][data[0]] = data
else:
newdata = np.zeros((size, 6))
newdata[data[0]] = data
self.data[key] = newdata | [
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249,130 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | DataStore.hashfile | def hashfile(name: str) -> str:
"""
Gets a hash of a file using block parsing
http://stackoverflow.com/questions/3431825/generating-a-md5-checksum-of-a-file
Using SHA512 for long-term support (hehehehe)
"""
hasher = hashlib.sha512()
with open(name, 'rb') as openfile:
for chunk in iter(lambda: openfile.read(4096), b''):
hasher.update(chunk)
return hasher.hexdigest() | python | def hashfile(name: str) -> str:
"""
Gets a hash of a file using block parsing
http://stackoverflow.com/questions/3431825/generating-a-md5-checksum-of-a-file
Using SHA512 for long-term support (hehehehe)
"""
hasher = hashlib.sha512()
with open(name, 'rb') as openfile:
for chunk in iter(lambda: openfile.read(4096), b''):
hasher.update(chunk)
return hasher.hexdigest() | [
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http://stackoverflow.com/questions/3431825/generating-a-md5-checksum-of-a-file
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249,131 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit._loadedges | def _loadedges(self) -> typing.Tuple[np.ndarray, np.ndarray, np.ndarray, float, np.ndarray]:
"""
Attempts to intelligently load the .mat file and take average of left and right edges
:return: left and right averages
:return: times for each column
:return: accept/reject for each column
:return: pixel-inch ratio
"""
data = sco.loadmat(self.filename)
datakeys = [k for k in data.keys()
if ('right' in k) or ('left' in k) or ('edge' in k)]
averagedata = ((data[datakeys[0]] + data[datakeys[1]]) / 2)
try:
times = (data['times'] - data['times'].min())[0]
except KeyError:
times = np.arange(len(data[datakeys[0]][0]))
try:
accept = data['accept']
except KeyError:
accept = np.zeros(len(times))
try:
ratio = data['ratio']
except KeyError:
ratio = 1
try:
viscosity = data['viscosity']
except KeyError:
viscosity = np.ones(len(times))
return averagedata, times, accept, ratio, viscosity | python | def _loadedges(self) -> typing.Tuple[np.ndarray, np.ndarray, np.ndarray, float, np.ndarray]:
"""
Attempts to intelligently load the .mat file and take average of left and right edges
:return: left and right averages
:return: times for each column
:return: accept/reject for each column
:return: pixel-inch ratio
"""
data = sco.loadmat(self.filename)
datakeys = [k for k in data.keys()
if ('right' in k) or ('left' in k) or ('edge' in k)]
averagedata = ((data[datakeys[0]] + data[datakeys[1]]) / 2)
try:
times = (data['times'] - data['times'].min())[0]
except KeyError:
times = np.arange(len(data[datakeys[0]][0]))
try:
accept = data['accept']
except KeyError:
accept = np.zeros(len(times))
try:
ratio = data['ratio']
except KeyError:
ratio = 1
try:
viscosity = data['viscosity']
except KeyError:
viscosity = np.ones(len(times))
return averagedata, times, accept, ratio, viscosity | [
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:return: left and right averages
:return: times for each column
:return: accept/reject for each column
:return: pixel-inch ratio | [
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249,132 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit.plot_file | def plot_file(self, name: str=None, time: int=None) -> None:
"""
Plot specific time for provided datafile.
If no time provided, will plot middle.
:param: savefile name
:param: time/data column
"""
if not time:
time = int(len(self.times) / 2)
if not name:
name = './img/' + self.filename + '.png'
yhat, residuals, residual_mean, noise = self._get_fit(time)
plt.figure()
plt.scatter(self.domain, self.averagedata[:, time], alpha=0.2)
plt.plot(yhat)
plt.savefig(name) | python | def plot_file(self, name: str=None, time: int=None) -> None:
"""
Plot specific time for provided datafile.
If no time provided, will plot middle.
:param: savefile name
:param: time/data column
"""
if not time:
time = int(len(self.times) / 2)
if not name:
name = './img/' + self.filename + '.png'
yhat, residuals, residual_mean, noise = self._get_fit(time)
plt.figure()
plt.scatter(self.domain, self.averagedata[:, time], alpha=0.2)
plt.plot(yhat)
plt.savefig(name) | [
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249,133 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit._gaussian_function | def _gaussian_function(self, datalength: int, values: np.ndarray,
height: int, index: int) -> np.ndarray:
"""
i'th Regression Model Gaussian
:param: len(x)
:param: x values
:param: height of gaussian
:param: position of gaussian
:return: gaussian bumps over domain
"""
return height * np.exp(-(1 / (self.spread_number * datalength)) *
(values - ((datalength / self.function_number) * index)) ** 2) | python | def _gaussian_function(self, datalength: int, values: np.ndarray,
height: int, index: int) -> np.ndarray:
"""
i'th Regression Model Gaussian
:param: len(x)
:param: x values
:param: height of gaussian
:param: position of gaussian
:return: gaussian bumps over domain
"""
return height * np.exp(-(1 / (self.spread_number * datalength)) *
(values - ((datalength / self.function_number) * index)) ** 2) | [
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249,134 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit._get_fit | def _get_fit(self, time: int) -> typing.Tuple[np.ndarray, np.ndarray, float, float]:
"""
Fit regression model to data
:param: time (column of data)
:return: predicted points
:return: residuals
:return: mean residual
:return: error
"""
rawdata = self.averagedata[:, time]
domain = np.arange(len(rawdata))
datalength = len(domain)
coefficients = np.zeros((datalength, self.function_number + 2))
coefficients[:, 0] = 1
coefficients[:, 1] = domain
for i in range(self.function_number):
coefficients[:, 2 + i] = self._gaussian_function(datalength, domain, 1, i)
betas = linalg.inv(coefficients.transpose().dot(coefficients)).dot(coefficients.transpose().dot(rawdata))
predicted_values = coefficients.dot(betas)
residuals = rawdata - predicted_values
error = np.sqrt(residuals.transpose().dot(residuals) / (datalength - (self.function_number + 2)))
return predicted_values, residuals, residuals.mean(), error | python | def _get_fit(self, time: int) -> typing.Tuple[np.ndarray, np.ndarray, float, float]:
"""
Fit regression model to data
:param: time (column of data)
:return: predicted points
:return: residuals
:return: mean residual
:return: error
"""
rawdata = self.averagedata[:, time]
domain = np.arange(len(rawdata))
datalength = len(domain)
coefficients = np.zeros((datalength, self.function_number + 2))
coefficients[:, 0] = 1
coefficients[:, 1] = domain
for i in range(self.function_number):
coefficients[:, 2 + i] = self._gaussian_function(datalength, domain, 1, i)
betas = linalg.inv(coefficients.transpose().dot(coefficients)).dot(coefficients.transpose().dot(rawdata))
predicted_values = coefficients.dot(betas)
residuals = rawdata - predicted_values
error = np.sqrt(residuals.transpose().dot(residuals) / (datalength - (self.function_number + 2)))
return predicted_values, residuals, residuals.mean(), error | [
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249,135 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit._get_noise | def _get_noise(self, residuals: np.ndarray) -> float:
"""
Determine Noise of Residuals.
:param: residuals
:return: noise
"""
return np.mean(np.abs(residuals)) | python | def _get_noise(self, residuals: np.ndarray) -> float:
"""
Determine Noise of Residuals.
:param: residuals
:return: noise
"""
return np.mean(np.abs(residuals)) | [
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249,136 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit.analyze | def analyze(self, time: int=None) -> typing.Tuple[float, float, int, int]:
"""
Determine noise, curvature, range, and domain of specified array.
:param: pixel to inch ratio
:param: time (column) to use.
:return: curvature
:return: noise
:return: range
:return: domain
"""
if not time:
time = int(len(self.times) / 2)
if self.domains[time] == 0:
yhat, residuals, mean_residual, error = self._get_fit(time)
yhat_p = self.ddiff(yhat)
yhat_pp = self.ddiff(yhat_p)
noise = self._get_noise(residuals)
curvature = (1 / self.ratio) * (1 / len(yhat_pp)) * np.sqrt(si.simps(yhat_pp ** 2))
rng = (self.ratio * (np.max(self.averagedata[:, time]) -
np.min(self.averagedata[:, time])))
dmn = self.ratio * len(self.averagedata[:, time])
self.noises[time] = np.log10(noise)
self.curves[time] = np.log10(curvature)
self.ranges[time] = np.log10(rng)
self.domains[time] = np.log10(dmn)
return self.noises[time], self.curves[time], self.ranges[time], self.domains[time] | python | def analyze(self, time: int=None) -> typing.Tuple[float, float, int, int]:
"""
Determine noise, curvature, range, and domain of specified array.
:param: pixel to inch ratio
:param: time (column) to use.
:return: curvature
:return: noise
:return: range
:return: domain
"""
if not time:
time = int(len(self.times) / 2)
if self.domains[time] == 0:
yhat, residuals, mean_residual, error = self._get_fit(time)
yhat_p = self.ddiff(yhat)
yhat_pp = self.ddiff(yhat_p)
noise = self._get_noise(residuals)
curvature = (1 / self.ratio) * (1 / len(yhat_pp)) * np.sqrt(si.simps(yhat_pp ** 2))
rng = (self.ratio * (np.max(self.averagedata[:, time]) -
np.min(self.averagedata[:, time])))
dmn = self.ratio * len(self.averagedata[:, time])
self.noises[time] = np.log10(noise)
self.curves[time] = np.log10(curvature)
self.ranges[time] = np.log10(rng)
self.domains[time] = np.log10(dmn)
return self.noises[time], self.curves[time], self.ranges[time], self.domains[time] | [
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249,137 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | LineFit.analyze_full | def analyze_full(self) -> typing.Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
"""
Determine noise, curvature, range, and domain of specified data.
Like analyze, except examines the entire file.
:param: float->pixel to inch ratio
:return: array->curvatures
:return: array->noises
:return: array->ranges
:return: array->domains
"""
if self.noises[0] == 0:
timelength = len(self.times)
for i in tqdm(range(timelength)):
self.analyze(time=i)
return self.noises, self.curves, self.ranges, self.domains | python | def analyze_full(self) -> typing.Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
"""
Determine noise, curvature, range, and domain of specified data.
Like analyze, except examines the entire file.
:param: float->pixel to inch ratio
:return: array->curvatures
:return: array->noises
:return: array->ranges
:return: array->domains
"""
if self.noises[0] == 0:
timelength = len(self.times)
for i in tqdm(range(timelength)):
self.analyze(time=i)
return self.noises, self.curves, self.ranges, self.domains | [
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249,138 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | ML.get_algo | def get_algo(self, args: argparse.Namespace, algo: str) -> object:
""" Returns machine learning algorithm based on arguments """
if algo == 'nn':
return NearestNeighbor(args.nnk) | python | def get_algo(self, args: argparse.Namespace, algo: str) -> object:
""" Returns machine learning algorithm based on arguments """
if algo == 'nn':
return NearestNeighbor(args.nnk) | [
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249,139 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | ML.plot_fitspace | def plot_fitspace(self, name: str, X: np.ndarray, y: np.ndarray, clf: object) -> None:
""" Plot 2dplane of fitspace """
cmap_light = ListedColormap(['#FFAAAA', '#AAFFAA', '#AAAAFF'])
cmap_bold = ListedColormap(['#FF0000', '#00FF00', '#0000FF'])
# Plot the decision boundary. For that, we will assign a color to each
# point in the mesh [x_min, m_max]x[y_min, y_max].
h = 0.01 # Mesh step size
x_min, x_max = X[:, 0].min() - 1, X[:, 0].max() + 1
y_min, y_max = X[:, 1].min() - 1, X[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, h),
np.arange(y_min, y_max, h))
Z = clf.predict(np.c_[xx.ravel(), yy.ravel()])
# Put the result into a color plot
Z = Z.reshape(xx.shape)
plt.figure()
plt.pcolormesh(xx, yy, Z, cmap=cmap_light)
# Plot also the training points
plt.scatter(X[:, 0], X[:, 1], c=y, cmap=cmap_bold)
plt.xlim(xx.min(), xx.max())
plt.ylim(yy.min(), yy.max())
plt.xlabel(r'$\log_{10}$ Noise')
plt.ylabel(r'$\log_{10}$ Curvature')
plt.savefig(name) | python | def plot_fitspace(self, name: str, X: np.ndarray, y: np.ndarray, clf: object) -> None:
""" Plot 2dplane of fitspace """
cmap_light = ListedColormap(['#FFAAAA', '#AAFFAA', '#AAAAFF'])
cmap_bold = ListedColormap(['#FF0000', '#00FF00', '#0000FF'])
# Plot the decision boundary. For that, we will assign a color to each
# point in the mesh [x_min, m_max]x[y_min, y_max].
h = 0.01 # Mesh step size
x_min, x_max = X[:, 0].min() - 1, X[:, 0].max() + 1
y_min, y_max = X[:, 1].min() - 1, X[:, 1].max() + 1
xx, yy = np.meshgrid(np.arange(x_min, x_max, h),
np.arange(y_min, y_max, h))
Z = clf.predict(np.c_[xx.ravel(), yy.ravel()])
# Put the result into a color plot
Z = Z.reshape(xx.shape)
plt.figure()
plt.pcolormesh(xx, yy, Z, cmap=cmap_light)
# Plot also the training points
plt.scatter(X[:, 0], X[:, 1], c=y, cmap=cmap_bold)
plt.xlim(xx.min(), xx.max())
plt.ylim(yy.min(), yy.max())
plt.xlabel(r'$\log_{10}$ Noise')
plt.ylabel(r'$\log_{10}$ Curvature')
plt.savefig(name) | [
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249,140 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | NearestNeighbor.train | def train(self, traindata: np.ndarray) -> None:
""" Trains on dataset """
self.clf.fit(traindata[:, 1:5], traindata[:, 5]) | python | def train(self, traindata: np.ndarray) -> None:
""" Trains on dataset """
self.clf.fit(traindata[:, 1:5], traindata[:, 5]) | [
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249,141 | Dispersive-Hydrodynamics-Lab/PACE | PACE/PACE.py | NearestNeighbor.predict | def predict(self, predictdata: np.ndarray) -> np.ndarray:
""" predict given points """
return self.clf.predict(predictdata) | python | def predict(self, predictdata: np.ndarray) -> np.ndarray:
""" predict given points """
return self.clf.predict(predictdata) | [
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249,142 | henrysher/kotocore | kotocore/session.py | Session.connect_to | def connect_to(self, service_name, **kwargs):
"""
Shortcut method to make instantiating the ``Connection`` classes
easier.
Forwards ``**kwargs`` like region, keys, etc. on to the constructor.
:param service_name: A string that specifies the name of the desired
service. Ex. ``sqs``, ``sns``, ``dynamodb``, etc.
:type service_name: string
:rtype: <kotocore.connection.Connection> instance
"""
service_class = self.get_connection(service_name)
return service_class.connect_to(**kwargs) | python | def connect_to(self, service_name, **kwargs):
"""
Shortcut method to make instantiating the ``Connection`` classes
easier.
Forwards ``**kwargs`` like region, keys, etc. on to the constructor.
:param service_name: A string that specifies the name of the desired
service. Ex. ``sqs``, ``sns``, ``dynamodb``, etc.
:type service_name: string
:rtype: <kotocore.connection.Connection> instance
"""
service_class = self.get_connection(service_name)
return service_class.connect_to(**kwargs) | [
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249,143 | minhhoit/yacms | yacms/forms/forms.py | FormForForm.save | def save(self, **kwargs):
"""
Create a ``FormEntry`` instance and related ``FieldEntry``
instances for each form field.
"""
entry = super(FormForForm, self).save(commit=False)
entry.form = self.form
entry.entry_time = now()
entry.save()
entry_fields = entry.fields.values_list("field_id", flat=True)
new_entry_fields = []
for field in self.form_fields:
field_key = "field_%s" % field.id
value = self.cleaned_data[field_key]
if value and self.fields[field_key].widget.needs_multipart_form:
value = fs.save(join("forms", str(uuid4()), value.name), value)
if isinstance(value, list):
value = ", ".join([v.strip() for v in value])
if field.id in entry_fields:
field_entry = entry.fields.get(field_id=field.id)
field_entry.value = value
field_entry.save()
else:
new = {"entry": entry, "field_id": field.id, "value": value}
new_entry_fields.append(FieldEntry(**new))
if new_entry_fields:
FieldEntry.objects.bulk_create(new_entry_fields)
return entry | python | def save(self, **kwargs):
"""
Create a ``FormEntry`` instance and related ``FieldEntry``
instances for each form field.
"""
entry = super(FormForForm, self).save(commit=False)
entry.form = self.form
entry.entry_time = now()
entry.save()
entry_fields = entry.fields.values_list("field_id", flat=True)
new_entry_fields = []
for field in self.form_fields:
field_key = "field_%s" % field.id
value = self.cleaned_data[field_key]
if value and self.fields[field_key].widget.needs_multipart_form:
value = fs.save(join("forms", str(uuid4()), value.name), value)
if isinstance(value, list):
value = ", ".join([v.strip() for v in value])
if field.id in entry_fields:
field_entry = entry.fields.get(field_id=field.id)
field_entry.value = value
field_entry.save()
else:
new = {"entry": entry, "field_id": field.id, "value": value}
new_entry_fields.append(FieldEntry(**new))
if new_entry_fields:
FieldEntry.objects.bulk_create(new_entry_fields)
return entry | [
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249,144 | minhhoit/yacms | yacms/forms/forms.py | FormForForm.email_to | def email_to(self):
"""
Return the value entered for the first field of type
``forms.EmailField``.
"""
for field in self.form_fields:
if issubclass(fields.CLASSES[field.field_type], forms.EmailField):
return self.cleaned_data["field_%s" % field.id]
return None | python | def email_to(self):
"""
Return the value entered for the first field of type
``forms.EmailField``.
"""
for field in self.form_fields:
if issubclass(fields.CLASSES[field.field_type], forms.EmailField):
return self.cleaned_data["field_%s" % field.id]
return None | [
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249,145 | minhhoit/yacms | yacms/forms/forms.py | EntriesForm.columns | def columns(self):
"""
Returns the list of selected column names.
"""
fields = [f.label for f in self.form_fields
if self.cleaned_data["field_%s_export" % f.id]]
if self.cleaned_data["field_0_export"]:
fields.append(self.entry_time_name)
return fields | python | def columns(self):
"""
Returns the list of selected column names.
"""
fields = [f.label for f in self.form_fields
if self.cleaned_data["field_%s_export" % f.id]]
if self.cleaned_data["field_0_export"]:
fields.append(self.entry_time_name)
return fields | [
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249,146 | WhereSoftwareGoesToDie/pymarquise | marquise/marquise.py | Marquise.close | def close(self):
"""Close the Marquise context, ensuring data is flushed and
spool files are closed.
This should always be closed explicitly, as there's no
guarantees that it will happen when the instance is deleted.
"""
if self.marquise_ctx is None:
self.__debug("Marquise handle is already closed, will do nothing.")
# Multiple close() calls are okay.
return
self.__debug("Shutting down Marquise handle spooling to %s and %s" % (self.spool_path_points, self.spool_path_contents))
# At the time of writing this always succeeds (returns 0).
MARQUISE_SHUTDOWN(self.marquise_ctx)
# Signal that our context is no longer valid.
self.marquise_ctx = None | python | def close(self):
"""Close the Marquise context, ensuring data is flushed and
spool files are closed.
This should always be closed explicitly, as there's no
guarantees that it will happen when the instance is deleted.
"""
if self.marquise_ctx is None:
self.__debug("Marquise handle is already closed, will do nothing.")
# Multiple close() calls are okay.
return
self.__debug("Shutting down Marquise handle spooling to %s and %s" % (self.spool_path_points, self.spool_path_contents))
# At the time of writing this always succeeds (returns 0).
MARQUISE_SHUTDOWN(self.marquise_ctx)
# Signal that our context is no longer valid.
self.marquise_ctx = None | [
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249,147 | WhereSoftwareGoesToDie/pymarquise | marquise/marquise.py | Marquise.update_source | def update_source(self, address, metadata_dict):
"""Pack the `metadata_dict` for an `address` into a data structure and ship it to the spool file.
Arguments:
address -- the address for which this metadata_dict applies.
metadata_dict -- a Python dict of arbitrary string key-value pairs.
"""
if self.marquise_ctx is None:
raise ValueError("Attempted to write to a closed Marquise handle.")
self.__debug("Supplied address: %s" % address)
# Sanity check the input, everything must be UTF8 strings (not
# yet confirmed), no Nonetypes or anything stupid like that.
#
# The keys of the key-value pairs are unique, by virtue of
# taking a dict as input.
if any([ x is None for x in metadata_dict.keys() ]):
raise TypeError("One of your metadata_dict keys is a Nonetype")
# Values are allowed to be None, coerce to empty strings.
metadata_dict = dict([ (x[0],"" if x[1] is None else x[1]) for x in metadata_dict.items() ])
# Cast each string to a C-string. This may have unusual results if your
# keys/vals aren't particularly stringy, such as Python classes,
# Exceptions, etc. They will get str()'d, and they may look stupid.
# pylint: disable=multiple-statements
try: c_fields = [ cstring(str(x)) for x in metadata_dict.keys() ]
except Exception as exc: raise TypeError("One of your metadata_dict keys couldn't be cast to a Cstring, %s" % exc)
try: c_values = [ cstring(str(x)) for x in metadata_dict.values() ]
except Exception as exc: raise TypeError("One of your metadata_dict values couldn't be cast to a Cstring, %s" % exc)
# pylint: enable=multiple-statements
# Get our source_dict data structure
source_dict = MARQUISE_NEW_SOURCE(c_fields, c_values, len(metadata_dict))
if is_cnull(source_dict):
raise ValueError("errno is set to EINVAL on invalid input, our errno is %d" % FFI.errno)
# If you do something stupid, like passing a string where an
# int (address) is meant to go, CFFI will explode. Which is
# fine, but that causes memory leaks. The explosion still
# occurs, but we cleanup after (before?) ourselves.
try:
success = MARQUISE_UPDATE_SOURCE(self.marquise_ctx, address, source_dict)
except TypeError as exc:
MARQUISE_FREE_SOURCE(source_dict)
raise
self.__debug("marquise_update_source returned %d" % success)
if success != 0:
MARQUISE_FREE_SOURCE(source_dict)
raise RuntimeError("marquise_update_source was unsuccessful, errno is %d" % FFI.errno)
MARQUISE_FREE_SOURCE(source_dict)
return True | python | def update_source(self, address, metadata_dict):
"""Pack the `metadata_dict` for an `address` into a data structure and ship it to the spool file.
Arguments:
address -- the address for which this metadata_dict applies.
metadata_dict -- a Python dict of arbitrary string key-value pairs.
"""
if self.marquise_ctx is None:
raise ValueError("Attempted to write to a closed Marquise handle.")
self.__debug("Supplied address: %s" % address)
# Sanity check the input, everything must be UTF8 strings (not
# yet confirmed), no Nonetypes or anything stupid like that.
#
# The keys of the key-value pairs are unique, by virtue of
# taking a dict as input.
if any([ x is None for x in metadata_dict.keys() ]):
raise TypeError("One of your metadata_dict keys is a Nonetype")
# Values are allowed to be None, coerce to empty strings.
metadata_dict = dict([ (x[0],"" if x[1] is None else x[1]) for x in metadata_dict.items() ])
# Cast each string to a C-string. This may have unusual results if your
# keys/vals aren't particularly stringy, such as Python classes,
# Exceptions, etc. They will get str()'d, and they may look stupid.
# pylint: disable=multiple-statements
try: c_fields = [ cstring(str(x)) for x in metadata_dict.keys() ]
except Exception as exc: raise TypeError("One of your metadata_dict keys couldn't be cast to a Cstring, %s" % exc)
try: c_values = [ cstring(str(x)) for x in metadata_dict.values() ]
except Exception as exc: raise TypeError("One of your metadata_dict values couldn't be cast to a Cstring, %s" % exc)
# pylint: enable=multiple-statements
# Get our source_dict data structure
source_dict = MARQUISE_NEW_SOURCE(c_fields, c_values, len(metadata_dict))
if is_cnull(source_dict):
raise ValueError("errno is set to EINVAL on invalid input, our errno is %d" % FFI.errno)
# If you do something stupid, like passing a string where an
# int (address) is meant to go, CFFI will explode. Which is
# fine, but that causes memory leaks. The explosion still
# occurs, but we cleanup after (before?) ourselves.
try:
success = MARQUISE_UPDATE_SOURCE(self.marquise_ctx, address, source_dict)
except TypeError as exc:
MARQUISE_FREE_SOURCE(source_dict)
raise
self.__debug("marquise_update_source returned %d" % success)
if success != 0:
MARQUISE_FREE_SOURCE(source_dict)
raise RuntimeError("marquise_update_source was unsuccessful, errno is %d" % FFI.errno)
MARQUISE_FREE_SOURCE(source_dict)
return True | [
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address -- the address for which this metadata_dict applies.
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249,148 | edeposit/edeposit.amqp.storage | src/edeposit/amqp/storage/storage_handler.py | StorageHandler._get_db_fields | def _get_db_fields(self, obj):
"""
Return list of database dictionaries, which are used as indexes for
each attributes.
Args:
cached (bool, default True): Use cached connection to database.
Returns:
list: List of OOBTree's for each item in :attr:`.COMMON_FIELDS`.
"""
for field in obj.indexes:
yield field, self._zeo_key(field) | python | def _get_db_fields(self, obj):
"""
Return list of database dictionaries, which are used as indexes for
each attributes.
Args:
cached (bool, default True): Use cached connection to database.
Returns:
list: List of OOBTree's for each item in :attr:`.COMMON_FIELDS`.
"""
for field in obj.indexes:
yield field, self._zeo_key(field) | [
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249,149 | edeposit/edeposit.amqp.storage | src/edeposit/amqp/storage/storage_handler.py | StorageHandler._check_obj_properties | def _check_obj_properties(self, pub, name="pub"):
"""
Make sure, that `pub` has the right interface.
Args:
pub (obj): Instance which will be checked.
name (str): Name of the instance. Used in exception. Default `pub`.
Raises:
InvalidType: When the `pub` is not instance of `obj_type`.
"""
if not hasattr(pub, "indexes"):
raise InvalidType("`%s` doesn't have .indexes property!" % name)
if not pub.indexes:
raise InvalidType("`%s.indexes` is not set!" % name)
if not hasattr(pub, "project_key"):
raise InvalidType(
"`%s` doesn't have .project_key property!" % name
)
if not pub.project_key:
raise InvalidType("`%s.project_key` is not set!" % name) | python | def _check_obj_properties(self, pub, name="pub"):
"""
Make sure, that `pub` has the right interface.
Args:
pub (obj): Instance which will be checked.
name (str): Name of the instance. Used in exception. Default `pub`.
Raises:
InvalidType: When the `pub` is not instance of `obj_type`.
"""
if not hasattr(pub, "indexes"):
raise InvalidType("`%s` doesn't have .indexes property!" % name)
if not pub.indexes:
raise InvalidType("`%s.indexes` is not set!" % name)
if not hasattr(pub, "project_key"):
raise InvalidType(
"`%s` doesn't have .project_key property!" % name
)
if not pub.project_key:
raise InvalidType("`%s.project_key` is not set!" % name) | [
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249,150 | edeposit/edeposit.amqp.storage | src/edeposit/amqp/storage/storage_handler.py | StorageHandler._put_into_indexes | def _put_into_indexes(self, obj):
"""
Put publication into all indexes.
Attr:
obj (obj): Indexable object.
Raises:
UnindexableObject: When there is no index (property) which can be
used to index `obj` in database.
"""
no_of_used_indexes = 0
for field_name, db_index in list(self._get_db_fields(obj)):
attr_value = getattr(obj, field_name)
if attr_value is None: # index only by set attributes
continue
container = db_index.get(attr_value, None)
if container is None:
container = OOTreeSet()
db_index[attr_value] = container
container.insert(obj)
no_of_used_indexes += 1
# make sure that atleast one `attr_value` was used
if no_of_used_indexes <= 0:
raise UnindexableObject(
"You have to use atleast one of the identificators!"
) | python | def _put_into_indexes(self, obj):
"""
Put publication into all indexes.
Attr:
obj (obj): Indexable object.
Raises:
UnindexableObject: When there is no index (property) which can be
used to index `obj` in database.
"""
no_of_used_indexes = 0
for field_name, db_index in list(self._get_db_fields(obj)):
attr_value = getattr(obj, field_name)
if attr_value is None: # index only by set attributes
continue
container = db_index.get(attr_value, None)
if container is None:
container = OOTreeSet()
db_index[attr_value] = container
container.insert(obj)
no_of_used_indexes += 1
# make sure that atleast one `attr_value` was used
if no_of_used_indexes <= 0:
raise UnindexableObject(
"You have to use atleast one of the identificators!"
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249,151 | edeposit/edeposit.amqp.storage | src/edeposit/amqp/storage/storage_handler.py | StorageHandler.store_object | def store_object(self, obj):
"""
Save `obj` into database and into proper indexes.
Attr:
obj (obj): Indexable object.
Raises:
InvalidType: When the `obj` doesn't have right properties.
Unindexableobjlication: When there is no indexes defined.
"""
self._check_obj_properties(obj)
with transaction.manager:
self._put_into_indexes(obj) | python | def store_object(self, obj):
"""
Save `obj` into database and into proper indexes.
Attr:
obj (obj): Indexable object.
Raises:
InvalidType: When the `obj` doesn't have right properties.
Unindexableobjlication: When there is no indexes defined.
"""
self._check_obj_properties(obj)
with transaction.manager:
self._put_into_indexes(obj) | [
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249,152 | edeposit/edeposit.amqp.storage | src/edeposit/amqp/storage/storage_handler.py | StorageHandler._get_subset_matches | def _get_subset_matches(self, query):
"""
Yield publications, at indexes defined by `query` property values.
Args:
query (obj): Object implementing proper interface.
Yields:
list: List of matching publications.
"""
for field_name, db_index in self._get_db_fields(query):
attr = getattr(query, field_name)
if attr is None: # don't use unset attributes
continue
results = db_index.get(attr, OOTreeSet())
if results:
yield results | python | def _get_subset_matches(self, query):
"""
Yield publications, at indexes defined by `query` property values.
Args:
query (obj): Object implementing proper interface.
Yields:
list: List of matching publications.
"""
for field_name, db_index in self._get_db_fields(query):
attr = getattr(query, field_name)
if attr is None: # don't use unset attributes
continue
results = db_index.get(attr, OOTreeSet())
if results:
yield results | [
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249,153 | pjanis/funtool | funtool/group_measure.py | _wrap_measure | def _wrap_measure(individual_group_measure_process, group_measure, loaded_processes):
"""
Creates a function on a state_collection, which creates analysis_collections for each group in the collection.
"""
def wrapped_measure(state_collection,overriding_parameters=None,loggers=None):
if loggers == None:
loggers = funtool.logger.set_default_loggers()
if loaded_processes != None :
if group_measure.grouping_selectors != None:
for grouping_selector_name in group_measure.grouping_selectors:
state_collection= funtool.state_collection.add_grouping(state_collection, grouping_selector_name, loaded_processes)
for group in funtool.state_collection.groups_in_grouping(state_collection, grouping_selector_name):
analysis_collection = funtool.analysis.AnalysisCollection(None,group,{},{})
if group_measure.analysis_selectors != None:
for analysis_selector in group_measure.analysis_selectors:
analysis_collection = loaded_processes["analysis_selector"][analysis_selector].process_function(analysis_collection,state_collection)
if analysis_collection != None:
individual_group_measure_process(analysis_collection,state_collection)
return state_collection
return wrapped_measure | python | def _wrap_measure(individual_group_measure_process, group_measure, loaded_processes):
"""
Creates a function on a state_collection, which creates analysis_collections for each group in the collection.
"""
def wrapped_measure(state_collection,overriding_parameters=None,loggers=None):
if loggers == None:
loggers = funtool.logger.set_default_loggers()
if loaded_processes != None :
if group_measure.grouping_selectors != None:
for grouping_selector_name in group_measure.grouping_selectors:
state_collection= funtool.state_collection.add_grouping(state_collection, grouping_selector_name, loaded_processes)
for group in funtool.state_collection.groups_in_grouping(state_collection, grouping_selector_name):
analysis_collection = funtool.analysis.AnalysisCollection(None,group,{},{})
if group_measure.analysis_selectors != None:
for analysis_selector in group_measure.analysis_selectors:
analysis_collection = loaded_processes["analysis_selector"][analysis_selector].process_function(analysis_collection,state_collection)
if analysis_collection != None:
individual_group_measure_process(analysis_collection,state_collection)
return state_collection
return wrapped_measure | [
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249,154 | unixorn/haze | haze/ec2.py | getAWSAccountID | def getAWSAccountID():
'''
Print an instance's AWS account number or 0 when not in EC2
'''
link = "http://169.254.169.254/latest/dynamic/instance-identity/document"
try:
conn = urllib2.urlopen(url=link, timeout=5)
except urllib2.URLError:
return '0'
jsonData = json.loads(conn.read())
return jsonData['accountId'] | python | def getAWSAccountID():
'''
Print an instance's AWS account number or 0 when not in EC2
'''
link = "http://169.254.169.254/latest/dynamic/instance-identity/document"
try:
conn = urllib2.urlopen(url=link, timeout=5)
except urllib2.URLError:
return '0'
jsonData = json.loads(conn.read())
return jsonData['accountId'] | [
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249,155 | unixorn/haze | haze/ec2.py | readInstanceTag | def readInstanceTag(instanceID, tagName="Name", connection=None):
"""
Load a tag from EC2
:param str instanceID: Instance ID to read the tag on
:param str tagName: Name of tag to load
:param connection: optional boto connection to use
:returns: the tag's value
:rtype: str
"""
assert isinstance(instanceID, basestring), ("instanceID must be a string but is %r" % instanceID)
assert isinstance(tagName, basestring), ("tagName must be a string but is %r" % tagName)
if not connection:
# Assume AWS credentials are in the environment or the instance is using an IAM role
connection = boto.ec2.connect_to_region(myRegion())
# Filter the tag values for our instance_id
# http://docs.aws.amazon.com/AWSEC2/latest/CommandLineReference/ApiReference-cmd-DescribeTags.html
tagData = connection.get_all_tags(filters={"resource-id": instanceID, "key": tagName})
if tagData:
tagValue = tagData[0].value
else:
raise RuntimeError, "%s: No such tag on %s" % (tagName, instanceID)
return tagValue | python | def readInstanceTag(instanceID, tagName="Name", connection=None):
"""
Load a tag from EC2
:param str instanceID: Instance ID to read the tag on
:param str tagName: Name of tag to load
:param connection: optional boto connection to use
:returns: the tag's value
:rtype: str
"""
assert isinstance(instanceID, basestring), ("instanceID must be a string but is %r" % instanceID)
assert isinstance(tagName, basestring), ("tagName must be a string but is %r" % tagName)
if not connection:
# Assume AWS credentials are in the environment or the instance is using an IAM role
connection = boto.ec2.connect_to_region(myRegion())
# Filter the tag values for our instance_id
# http://docs.aws.amazon.com/AWSEC2/latest/CommandLineReference/ApiReference-cmd-DescribeTags.html
tagData = connection.get_all_tags(filters={"resource-id": instanceID, "key": tagName})
if tagData:
tagValue = tagData[0].value
else:
raise RuntimeError, "%s: No such tag on %s" % (tagName, instanceID)
return tagValue | [
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249,156 | unixorn/haze | haze/ec2.py | readMyEC2Tag | def readMyEC2Tag(tagName, connection=None):
"""
Load an EC2 tag for the running instance & print it.
:param str tagName: Name of the tag to read
:param connection: Optional boto connection
"""
assert isinstance(tagName, basestring), ("tagName must be a string but is %r" % tagName)
# Load metadata. if == {} we are on localhost
# http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AESDG-chapter-instancedata.html
if not connection:
# Assume AWS credentials are in the environment or the instance is using an IAM role
connection = boto.ec2.connect_to_region(myRegion())
return readInstanceTag(connection=connection,
instanceID=myInstanceID(),
tagName=tagName) | python | def readMyEC2Tag(tagName, connection=None):
"""
Load an EC2 tag for the running instance & print it.
:param str tagName: Name of the tag to read
:param connection: Optional boto connection
"""
assert isinstance(tagName, basestring), ("tagName must be a string but is %r" % tagName)
# Load metadata. if == {} we are on localhost
# http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/AESDG-chapter-instancedata.html
if not connection:
# Assume AWS credentials are in the environment or the instance is using an IAM role
connection = boto.ec2.connect_to_region(myRegion())
return readInstanceTag(connection=connection,
instanceID=myInstanceID(),
tagName=tagName) | [
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249,157 | vuolter/autoupgrade | autoupgrade/utils.py | ver_to_tuple | def ver_to_tuple(value):
"""
Convert version like string to a tuple of integers.
"""
return tuple(int(_f) for _f in re.split(r'\D+', value) if _f) | python | def ver_to_tuple(value):
"""
Convert version like string to a tuple of integers.
"""
return tuple(int(_f) for _f in re.split(r'\D+', value) if _f) | [
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249,158 | rinocloud/rinocloud-python | rinocloud/object.py | Object.increment_name | def increment_name(self, name, i):
"""
takes something like
test.txt
and returns
test1.txt
"""
if i == 0:
return name
if '.' in name:
split = name.split('.')
split[-2] = split[-2] + str(i)
return '.'.join(split)
else:
return name + str(i) | python | def increment_name(self, name, i):
"""
takes something like
test.txt
and returns
test1.txt
"""
if i == 0:
return name
if '.' in name:
split = name.split('.')
split[-2] = split[-2] + str(i)
return '.'.join(split)
else:
return name + str(i) | [
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249,159 | rinocloud/rinocloud-python | rinocloud/object.py | Object.save_local_metadata | def save_local_metadata(self):
"""
save all the exposed variables to a json file
"""
# save to the set local path and add .json
with open(self.filepath + '.json', 'w+') as outfile:
json.dump(self._prep_metadata(), outfile, indent=4) | python | def save_local_metadata(self):
"""
save all the exposed variables to a json file
"""
# save to the set local path and add .json
with open(self.filepath + '.json', 'w+') as outfile:
json.dump(self._prep_metadata(), outfile, indent=4) | [
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249,160 | jrheard/madison_axi | madison_axi/axi.py | move_forward | def move_forward(num_steps):
"""Moves the pen forward a few steps in the direction that its "turtle" is facing.
Arguments:
num_steps - a number like 20. A bigger number makes the pen move farther.
"""
assert int(num_steps) == num_steps, "move_forward() only accepts integers, but you gave it " + str(num_steps)
_make_cnc_request("move.forward./" + str(num_steps))
state['turtle'].forward(num_steps) | python | def move_forward(num_steps):
"""Moves the pen forward a few steps in the direction that its "turtle" is facing.
Arguments:
num_steps - a number like 20. A bigger number makes the pen move farther.
"""
assert int(num_steps) == num_steps, "move_forward() only accepts integers, but you gave it " + str(num_steps)
_make_cnc_request("move.forward./" + str(num_steps))
state['turtle'].forward(num_steps) | [
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249,161 | pjuren/pyokit | src/pyokit/statistics/online.py | RollingMean.add | def add(self, v):
"""Add a new value."""
self._vals_added += 1
if self._mean is None:
self._mean = v
self._mean = self._mean + ((v - self._mean) / float(self._vals_added)) | python | def add(self, v):
"""Add a new value."""
self._vals_added += 1
if self._mean is None:
self._mean = v
self._mean = self._mean + ((v - self._mean) / float(self._vals_added)) | [
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249,162 | pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | _build_trees_by_chrom | def _build_trees_by_chrom(blocks, verbose=False):
"""
Construct set of interval trees from an iterable of genome alignment blocks.
:return: a dictionary indexed by chromosome name where each entry is an
interval tree for that chromosome.
"""
if verbose:
sys.stderr.write("separating blocks by chromosome... ")
by_chrom = {}
for b in blocks:
if b.chrom not in by_chrom:
by_chrom[b.chrom] = []
by_chrom[b.chrom].append(b)
if verbose:
sys.stderr.write("done\n")
if verbose:
sys.stderr.write("building interval trees by chromosome... ")
res = {}
for c in by_chrom:
res[c] = IntervalTree(by_chrom[c], openEnded=True)
if verbose:
sys.stderr.write("done\n")
return res | python | def _build_trees_by_chrom(blocks, verbose=False):
"""
Construct set of interval trees from an iterable of genome alignment blocks.
:return: a dictionary indexed by chromosome name where each entry is an
interval tree for that chromosome.
"""
if verbose:
sys.stderr.write("separating blocks by chromosome... ")
by_chrom = {}
for b in blocks:
if b.chrom not in by_chrom:
by_chrom[b.chrom] = []
by_chrom[b.chrom].append(b)
if verbose:
sys.stderr.write("done\n")
if verbose:
sys.stderr.write("building interval trees by chromosome... ")
res = {}
for c in by_chrom:
res[c] = IntervalTree(by_chrom[c], openEnded=True)
if verbose:
sys.stderr.write("done\n")
return res | [
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interval tree for that chromosome. | [
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249,163 | pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | GenomeAlignmentBlock.get_column_absolute | def get_column_absolute(self, position,
miss_seqs=MissingSequenceHandler.TREAT_AS_ALL_GAPS,
species=None):
"""
return a column from the block as dictionary indexed by seq. name.
:param position: the index to extract from the block; must be absolute
coordinates (i.e. between self.start and self.end, not
inclusive of the end).
:param miss_seqs: how to treat sequence with no actual sequence data for
the column.
:return: dictionary where keys are sequence names and values are
nucleotides (raw strings).
"""
if position < self.start or position >= self.end:
raise ValueError("getting column at genomic locus " + self._chrom + " " +
str(position) + " failed; locus is outside of genome " +
"alignment block")
rel_coord = self.sequence_to_alignment_coords(self.reference_sequence_name,
position, position + 1)
assert(len(rel_coord) == 1)
rel_start, rel_end = rel_coord[0]
assert(rel_end == rel_start + 1)
raw_col = self.get_column(rel_start, miss_seqs)
if species is None:
return raw_col
res = {}
for k in raw_col:
name_parts = k.split(".")
if name_parts[0] in species:
res[k] = raw_col[k]
return res | python | def get_column_absolute(self, position,
miss_seqs=MissingSequenceHandler.TREAT_AS_ALL_GAPS,
species=None):
"""
return a column from the block as dictionary indexed by seq. name.
:param position: the index to extract from the block; must be absolute
coordinates (i.e. between self.start and self.end, not
inclusive of the end).
:param miss_seqs: how to treat sequence with no actual sequence data for
the column.
:return: dictionary where keys are sequence names and values are
nucleotides (raw strings).
"""
if position < self.start or position >= self.end:
raise ValueError("getting column at genomic locus " + self._chrom + " " +
str(position) + " failed; locus is outside of genome " +
"alignment block")
rel_coord = self.sequence_to_alignment_coords(self.reference_sequence_name,
position, position + 1)
assert(len(rel_coord) == 1)
rel_start, rel_end = rel_coord[0]
assert(rel_end == rel_start + 1)
raw_col = self.get_column(rel_start, miss_seqs)
if species is None:
return raw_col
res = {}
for k in raw_col:
name_parts = k.split(".")
if name_parts[0] in species:
res[k] = raw_col[k]
return res | [
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:param position: the index to extract from the block; must be absolute
coordinates (i.e. between self.start and self.end, not
inclusive of the end).
:param miss_seqs: how to treat sequence with no actual sequence data for
the column.
:return: dictionary where keys are sequence names and values are
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249,164 | pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | GenomeAlignment.get_column | def get_column(self, chrom, position,
missing_seqs=MissingSequenceHandler.TREAT_AS_ALL_GAPS,
species=None):
"""Get the alignment column at the specified chromosome and position."""
blocks = self.get_blocks(chrom, position, position + 1)
if len(blocks) == 0:
raise NoSuchAlignmentColumnError("Request for column on chrom " +
chrom + " at position " +
str(position) + " not possible; " +
"genome alignment not defined at " +
"that locus.")
if len(blocks) > 1:
raise NoUniqueColumnError("Request for column on chrom " + chrom +
" at position " + str(position) + "not " +
"possible; ambiguous alignment of that locus.")
return blocks[0].get_column_absolute(position, missing_seqs, species) | python | def get_column(self, chrom, position,
missing_seqs=MissingSequenceHandler.TREAT_AS_ALL_GAPS,
species=None):
"""Get the alignment column at the specified chromosome and position."""
blocks = self.get_blocks(chrom, position, position + 1)
if len(blocks) == 0:
raise NoSuchAlignmentColumnError("Request for column on chrom " +
chrom + " at position " +
str(position) + " not possible; " +
"genome alignment not defined at " +
"that locus.")
if len(blocks) > 1:
raise NoUniqueColumnError("Request for column on chrom " + chrom +
" at position " + str(position) + "not " +
"possible; ambiguous alignment of that locus.")
return blocks[0].get_column_absolute(position, missing_seqs, species) | [
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249,165 | cogniteev/docido-python-sdk | docido_sdk/toolbox/decorators.py | decorate_instance_methods | def decorate_instance_methods(obj, decorator, includes=None, excludes=None):
"""Decorator instance methods of an object.
:param obj: Python object whose instance methods have to be decorated
:param decorator:
instance method decorator.
>>> def decorate(name, f):
>>> def __wrap(*args, **kwargs)
>>> print '--> entering instance method {}'.format(name)
>>> eax = f(*args, **kwargs)
>>> print '<-- leaving instance method {}'.format(name)
:param string list includes:
restrict wrapped instance methods. Default is `None` meaning
that all instance method are wrapped.
:param string list excludes:
used to prevent some instance methods to be wrapped. Default is `None`
:return: new class that inherits the `clazz` specified in parameter.
"""
class InstanceMethodDecorator(object):
def __getattribute__(self, name):
value = obj.__getattribute__(name)
if excludes and name in excludes:
return value
if includes and name not in includes:
return value
if inspect.ismethod(value):
value = decorator(name, value)
return value
return InstanceMethodDecorator() | python | def decorate_instance_methods(obj, decorator, includes=None, excludes=None):
"""Decorator instance methods of an object.
:param obj: Python object whose instance methods have to be decorated
:param decorator:
instance method decorator.
>>> def decorate(name, f):
>>> def __wrap(*args, **kwargs)
>>> print '--> entering instance method {}'.format(name)
>>> eax = f(*args, **kwargs)
>>> print '<-- leaving instance method {}'.format(name)
:param string list includes:
restrict wrapped instance methods. Default is `None` meaning
that all instance method are wrapped.
:param string list excludes:
used to prevent some instance methods to be wrapped. Default is `None`
:return: new class that inherits the `clazz` specified in parameter.
"""
class InstanceMethodDecorator(object):
def __getattribute__(self, name):
value = obj.__getattribute__(name)
if excludes and name in excludes:
return value
if includes and name not in includes:
return value
if inspect.ismethod(value):
value = decorator(name, value)
return value
return InstanceMethodDecorator() | [
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:param obj: Python object whose instance methods have to be decorated
:param decorator:
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>>> def decorate(name, f):
>>> def __wrap(*args, **kwargs)
>>> print '--> entering instance method {}'.format(name)
>>> eax = f(*args, **kwargs)
>>> print '<-- leaving instance method {}'.format(name)
:param string list includes:
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:param string list excludes:
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] | 58ecb6c6f5757fd40c0601657ab18368da7ddf33 | https://github.com/cogniteev/docido-python-sdk/blob/58ecb6c6f5757fd40c0601657ab18368da7ddf33/docido_sdk/toolbox/decorators.py#L33-L63 |
249,166 | cogniteev/docido-python-sdk | docido_sdk/toolbox/decorators.py | reraise | def reraise(clazz):
""" Decorator catching every exception that might be raised by wrapped
function and raise another exception instead.
Exception initially raised is passed in first argument of the raised
exception.
:param: Exception class: clazz:
Python exception class to raise
"""
def _decorator(f):
@functools.wraps(f)
def _wrap(*args, **kwargs):
try:
return f(*args, **kwargs)
except Exception as e:
raise clazz(e), None, sys.exc_info()[2]
return _wrap
return _decorator | python | def reraise(clazz):
""" Decorator catching every exception that might be raised by wrapped
function and raise another exception instead.
Exception initially raised is passed in first argument of the raised
exception.
:param: Exception class: clazz:
Python exception class to raise
"""
def _decorator(f):
@functools.wraps(f)
def _wrap(*args, **kwargs):
try:
return f(*args, **kwargs)
except Exception as e:
raise clazz(e), None, sys.exc_info()[2]
return _wrap
return _decorator | [
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Exception initially raised is passed in first argument of the raised
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249,167 | edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | getListOfBases | def getListOfBases():
"""
This function is here mainly for purposes of unittest
Returns:
list of str: Valid bases as they are used as URL parameters in links at
Aleph main page.
"""
downer = Downloader()
data = downer.download(ALEPH_URL + "/F/?func=file&file_name=base-list")
dom = dhtmlparser.parseString(data.lower())
# from default aleph page filter links containing local_base in their href
base_links = filter(
lambda x: "href" in x.params and "local_base" in x.params["href"],
dom.find("a")
)
# split links by & - we will need only XXX from link.tld/..&local_base=XXX
base_links = map(
lambda x: x.params["href"].replace("?", "&", 1).split("&"),
base_links
)
# filter only sections containing bases
bases = map(
lambda link: filter(lambda base: "local_base=" in base, link)[0],
base_links
)
# filter bases from base sections
bases = map(lambda x: x.split("=")[1].strip(), bases)
return list(set(bases)) | python | def getListOfBases():
"""
This function is here mainly for purposes of unittest
Returns:
list of str: Valid bases as they are used as URL parameters in links at
Aleph main page.
"""
downer = Downloader()
data = downer.download(ALEPH_URL + "/F/?func=file&file_name=base-list")
dom = dhtmlparser.parseString(data.lower())
# from default aleph page filter links containing local_base in their href
base_links = filter(
lambda x: "href" in x.params and "local_base" in x.params["href"],
dom.find("a")
)
# split links by & - we will need only XXX from link.tld/..&local_base=XXX
base_links = map(
lambda x: x.params["href"].replace("?", "&", 1).split("&"),
base_links
)
# filter only sections containing bases
bases = map(
lambda link: filter(lambda base: "local_base=" in base, link)[0],
base_links
)
# filter bases from base sections
bases = map(lambda x: x.split("=")[1].strip(), bases)
return list(set(bases)) | [
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249,168 | edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | searchInAleph | def searchInAleph(base, phrase, considerSimilar, field):
"""
Send request to the aleph search engine.
Request itself is pretty useless, but it can be later used as parameter
for :func:`getDocumentIDs`, which can fetch records from Aleph.
Args:
base (str): which database you want to use
phrase (str): what do you want to search
considerSimilar (bool): fuzzy search, which is not working at all, so
don't use it
field (str): where you want to look (see: :attr:`VALID_ALEPH_FIELDS`)
Returns:
dictionary: consisting from following fields:
| error (optional): present if there was some form of error
| no_entries (int): number of entries that can be fetch from aleph
| no_records (int): no idea what is this, but it is always >= than
`no_entries`
| set_number (int): important - something like ID of your request
| session-id (str): used to count users for licensing purposes
Example:
Returned dict::
{
'session-id': 'YLI54HBQJESUTS678YYUNKEU4BNAUJDKA914GMF39J6K89VSCB',
'set_number': 36520,
'no_records': 1,
'no_entries': 1
}
Raises:
AlephException: if Aleph doesn't return any information
InvalidAlephFieldException: if specified field is not valid
"""
downer = Downloader()
if field.lower() not in VALID_ALEPH_FIELDS:
raise InvalidAlephFieldException("Unknown field '" + field + "'!")
param_url = Template(SEARCH_URL_TEMPLATE).substitute(
PHRASE=quote_plus(phrase), # urlencode phrase
BASE=base,
FIELD=field,
SIMILAR="Y" if considerSimilar else "N"
)
result = downer.download(ALEPH_URL + param_url)
dom = dhtmlparser.parseString(result)
find = dom.find("find") # find <find> element :)
if len(find) <= 0:
raise AlephException("Aleph didn't returned any information.")
find = find[0]
# convert aleph result into dictionary
result = _alephResultToDict(find)
# add informations about base into result
result["base"] = base
if "error" not in result:
return result
# handle errors
if result["error"] == "empty set":
result["no_entries"] = 0 # empty set have 0 entries
return result
else:
raise AlephException(result["error"]) | python | def searchInAleph(base, phrase, considerSimilar, field):
"""
Send request to the aleph search engine.
Request itself is pretty useless, but it can be later used as parameter
for :func:`getDocumentIDs`, which can fetch records from Aleph.
Args:
base (str): which database you want to use
phrase (str): what do you want to search
considerSimilar (bool): fuzzy search, which is not working at all, so
don't use it
field (str): where you want to look (see: :attr:`VALID_ALEPH_FIELDS`)
Returns:
dictionary: consisting from following fields:
| error (optional): present if there was some form of error
| no_entries (int): number of entries that can be fetch from aleph
| no_records (int): no idea what is this, but it is always >= than
`no_entries`
| set_number (int): important - something like ID of your request
| session-id (str): used to count users for licensing purposes
Example:
Returned dict::
{
'session-id': 'YLI54HBQJESUTS678YYUNKEU4BNAUJDKA914GMF39J6K89VSCB',
'set_number': 36520,
'no_records': 1,
'no_entries': 1
}
Raises:
AlephException: if Aleph doesn't return any information
InvalidAlephFieldException: if specified field is not valid
"""
downer = Downloader()
if field.lower() not in VALID_ALEPH_FIELDS:
raise InvalidAlephFieldException("Unknown field '" + field + "'!")
param_url = Template(SEARCH_URL_TEMPLATE).substitute(
PHRASE=quote_plus(phrase), # urlencode phrase
BASE=base,
FIELD=field,
SIMILAR="Y" if considerSimilar else "N"
)
result = downer.download(ALEPH_URL + param_url)
dom = dhtmlparser.parseString(result)
find = dom.find("find") # find <find> element :)
if len(find) <= 0:
raise AlephException("Aleph didn't returned any information.")
find = find[0]
# convert aleph result into dictionary
result = _alephResultToDict(find)
# add informations about base into result
result["base"] = base
if "error" not in result:
return result
# handle errors
if result["error"] == "empty set":
result["no_entries"] = 0 # empty set have 0 entries
return result
else:
raise AlephException(result["error"]) | [
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Request itself is pretty useless, but it can be later used as parameter
for :func:`getDocumentIDs`, which can fetch records from Aleph.
Args:
base (str): which database you want to use
phrase (str): what do you want to search
considerSimilar (bool): fuzzy search, which is not working at all, so
don't use it
field (str): where you want to look (see: :attr:`VALID_ALEPH_FIELDS`)
Returns:
dictionary: consisting from following fields:
| error (optional): present if there was some form of error
| no_entries (int): number of entries that can be fetch from aleph
| no_records (int): no idea what is this, but it is always >= than
`no_entries`
| set_number (int): important - something like ID of your request
| session-id (str): used to count users for licensing purposes
Example:
Returned dict::
{
'session-id': 'YLI54HBQJESUTS678YYUNKEU4BNAUJDKA914GMF39J6K89VSCB',
'set_number': 36520,
'no_records': 1,
'no_entries': 1
}
Raises:
AlephException: if Aleph doesn't return any information
InvalidAlephFieldException: if specified field is not valid | [
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] | 360342c0504d5daa2344e864762cdf938d4149c7 | https://github.com/edeposit/edeposit.amqp.aleph/blob/360342c0504d5daa2344e864762cdf938d4149c7/src/edeposit/amqp/aleph/aleph.py#L316-L388 |
249,169 | edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | downloadRecords | def downloadRecords(search_result, from_doc=1):
"""
Download `MAX_RECORDS` documents from `search_result` starting from
`from_doc`.
Attr:
search_result (dict): returned from :func:`searchInAleph`.
from_doc (int, default 1): Start from document number `from_doc`.
Returns:
list: List of XML strings with documents in MARC OAI.
"""
downer = Downloader()
if "set_number" not in search_result:
return []
# set numbers should be probably aligned to some length
set_number = str(search_result["set_number"])
if len(set_number) < 6:
set_number = (6 - len(set_number)) * "0" + set_number
# download all no_records
records = []
for cnt in range(search_result["no_records"]):
doc_number = from_doc + cnt
if cnt >= MAX_RECORDS or doc_number > search_result["no_records"]:
break
set_data = downer.download(
ALEPH_URL + Template(RECORD_URL_TEMPLATE).substitute(
SET_NUM=set_number,
RECORD_NUM=doc_number,
)
)
records.append(set_data)
return records | python | def downloadRecords(search_result, from_doc=1):
"""
Download `MAX_RECORDS` documents from `search_result` starting from
`from_doc`.
Attr:
search_result (dict): returned from :func:`searchInAleph`.
from_doc (int, default 1): Start from document number `from_doc`.
Returns:
list: List of XML strings with documents in MARC OAI.
"""
downer = Downloader()
if "set_number" not in search_result:
return []
# set numbers should be probably aligned to some length
set_number = str(search_result["set_number"])
if len(set_number) < 6:
set_number = (6 - len(set_number)) * "0" + set_number
# download all no_records
records = []
for cnt in range(search_result["no_records"]):
doc_number = from_doc + cnt
if cnt >= MAX_RECORDS or doc_number > search_result["no_records"]:
break
set_data = downer.download(
ALEPH_URL + Template(RECORD_URL_TEMPLATE).substitute(
SET_NUM=set_number,
RECORD_NUM=doc_number,
)
)
records.append(set_data)
return records | [
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`from_doc`.
Attr:
search_result (dict): returned from :func:`searchInAleph`.
from_doc (int, default 1): Start from document number `from_doc`.
Returns:
list: List of XML strings with documents in MARC OAI. | [
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249,170 | edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | getDocumentIDs | def getDocumentIDs(aleph_search_result, number_of_docs=-1):
"""
Get IDs, which can be used as parameters for other functions.
Args:
aleph_search_result (dict): returned from :func:`searchInAleph`
number_of_docs (int, optional): how many :class:`DocumentID` from set
given by `aleph_search_result` should be returned.
Default -1 for all of them.
Returns:
list: :class:`DocumentID` named tuples to given `aleph_search_result`.
Raises:
AlephException: If Aleph returns unknown format of data.
Note:
Returned :class:`DocumentID` can be used as parameters to
:func:`downloadMARCXML`.
"""
downer = Downloader()
if "set_number" not in aleph_search_result:
return []
# set numbers should be probably aligned to some length
set_number = str(aleph_search_result["set_number"])
if len(set_number) < 6:
set_number = (6 - len(set_number)) * "0" + set_number
# limit number of fetched documents, if -1, download all
if number_of_docs <= 0:
number_of_docs = aleph_search_result["no_entries"]
# download data about given set
set_data = downer.download(
ALEPH_URL + Template(SET_URL_TEMPLATE).substitute(
SET_NUMBER=set_number,
NUMBER_OF_DOCS=number_of_docs,
)
)
# parse data
dom = dhtmlparser.parseString(set_data)
set_data = dom.find("ill-get-set")
# there should be at least one <ill-get-set> field
if len(set_data) <= 0:
raise AlephException("Aleph didn't returned set data.")
ids = []
for library in set_data:
documents = _alephResultToDict(library)
if "error" in documents:
raise AlephException("getDocumentIDs: " + documents["error"])
# convert all document records to DocumentID named tuple and extend
# them to 'ids' array
if isinstance(documents["doc-number"], list):
ids.extend(
map(
lambda x: DocumentID(
x,
documents["set-library"],
aleph_search_result["base"]
),
set(documents["doc-number"])
)
)
else:
ids.append(
DocumentID(
documents["doc-number"],
documents["set-library"],
aleph_search_result["base"]
)
)
return ids | python | def getDocumentIDs(aleph_search_result, number_of_docs=-1):
"""
Get IDs, which can be used as parameters for other functions.
Args:
aleph_search_result (dict): returned from :func:`searchInAleph`
number_of_docs (int, optional): how many :class:`DocumentID` from set
given by `aleph_search_result` should be returned.
Default -1 for all of them.
Returns:
list: :class:`DocumentID` named tuples to given `aleph_search_result`.
Raises:
AlephException: If Aleph returns unknown format of data.
Note:
Returned :class:`DocumentID` can be used as parameters to
:func:`downloadMARCXML`.
"""
downer = Downloader()
if "set_number" not in aleph_search_result:
return []
# set numbers should be probably aligned to some length
set_number = str(aleph_search_result["set_number"])
if len(set_number) < 6:
set_number = (6 - len(set_number)) * "0" + set_number
# limit number of fetched documents, if -1, download all
if number_of_docs <= 0:
number_of_docs = aleph_search_result["no_entries"]
# download data about given set
set_data = downer.download(
ALEPH_URL + Template(SET_URL_TEMPLATE).substitute(
SET_NUMBER=set_number,
NUMBER_OF_DOCS=number_of_docs,
)
)
# parse data
dom = dhtmlparser.parseString(set_data)
set_data = dom.find("ill-get-set")
# there should be at least one <ill-get-set> field
if len(set_data) <= 0:
raise AlephException("Aleph didn't returned set data.")
ids = []
for library in set_data:
documents = _alephResultToDict(library)
if "error" in documents:
raise AlephException("getDocumentIDs: " + documents["error"])
# convert all document records to DocumentID named tuple and extend
# them to 'ids' array
if isinstance(documents["doc-number"], list):
ids.extend(
map(
lambda x: DocumentID(
x,
documents["set-library"],
aleph_search_result["base"]
),
set(documents["doc-number"])
)
)
else:
ids.append(
DocumentID(
documents["doc-number"],
documents["set-library"],
aleph_search_result["base"]
)
)
return ids | [
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Args:
aleph_search_result (dict): returned from :func:`searchInAleph`
number_of_docs (int, optional): how many :class:`DocumentID` from set
given by `aleph_search_result` should be returned.
Default -1 for all of them.
Returns:
list: :class:`DocumentID` named tuples to given `aleph_search_result`.
Raises:
AlephException: If Aleph returns unknown format of data.
Note:
Returned :class:`DocumentID` can be used as parameters to
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249,171 | edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | downloadMARCXML | def downloadMARCXML(doc_id, library, base="nkc"):
"""
Download MARC XML document with given `doc_id` from given `library`.
Args:
doc_id (DocumentID): You will get this from :func:`getDocumentIDs`.
library (str): "``NKC01``" in our case, but don't worry,
:func:`getDocumentIDs` adds library specification into
:class:`DocumentID` named tuple.
Returns:
str: MARC XML unicode string.
Raises:
LibraryNotFoundException
DocumentNotFoundException
"""
downer = Downloader()
data = downer.download(
ALEPH_URL + Template(DOC_URL_TEMPLATE).substitute(
DOC_ID=doc_id,
LIBRARY=library
)
)
dom = dhtmlparser.parseString(data)
# check if there are any errors
# bad library error
error = dom.find("login")
if error:
error_msg = error[0].find("error")
if error_msg:
raise LibraryNotFoundException(
"Can't download document doc_id: '" + str(doc_id) + "' " +
"(probably bad library: '" + library + "')!\nMessage: " +
"\n".join(map(lambda x: x.getContent(), error_msg))
)
# another error - document not found
error = dom.find("ill-get-doc")
if error:
error_msg = error[0].find("error")
if error_msg:
raise DocumentNotFoundException(
"\n".join(map(lambda x: x.getContent(), error_msg))
)
return data | python | def downloadMARCXML(doc_id, library, base="nkc"):
"""
Download MARC XML document with given `doc_id` from given `library`.
Args:
doc_id (DocumentID): You will get this from :func:`getDocumentIDs`.
library (str): "``NKC01``" in our case, but don't worry,
:func:`getDocumentIDs` adds library specification into
:class:`DocumentID` named tuple.
Returns:
str: MARC XML unicode string.
Raises:
LibraryNotFoundException
DocumentNotFoundException
"""
downer = Downloader()
data = downer.download(
ALEPH_URL + Template(DOC_URL_TEMPLATE).substitute(
DOC_ID=doc_id,
LIBRARY=library
)
)
dom = dhtmlparser.parseString(data)
# check if there are any errors
# bad library error
error = dom.find("login")
if error:
error_msg = error[0].find("error")
if error_msg:
raise LibraryNotFoundException(
"Can't download document doc_id: '" + str(doc_id) + "' " +
"(probably bad library: '" + library + "')!\nMessage: " +
"\n".join(map(lambda x: x.getContent(), error_msg))
)
# another error - document not found
error = dom.find("ill-get-doc")
if error:
error_msg = error[0].find("error")
if error_msg:
raise DocumentNotFoundException(
"\n".join(map(lambda x: x.getContent(), error_msg))
)
return data | [
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Returns:
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Raises:
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249,172 | KnowledgeLinks/rdfframework | rdfframework/search/esloaders_temp.py | EsRdfBulkLoader._index_item | def _index_item(self, uri, num, batch_num):
""" queries the triplestore for an item sends it to elasticsearch """
data = RdfDataset(get_all_item_data(uri, self.namespace),
uri).base_class.es_json()
self.batch_data[batch_num].append(data)
self.count += 1 | python | def _index_item(self, uri, num, batch_num):
""" queries the triplestore for an item sends it to elasticsearch """
data = RdfDataset(get_all_item_data(uri, self.namespace),
uri).base_class.es_json()
self.batch_data[batch_num].append(data)
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249,173 | StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | share_with_org | def share_with_org(project_ids, org, access_level, suppress_email_notification=False):
"""
Shares one or more DNAnexus projects with an organization.
Args:
project_ids: `list`. One or more DNAnexus project identifiers, where each project ID is in
the form "project-FXq6B809p5jKzp2vJkjkKvg3".
org: `str`. The name of the DNAnexus org with which to share the projects.
access_level: The permission level to give to members of the org - one of
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suppress_email_notification: `bool`. True means to allow the DNAnexus platform to send an
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"""
for p in project_ids:
dxpy.api.project_invite(object_id=p,input_params={"invitee": org,"level": access_level,"suppressEmailNotification": suppress_email_notification}) | python | def share_with_org(project_ids, org, access_level, suppress_email_notification=False):
"""
Shares one or more DNAnexus projects with an organization.
Args:
project_ids: `list`. One or more DNAnexus project identifiers, where each project ID is in
the form "project-FXq6B809p5jKzp2vJkjkKvg3".
org: `str`. The name of the DNAnexus org with which to share the projects.
access_level: The permission level to give to members of the org - one of
["VIEW","UPLOAD","CONTRIBUTE","ADMINISTER"].
suppress_email_notification: `bool`. True means to allow the DNAnexus platform to send an
email notification for each shared project.
"""
for p in project_ids:
dxpy.api.project_invite(object_id=p,input_params={"invitee": org,"level": access_level,"suppressEmailNotification": suppress_email_notification}) | [
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249,174 | amcfague/webunit2 | webunit2/utils.py | parse_url | def parse_url(url):
""" Takes a URL string and returns its protocol and server """
# Verify that the protocol makes sense. We shouldn't guess!
if not RE_PROTOCOL_SERVER.match(url):
raise Exception("URL should begin with `protocol://domain`")
protocol, server, path, _, _, _ = urlparse.urlparse(url)
return protocol, server | python | def parse_url(url):
""" Takes a URL string and returns its protocol and server """
# Verify that the protocol makes sense. We shouldn't guess!
if not RE_PROTOCOL_SERVER.match(url):
raise Exception("URL should begin with `protocol://domain`")
protocol, server, path, _, _, _ = urlparse.urlparse(url)
return protocol, server | [
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249,175 | msuozzo/Aduro | aduro/store.py | EventStore.record_event | def record_event(self, event):
"""Records the ``KindleEvent`` `event` in the store
"""
with open(self._path, 'a') as file_:
file_.write(str(event) + '\n') | python | def record_event(self, event):
"""Records the ``KindleEvent`` `event` in the store
"""
with open(self._path, 'a') as file_:
file_.write(str(event) + '\n') | [
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249,176 | msuozzo/Aduro | aduro/store.py | EventStore.get_events | def get_events(self):
"""Returns a list of all ``KindleEvent``s held in the store
"""
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file_lines = file_.read().splitlines()
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try:
event = event_cls.from_str(event_line)
except EventParseError:
pass
else:
events.append(event)
return events | python | def get_events(self):
"""Returns a list of all ``KindleEvent``s held in the store
"""
with open(self._path, 'r') as file_:
file_lines = file_.read().splitlines()
event_lines = [line for line in file_lines if line]
events = []
for event_line in event_lines:
for event_cls in (AddEvent, SetReadingEvent, ReadEvent,
SetFinishedEvent):
try:
event = event_cls.from_str(event_line)
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events.append(event)
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249,177 | b3j0f/conf | b3j0f/conf/model/param.py | Parameter.name | def name(self, value):
"""Set parameter name.
:param str value: name value.
"""
if isinstance(value, string_types):
match = Parameter._PARAM_NAME_COMPILER_MATCHER(value)
if match is None or match.group() != value:
value = re_compile(value)
self._name = value | python | def name(self, value):
"""Set parameter name.
:param str value: name value.
"""
if isinstance(value, string_types):
match = Parameter._PARAM_NAME_COMPILER_MATCHER(value)
if match is None or match.group() != value:
value = re_compile(value)
self._name = value | [
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249,178 | b3j0f/conf | b3j0f/conf/model/param.py | Parameter.svalue | def svalue(self):
"""Get serialized value.
:rtype: str
"""
result = self._svalue
if result is None: # try to get svalue from value if svalue is None
try:
value = self.value
except Parameter.Error:
pass
else:
result = self._svalue = self.serializer(value)
return result | python | def svalue(self):
"""Get serialized value.
:rtype: str
"""
result = self._svalue
if result is None: # try to get svalue from value if svalue is None
try:
value = self.value
except Parameter.Error:
pass
else:
result = self._svalue = self.serializer(value)
return result | [
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249,179 | b3j0f/conf | b3j0f/conf/model/param.py | Parameter.svalue | def svalue(self, value):
"""Change of serialized value.
Nonify this value as well.
:param str value: serialized value to use.
"""
if value is not None: # if value is not None
self._value = None
self._error = None
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"""Change of serialized value.
Nonify this value as well.
:param str value: serialized value to use.
"""
if value is not None: # if value is not None
self._value = None
self._error = None
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249,180 | b3j0f/conf | b3j0f/conf/model/param.py | Parameter.resolve | def resolve(
self,
configurable=None, conf=None, scope=None, ptype=None,
parser=None, error=True, svalue=None,
safe=None, besteffort=None
):
"""Resolve this parameter value related to a configurable and a
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Save error in this attribute `error` in case of failure.
:param str svalue: serialized value too resolve. Default is this svalue.
:param Configurable configurable: configurable to use for foreign
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:param Configuration conf: configuration to use for
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:param dict scope: variables to use for local expression evaluation.
:param type ptype: return type. Default is this ptype.
:param parser: specific parser to use. Default this parser.
:param bool error: raise an error if True (False by default).
:param bool safe: if True (default) resolve without builtins functions.
:param bool besteffort: best effort flag. Default is this besteffort.
:return: newly resolved value.
:raises: Parameter.Error for any raised exception.
"""
result = self._value
# if cached value is None and serialiazed value exists
if self._value is None and self._svalue is not None:
self._error = None # nonify error.
if ptype is None:
ptype = self.ptype
if parser is None: # init parser
parser = self.parser
if svalue is None:
svalue = self._svalue
if conf is None: # init conf
conf = self.conf
if configurable is None: # init configurable
configurable = self.configurable
if scope is None:
scope = self.scope
else:
scope, selfscope = self.scope.copy(), scope
scope.update(selfscope)
if safe is None:
safe = self.safe
if besteffort is None:
besteffort = self.besteffort
# parse value if str and if parser exists
try:
result = self._value = parser(
svalue=svalue, conf=conf,
configurable=configurable, ptype=ptype,
scope=scope, safe=safe, besteffort=besteffort
)
except Exception as ex:
self._error = ex
if error:
msg = 'Impossible to parse value ({0}) with {1}.'
msg = msg.format(self._svalue, self.parser)
reraise(Parameter.Error, Parameter.Error(msg))
return result | python | def resolve(
self,
configurable=None, conf=None, scope=None, ptype=None,
parser=None, error=True, svalue=None,
safe=None, besteffort=None
):
"""Resolve this parameter value related to a configurable and a
configuration.
Save error in this attribute `error` in case of failure.
:param str svalue: serialized value too resolve. Default is this svalue.
:param Configurable configurable: configurable to use for foreign
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:param Configuration conf: configuration to use for
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:param dict scope: variables to use for local expression evaluation.
:param type ptype: return type. Default is this ptype.
:param parser: specific parser to use. Default this parser.
:param bool error: raise an error if True (False by default).
:param bool safe: if True (default) resolve without builtins functions.
:param bool besteffort: best effort flag. Default is this besteffort.
:return: newly resolved value.
:raises: Parameter.Error for any raised exception.
"""
result = self._value
# if cached value is None and serialiazed value exists
if self._value is None and self._svalue is not None:
self._error = None # nonify error.
if ptype is None:
ptype = self.ptype
if parser is None: # init parser
parser = self.parser
if svalue is None:
svalue = self._svalue
if conf is None: # init conf
conf = self.conf
if configurable is None: # init configurable
configurable = self.configurable
if scope is None:
scope = self.scope
else:
scope, selfscope = self.scope.copy(), scope
scope.update(selfscope)
if safe is None:
safe = self.safe
if besteffort is None:
besteffort = self.besteffort
# parse value if str and if parser exists
try:
result = self._value = parser(
svalue=svalue, conf=conf,
configurable=configurable, ptype=ptype,
scope=scope, safe=safe, besteffort=besteffort
)
except Exception as ex:
self._error = ex
if error:
msg = 'Impossible to parse value ({0}) with {1}.'
msg = msg.format(self._svalue, self.parser)
reraise(Parameter.Error, Parameter.Error(msg))
return result | [
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] | Resolve this parameter value related to a configurable and a
configuration.
Save error in this attribute `error` in case of failure.
:param str svalue: serialized value too resolve. Default is this svalue.
:param Configurable configurable: configurable to use for foreign
parameter resolution.
:param Configuration conf: configuration to use for
cross-value resolution.
:param dict scope: variables to use for local expression evaluation.
:param type ptype: return type. Default is this ptype.
:param parser: specific parser to use. Default this parser.
:param bool error: raise an error if True (False by default).
:param bool safe: if True (default) resolve without builtins functions.
:param bool besteffort: best effort flag. Default is this besteffort.
:return: newly resolved value.
:raises: Parameter.Error for any raised exception. | [
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249,181 | b3j0f/conf | b3j0f/conf/model/param.py | Parameter.value | def value(self):
"""Get parameter value.
If this cached value is None and this serialized value is not None,
calculate the new value from the serialized one.
:return: parameter value.
:raises: TypeError if serialized value is not an instance of self ptype
. ParserError if parsing step raised an error.
"""
result = self._value
if result is None and self._svalue is not None:
try:
result = self._value = self.resolve()
except Exception as e:
reraise(
Parameter.Error,
Parameter.Error('Call the method "resolve" first.')
)
return result | python | def value(self):
"""Get parameter value.
If this cached value is None and this serialized value is not None,
calculate the new value from the serialized one.
:return: parameter value.
:raises: TypeError if serialized value is not an instance of self ptype
. ParserError if parsing step raised an error.
"""
result = self._value
if result is None and self._svalue is not None:
try:
result = self._value = self.resolve()
except Exception as e:
reraise(
Parameter.Error,
Parameter.Error('Call the method "resolve" first.')
)
return result | [
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249,182 | b3j0f/conf | b3j0f/conf/model/param.py | Parameter.value | def value(self, value):
"""Change of parameter value.
If an error occured, it is stored in this error attribute.
:param value: new value to use. If input value is not an instance of
self.ptype, self error
:raises: TypeError if input value is not an instance of self ptype.
"""
if value is None or (
self.ptype is None or isinstance(value, self.ptype)
):
self._value = value
else:
# raise wrong type error
error = TypeError(
'Wrong value type of {0} ({1}). {2} expected.'.format(
self.name, value, self.ptype
)
)
self._error = error
raise error | python | def value(self, value):
"""Change of parameter value.
If an error occured, it is stored in this error attribute.
:param value: new value to use. If input value is not an instance of
self.ptype, self error
:raises: TypeError if input value is not an instance of self ptype.
"""
if value is None or (
self.ptype is None or isinstance(value, self.ptype)
):
self._value = value
else:
# raise wrong type error
error = TypeError(
'Wrong value type of {0} ({1}). {2} expected.'.format(
self.name, value, self.ptype
)
)
self._error = error
raise error | [
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249,183 | ericmjl/polcart | polcart/polcart.py | to_cartesian | def to_cartesian(r, theta, theta_units="radians"):
"""
Converts polar r, theta to cartesian x, y.
"""
assert theta_units in ['radians', 'degrees'],\
"kwarg theta_units must specified in radians or degrees"
# Convert to radians
if theta_units == "degrees":
theta = to_radians(theta)
theta = to_proper_radians(theta)
x = r * cos(theta)
y = r * sin(theta)
return x, y | python | def to_cartesian(r, theta, theta_units="radians"):
"""
Converts polar r, theta to cartesian x, y.
"""
assert theta_units in ['radians', 'degrees'],\
"kwarg theta_units must specified in radians or degrees"
# Convert to radians
if theta_units == "degrees":
theta = to_radians(theta)
theta = to_proper_radians(theta)
x = r * cos(theta)
y = r * sin(theta)
return x, y | [
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249,184 | rraadd88/meld | meld/dfs.py | set_index | def set_index(data,col_index):
"""
Sets the index if the index is not present
:param data: pandas table
:param col_index: column name which will be assigned as a index
"""
if col_index in data:
data=data.reset_index().set_index(col_index)
if 'index' in data:
del data['index']
return data
elif data.index.name==col_index:
return data
else:
logging.error("something's wrong with the df")
df2info(data) | python | def set_index(data,col_index):
"""
Sets the index if the index is not present
:param data: pandas table
:param col_index: column name which will be assigned as a index
"""
if col_index in data:
data=data.reset_index().set_index(col_index)
if 'index' in data:
del data['index']
return data
elif data.index.name==col_index:
return data
else:
logging.error("something's wrong with the df")
df2info(data) | [
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249,185 | rraadd88/meld | meld/dfs.py | fhs2data_combo | def fhs2data_combo(fhs,cols,index,labels=None,col_sep=': '):
"""
Collates data from multiple csv files
:param fhs: list of paths to csv files
:param cols: list of column names to concatenate
:param index: name of the column name to be used as the common index of the output pandas table
"""
if labels is None:
labels=[basename(fh) for fh in fhs]
if len(fhs)>0:
for fhi,fh in enumerate(fhs):
label=labels[fhi]
data=pd.read_csv(fh).set_index(index)
if fhi==0:
data_combo=pd.DataFrame(index=data.index)
for col in cols:
data_combo.loc[:,'%s%s%s' % (label,col_sep,col)]=data.loc[:,col]
else:
for col in cols:
data_combo.loc[:,'%s%s%s' % (label,col_sep,col)]=data.loc[:,col]
return data_combo
else:
logging.error('no fhs found: len(fhs)=0') | python | def fhs2data_combo(fhs,cols,index,labels=None,col_sep=': '):
"""
Collates data from multiple csv files
:param fhs: list of paths to csv files
:param cols: list of column names to concatenate
:param index: name of the column name to be used as the common index of the output pandas table
"""
if labels is None:
labels=[basename(fh) for fh in fhs]
if len(fhs)>0:
for fhi,fh in enumerate(fhs):
label=labels[fhi]
data=pd.read_csv(fh).set_index(index)
if fhi==0:
data_combo=pd.DataFrame(index=data.index)
for col in cols:
data_combo.loc[:,'%s%s%s' % (label,col_sep,col)]=data.loc[:,col]
else:
for col in cols:
data_combo.loc[:,'%s%s%s' % (label,col_sep,col)]=data.loc[:,col]
return data_combo
else:
logging.error('no fhs found: len(fhs)=0') | [
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249,186 | DoWhileGeek/authentise-services | authentise_services/session.py | Session.__create_session | def __create_session(username=None, password=None):
"""grabs the configuration, and makes the call to Authentise to create the session"""
config = Config()
if not username or not password:
username = config.username
password = config.password
payload = {
"username": username,
"password": password,
}
session_resp = requests.post("https://users.{}/sessions/".format(config.host), json=payload)
if session_resp.status_code == 403:
raise errors.ResourceError("bad user credentials")
return session_resp.cookies["session"] | python | def __create_session(username=None, password=None):
"""grabs the configuration, and makes the call to Authentise to create the session"""
config = Config()
if not username or not password:
username = config.username
password = config.password
payload = {
"username": username,
"password": password,
}
session_resp = requests.post("https://users.{}/sessions/".format(config.host), json=payload)
if session_resp.status_code == 403:
raise errors.ResourceError("bad user credentials")
return session_resp.cookies["session"] | [
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249,187 | DoWhileGeek/authentise-services | authentise_services/session.py | Session.create_user | def create_user(cls, username, password, name, email):
"""utility class method to create a user"""
config = Config()
payload = {"username": username,
"email": email,
"name": name,
"password": password, }
user_creation_resp = requests.post("https://users.{}/users/".format(config.host),
json=payload)
if user_creation_resp.status_code != 201:
raise errors.ResourceError("couldnt create user") | python | def create_user(cls, username, password, name, email):
"""utility class method to create a user"""
config = Config()
payload = {"username": username,
"email": email,
"name": name,
"password": password, }
user_creation_resp = requests.post("https://users.{}/users/".format(config.host),
json=payload)
if user_creation_resp.status_code != 201:
raise errors.ResourceError("couldnt create user") | [
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249,188 | mush42/mezzanine-live-tile | mezzanine_live_tile/templatetags/tile_tags.py | wrap_text | def wrap_text(paragraph, line_count, min_char_per_line=0):
"""Wraps the given text to the specified number of lines."""
one_string = strip_all_white_space(paragraph)
if min_char_per_line:
lines = wrap(one_string, width=min_char_per_line)
try:
return lines[:line_count]
except IndexError:
return lines
else:
return wrap(one_string, len(one_string)/line_count) | python | def wrap_text(paragraph, line_count, min_char_per_line=0):
"""Wraps the given text to the specified number of lines."""
one_string = strip_all_white_space(paragraph)
if min_char_per_line:
lines = wrap(one_string, width=min_char_per_line)
try:
return lines[:line_count]
except IndexError:
return lines
else:
return wrap(one_string, len(one_string)/line_count) | [
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249,189 | neuroticnerd/armory | armory/serialize.py | jsonify | def jsonify(data, pretty=False, **kwargs):
"""Serialize Python objects to JSON with optional 'pretty' formatting
Raises:
TypeError: from :mod:`json` lib
ValueError: from :mod:`json` lib
JSONDecodeError: from :mod:`json` lib
"""
isod = isinstance(data, OrderedDict)
params = {
'for_json': True,
'default': _complex_encode,
}
if pretty:
params['indent'] = 2
params['sort_keys'] = False if isod else True
params.update(kwargs)
try:
return json.dumps(data, ensure_ascii=False, **params)
except UnicodeDecodeError:
return json.dumps(data, **params) | python | def jsonify(data, pretty=False, **kwargs):
"""Serialize Python objects to JSON with optional 'pretty' formatting
Raises:
TypeError: from :mod:`json` lib
ValueError: from :mod:`json` lib
JSONDecodeError: from :mod:`json` lib
"""
isod = isinstance(data, OrderedDict)
params = {
'for_json': True,
'default': _complex_encode,
}
if pretty:
params['indent'] = 2
params['sort_keys'] = False if isod else True
params.update(kwargs)
try:
return json.dumps(data, ensure_ascii=False, **params)
except UnicodeDecodeError:
return json.dumps(data, **params) | [
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249,190 | soasme/rio-client | rio_client/transports/base.py | Transport.get_emit_api | def get_emit_api(self, action):
"""Build emit api."""
args = {'action': action}
args.update(self.context)
return (
'%(scheme)s://%(sender)s:%(token)s@%(domain)s:%(port)d'
'/event/%(project)s/emit/%(action)s' % args
) | python | def get_emit_api(self, action):
"""Build emit api."""
args = {'action': action}
args.update(self.context)
return (
'%(scheme)s://%(sender)s:%(token)s@%(domain)s:%(port)d'
'/event/%(project)s/emit/%(action)s' % args
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249,191 | tmacwill/stellata | stellata/model.py | serialize | def serialize(data, format: str = 'json', pretty: bool = False):
"""Serialize a stellata object to a string format."""
def encode(obj):
if isinstance(obj, stellata.model.Model):
return obj.to_dict()
elif isinstance(obj, datetime.datetime):
return int(obj.timestamp())
elif isinstance(obj, datetime.date):
return obj.isoformat()
elif isinstance(obj, decimal.Decimal):
return float(obj)
elif hasattr(obj, 'serialize'):
return obj.serialize()
return obj
if format == 'msgpack':
return msgpack.packb(data, default=encode)
if format == 'json':
if pretty:
return json.dumps(data, default=encode, indent=4)
return json.dumps(data, default=encode)
return data | python | def serialize(data, format: str = 'json', pretty: bool = False):
"""Serialize a stellata object to a string format."""
def encode(obj):
if isinstance(obj, stellata.model.Model):
return obj.to_dict()
elif isinstance(obj, datetime.datetime):
return int(obj.timestamp())
elif isinstance(obj, datetime.date):
return obj.isoformat()
elif isinstance(obj, decimal.Decimal):
return float(obj)
elif hasattr(obj, 'serialize'):
return obj.serialize()
return obj
if format == 'msgpack':
return msgpack.packb(data, default=encode)
if format == 'json':
if pretty:
return json.dumps(data, default=encode, indent=4)
return json.dumps(data, default=encode)
return data | [
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249,192 | dabercro/customdocs | customdocs/__init__.py | pretty_exe_doc | def pretty_exe_doc(program, parser, stack=1, under='-'):
"""
Takes the name of a script and a parser that will give the help message for it.
The module that called this function will then add a header to the docstring
of the script, followed immediately by the help message generated
by the OptionParser
:param str program: Name of the program that we want to make the header
:param optparser.Option parser: Either a parser or a callable with no arguments
that will give the desired parser
:param int stack: How far up the stack to get the docstring to change
:param str under: The character you want for the program underline
"""
if os.path.basename(sys.argv[0]) == 'sphinx-build':
# Get the calling module
mod = inspect.getmodule(inspect.stack()[stack][0])
# Get parser
_parser = parser() if '__call__' in dir(parser) else parser
# Make the parser use the correct program
_parser.set_usage(mod.__usage__.replace('%prog', program))
# Modify docs by adding a header and usate
mod.__doc__ = '\n'.join(['', program, under * len(program), '::', ''] +
[' %s' % l for l in _parser.format_help().split('\n')]) + \
mod.__doc__ | python | def pretty_exe_doc(program, parser, stack=1, under='-'):
"""
Takes the name of a script and a parser that will give the help message for it.
The module that called this function will then add a header to the docstring
of the script, followed immediately by the help message generated
by the OptionParser
:param str program: Name of the program that we want to make the header
:param optparser.Option parser: Either a parser or a callable with no arguments
that will give the desired parser
:param int stack: How far up the stack to get the docstring to change
:param str under: The character you want for the program underline
"""
if os.path.basename(sys.argv[0]) == 'sphinx-build':
# Get the calling module
mod = inspect.getmodule(inspect.stack()[stack][0])
# Get parser
_parser = parser() if '__call__' in dir(parser) else parser
# Make the parser use the correct program
_parser.set_usage(mod.__usage__.replace('%prog', program))
# Modify docs by adding a header and usate
mod.__doc__ = '\n'.join(['', program, under * len(program), '::', ''] +
[' %s' % l for l in _parser.format_help().split('\n')]) + \
mod.__doc__ | [
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249,193 | uw-it-aca/uw-restclients-kws | uw_kws/__init__.py | KWS.get_key | def get_key(self, key_id):
"""
Returns a restclients.Key object for the given key ID. If the
key ID isn't found, or if there is an error communicating with the
KWS, a DataFailureException will be thrown.
"""
url = ENCRYPTION_KEY_URL.format(key_id)
return self._key_from_json(self._get_resource(url)) | python | def get_key(self, key_id):
"""
Returns a restclients.Key object for the given key ID. If the
key ID isn't found, or if there is an error communicating with the
KWS, a DataFailureException will be thrown.
"""
url = ENCRYPTION_KEY_URL.format(key_id)
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249,194 | uw-it-aca/uw-restclients-kws | uw_kws/__init__.py | KWS.get_current_key | def get_current_key(self, resource_name):
"""
Returns a restclients.Key object for the given resource. If the
resource isn't found, or if there is an error communicating with the
KWS, a DataFailureException will be thrown.
"""
url = ENCRYPTION_CURRENT_KEY_URL.format(resource_name)
return self._key_from_json(self._get_resource(url)) | python | def get_current_key(self, resource_name):
"""
Returns a restclients.Key object for the given resource. If the
resource isn't found, or if there is an error communicating with the
KWS, a DataFailureException will be thrown.
"""
url = ENCRYPTION_CURRENT_KEY_URL.format(resource_name)
return self._key_from_json(self._get_resource(url)) | [
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249,195 | uw-it-aca/uw-restclients-kws | uw_kws/__init__.py | KWS._key_from_json | def _key_from_json(self, data):
"""
Internal method, for creating the Key object.
"""
key = Key()
key.algorithm = data["Algorithm"]
key.cipher_mode = data["CipherMode"]
key.expiration = datetime.strptime(data["Expiration"].split(".")[0],
"%Y-%m-%dT%H:%M:%S")
key.key_id = data["ID"]
key.key = data["Key"]
key.size = data["KeySize"]
key.url = data["KeyUrl"]
return key | python | def _key_from_json(self, data):
"""
Internal method, for creating the Key object.
"""
key = Key()
key.algorithm = data["Algorithm"]
key.cipher_mode = data["CipherMode"]
key.expiration = datetime.strptime(data["Expiration"].split(".")[0],
"%Y-%m-%dT%H:%M:%S")
key.key_id = data["ID"]
key.key = data["Key"]
key.size = data["KeySize"]
key.url = data["KeyUrl"]
return key | [
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249,196 | jmgilman/Neolib | neolib/http/Page.py | Page.newSession | def newSession():
""" Returns a new Requests session with pre-loaded default HTTP Headers
Generates a new Requests session and consults with the Configuration class
to determine if a Configuration exists and attempts to use the configured
HTTP Request headers first. If this fails, it attempts to create a new
default configuration and use those values. Finally, if a configuration
cannot be initiaized it uses the hard-coded Mozilla headers.
Returns
request-client - The configured Requests session
Raises
HTTPException
"""
from neolib.config.Configuration import Configuration
s = requests.session()
if not Configuration.loaded():
if not Configuration.initialize():
s.headers.update(Page._defaultVars)
else:
s.headers.update(Configuration.getConfig().core.HTTPHeaders.toDict())
else:
s.headers.update(Configuration.getConfig().core.HTTPHeaders.toDict())
return requests.session() | python | def newSession():
""" Returns a new Requests session with pre-loaded default HTTP Headers
Generates a new Requests session and consults with the Configuration class
to determine if a Configuration exists and attempts to use the configured
HTTP Request headers first. If this fails, it attempts to create a new
default configuration and use those values. Finally, if a configuration
cannot be initiaized it uses the hard-coded Mozilla headers.
Returns
request-client - The configured Requests session
Raises
HTTPException
"""
from neolib.config.Configuration import Configuration
s = requests.session()
if not Configuration.loaded():
if not Configuration.initialize():
s.headers.update(Page._defaultVars)
else:
s.headers.update(Configuration.getConfig().core.HTTPHeaders.toDict())
else:
s.headers.update(Configuration.getConfig().core.HTTPHeaders.toDict())
return requests.session() | [
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249,197 | treycucco/bidon | bidon/db/access/model_access.py | get_model_id_constraints | def get_model_id_constraints(model):
"""Returns constraints to target a specific model."""
pkname = model.primary_key_name
pkey = model.primary_key
return get_id_constraints(pkname, pkey) | python | def get_model_id_constraints(model):
"""Returns constraints to target a specific model."""
pkname = model.primary_key_name
pkey = model.primary_key
return get_id_constraints(pkname, pkey) | [
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249,198 | treycucco/bidon | bidon/db/access/model_access.py | get_id_constraints | def get_id_constraints(pkname, pkey):
"""Returns primary key consraints.
:pkname: if a string, returns a dict with pkname=pkey. pkname and pkey must be enumerables of
matching length.
"""
if isinstance(pkname, str):
return {pkname: pkey}
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return dict(zip(pkname, pkey)) | python | def get_id_constraints(pkname, pkey):
"""Returns primary key consraints.
:pkname: if a string, returns a dict with pkname=pkey. pkname and pkey must be enumerables of
matching length.
"""
if isinstance(pkname, str):
return {pkname: pkey}
else:
return dict(zip(pkname, pkey)) | [
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249,199 | treycucco/bidon | bidon/db/access/model_access.py | ModelAccess._find_model | def _find_model(self, constructor, table_name, constraints=None, *, columns=None, order_by=None):
"""Calls DataAccess.find and passes the results to the given constructor."""
data = self.find(table_name, constraints, columns=columns, order_by=order_by)
return constructor(data) if data else None | python | def _find_model(self, constructor, table_name, constraints=None, *, columns=None, order_by=None):
"""Calls DataAccess.find and passes the results to the given constructor."""
data = self.find(table_name, constraints, columns=columns, order_by=order_by)
return constructor(data) if data else None | [
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Subsets and Splits