id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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48,100 | ungarj/s2reader | s2reader/s2reader.py | SentinelDataSet.footprint | def footprint(self):
"""Return product footprint."""
product_footprint = self._product_metadata.iter("Product_Footprint")
# I don't know why two "Product_Footprint" items are found.
for element in product_footprint:
global_footprint = None
for global_footprint in ... | python | def footprint(self):
"""Return product footprint."""
product_footprint = self._product_metadata.iter("Product_Footprint")
# I don't know why two "Product_Footprint" items are found.
for element in product_footprint:
global_footprint = None
for global_footprint in ... | [
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48,101 | ungarj/s2reader | s2reader/s2reader.py | SentinelDataSet.granules | def granules(self):
"""Return list of SentinelGranule objects."""
for element in self._product_metadata.iter("Product_Info"):
product_organisation = element.find("Product_Organisation")
if self.product_format == 'SAFE':
return [
SentinelGranule(_id.find("G... | python | def granules(self):
"""Return list of SentinelGranule objects."""
for element in self._product_metadata.iter("Product_Info"):
product_organisation = element.find("Product_Organisation")
if self.product_format == 'SAFE':
return [
SentinelGranule(_id.find("G... | [
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48,102 | ungarj/s2reader | s2reader/s2reader.py | SentinelDataSet.granule_paths | def granule_paths(self, band_id):
"""Return the path of all granules of a given band."""
band_id = str(band_id).zfill(2)
try:
assert isinstance(band_id, str)
assert band_id in BAND_IDS
except AssertionError:
raise AttributeError(
"band ... | python | def granule_paths(self, band_id):
"""Return the path of all granules of a given band."""
band_id = str(band_id).zfill(2)
try:
assert isinstance(band_id, str)
assert band_id in BAND_IDS
except AssertionError:
raise AttributeError(
"band ... | [
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48,103 | ungarj/s2reader | s2reader/s2reader.py | SentinelGranule.metadata_path | def metadata_path(self):
"""Determine the metadata path."""
xml_name = _granule_identifier_to_xml_name(self.granule_identifier)
metadata_path = os.path.join(self.granule_path, xml_name)
try:
assert os.path.isfile(metadata_path) or \
metadata_path in self.datas... | python | def metadata_path(self):
"""Determine the metadata path."""
xml_name = _granule_identifier_to_xml_name(self.granule_identifier)
metadata_path = os.path.join(self.granule_path, xml_name)
try:
assert os.path.isfile(metadata_path) or \
metadata_path in self.datas... | [
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48,104 | ungarj/s2reader | s2reader/s2reader.py | SentinelGranule.tci_path | def tci_path(self):
"""Return the path to the granules TrueColorImage."""
tci_paths = [
path for path in self.dataset._product_metadata.xpath(
".//Granule[@granuleIdentifier='%s']/IMAGE_FILE/text()"
% self.granule_identifier
) if path.endswith('TCI... | python | def tci_path(self):
"""Return the path to the granules TrueColorImage."""
tci_paths = [
path for path in self.dataset._product_metadata.xpath(
".//Granule[@granuleIdentifier='%s']/IMAGE_FILE/text()"
% self.granule_identifier
) if path.endswith('TCI... | [
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48,105 | ungarj/s2reader | s2reader/s2reader.py | SentinelGranule.cloud_percent | def cloud_percent(self):
"""Return percentage of cloud coverage."""
image_content_qi = self._metadata.findtext(
(
"""n1:Quality_Indicators_Info/Image_Content_QI/"""
"""CLOUDY_PIXEL_PERCENTAGE"""
),
namespaces=self._nsmap)
return... | python | def cloud_percent(self):
"""Return percentage of cloud coverage."""
image_content_qi = self._metadata.findtext(
(
"""n1:Quality_Indicators_Info/Image_Content_QI/"""
"""CLOUDY_PIXEL_PERCENTAGE"""
),
namespaces=self._nsmap)
return... | [
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48,106 | ungarj/s2reader | s2reader/s2reader.py | SentinelGranule.footprint | def footprint(self):
"""Find and return footprint as Shapely Polygon."""
# Check whether product or granule footprint needs to be calculated.
tile_geocoding = self._metadata.iter("Tile_Geocoding").next()
resolution = 10
searchstring = ".//*[@resolution='%s']" % resolution
... | python | def footprint(self):
"""Find and return footprint as Shapely Polygon."""
# Check whether product or granule footprint needs to be calculated.
tile_geocoding = self._metadata.iter("Tile_Geocoding").next()
resolution = 10
searchstring = ".//*[@resolution='%s']" % resolution
... | [
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48,107 | ungarj/s2reader | s2reader/s2reader.py | SentinelGranule.cloudmask | def cloudmask(self):
"""Return cloudmask as a shapely geometry."""
polys = list(self._get_mask(mask_type="MSK_CLOUDS"))
return MultiPolygon([
poly["geometry"]
for poly in polys
if poly["attributes"]["maskType"] == "OPAQUE"
]).buffer(0) | python | def cloudmask(self):
"""Return cloudmask as a shapely geometry."""
polys = list(self._get_mask(mask_type="MSK_CLOUDS"))
return MultiPolygon([
poly["geometry"]
for poly in polys
if poly["attributes"]["maskType"] == "OPAQUE"
]).buffer(0) | [
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48,108 | ungarj/s2reader | s2reader/s2reader.py | SentinelGranule.band_path | def band_path(self, band_id, for_gdal=False, absolute=False):
"""Return paths of given band's jp2 files for all granules."""
band_id = str(band_id).zfill(2)
if not isinstance(band_id, str) or band_id not in BAND_IDS:
raise ValueError("band ID not valid: %s" % band_id)
if self... | python | def band_path(self, band_id, for_gdal=False, absolute=False):
"""Return paths of given band's jp2 files for all granules."""
band_id = str(band_id).zfill(2)
if not isinstance(band_id, str) or band_id not in BAND_IDS:
raise ValueError("band ID not valid: %s" % band_id)
if self... | [
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48,109 | buckhx/QuadKey | quadkey/tile_system.py | TileSystem.geo_to_pixel | def geo_to_pixel(geo, level):
"""Transform from geo coordinates to pixel coordinates"""
lat, lon = float(geo[0]), float(geo[1])
lat = TileSystem.clip(lat, TileSystem.LATITUDE_RANGE)
lon = TileSystem.clip(lon, TileSystem.LONGITUDE_RANGE)
x = (lon + 180) / 360
sin_lat = sin... | python | def geo_to_pixel(geo, level):
"""Transform from geo coordinates to pixel coordinates"""
lat, lon = float(geo[0]), float(geo[1])
lat = TileSystem.clip(lat, TileSystem.LATITUDE_RANGE)
lon = TileSystem.clip(lon, TileSystem.LONGITUDE_RANGE)
x = (lon + 180) / 360
sin_lat = sin... | [
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48,110 | buckhx/QuadKey | quadkey/tile_system.py | TileSystem.pixel_to_geo | def pixel_to_geo(pixel, level):
"""Transform from pixel to geo coordinates"""
pixel_x = pixel[0]
pixel_y = pixel[1]
map_size = float(TileSystem.map_size(level))
x = (TileSystem.clip(pixel_x, (0, map_size - 1)) / map_size) - 0.5
y = 0.5 - (TileSystem.clip(pixel_y, (0, map_... | python | def pixel_to_geo(pixel, level):
"""Transform from pixel to geo coordinates"""
pixel_x = pixel[0]
pixel_y = pixel[1]
map_size = float(TileSystem.map_size(level))
x = (TileSystem.clip(pixel_x, (0, map_size - 1)) / map_size) - 0.5
y = 0.5 - (TileSystem.clip(pixel_y, (0, map_... | [
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48,111 | buckhx/QuadKey | quadkey/tile_system.py | TileSystem.tile_to_pixel | def tile_to_pixel(tile, centered=False):
"""Transform tile to pixel coordinates"""
pixel = [tile[0] * 256, tile[1] * 256]
if centered:
# should clip on max map size
pixel = [pix + 128 for pix in pixel]
return pixel[0], pixel[1] | python | def tile_to_pixel(tile, centered=False):
"""Transform tile to pixel coordinates"""
pixel = [tile[0] * 256, tile[1] * 256]
if centered:
# should clip on max map size
pixel = [pix + 128 for pix in pixel]
return pixel[0], pixel[1] | [
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48,112 | buckhx/QuadKey | quadkey/tile_system.py | TileSystem.tile_to_quadkey | def tile_to_quadkey(tile, level):
"""Transform tile coordinates to a quadkey"""
tile_x = tile[0]
tile_y = tile[1]
quadkey = ""
for i in xrange(level):
bit = level - i
digit = ord('0')
mask = 1 << (bit - 1) # if (bit - 1) > 0 else 1 >> (bit - 1... | python | def tile_to_quadkey(tile, level):
"""Transform tile coordinates to a quadkey"""
tile_x = tile[0]
tile_y = tile[1]
quadkey = ""
for i in xrange(level):
bit = level - i
digit = ord('0')
mask = 1 << (bit - 1) # if (bit - 1) > 0 else 1 >> (bit - 1... | [
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48,113 | buckhx/QuadKey | quadkey/tile_system.py | TileSystem.quadkey_to_tile | def quadkey_to_tile(quadkey):
"""Transform quadkey to tile coordinates"""
tile_x, tile_y = (0, 0)
level = len(quadkey)
for i in xrange(level):
bit = level - i
mask = 1 << (bit - 1)
if quadkey[level - bit] == '1':
tile_x |= mask
... | python | def quadkey_to_tile(quadkey):
"""Transform quadkey to tile coordinates"""
tile_x, tile_y = (0, 0)
level = len(quadkey)
for i in xrange(level):
bit = level - i
mask = 1 << (bit - 1)
if quadkey[level - bit] == '1':
tile_x |= mask
... | [
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48,114 | hanguokai/youku | youku/youku_oauth.py | YoukuOauth.authorize_url | def authorize_url(self, state=''):
""" return user authorize url
"""
url = 'https://openapi.youku.com/v2/oauth2/authorize?'
params = {
'client_id': self.client_id,
'response_type': 'code',
'state': state,
'redirect_uri': self.redirect_uri
... | python | def authorize_url(self, state=''):
""" return user authorize url
"""
url = 'https://openapi.youku.com/v2/oauth2/authorize?'
params = {
'client_id': self.client_id,
'response_type': 'code',
'state': state,
'redirect_uri': self.redirect_uri
... | [
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48,115 | hanguokai/youku | youku/util.py | remove_none_value | def remove_none_value(data):
"""remove item from dict if value is None.
return new dict.
"""
return dict((k, v) for k, v in data.items() if v is not None) | python | def remove_none_value(data):
"""remove item from dict if value is None.
return new dict.
"""
return dict((k, v) for k, v in data.items() if v is not None) | [
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48,116 | wiheto/fetchopenfmri | fetchopenfmri/fetch.py | get_dataset | def get_dataset(ds,dataDir,removecompressed=1):
"""
A function which attempts downloads and uncompresses the latest version of an openfmri.fmri dataset.
PARAMETERS
:ds: dataset number of the openfMRI.org dataset (integer) without zero padding. I.e. can just be 212 (doesn't need to be 000212).
:da... | python | def get_dataset(ds,dataDir,removecompressed=1):
"""
A function which attempts downloads and uncompresses the latest version of an openfmri.fmri dataset.
PARAMETERS
:ds: dataset number of the openfMRI.org dataset (integer) without zero padding. I.e. can just be 212 (doesn't need to be 000212).
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48,117 | hanguokai/youku | youku/youku_upload.py | YoukuUpload.prepare_video_params | def prepare_video_params(self, title=None, tags='Others', description='',
copyright_type='original', public_type='all',
category=None, watch_password=None,
latitude=None, longitude=None, shoot_time=None
)... | python | def prepare_video_params(self, title=None, tags='Others', description='',
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48,118 | hanguokai/youku | youku/youku_upload.py | YoukuUpload._save_upload_state_to_file | def _save_upload_state_to_file(self):
"""if create and create_file has execute, save upload state
to file for next resume upload if current upload process is
interrupted.
"""
if os.access(self.file_dir, os.W_OK | os.R_OK | os.X_OK):
save_file = self.file + '.upload'
... | python | def _save_upload_state_to_file(self):
"""if create and create_file has execute, save upload state
to file for next resume upload if current upload process is
interrupted.
"""
if os.access(self.file_dir, os.W_OK | os.R_OK | os.X_OK):
save_file = self.file + '.upload'
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48,119 | hanguokai/youku | youku/youku_upload.py | YoukuUpload.upload | def upload(self, params={}):
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Args:
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48,120 | jbittel/django-ldap-sync | ldap_sync/sync.py | SyncLDAP.sync_users | def sync_users(self):
"""Synchronize LDAP users with local user model."""
if self.settings.USER_FILTER:
user_attributes = self.settings.USER_ATTRIBUTES.keys() + self.settings.USER_EXTRA_ATTRIBUTES
ldap_users = self.ldap.search(self.settings.USER_FILTER, user_attributes)
... | python | def sync_users(self):
"""Synchronize LDAP users with local user model."""
if self.settings.USER_FILTER:
user_attributes = self.settings.USER_ATTRIBUTES.keys() + self.settings.USER_EXTRA_ATTRIBUTES
ldap_users = self.ldap.search(self.settings.USER_FILTER, user_attributes)
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48,121 | ungarj/s2reader | s2reader/cli/transform.py | main | def main(args=sys.argv[1:]):
"""Generate EO O&M XML metadata."""
parser = argparse.ArgumentParser()
parser.add_argument("filename", nargs=1)
parser.add_argument("--granule-id", dest="granule_id",
help=(
"Optional. Specify a granule to export metadata from."
)
)
parser... | python | def main(args=sys.argv[1:]):
"""Generate EO O&M XML metadata."""
parser = argparse.ArgumentParser()
parser.add_argument("filename", nargs=1)
parser.add_argument("--granule-id", dest="granule_id",
help=(
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48,122 | buckhx/QuadKey | quadkey/__init__.py | QuadKey.is_ancestor | def is_ancestor(self, node):
"""
If node is ancestor of self
Get the difference in level
If not, None
"""
if self.level <= node.level or self.key[:len(node.key)] != node.key:
return None
return self.level - node.level | python | def is_ancestor(self, node):
"""
If node is ancestor of self
Get the difference in level
If not, None
"""
if self.level <= node.level or self.key[:len(node.key)] != node.key:
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48,123 | buckhx/QuadKey | quadkey/__init__.py | QuadKey.xdifference | def xdifference(self, to):
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Only works with quadkeys of same level
"""
x,y = 0,1
assert self.level == to.level
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48,124 | buckhx/QuadKey | quadkey/__init__.py | QuadKey.unwind | def unwind(self):
""" Get a list of all ancestors in descending order of level, including a new instance of self
"""
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""" Get a list of all ancestors in descending order of level, including a new instance of self
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48,125 | jbittel/django-ldap-sync | ldap_sync/settings.py | LDAPSettings.validate | def validate(self):
"""Apply validation rules for loaded settings."""
if self.GROUP_ATTRIBUTES and self.GROUPNAME_FIELD not in self.GROUP_ATTRIBUTES.values():
raise ImproperlyConfigured("LDAP_SYNC_GROUP_ATTRIBUTES must contain '%s'" % self.GROUPNAME_FIELD)
if not self.model._meta.ge... | python | def validate(self):
"""Apply validation rules for loaded settings."""
if self.GROUP_ATTRIBUTES and self.GROUPNAME_FIELD not in self.GROUP_ATTRIBUTES.values():
raise ImproperlyConfigured("LDAP_SYNC_GROUP_ATTRIBUTES must contain '%s'" % self.GROUPNAME_FIELD)
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48,126 | jbittel/django-ldap-sync | ldap_sync/search.py | LDAPSearch.search | def search(self, filterstr, attrlist):
"""Query the configured LDAP server."""
return self._paged_search_ext_s(self.settings.BASE, ldap.SCOPE_SUBTREE, filterstr=filterstr,
attrlist=attrlist, page_size=self.settings.PAGE_SIZE) | python | def search(self, filterstr, attrlist):
"""Query the configured LDAP server."""
return self._paged_search_ext_s(self.settings.BASE, ldap.SCOPE_SUBTREE, filterstr=filterstr,
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48,127 | tsroten/yweather | yweather.py | Client.fetch_lid | def fetch_lid(self, woeid):
"""Fetch a location's corresponding LID.
Args:
woeid: (string) the location's WOEID.
Returns:
a string containing the requested LID or None if the LID could
not be found.
Raises:
urllib.error.URLError: urllib.... | python | def fetch_lid(self, woeid):
"""Fetch a location's corresponding LID.
Args:
woeid: (string) the location's WOEID.
Returns:
a string containing the requested LID or None if the LID could
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48,128 | tsroten/yweather | yweather.py | Client.fetch_woeid | def fetch_woeid(self, location):
"""Fetch a location's corresponding WOEID.
Args:
location: (string) a location (e.g. 23454 or Berlin, Germany).
Returns:
a string containing the location's corresponding WOEID or None if
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... | python | def fetch_woeid(self, location):
"""Fetch a location's corresponding WOEID.
Args:
location: (string) a location (e.g. 23454 or Berlin, Germany).
Returns:
a string containing the location's corresponding WOEID or None if
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48,129 | tsroten/yweather | yweather.py | Client._degrees_to_direction | def _degrees_to_direction(self, degrees):
"""Convert wind direction from degrees to compass direction."""
try:
degrees = float(degrees)
except ValueError:
return None
if degrees < 0 or degrees > 360:
return None
if degrees <= 11.25 or degrees >... | python | def _degrees_to_direction(self, degrees):
"""Convert wind direction from degrees to compass direction."""
try:
degrees = float(degrees)
except ValueError:
return None
if degrees < 0 or degrees > 360:
return None
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48,130 | tsroten/yweather | yweather.py | Client._fetch_xml | def _fetch_xml(self, url):
"""Fetch a url and parse the document's XML."""
with contextlib.closing(urlopen(url)) as f:
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"""Fetch a url and parse the document's XML."""
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48,131 | galaxy-genome-annotation/python-apollo | apollo/cannedvalues/__init__.py | CannedValuesClient.show_value | def show_value(self, value):
"""
Get a specific canned value
:type value: str
:param value: Canned value to show
:rtype: dict
:return: A dictionnary containing canned value description
"""
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"""
Get a specific canned value
:type value: str
:param value: Canned value to show
:rtype: dict
:return: A dictionnary containing canned value description
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48,132 | galaxy-genome-annotation/python-apollo | apollo/cannedkeys/__init__.py | CannedKeysClient.show_key | def show_key(self, value):
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:return: A dictionnary containing canned key description
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48,133 | cytomine/Cytomine-python-client | cytomine/models/image.py | ImageInstance.download | def download(self, dest_pattern="{originalFilename}", override=True, parent=False):
"""
Download the original image.
Parameters
----------
dest_pattern : str, optional
Destination path for the downloaded image. "{X}" patterns are replaced by the value of X attribute
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Download the original image.
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48,134 | cytomine/Cytomine-python-client | cytomine/models/image.py | ImageInstance.dump | def dump(self, dest_pattern="{id}.jpg", override=True, max_size=None, bits=8, contrast=None, gamma=None,
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Download the image with optional image modifications.
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48,135 | pyecore/pyecoregen | pyecoregen/ecore.py | EcoreTask.filtered_elements | def filtered_elements(self, model):
"""Return iterator based on `element_type`."""
if isinstance(model, self.element_type):
yield model
yield from (e for e in model.eAllContents() if isinstance(e, self.element_type)) | python | def filtered_elements(self, model):
"""Return iterator based on `element_type`."""
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yield model
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48,136 | pyecore/pyecoregen | pyecoregen/ecore.py | EcoreTask.folder_path_for_package | def folder_path_for_package(cls, package: ecore.EPackage):
"""Returns path to folder holding generated artifact for given element."""
parent = package.eContainer()
if parent:
return os.path.join(cls.folder_path_for_package(parent), package.name)
return package.name | python | def folder_path_for_package(cls, package: ecore.EPackage):
"""Returns path to folder holding generated artifact for given element."""
parent = package.eContainer()
if parent:
return os.path.join(cls.folder_path_for_package(parent), package.name)
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48,137 | pyecore/pyecoregen | pyecoregen/ecore.py | EcorePackageInitTask.imported_classifiers_package | def imported_classifiers_package(p: ecore.EPackage):
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references = itertools.chain(*(c.eAllReferences() for c in classes))
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"""Determines which classifiers have to be imported into given package."""
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references = itertools.chain(*(c.eAllReferences() for c in classes))
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48,138 | pyecore/pyecoregen | pyecoregen/ecore.py | EcorePackageModuleTask.imported_classifiers | def imported_classifiers(p: ecore.EPackage):
"""Determines which classifiers have to be imported into given module."""
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"""Determines which classifiers have to be imported into given module."""
classes = {c for c in p.eClassifiers if isinstance(c, ecore.EClass)}
supertypes = itertools.chain(*(c.eAllSuperTypes() for c in classes))
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48,139 | pyecore/pyecoregen | pyecoregen/ecore.py | EcorePackageModuleTask.classes | def classes(p: ecore.EPackage):
"""Returns classes in package in ordered by number of bases."""
classes = (c for c in p.eClassifiers if isinstance(c, ecore.EClass))
return sorted(classes, key=lambda c: len(set(c.eAllSuperTypes()))) | python | def classes(p: ecore.EPackage):
"""Returns classes in package in ordered by number of bases."""
classes = (c for c in p.eClassifiers if isinstance(c, ecore.EClass))
return sorted(classes, key=lambda c: len(set(c.eAllSuperTypes()))) | [
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48,140 | pyecore/pyecoregen | pyecoregen/ecore.py | EcoreGenerator.filter_pyfqn | def filter_pyfqn(cls, value, relative_to=0):
"""
Returns Python form of fully qualified name.
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relative_to: If greater 0, the returned path is relative to the first n directories.
"""
def collect_packages(element, packages):
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48,141 | pyecore/pyecoregen | pyecoregen/ecore.py | EcoreGenerator.create_environment | def create_environment(self, **kwargs):
"""
Return a new Jinja environment.
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loader type.
"""
environment = super().create_environment(**kwargs)
environment.tests.update({
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"""
Return a new Jinja environment.
Derived classes may override method to pass additional parameters or to change the template
loader type.
"""
environment = super().create_environment(**kwargs)
environment.tests.update({
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48,142 | pyecore/pyecoregen | pyecoregen/ecore.py | EcoreGenerator.generate | def generate(self, model, outfolder, *, exclude=None):
"""
Generate model code.
Args:
model: The meta-model to generate code for.
outfolder: Path to the directoty that will contain the generated code.
exclude: List of referenced resources for which code was a... | python | def generate(self, model, outfolder, *, exclude=None):
"""
Generate model code.
Args:
model: The meta-model to generate code for.
outfolder: Path to the directoty that will contain the generated code.
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48,143 | galaxy-genome-annotation/python-apollo | apollo/groups/__init__.py | GroupsClient.show_group | def show_group(self, group_id):
"""
Get information about a group
:type group_id: int
:param group_id: Group ID Number
:rtype: dict
:return: a dictionary containing group information
"""
res = self.post('loadGroups', {'groupId': group_id})
if isi... | python | def show_group(self, group_id):
"""
Get information about a group
:type group_id: int
:param group_id: Group ID Number
:rtype: dict
:return: a dictionary containing group information
"""
res = self.post('loadGroups', {'groupId': group_id})
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48,144 | galaxy-genome-annotation/python-apollo | apollo/groups/__init__.py | GroupsClient.get_organism_permissions | def get_organism_permissions(self, group):
"""
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:type group: str
:param group: group name
:rtype: list
:return: a list containing organism permissions (if any)
"""
data = {
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}
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"""
Get the group's organism permissions
:type group: str
:param group: group name
:rtype: list
:return: a list containing organism permissions (if any)
"""
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48,145 | galaxy-genome-annotation/python-apollo | apollo/groups/__init__.py | GroupsClient.get_group_admin | def get_group_admin(self, group):
"""
Get the group's admins
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:param group: group name
:rtype: list
:return: a list containing group admins
"""
data = {
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response = _fix_group(self.post('getGrou... | python | def get_group_admin(self, group):
"""
Get the group's admins
:type group: str
:param group: group name
:rtype: list
:return: a list containing group admins
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data = {
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48,146 | galaxy-genome-annotation/python-apollo | apollo/groups/__init__.py | GroupsClient.get_group_creator | def get_group_creator(self, group):
"""
Get the group's creator
:type group: str
:param group: group name
:rtype: list
:return: creator userId
"""
data = {
'name': group,
}
response = _fix_group(self.post('getGroupCreator', da... | python | def get_group_creator(self, group):
"""
Get the group's creator
:type group: str
:param group: group name
:rtype: list
:return: creator userId
"""
data = {
'name': group,
}
response = _fix_group(self.post('getGroupCreator', da... | [
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48,147 | globocom/tornado-es | tornadoes/__init__.py | ESConnection._create_query_string | def _create_query_string(params):
"""
Support Elasticsearch 5.X
"""
parameters = params or {}
for param, value in parameters.items():
param_value = str(value).lower() if isinstance(value, bool) else value
parameters[param] = param_value
return ur... | python | def _create_query_string(params):
"""
Support Elasticsearch 5.X
"""
parameters = params or {}
for param, value in parameters.items():
param_value = str(value).lower() if isinstance(value, bool) else value
parameters[param] = param_value
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48,148 | galaxy-genome-annotation/python-apollo | apollo/status/__init__.py | StatusClient.show_status | def show_status(self, status):
"""
Get a specific status
:type status: str
:param status: Status to show
:rtype: dict
:return: A dictionnary containing status description
"""
statuses = self.get_statuses()
statuses = [x for x in statuses if x['va... | python | def show_status(self, status):
"""
Get a specific status
:type status: str
:param status: Status to show
:rtype: dict
:return: A dictionnary containing status description
"""
statuses = self.get_statuses()
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48,149 | galaxy-genome-annotation/python-apollo | apollo/annotations/__init__.py | AnnotationsClient.add_attribute | def add_attribute(self, feature_id, attribute_key, attribute_value, organism=None, sequence=None):
"""
Add an attribute to a feature
:type feature_id: str
:param feature_id: Feature UUID
:type attribute_key: str
:param attribute_key: Attribute Key
:type attribu... | python | def add_attribute(self, feature_id, attribute_key, attribute_value, organism=None, sequence=None):
"""
Add an attribute to a feature
:type feature_id: str
:param feature_id: Feature UUID
:type attribute_key: str
:param attribute_key: Attribute Key
:type attribu... | [
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48,150 | galaxy-genome-annotation/python-apollo | apollo/annotations/__init__.py | AnnotationsClient.add_dbxref | def add_dbxref(self, feature_id, db, accession, organism=None, sequence=None):
"""
Add a dbxref to a feature
:type feature_id: str
:param feature_id: Feature UUID
:type db: str
:param db: DB Name (e.g. PMID)
:type accession: str
:param accession: Access... | python | def add_dbxref(self, feature_id, db, accession, organism=None, sequence=None):
"""
Add a dbxref to a feature
:type feature_id: str
:param feature_id: Feature UUID
:type db: str
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:param accession: Access... | [
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:param accession: Accession Value
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48,151 | galaxy-genome-annotation/python-apollo | apollo/users/__init__.py | UsersClient._handle_empty | def _handle_empty(self, user, response):
"""Apollo likes to return empty user arrays, even when you REALLY
want a user response back... like creating a user."""
if len(response.keys()) == 0:
response = self.show_user(user)
# And sometimes show_user can return nothing. As... | python | def _handle_empty(self, user, response):
"""Apollo likes to return empty user arrays, even when you REALLY
want a user response back... like creating a user."""
if len(response.keys()) == 0:
response = self.show_user(user)
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48,152 | galaxy-genome-annotation/python-apollo | apollo/users/__init__.py | UsersClient.show_user | def show_user(self, user):
"""
Get a specific user
:type user: str
:param user: User Email
:rtype: dict
:return: a dictionary containing user information
"""
res = self.post('loadUsers', {'userId': user})
if isinstance(res, list) and len(res) > 0... | python | def show_user(self, user):
"""
Get a specific user
:type user: str
:param user: User Email
:rtype: dict
:return: a dictionary containing user information
"""
res = self.post('loadUsers', {'userId': user})
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48,153 | galaxy-genome-annotation/python-apollo | apollo/__init__.py | require_user | def require_user(wa, email):
"""Require that the user has an account"""
cache_key = 'user-list'
try:
# Get the cached value
data = userCache[cache_key]
except KeyError:
# If we hit a key error above, indicating that
# we couldn't find the key, we'll simply re-request
... | python | def require_user(wa, email):
"""Require that the user has an account"""
cache_key = 'user-list'
try:
# Get the cached value
data = userCache[cache_key]
except KeyError:
# If we hit a key error above, indicating that
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48,154 | galaxy-genome-annotation/python-apollo | apollo/__init__.py | accessible_organisms | def accessible_organisms(user, orgs):
"""Get the list of organisms accessible to a user, filtered by `orgs`"""
permission_map = {
x['organism']: x['permissions']
for x in user.organismPermissions
if 'WRITE' in x['permissions'] or
'READ' in x['permissions'] or
'ADMINISTRAT... | python | def accessible_organisms(user, orgs):
"""Get the list of organisms accessible to a user, filtered by `orgs`"""
permission_map = {
x['organism']: x['permissions']
for x in user.organismPermissions
if 'WRITE' in x['permissions'] or
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48,155 | cytomine/Cytomine-python-client | cytomine/cytomine.py | Cytomine.connect | def connect(cls, host, public_key, private_key, verbose=0, use_cache=True):
"""
Connect the client with the given host and the provided credentials.
Parameters
----------
host : str
The Cytomine host (without protocol).
public_key : str
The Cytomi... | python | def connect(cls, host, public_key, private_key, verbose=0, use_cache=True):
"""
Connect the client with the given host and the provided credentials.
Parameters
----------
host : str
The Cytomine host (without protocol).
public_key : str
The Cytomi... | [
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48,156 | cytomine/Cytomine-python-client | cytomine/cytomine.py | Cytomine.connect_from_cli | def connect_from_cli(cls, argv, use_cache=True):
"""
Connect with data taken from a command line interface.
Parameters
----------
argv: list
Command line parameters (executable name excluded)
use_cache : bool
True to use HTTP cache, False otherwis... | python | def connect_from_cli(cls, argv, use_cache=True):
"""
Connect with data taken from a command line interface.
Parameters
----------
argv: list
Command line parameters (executable name excluded)
use_cache : bool
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48,157 | cytomine/Cytomine-python-client | cytomine/cytomine.py | Cytomine._parse_url | def _parse_url(host, provided_protocol=None):
"""
Process the provided host and protocol to return them in a standardized
way that can be subsequently used by Cytomine methods.
If the protocol is not specified, HTTP is the default.
Only HTTP and HTTPS schemes are supported.
... | python | def _parse_url(host, provided_protocol=None):
"""
Process the provided host and protocol to return them in a standardized
way that can be subsequently used by Cytomine methods.
If the protocol is not specified, HTTP is the default.
Only HTTP and HTTPS schemes are supported.
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48,158 | cytomine/Cytomine-python-client | cytomine/cytomine.py | Cytomine.upload_crop | def upload_crop(self, ims_host, filename, id_annot, id_storage,
id_project=None, sync=False, protocol=None):
"""
Upload the crop associated with an annotation as a new image.
Parameters
----------
ims_host: str
Cytomine IMS host, with or without the ... | python | def upload_crop(self, ims_host, filename, id_annot, id_storage,
id_project=None, sync=False, protocol=None):
"""
Upload the crop associated with an annotation as a new image.
Parameters
----------
ims_host: str
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48,159 | galaxy-genome-annotation/python-apollo | apollo/cannedcomments/__init__.py | CannedCommentsClient.show_comment | def show_comment(self, value):
"""
Get a specific canned comment
:type value: str
:param value: Canned comment to show
:rtype: dict
:return: A dictionnary containing canned comment description
"""
comments = self.get_comments()
comments = [x for ... | python | def show_comment(self, value):
"""
Get a specific canned comment
:type value: str
:param value: Canned comment to show
:rtype: dict
:return: A dictionnary containing canned comment description
"""
comments = self.get_comments()
comments = [x for ... | [
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48,160 | galaxy-genome-annotation/python-apollo | arrow/cli.py | arrow | def arrow(ctx, apollo_instance, verbose, log_level):
"""Command line wrappers around Apollo functions. While this sounds
unexciting, with arrow and jq you can easily build powerful command line
scripts."""
set_logging_level(log_level)
# We abuse this, knowing that calls to one will fail.
try:
... | python | def arrow(ctx, apollo_instance, verbose, log_level):
"""Command line wrappers around Apollo functions. While this sounds
unexciting, with arrow and jq you can easily build powerful command line
scripts."""
set_logging_level(log_level)
# We abuse this, knowing that calls to one will fail.
try:
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48,161 | galaxy-genome-annotation/python-apollo | arrow/cli.py | json_loads | def json_loads(data):
"""Load json data, allowing - to represent stdin."""
if data is None:
return ""
if data == "-":
return json.load(sys.stdin)
elif os.path.exists(data):
with open(data, 'r') as handle:
return json.load(handle)
else:
return json.loads(d... | python | def json_loads(data):
"""Load json data, allowing - to represent stdin."""
if data is None:
return ""
if data == "-":
return json.load(sys.stdin)
elif os.path.exists(data):
with open(data, 'r') as handle:
return json.load(handle)
else:
return json.loads(d... | [
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48,162 | maykinmedia/django-timeline-logger | timeline_logger/management/commands/report_mailing.py | Command.get_queryset | def get_queryset(self, **options):
"""
Filters the list of log objects to display
"""
days = options.get('days')
queryset = TimelineLog.objects.order_by('-timestamp')
if days:
try:
start = timezone.now() - timedelta(days=days)
excep... | python | def get_queryset(self, **options):
"""
Filters the list of log objects to display
"""
days = options.get('days')
queryset = TimelineLog.objects.order_by('-timestamp')
if days:
try:
start = timezone.now() - timedelta(days=days)
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48,163 | maykinmedia/django-timeline-logger | timeline_logger/management/commands/report_mailing.py | Command.get_recipients | def get_recipients(self, **options):
"""
Figures out the recipients
"""
if options['recipients_from_setting']:
return settings.TIMELINE_DIGEST_EMAIL_RECIPIENTS
users = get_user_model()._default_manager.all()
if options['staff']:
users = users.filt... | python | def get_recipients(self, **options):
"""
Figures out the recipients
"""
if options['recipients_from_setting']:
return settings.TIMELINE_DIGEST_EMAIL_RECIPIENTS
users = get_user_model()._default_manager.all()
if options['staff']:
users = users.filt... | [
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48,164 | bouncer-app/bouncer | bouncer/models.py | Ability.expand_actions | def expand_actions(self, actions):
"""Accepts an array of actions and returns an array of actions which match.
This should be called before "matches?" and other checking methods since they
rely on the actions to be expanded."""
results = list()
for action in actions:
... | python | def expand_actions(self, actions):
"""Accepts an array of actions and returns an array of actions which match.
This should be called before "matches?" and other checking methods since they
rely on the actions to be expanded."""
results = list()
for action in actions:
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48,165 | cytomine/Cytomine-python-client | cytomine/cytomine_job.py | _software_params_to_argparse | def _software_params_to_argparse(parameters):
"""
Converts a SoftwareParameterCollection into an ArgumentParser object.
Parameters
----------
parameters: SoftwareParameterCollection
The software parameters
Returns
-------
argparse: ArgumentParser
An initialized argument ... | python | def _software_params_to_argparse(parameters):
"""
Converts a SoftwareParameterCollection into an ArgumentParser object.
Parameters
----------
parameters: SoftwareParameterCollection
The software parameters
Returns
-------
argparse: ArgumentParser
An initialized argument ... | [
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48,166 | cytomine/Cytomine-python-client | cytomine/cytomine_job.py | CytomineJob.start | def start(self):
"""
Connect to the Cytomine server and switch to job connection
Incurs dataflows
"""
run_by_ui = False
if not self.current_user.algo:
# If user connects as a human (CLI execution)
self._job = Job(self._project.id, self._software.i... | python | def start(self):
"""
Connect to the Cytomine server and switch to job connection
Incurs dataflows
"""
run_by_ui = False
if not self.current_user.algo:
# If user connects as a human (CLI execution)
self._job = Job(self._project.id, self._software.i... | [
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48,167 | cytomine/Cytomine-python-client | cytomine/cytomine_job.py | CytomineJob.close | def close(self, value):
"""
Notify the Cytomine server of the job's end
Incurs a dataflows
"""
if value is None:
status = Job.TERMINATED
status_comment = "Job successfully terminated"
else:
status = Job.FAILED
status_comment... | python | def close(self, value):
"""
Notify the Cytomine server of the job's end
Incurs a dataflows
"""
if value is None:
status = Job.TERMINATED
status_comment = "Job successfully terminated"
else:
status = Job.FAILED
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48,168 | pyecore/pyecoregen | pyecoregen/cli.py | generate_from_cli | def generate_from_cli(args):
"""CLI entry point."""
parser = argparse.ArgumentParser(description="Generate Python classes from an Ecore model.")
parser.add_argument(
'--ecore-model',
'-e',
help="Path to Ecore XMI file.",
required=True
)
parser.add_argument(
'-... | python | def generate_from_cli(args):
"""CLI entry point."""
parser = argparse.ArgumentParser(description="Generate Python classes from an Ecore model.")
parser.add_argument(
'--ecore-model',
'-e',
help="Path to Ecore XMI file.",
required=True
)
parser.add_argument(
'-... | [
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48,169 | pyecore/pyecoregen | pyecoregen/cli.py | select_uri_implementation | def select_uri_implementation(ecore_model_path):
"""Select the right URI implementation regarding the Ecore model path schema."""
if URL_PATTERN.match(ecore_model_path):
return pyecore.resources.resource.HttpURI
return pyecore.resources.URI | python | def select_uri_implementation(ecore_model_path):
"""Select the right URI implementation regarding the Ecore model path schema."""
if URL_PATTERN.match(ecore_model_path):
return pyecore.resources.resource.HttpURI
return pyecore.resources.URI | [
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48,170 | pyecore/pyecoregen | pyecoregen/cli.py | load_model | def load_model(ecore_model_path):
"""Load a single Ecore model and return the root package."""
rset = pyecore.resources.ResourceSet()
uri_implementation = select_uri_implementation(ecore_model_path)
resource = rset.get_resource(uri_implementation(ecore_model_path))
return resource.contents[0] | python | def load_model(ecore_model_path):
"""Load a single Ecore model and return the root package."""
rset = pyecore.resources.ResourceSet()
uri_implementation = select_uri_implementation(ecore_model_path)
resource = rset.get_resource(uri_implementation(ecore_model_path))
return resource.contents[0] | [
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48,171 | galaxy-genome-annotation/python-apollo | apollo/client.py | Client.post | def post(self, client_method, data, post_params=None, is_json=True):
"""Make a POST request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
if post_params is None:
post_params = {}
headers = {
'Content-Type': 'application/json'
}
... | python | def post(self, client_method, data, post_params=None, is_json=True):
"""Make a POST request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
if post_params is None:
post_params = {}
headers = {
'Content-Type': 'application/json'
}
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48,172 | galaxy-genome-annotation/python-apollo | apollo/client.py | Client.get | def get(self, client_method, get_params, is_json=True):
"""Make a GET request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
headers = {}
response = requests.get(url, headers=headers,
verify=self.__verify, params=get_params,
... | python | def get(self, client_method, get_params, is_json=True):
"""Make a GET request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
headers = {}
response = requests.get(url, headers=headers,
verify=self.__verify, params=get_params,
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48,173 | bouncer-app/bouncer | bouncer/__init__.py | can | def can(user, action, subject):
"""Checks if a given user has the ability to perform the action on a subject
:param user: A user object
:param action: an action string, typically 'read', 'edit', 'manage'. Use bouncer.constants for readability
:param subject: the resource in question. Either a Class o... | python | def can(user, action, subject):
"""Checks if a given user has the ability to perform the action on a subject
:param user: A user object
:param action: an action string, typically 'read', 'edit', 'manage'. Use bouncer.constants for readability
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48,174 | bouncer-app/bouncer | bouncer/__init__.py | cannot | def cannot(user, action, subject):
"""inverse of ``can``"""
ability = Ability(user, get_authorization_method())
return ability.cannot(action, subject) | python | def cannot(user, action, subject):
"""inverse of ``can``"""
ability = Ability(user, get_authorization_method())
return ability.cannot(action, subject) | [
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48,175 | bouncer-app/bouncer | bouncer/__init__.py | ensure | def ensure(user, action, subject):
""" Similar to ``can`` but will raise a AccessDenied Exception if does not have access"""
ability = Ability(user, get_authorization_method())
if ability.cannot(action, subject):
raise AccessDenied() | python | def ensure(user, action, subject):
""" Similar to ``can`` but will raise a AccessDenied Exception if does not have access"""
ability = Ability(user, get_authorization_method())
if ability.cannot(action, subject):
raise AccessDenied() | [
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48,176 | cytomine/Cytomine-python-client | cytomine/models/annotation.py | Annotation.dump | def dump(self, dest_pattern="{id}.jpg", override=True, mask=False, alpha=False, bits=8,
zoom=None, max_size=None, increase_area=None, contrast=None, gamma=None, colormap=None, inverse=None):
"""
Download the annotation crop, with optional image modifications.
Parameters
---... | python | def dump(self, dest_pattern="{id}.jpg", override=True, mask=False, alpha=False, bits=8,
zoom=None, max_size=None, increase_area=None, contrast=None, gamma=None, colormap=None, inverse=None):
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Download the annotation crop, with optional image modifications.
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] | bac19722b900dd32c6cfd6bdb9354fc784d33bc4 | https://github.com/cytomine/Cytomine-python-client/blob/bac19722b900dd32c6cfd6bdb9354fc784d33bc4/cytomine/models/annotation.py#L62-L144 |
48,177 | galaxy-genome-annotation/python-apollo | arrow/commands/annotations/set_sequence.py | cli | def cli(ctx, organism, sequence):
"""Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.
Output:
None
"""
return ctx.gi.annotations.set_sequence(organism, sequence) | python | def cli(ctx, organism, sequence):
"""Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.
Output:
None
"""
return ctx.gi.annotations.set_sequence(organism, sequence) | [
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48,178 | hearsaycorp/normalize | normalize/selector.py | MultiFieldSelector.path | def path(self):
"""The path attribute returns a stringified, concise representation of
the MultiFieldSelector. It can be reversed by the ``from_path``
constructor.
"""
if len(self.heads) == 1:
return _fmt_mfs_path(self.heads.keys()[0], self.heads.values()[0])
... | python | def path(self):
"""The path attribute returns a stringified, concise representation of
the MultiFieldSelector. It can be reversed by the ``from_path``
constructor.
"""
if len(self.heads) == 1:
return _fmt_mfs_path(self.heads.keys()[0], self.heads.values()[0])
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48,179 | hearsaycorp/normalize | normalize/selector.py | MultiFieldSelector.get | def get(self, obj):
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"""
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"""Creates a copy of the passed object which only contains the parts
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48,180 | hearsaycorp/normalize | normalize/selector.py | MultiFieldSelector.delete | def delete(self, obj, force=False):
"""Deletes all of the fields at the specified locations.
args:
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``force=``\ *BOOL*
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"""Deletes all of the fields at the specified locations.
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48,181 | merll/docker-fabric | dockerfabric/tasks.py | reset_socat | def reset_socat(use_sudo=False):
"""
Finds and closes all processes of `socat`.
:param use_sudo: Use `sudo` command. As Docker-Fabric does not run `socat` with `sudo`, this is by default set to
``False``. Setting it to ``True`` could unintentionally remove instances from other users.
:type use_su... | python | def reset_socat(use_sudo=False):
"""
Finds and closes all processes of `socat`.
:param use_sudo: Use `sudo` command. As Docker-Fabric does not run `socat` with `sudo`, this is by default set to
``False``. Setting it to ``True`` could unintentionally remove instances from other users.
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48,182 | merll/docker-fabric | dockerfabric/tasks.py | version | def version():
"""
Shows version information of the remote Docker service, similar to ``docker version``.
"""
output = docker_fabric().version()
col_len = max(map(len, output.keys())) + 1
puts('')
for k, v in six.iteritems(output):
fastprint('{0:{1}} {2}'.format(''.join((k, ':')), co... | python | def version():
"""
Shows version information of the remote Docker service, similar to ``docker version``.
"""
output = docker_fabric().version()
col_len = max(map(len, output.keys())) + 1
puts('')
for k, v in six.iteritems(output):
fastprint('{0:{1}} {2}'.format(''.join((k, ':')), co... | [
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48,183 | merll/docker-fabric | dockerfabric/tasks.py | list_images | def list_images(list_all=False, full_ids=False):
"""
Lists images on the Docker remote host, similar to ``docker images``.
:param list_all: Lists all images (e.g. dependencies). Default is ``False``, only shows named images.
:type list_all: bool
:param full_ids: Shows the full ids. When ``False`` (... | python | def list_images(list_all=False, full_ids=False):
"""
Lists images on the Docker remote host, similar to ``docker images``.
:param list_all: Lists all images (e.g. dependencies). Default is ``False``, only shows named images.
:type list_all: bool
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48,184 | merll/docker-fabric | dockerfabric/tasks.py | list_containers | def list_containers(list_all=True, short_image=True, full_ids=False, full_cmd=False):
"""
Lists containers on the Docker remote host, similar to ``docker ps``.
:param list_all: Shows all containers. Default is ``False``, which omits exited containers.
:type list_all: bool
:param short_image: Hides ... | python | def list_containers(list_all=True, short_image=True, full_ids=False, full_cmd=False):
"""
Lists containers on the Docker remote host, similar to ``docker ps``.
:param list_all: Shows all containers. Default is ``False``, which omits exited containers.
:type list_all: bool
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48,185 | merll/docker-fabric | dockerfabric/tasks.py | list_networks | def list_networks(full_ids=False):
"""
Lists networks on the Docker remote host, similar to ``docker network ls``.
:param full_ids: Shows the full network ids. When ``False`` (default) only shows the first 12 characters.
:type full_ids: bool
"""
networks = docker_fabric().networks()
_format... | python | def list_networks(full_ids=False):
"""
Lists networks on the Docker remote host, similar to ``docker network ls``.
:param full_ids: Shows the full network ids. When ``False`` (default) only shows the first 12 characters.
:type full_ids: bool
"""
networks = docker_fabric().networks()
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48,186 | merll/docker-fabric | dockerfabric/tasks.py | cleanup_containers | def cleanup_containers(**kwargs):
"""
Removes all containers that have finished running. Similar to the ``prune`` functionality in newer Docker versions.
"""
containers = docker_fabric().cleanup_containers(**kwargs)
if kwargs.get('list_only'):
puts('Existing containers:')
for c_id, c... | python | def cleanup_containers(**kwargs):
"""
Removes all containers that have finished running. Similar to the ``prune`` functionality in newer Docker versions.
"""
containers = docker_fabric().cleanup_containers(**kwargs)
if kwargs.get('list_only'):
puts('Existing containers:')
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48,187 | merll/docker-fabric | dockerfabric/tasks.py | cleanup_images | def cleanup_images(remove_old=False, **kwargs):
"""
Removes all images that have no name, and that are not references as dependency by any other named image. Similar
to the ``prune`` functionality in newer Docker versions, but supports more filters.
:param remove_old: Also remove images that do have a ... | python | def cleanup_images(remove_old=False, **kwargs):
"""
Removes all images that have no name, and that are not references as dependency by any other named image. Similar
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48,188 | merll/docker-fabric | dockerfabric/tasks.py | save_image | def save_image(image, filename=None):
"""
Saves a Docker image from the remote to a local files. For performance reasons, uses the Docker command line client
on the host, generates a gzip-tarball and downloads that.
:param image: Image name or id.
:type image: unicode
:param filename: File name... | python | def save_image(image, filename=None):
"""
Saves a Docker image from the remote to a local files. For performance reasons, uses the Docker command line client
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:param image: Image name or id.
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48,189 | merll/docker-fabric | dockerfabric/tasks.py | load_image | def load_image(filename, timeout=120):
"""
Uploads an image from a local file to a Docker remote. Note that this temporarily has to extend the service timeout
period.
:param filename: Local file name.
:type filename: unicode
:param timeout: Timeout in seconds to set temporarily for the upload.
... | python | def load_image(filename, timeout=120):
"""
Uploads an image from a local file to a Docker remote. Note that this temporarily has to extend the service timeout
period.
:param filename: Local file name.
:type filename: unicode
:param timeout: Timeout in seconds to set temporarily for the upload.
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48,190 | hearsaycorp/normalize | normalize/record/__init__.py | Record.diff_iter | def diff_iter(self, other, **kwargs):
"""Generator method which returns the differences from the invocant to
the argument.
args:
``other=``\ *Record*\ \|\ *Anything*
The thing to compare against; the types must match, unless
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48,191 | zhanglab/psamm | psamm/commands/primarypairs.py | _parse_weights | def _parse_weights(weight_args, default_weight=0.6):
"""Parse list of weight assignments."""
weights_dict = {}
r_group_weight = default_weight
for weight_arg in weight_args:
for weight_assignment in weight_arg.split(','):
if '=' not in weight_assignment:
raise ValueEr... | python | def _parse_weights(weight_args, default_weight=0.6):
"""Parse list of weight assignments."""
weights_dict = {}
r_group_weight = default_weight
for weight_arg in weight_args:
for weight_assignment in weight_arg.split(','):
if '=' not in weight_assignment:
raise ValueEr... | [
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48,192 | zhanglab/psamm | psamm/commands/primarypairs.py | PrimaryPairsCommand._combine_transfers | def _combine_transfers(self, result):
"""Combine multiple pair transfers into one."""
transfers = {}
for reaction_id, c1, c2, form in result:
key = reaction_id, c1, c2
combined_form = transfers.setdefault(key, Formula())
transfers[key] = combined_form | form
... | python | def _combine_transfers(self, result):
"""Combine multiple pair transfers into one."""
transfers = {}
for reaction_id, c1, c2, form in result:
key = reaction_id, c1, c2
combined_form = transfers.setdefault(key, Formula())
transfers[key] = combined_form | form
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48,193 | merll/docker-fabric | dockerfabric/cli.py | copy_resource | def copy_resource(container, resource, local_filename, contents_only=True):
"""
Copies a resource from a container to a compressed tarball and downloads it.
:param container: Container name or id.
:type container: unicode
:param resource: Name of resource to copy.
:type resource: unicode
:p... | python | def copy_resource(container, resource, local_filename, contents_only=True):
"""
Copies a resource from a container to a compressed tarball and downloads it.
:param container: Container name or id.
:type container: unicode
:param resource: Name of resource to copy.
:type resource: unicode
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48,194 | merll/docker-fabric | dockerfabric/cli.py | save_image | def save_image(image, local_filename):
"""
Saves a Docker image as a compressed tarball. This command line client method is a suitable alternative, if the
Remove API method is too slow.
:param image: Image id or tag.
:type image: unicode
:param local_filename: Local file name to store the image... | python | def save_image(image, local_filename):
"""
Saves a Docker image as a compressed tarball. This command line client method is a suitable alternative, if the
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:param image: Image id or tag.
:type image: unicode
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48,195 | zhanglab/psamm | psamm/datasource/modelseed.py | decode_name | def decode_name(s):
"""Decode names in ModelSEED files"""
# Some names contain XML-like entity codes
return re.sub(r'&#(\d+);', lambda x: chr(int(x.group(1))), s) | python | def decode_name(s):
"""Decode names in ModelSEED files"""
# Some names contain XML-like entity codes
return re.sub(r'&#(\d+);', lambda x: chr(int(x.group(1))), s) | [
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48,196 | zhanglab/psamm | psamm/datasource/modelseed.py | parse_compound_file | def parse_compound_file(f, context=None):
"""Iterate over the compound entries in the given file"""
f.readline() # Skip header
for lineno, row in enumerate(csv.reader(f, delimiter='\t')):
compound_id, names, formula = row[:3]
names = (decode_name(name) for name in names.split(',<br>'))
... | python | def parse_compound_file(f, context=None):
"""Iterate over the compound entries in the given file"""
f.readline() # Skip header
for lineno, row in enumerate(csv.reader(f, delimiter='\t')):
compound_id, names, formula = row[:3]
names = (decode_name(name) for name in names.split(',<br>'))
... | [
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48,197 | zhanglab/psamm | psamm/commands/search.py | SearchCommand.init_parser | def init_parser(cls, parser):
"""Initialize argument parser"""
subparsers = parser.add_subparsers(title='Search domain')
# Compound subcommand
parser_compound = subparsers.add_parser(
'compound', help='Search in compounds')
parser_compound.set_defaults(which='compoun... | python | def init_parser(cls, parser):
"""Initialize argument parser"""
subparsers = parser.add_subparsers(title='Search domain')
# Compound subcommand
parser_compound = subparsers.add_parser(
'compound', help='Search in compounds')
parser_compound.set_defaults(which='compoun... | [
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48,198 | zhanglab/psamm | psamm/commands/search.py | SearchCommand.run | def run(self):
"""Run search command."""
which_command = self._args.which
if which_command == 'compound':
self._search_compound()
elif which_command == 'reaction':
self._search_reaction() | python | def run(self):
"""Run search command."""
which_command = self._args.which
if which_command == 'compound':
self._search_compound()
elif which_command == 'reaction':
self._search_reaction() | [
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48,199 | hearsaycorp/normalize | normalize/property/json.py | JsonProperty.to_json | def to_json(self, propval, extraneous=False, to_json_func=None):
"""This function calls the ``json_out`` function, if it was specified,
otherwise continues with JSON conversion of the value in the slot by
calling ``to_json_func`` on it.
"""
if self.json_out:
return se... | python | def to_json(self, propval, extraneous=False, to_json_func=None):
"""This function calls the ``json_out`` function, if it was specified,
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