partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
valid | BELNamespaceManagerMixin.write_bel_namespace | Write as a BEL namespace file. | src/bio2bel/manager/namespace_manager.py | def write_bel_namespace(self, file: TextIO, use_names: bool = False) -> None:
"""Write as a BEL namespace file."""
if not self.is_populated():
self.populate()
if use_names and not self.has_names:
raise ValueError
values = (
self._get_namespace_name_t... | def write_bel_namespace(self, file: TextIO, use_names: bool = False) -> None:
"""Write as a BEL namespace file."""
if not self.is_populated():
self.populate()
if use_names and not self.has_names:
raise ValueError
values = (
self._get_namespace_name_t... | [
"Write",
"as",
"a",
"BEL",
"namespace",
"file",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/namespace_manager.py#L345-L365 | [
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valid | BELNamespaceManagerMixin.write_bel_annotation | Write as a BEL annotation file. | src/bio2bel/manager/namespace_manager.py | def write_bel_annotation(self, file: TextIO) -> None:
"""Write as a BEL annotation file."""
if not self.is_populated():
self.populate()
values = self._get_namespace_name_to_encoding(desc='writing names')
write_annotation(
keyword=self._get_namespace_keyword(),
... | def write_bel_annotation(self, file: TextIO) -> None:
"""Write as a BEL annotation file."""
if not self.is_populated():
self.populate()
values = self._get_namespace_name_to_encoding(desc='writing names')
write_annotation(
keyword=self._get_namespace_keyword(),
... | [
"Write",
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"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/namespace_manager.py#L367-L380 | [
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valid | BELNamespaceManagerMixin.write_bel_namespace_mappings | Write a BEL namespace mapping file. | src/bio2bel/manager/namespace_manager.py | def write_bel_namespace_mappings(self, file: TextIO, **kwargs) -> None:
"""Write a BEL namespace mapping file."""
json.dump(self._get_namespace_identifier_to_name(**kwargs), file, indent=2, sort_keys=True) | def write_bel_namespace_mappings(self, file: TextIO, **kwargs) -> None:
"""Write a BEL namespace mapping file."""
json.dump(self._get_namespace_identifier_to_name(**kwargs), file, indent=2, sort_keys=True) | [
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valid | BELNamespaceManagerMixin.write_directory | Write a BEL namespace for identifiers, names, name hash, and mappings to the given directory. | src/bio2bel/manager/namespace_manager.py | def write_directory(self, directory: str) -> bool:
"""Write a BEL namespace for identifiers, names, name hash, and mappings to the given directory."""
current_md5_hash = self.get_namespace_hash()
md5_hash_path = os.path.join(directory, f'{self.module_name}.belns.md5')
if not os.path.exi... | def write_directory(self, directory: str) -> bool:
"""Write a BEL namespace for identifiers, names, name hash, and mappings to the given directory."""
current_md5_hash = self.get_namespace_hash()
md5_hash_path = os.path.join(directory, f'{self.module_name}.belns.md5')
if not os.path.exi... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/namespace_manager.py#L386-L413 | [
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valid | BELNamespaceManagerMixin.get_namespace_hash | Get the namespace hash.
Defaults to MD5. | src/bio2bel/manager/namespace_manager.py | def get_namespace_hash(self, hash_fn=hashlib.md5) -> str:
"""Get the namespace hash.
Defaults to MD5.
"""
m = hash_fn()
if self.has_names:
items = self._get_namespace_name_to_encoding(desc='getting hash').items()
else:
items = self._get_namespace... | def get_namespace_hash(self, hash_fn=hashlib.md5) -> str:
"""Get the namespace hash.
Defaults to MD5.
"""
m = hash_fn()
if self.has_names:
items = self._get_namespace_name_to_encoding(desc='getting hash').items()
else:
items = self._get_namespace... | [
"Get",
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/namespace_manager.py#L433-L447 | [
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valid | BELNamespaceManagerMixin.get_cli | Get a :mod:`click` main function with added BEL namespace commands. | src/bio2bel/manager/namespace_manager.py | def get_cli(cls) -> click.Group:
"""Get a :mod:`click` main function with added BEL namespace commands."""
main = super().get_cli()
if cls.is_namespace:
@main.group()
def belns():
"""Manage BEL namespace."""
cls._cli_add_to_bel_namespace(beln... | def get_cli(cls) -> click.Group:
"""Get a :mod:`click` main function with added BEL namespace commands."""
main = super().get_cli()
if cls.is_namespace:
@main.group()
def belns():
"""Manage BEL namespace."""
cls._cli_add_to_bel_namespace(beln... | [
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valid | get_long_description | Get the long_description from the README.rst file. Assume UTF-8 encoding. | setup.py | def get_long_description():
"""Get the long_description from the README.rst file. Assume UTF-8 encoding."""
with codecs.open(os.path.join(HERE, 'README.rst'), encoding='utf-8') as f:
long_description = f.read()
return long_description | def get_long_description():
"""Get the long_description from the README.rst file. Assume UTF-8 encoding."""
with codecs.open(os.path.join(HERE, 'README.rst'), encoding='utf-8') as f:
long_description = f.read()
return long_description | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/setup.py#L89-L93 | [
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | dropbox_post_factory | receives a UUID via the request and returns either a fresh or an existing dropbox
for it | application/briefkasten/__init__.py | def dropbox_post_factory(request):
"""receives a UUID via the request and returns either a fresh or an existing dropbox
for it"""
try:
max_age = int(request.registry.settings.get('post_token_max_age_seconds'))
except Exception:
max_age = 300
try:
drop_id = parse_post_token(
... | def dropbox_post_factory(request):
"""receives a UUID via the request and returns either a fresh or an existing dropbox
for it"""
try:
max_age = int(request.registry.settings.get('post_token_max_age_seconds'))
except Exception:
max_age = 300
try:
drop_id = parse_post_token(
... | [
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valid | dropbox_factory | expects the id of an existing dropbox and returns its instance | application/briefkasten/__init__.py | def dropbox_factory(request):
""" expects the id of an existing dropbox and returns its instance"""
try:
return request.registry.settings['dropbox_container'].get_dropbox(request.matchdict['drop_id'])
except KeyError:
raise HTTPNotFound('no such dropbox') | def dropbox_factory(request):
""" expects the id of an existing dropbox and returns its instance"""
try:
return request.registry.settings['dropbox_container'].get_dropbox(request.matchdict['drop_id'])
except KeyError:
raise HTTPNotFound('no such dropbox') | [
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valid | is_equal | a constant time comparison implementation taken from
http://codahale.com/a-lesson-in-timing-attacks/ and
Django's `util` module https://github.com/django/django/blob/master/django/utils/crypto.py#L82 | application/briefkasten/__init__.py | def is_equal(a, b):
""" a constant time comparison implementation taken from
http://codahale.com/a-lesson-in-timing-attacks/ and
Django's `util` module https://github.com/django/django/blob/master/django/utils/crypto.py#L82
"""
if len(a) != len(b):
return False
result = 0
fo... | def is_equal(a, b):
""" a constant time comparison implementation taken from
http://codahale.com/a-lesson-in-timing-attacks/ and
Django's `util` module https://github.com/django/django/blob/master/django/utils/crypto.py#L82
"""
if len(a) != len(b):
return False
result = 0
fo... | [
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valid | dropbox_editor_factory | this factory also requires the editor token | application/briefkasten/__init__.py | def dropbox_editor_factory(request):
""" this factory also requires the editor token"""
dropbox = dropbox_factory(request)
if is_equal(dropbox.editor_token, request.matchdict['editor_token'].encode('utf-8')):
return dropbox
else:
raise HTTPNotFound('invalid editor token') | def dropbox_editor_factory(request):
""" this factory also requires the editor token"""
dropbox = dropbox_factory(request)
if is_equal(dropbox.editor_token, request.matchdict['editor_token'].encode('utf-8')):
return dropbox
else:
raise HTTPNotFound('invalid editor token') | [
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valid | CliMixin.get_cli | Build a :mod:`click` CLI main function.
:param Type[AbstractManager] cls: A Manager class
:return: The main function for click | src/bio2bel/manager/cli_manager.py | def get_cli(cls) -> click.Group:
"""Build a :mod:`click` CLI main function.
:param Type[AbstractManager] cls: A Manager class
:return: The main function for click
"""
group_help = 'Default connection at {}\n\nusing Bio2BEL v{}'.format(cls._get_connection(), get_version())
... | def get_cli(cls) -> click.Group:
"""Build a :mod:`click` CLI main function.
:param Type[AbstractManager] cls: A Manager class
:return: The main function for click
"""
group_help = 'Default connection at {}\n\nusing Bio2BEL v{}'.format(cls._get_connection(), get_version())
... | [
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valid | sanitize_filename | preserve the file ending, but replace the name with a random token | application/briefkasten/dropbox.py | def sanitize_filename(filename):
"""preserve the file ending, but replace the name with a random token """
# TODO: fix broken splitext (it reveals everything of the filename after the first `.` - doh!)
token = generate_drop_id()
name, extension = splitext(filename)
if extension:
return '%s%s... | def sanitize_filename(filename):
"""preserve the file ending, but replace the name with a random token """
# TODO: fix broken splitext (it reveals everything of the filename after the first `.` - doh!)
token = generate_drop_id()
name, extension = splitext(filename)
if extension:
return '%s%s... | [
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valid | Dropbox.process | Calls the external cleanser scripts to (optionally) purge the meta data and then
send the contents of the dropbox via email. | application/briefkasten/dropbox.py | def process(self):
""" Calls the external cleanser scripts to (optionally) purge the meta data and then
send the contents of the dropbox via email.
"""
if self.num_attachments > 0:
self.status = u'100 processor running'
fs_dirty_archive = self._create_backup(... | def process(self):
""" Calls the external cleanser scripts to (optionally) purge the meta data and then
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"""
if self.num_attachments > 0:
self.status = u'100 processor running'
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valid | Dropbox.cleanup | ensures that no data leaks from drop after processing by
removing all data except the status file | application/briefkasten/dropbox.py | def cleanup(self):
""" ensures that no data leaks from drop after processing by
removing all data except the status file"""
try:
remove(join(self.fs_path, u'message'))
remove(join(self.fs_path, 'dirty.zip.pgp'))
except OSError:
pass
shutil.rmtr... | def cleanup(self):
""" ensures that no data leaks from drop after processing by
removing all data except the status file"""
try:
remove(join(self.fs_path, u'message'))
remove(join(self.fs_path, 'dirty.zip.pgp'))
except OSError:
pass
shutil.rmtr... | [
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valid | Dropbox._create_encrypted_zip | creates a zip file from the drop and encrypts it to the editors.
the encrypted archive is created inside fs_target_dir | application/briefkasten/dropbox.py | def _create_encrypted_zip(self, source='dirty', fs_target_dir=None):
""" creates a zip file from the drop and encrypts it to the editors.
the encrypted archive is created inside fs_target_dir"""
backup_recipients = [r for r in self.editors if checkRecipient(self.gpg_context, r)]
# this ... | def _create_encrypted_zip(self, source='dirty', fs_target_dir=None):
""" creates a zip file from the drop and encrypts it to the editors.
the encrypted archive is created inside fs_target_dir"""
backup_recipients = [r for r in self.editors if checkRecipient(self.gpg_context, r)]
# this ... | [
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valid | Dropbox._create_archive | creates an encrypted archive of the dropbox outside of the drop directory. | application/briefkasten/dropbox.py | def _create_archive(self):
""" creates an encrypted archive of the dropbox outside of the drop directory.
"""
self.status = u'270 creating final encrypted backup of cleansed attachments'
return self._create_encrypted_zip(source='clean', fs_target_dir=self.container.fs_archive_cleansed) | def _create_archive(self):
""" creates an encrypted archive of the dropbox outside of the drop directory.
"""
self.status = u'270 creating final encrypted backup of cleansed attachments'
return self._create_encrypted_zip(source='clean', fs_target_dir=self.container.fs_archive_cleansed) | [
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valid | Dropbox.size_attachments | returns the number of bytes that the cleansed attachments take up on disk | application/briefkasten/dropbox.py | def size_attachments(self):
"""returns the number of bytes that the cleansed attachments take up on disk"""
total_size = 0
for attachment in self.fs_cleansed_attachments:
total_size += stat(attachment).st_size
return total_size | def size_attachments(self):
"""returns the number of bytes that the cleansed attachments take up on disk"""
total_size = 0
for attachment in self.fs_cleansed_attachments:
total_size += stat(attachment).st_size
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valid | Dropbox.replies | returns a list of strings | application/briefkasten/dropbox.py | def replies(self):
""" returns a list of strings """
fs_reply_path = join(self.fs_replies_path, 'message_001.txt')
if exists(fs_reply_path):
return [load(open(fs_reply_path, 'r'))]
else:
return [] | def replies(self):
""" returns a list of strings """
fs_reply_path = join(self.fs_replies_path, 'message_001.txt')
if exists(fs_reply_path):
return [load(open(fs_reply_path, 'r'))]
else:
return [] | [
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valid | Dropbox.message | returns the user submitted text | application/briefkasten/dropbox.py | def message(self):
""" returns the user submitted text
"""
try:
with open(join(self.fs_path, u'message')) as message_file:
return u''.join([line.decode('utf-8') for line in message_file.readlines()])
except IOError:
return u'' | def message(self):
""" returns the user submitted text
"""
try:
with open(join(self.fs_path, u'message')) as message_file:
return u''.join([line.decode('utf-8') for line in message_file.readlines()])
except IOError:
return u'' | [
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valid | Dropbox.fs_dirty_attachments | returns a list of absolute paths to the attachements | application/briefkasten/dropbox.py | def fs_dirty_attachments(self):
""" returns a list of absolute paths to the attachements"""
if exists(self.fs_attachment_container):
return [join(self.fs_attachment_container, attachment)
for attachment in listdir(self.fs_attachment_container)]
else:
r... | def fs_dirty_attachments(self):
""" returns a list of absolute paths to the attachements"""
if exists(self.fs_attachment_container):
return [join(self.fs_attachment_container, attachment)
for attachment in listdir(self.fs_attachment_container)]
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valid | Dropbox.fs_cleansed_attachments | returns a list of absolute paths to the cleansed attachements | application/briefkasten/dropbox.py | def fs_cleansed_attachments(self):
""" returns a list of absolute paths to the cleansed attachements"""
if exists(self.fs_cleansed_attachment_container):
return [join(self.fs_cleansed_attachment_container, attachment)
for attachment in listdir(self.fs_cleansed_attachment_... | def fs_cleansed_attachments(self):
""" returns a list of absolute paths to the cleansed attachements"""
if exists(self.fs_cleansed_attachment_container):
return [join(self.fs_cleansed_attachment_container, attachment)
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valid | reset_cleansers | destroys all cleanser slaves and their rollback snapshots, as well as the initial master
snapshot - this allows re-running the jailhost deployment to recreate fresh cleansers. | deployment/jailhost.py | def reset_cleansers(confirm=True):
"""destroys all cleanser slaves and their rollback snapshots, as well as the initial master
snapshot - this allows re-running the jailhost deployment to recreate fresh cleansers."""
if value_asbool(confirm) and not yesno("""\nObacht!
This will destroy any exis... | def reset_cleansers(confirm=True):
"""destroys all cleanser slaves and their rollback snapshots, as well as the initial master
snapshot - this allows re-running the jailhost deployment to recreate fresh cleansers."""
if value_asbool(confirm) and not yesno("""\nObacht!
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valid | reset_jails | stops, deletes and re-creates all jails.
since the cleanser master is rather large, that one is omitted by default. | deployment/jailhost.py | def reset_jails(confirm=True, keep_cleanser_master=True):
""" stops, deletes and re-creates all jails.
since the cleanser master is rather large, that one is omitted by default.
"""
if value_asbool(confirm) and not yesno("""\nObacht!
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""" stops, deletes and re-creates all jails.
since the cleanser master is rather large, that one is omitted by default.
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valid | dict_dumper | Dump a provider to a format that can be passed to a
:class:`skosprovider.providers.DictionaryProvider`.
:param skosprovider.providers.VocabularyProvider provider: The provider
that wil be turned into a `dict`.
:rtype: A list of dicts.
.. versionadded:: 0.2.0 | skosprovider/utils.py | def dict_dumper(provider):
'''
Dump a provider to a format that can be passed to a
:class:`skosprovider.providers.DictionaryProvider`.
:param skosprovider.providers.VocabularyProvider provider: The provider
that wil be turned into a `dict`.
:rtype: A list of dicts.
.. versionadded:: 0.... | def dict_dumper(provider):
'''
Dump a provider to a format that can be passed to a
:class:`skosprovider.providers.DictionaryProvider`.
:param skosprovider.providers.VocabularyProvider provider: The provider
that wil be turned into a `dict`.
:rtype: A list of dicts.
.. versionadded:: 0.... | [
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valid | add_cli_flask | Add a ``web`` comand main :mod:`click` function. | src/bio2bel/manager/flask_manager.py | def add_cli_flask(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``web`` comand main :mod:`click` function."""
@main.command()
@click.option('-v', '--debug', is_flag=True)
@click.option('-p', '--port')
@click.option('-h', '--host')
@click.option('-k', '--secret-key', default=os.urand... | def add_cli_flask(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``web`` comand main :mod:`click` function."""
@main.command()
@click.option('-v', '--debug', is_flag=True)
@click.option('-p', '--port')
@click.option('-h', '--host')
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valid | FlaskMixin._add_admin | Add a Flask Admin interface to an application.
:param flask.Flask app: A Flask application
:param kwargs: Keyword arguments are passed through to :class:`flask_admin.Admin`
:rtype: flask_admin.Admin | src/bio2bel/manager/flask_manager.py | def _add_admin(self, app, **kwargs):
"""Add a Flask Admin interface to an application.
:param flask.Flask app: A Flask application
:param kwargs: Keyword arguments are passed through to :class:`flask_admin.Admin`
:rtype: flask_admin.Admin
"""
from flask_admin import Admi... | def _add_admin(self, app, **kwargs):
"""Add a Flask Admin interface to an application.
:param flask.Flask app: A Flask application
:param kwargs: Keyword arguments are passed through to :class:`flask_admin.Admin`
:rtype: flask_admin.Admin
"""
from flask_admin import Admi... | [
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valid | FlaskMixin.get_flask_admin_app | Create a Flask application.
:param url: Optional mount point of the admin application. Defaults to ``'/'``.
:rtype: flask.Flask | src/bio2bel/manager/flask_manager.py | def get_flask_admin_app(self, url: Optional[str] = None, secret_key: Optional[str] = None):
"""Create a Flask application.
:param url: Optional mount point of the admin application. Defaults to ``'/'``.
:rtype: flask.Flask
"""
from flask import Flask
app = Flask(__name_... | def get_flask_admin_app(self, url: Optional[str] = None, secret_key: Optional[str] = None):
"""Create a Flask application.
:param url: Optional mount point of the admin application. Defaults to ``'/'``.
:rtype: flask.Flask
"""
from flask import Flask
app = Flask(__name_... | [
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valid | FlaskMixin.get_cli | Add a :mod:`click` main function to use as a command line interface. | src/bio2bel/manager/flask_manager.py | def get_cli(cls) -> click.Group:
"""Add a :mod:`click` main function to use as a command line interface."""
main = super().get_cli()
cls._cli_add_flask(main)
return main | def get_cli(cls) -> click.Group:
"""Add a :mod:`click` main function to use as a command line interface."""
main = super().get_cli()
cls._cli_add_flask(main)
return main | [
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valid | Alarm._handle_system_status_event | DISARMED -> ARMED_AWAY -> EXIT_DELAY_START -> EXIT_DELAY_END
(trip): -> ALARM -> OUTPUT_ON -> ALARM_RESTORE
(disarm): -> DISARMED -> OUTPUT_OFF
(disarm): -> DISARMED
(disarm before EXIT_DELAY_END): -> DISARMED -> EXIT_DELAY_END
TODO(NW): Check ALARM_RESTORE state transiti... | nessclient/alarm.py | def _handle_system_status_event(self, event: SystemStatusEvent) -> None:
"""
DISARMED -> ARMED_AWAY -> EXIT_DELAY_START -> EXIT_DELAY_END
(trip): -> ALARM -> OUTPUT_ON -> ALARM_RESTORE
(disarm): -> DISARMED -> OUTPUT_OFF
(disarm): -> DISARMED
(disarm before EXIT_DE... | def _handle_system_status_event(self, event: SystemStatusEvent) -> None:
"""
DISARMED -> ARMED_AWAY -> EXIT_DELAY_START -> EXIT_DELAY_END
(trip): -> ALARM -> OUTPUT_ON -> ALARM_RESTORE
(disarm): -> DISARMED -> OUTPUT_OFF
(disarm): -> DISARMED
(disarm before EXIT_DE... | [
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"OUTPUT_O... | nickw444/nessclient | python | https://github.com/nickw444/nessclient/blob/9a2e3d450448312f56e708b8c7adeaef878cc28a/nessclient/alarm.py#L90-L125 | [
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valid | dropbox_form | generates a dropbox uid and renders the submission form with a signed version of that id | application/briefkasten/views.py | def dropbox_form(request):
""" generates a dropbox uid and renders the submission form with a signed version of that id"""
from briefkasten import generate_post_token
token = generate_post_token(secret=request.registry.settings['post_secret'])
return dict(
action=request.route_url('dropbox_form_... | def dropbox_form(request):
""" generates a dropbox uid and renders the submission form with a signed version of that id"""
from briefkasten import generate_post_token
token = generate_post_token(secret=request.registry.settings['post_secret'])
return dict(
action=request.route_url('dropbox_form_... | [
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] | ZeitOnline/briefkasten | python | https://github.com/ZeitOnline/briefkasten/blob/ce6b6eeb89196014fe21d68614c20059d02daa11/application/briefkasten/views.py#L50-L57 | [
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valid | dropbox_fileupload | accepts a single file upload and adds it to the dropbox as attachment | application/briefkasten/views.py | def dropbox_fileupload(dropbox, request):
""" accepts a single file upload and adds it to the dropbox as attachment"""
attachment = request.POST['attachment']
attached = dropbox.add_attachment(attachment)
return dict(
files=[dict(
name=attached,
type=attachment.type,
... | def dropbox_fileupload(dropbox, request):
""" accepts a single file upload and adds it to the dropbox as attachment"""
attachment = request.POST['attachment']
attached = dropbox.add_attachment(attachment)
return dict(
files=[dict(
name=attached,
type=attachment.type,
... | [
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] | ZeitOnline/briefkasten | python | https://github.com/ZeitOnline/briefkasten/blob/ce6b6eeb89196014fe21d68614c20059d02daa11/application/briefkasten/views.py#L65-L74 | [
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valid | dropbox_submission | handles the form submission, redirects to the dropbox's status page. | application/briefkasten/views.py | def dropbox_submission(dropbox, request):
""" handles the form submission, redirects to the dropbox's status page."""
try:
data = dropbox_schema.deserialize(request.POST)
except Exception:
return HTTPFound(location=request.route_url('dropbox_form'))
# set the message
dropbox.message... | def dropbox_submission(dropbox, request):
""" handles the form submission, redirects to the dropbox's status page."""
try:
data = dropbox_schema.deserialize(request.POST)
except Exception:
return HTTPFound(location=request.route_url('dropbox_form'))
# set the message
dropbox.message... | [
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... | ce6b6eeb89196014fe21d68614c20059d02daa11 |
valid | make_obo_getter | Build a function that handles downloading OBO data and parsing it into a NetworkX object.
:param data_url: The URL of the data
:param data_path: The path where the data should get stored
:param preparsed_path: The optional path to cache a pre-parsed json version | src/bio2bel/obo.py | def make_obo_getter(data_url: str,
data_path: str,
*,
preparsed_path: Optional[str] = None,
) -> Callable[[Optional[str], bool, bool], MultiDiGraph]:
"""Build a function that handles downloading OBO data and parsing it into a NetworkX o... | def make_obo_getter(data_url: str,
data_path: str,
*,
preparsed_path: Optional[str] = None,
) -> Callable[[Optional[str], bool, bool], MultiDiGraph]:
"""Build a function that handles downloading OBO data and parsing it into a NetworkX o... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/obo.py#L21-L54 | [
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valid | belns | Write as a BEL namespace. | src/bio2bel/obo.py | def belns(keyword: str, file: TextIO, encoding: Optional[str], use_names: bool):
"""Write as a BEL namespace."""
directory = get_data_dir(keyword)
obo_url = f'http://purl.obolibrary.org/obo/{keyword}.obo'
obo_path = os.path.join(directory, f'{keyword}.obo')
obo_cache_path = os.path.join(directory, f... | def belns(keyword: str, file: TextIO, encoding: Optional[str], use_names: bool):
"""Write as a BEL namespace."""
directory = get_data_dir(keyword)
obo_url = f'http://purl.obolibrary.org/obo/{keyword}.obo'
obo_path = os.path.join(directory, f'{keyword}.obo')
obo_cache_path = os.path.join(directory, f... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/obo.py#L67-L81 | [
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valid | belanno | Write as a BEL annotation. | src/bio2bel/obo.py | def belanno(keyword: str, file: TextIO):
"""Write as a BEL annotation."""
directory = get_data_dir(keyword)
obo_url = f'http://purl.obolibrary.org/obo/{keyword}.obo'
obo_path = os.path.join(directory, f'{keyword}.obo')
obo_cache_path = os.path.join(directory, f'{keyword}.obo.pickle')
obo_getter... | def belanno(keyword: str, file: TextIO):
"""Write as a BEL annotation."""
directory = get_data_dir(keyword)
obo_url = f'http://purl.obolibrary.org/obo/{keyword}.obo'
obo_path = os.path.join(directory, f'{keyword}.obo')
obo_cache_path = os.path.join(directory, f'{keyword}.obo.pickle')
obo_getter... | [
"Write",
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/obo.py#L87-L99 | [
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | _store_helper | Help store an action. | src/bio2bel/models.py | def _store_helper(model: Action, session: Optional[Session] = None) -> None:
"""Help store an action."""
if session is None:
session = _make_session()
session.add(model)
session.commit()
session.close() | def _store_helper(model: Action, session: Optional[Session] = None) -> None:
"""Help store an action."""
if session is None:
session = _make_session()
session.add(model)
session.commit()
session.close() | [
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | _make_session | Make a session. | src/bio2bel/models.py | def _make_session(connection: Optional[str] = None) -> Session:
"""Make a session."""
if connection is None:
connection = get_global_connection()
engine = create_engine(connection)
create_all(engine)
session_cls = sessionmaker(bind=engine)
session = session_cls()
return session | def _make_session(connection: Optional[str] = None) -> Session:
"""Make a session."""
if connection is None:
connection = get_global_connection()
engine = create_engine(connection)
create_all(engine)
session_cls = sessionmaker(bind=engine)
session = session_cls()
return session | [
"Make",
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valid | create_all | Create the tables for Bio2BEL. | src/bio2bel/models.py | def create_all(engine, checkfirst=True):
"""Create the tables for Bio2BEL."""
Base.metadata.create_all(bind=engine, checkfirst=checkfirst) | def create_all(engine, checkfirst=True):
"""Create the tables for Bio2BEL."""
Base.metadata.create_all(bind=engine, checkfirst=checkfirst) | [
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] | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | Action.store_populate | Store a "populate" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_populate('hgnc') | src/bio2bel/models.py | def store_populate(cls, resource: str, session: Optional[Session] = None) -> 'Action':
"""Store a "populate" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_populate('hgnc')
"""
... | def store_populate(cls, resource: str, session: Optional[Session] = None) -> 'Action':
"""Store a "populate" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_populate('hgnc')
"""
... | [
"Store",
"a",
"populate",
"event",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/models.py#L69-L81 | [
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valid | Action.store_populate_failed | Store a "populate failed" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_populate_failed('hgnc') | src/bio2bel/models.py | def store_populate_failed(cls, resource: str, session: Optional[Session] = None) -> 'Action':
"""Store a "populate failed" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_populate_failed('hgnc... | def store_populate_failed(cls, resource: str, session: Optional[Session] = None) -> 'Action':
"""Store a "populate failed" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_populate_failed('hgnc... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/models.py#L84-L96 | [
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valid | Action.store_drop | Store a "drop" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_drop('hgnc') | src/bio2bel/models.py | def store_drop(cls, resource: str, session: Optional[Session] = None) -> 'Action':
"""Store a "drop" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_drop('hgnc')
"""
action = c... | def store_drop(cls, resource: str, session: Optional[Session] = None) -> 'Action':
"""Store a "drop" event.
:param resource: The normalized name of the resource to store
Example:
>>> from bio2bel.models import Action
>>> Action.store_drop('hgnc')
"""
action = c... | [
"Store",
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/models.py#L99-L111 | [
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valid | Action.ls | Get all actions. | src/bio2bel/models.py | def ls(cls, session: Optional[Session] = None) -> List['Action']:
"""Get all actions."""
if session is None:
session = _make_session()
actions = session.query(cls).order_by(cls.created.desc()).all()
session.close()
return actions | def ls(cls, session: Optional[Session] = None) -> List['Action']:
"""Get all actions."""
if session is None:
session = _make_session()
actions = session.query(cls).order_by(cls.created.desc()).all()
session.close()
return actions | [
"Get",
"all",
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | Action.count | Count all actions. | src/bio2bel/models.py | def count(cls, session: Optional[Session] = None) -> int:
"""Count all actions."""
if session is None:
session = _make_session()
count = session.query(cls).count()
session.close()
return count | def count(cls, session: Optional[Session] = None) -> int:
"""Count all actions."""
if session is None:
session = _make_session()
count = session.query(cls).count()
session.close()
return count | [
"Count",
"all",
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"."
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valid | get_data_dir | Ensure the appropriate Bio2BEL data directory exists for the given module, then returns the file path.
:param module_name: The name of the module. Ex: 'chembl'
:return: The module's data directory | src/bio2bel/utils.py | def get_data_dir(module_name: str) -> str:
"""Ensure the appropriate Bio2BEL data directory exists for the given module, then returns the file path.
:param module_name: The name of the module. Ex: 'chembl'
:return: The module's data directory
"""
module_name = module_name.lower()
data_dir = os.... | def get_data_dir(module_name: str) -> str:
"""Ensure the appropriate Bio2BEL data directory exists for the given module, then returns the file path.
:param module_name: The name of the module. Ex: 'chembl'
:return: The module's data directory
"""
module_name = module_name.lower()
data_dir = os.... | [
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | get_module_config_cls | Build a module configuration class. | src/bio2bel/utils.py | def get_module_config_cls(module_name: str) -> Type[_AbstractModuleConfig]: # noqa: D202
"""Build a module configuration class."""
class ModuleConfig(_AbstractModuleConfig):
NAME = f'bio2bel:{module_name}'
FILES = DEFAULT_CONFIG_PATHS + [
os.path.join(DEFAULT_CONFIG_DIRECTORY, modu... | def get_module_config_cls(module_name: str) -> Type[_AbstractModuleConfig]: # noqa: D202
"""Build a module configuration class."""
class ModuleConfig(_AbstractModuleConfig):
NAME = f'bio2bel:{module_name}'
FILES = DEFAULT_CONFIG_PATHS + [
os.path.join(DEFAULT_CONFIG_DIRECTORY, modu... | [
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valid | get_connection | Return the SQLAlchemy connection string if it is set.
Order of operations:
1. Return the connection if given as a parameter
2. Check the environment for BIO2BEL_{module_name}_CONNECTION
3. Look in the bio2bel config file for module-specific connection. Create if doesn't exist. Check the
module-... | src/bio2bel/utils.py | def get_connection(module_name: str, connection: Optional[str] = None) -> str:
"""Return the SQLAlchemy connection string if it is set.
Order of operations:
1. Return the connection if given as a parameter
2. Check the environment for BIO2BEL_{module_name}_CONNECTION
3. Look in the bio2bel config ... | def get_connection(module_name: str, connection: Optional[str] = None) -> str:
"""Return the SQLAlchemy connection string if it is set.
Order of operations:
1. Return the connection if given as a parameter
2. Check the environment for BIO2BEL_{module_name}_CONNECTION
3. Look in the bio2bel config ... | [
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valid | get_modules | Get all Bio2BEL modules. | src/bio2bel/utils.py | def get_modules() -> Mapping:
"""Get all Bio2BEL modules."""
modules = {}
for entry_point in iter_entry_points(group='bio2bel', name=None):
entry = entry_point.name
try:
modules[entry] = entry_point.load()
except VersionConflict as exc:
log.warning('Version ... | def get_modules() -> Mapping:
"""Get all Bio2BEL modules."""
modules = {}
for entry_point in iter_entry_points(group='bio2bel', name=None):
entry = entry_point.name
try:
modules[entry] = entry_point.load()
except VersionConflict as exc:
log.warning('Version ... | [
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valid | clear_cache | Clear all downloaded files. | src/bio2bel/utils.py | def clear_cache(module_name: str, keep_database: bool = True) -> None:
"""Clear all downloaded files."""
data_dir = get_data_dir(module_name)
if not os.path.exists(data_dir):
return
for name in os.listdir(data_dir):
if name in {'config.ini', 'cfg.ini'}:
continue
if na... | def clear_cache(module_name: str, keep_database: bool = True) -> None:
"""Clear all downloaded files."""
data_dir = get_data_dir(module_name)
if not os.path.exists(data_dir):
return
for name in os.listdir(data_dir):
if name in {'config.ini', 'cfg.ini'}:
continue
if na... | [
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valid | add_cli_populate | Add a ``populate`` command to main :mod:`click` function. | src/bio2bel/manager/abstract_manager.py | def add_cli_populate(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``populate`` command to main :mod:`click` function."""
@main.command()
@click.option('--reset', is_flag=True, help='Nuke database first')
@click.option('--force', is_flag=True, help='Force overwrite if already populated')
... | def add_cli_populate(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``populate`` command to main :mod:`click` function."""
@main.command()
@click.option('--reset', is_flag=True, help='Nuke database first')
@click.option('--force', is_flag=True, help='Force overwrite if already populated')
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valid | add_cli_drop | Add a ``drop`` command to main :mod:`click` function. | src/bio2bel/manager/abstract_manager.py | def add_cli_drop(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``drop`` command to main :mod:`click` function."""
@main.command()
@click.confirmation_option(prompt='Are you sure you want to drop the db?')
@click.pass_obj
def drop(manager):
"""Drop the database."""
manage... | def add_cli_drop(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``drop`` command to main :mod:`click` function."""
@main.command()
@click.confirmation_option(prompt='Are you sure you want to drop the db?')
@click.pass_obj
def drop(manager):
"""Drop the database."""
manage... | [
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"'Are you sure you want to drop the db?'... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | add_cli_cache | Add several commands to main :mod:`click` function for handling the cache. | src/bio2bel/manager/abstract_manager.py | def add_cli_cache(main: click.Group) -> click.Group: # noqa: D202
"""Add several commands to main :mod:`click` function for handling the cache."""
@main.group()
def cache():
"""Manage cached data."""
@cache.command()
@click.pass_obj
def locate(manager):
"""Print the location o... | def add_cli_cache(main: click.Group) -> click.Group: # noqa: D202
"""Add several commands to main :mod:`click` function for handling the cache."""
@main.group()
def cache():
"""Manage cached data."""
@cache.command()
@click.pass_obj
def locate(manager):
"""Print the location o... | [
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valid | add_cli_summarize | Add a ``summarize`` command to main :mod:`click` function. | src/bio2bel/manager/abstract_manager.py | def add_cli_summarize(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``summarize`` command to main :mod:`click` function."""
@main.command()
@click.pass_obj
def summarize(manager: AbstractManager):
"""Summarize the contents of the database."""
if not manager.is_populated():
... | def add_cli_summarize(main: click.Group) -> click.Group: # noqa: D202
"""Add a ``summarize`` command to main :mod:`click` function."""
@main.command()
@click.pass_obj
def summarize(manager: AbstractManager):
"""Summarize the contents of the database."""
if not manager.is_populated():
... | [
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valid | AbstractManager.create_all | Create the empty database (tables).
:param bool check_first: Defaults to True, don't issue CREATEs for tables already present
in the target database. Defers to :meth:`sqlalchemy.sql.schema.MetaData.create_all` | src/bio2bel/manager/abstract_manager.py | def create_all(self, check_first: bool = True):
"""Create the empty database (tables).
:param bool check_first: Defaults to True, don't issue CREATEs for tables already present
in the target database. Defers to :meth:`sqlalchemy.sql.schema.MetaData.create_all`
"""
self._metadat... | def create_all(self, check_first: bool = True):
"""Create the empty database (tables).
:param bool check_first: Defaults to True, don't issue CREATEs for tables already present
in the target database. Defers to :meth:`sqlalchemy.sql.schema.MetaData.create_all`
"""
self._metadat... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/abstract_manager.py#L229-L235 | [
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valid | AbstractManager.drop_all | Drop all tables from the database.
:param bool check_first: Defaults to True, only issue DROPs for tables confirmed to be
present in the target database. Defers to :meth:`sqlalchemy.sql.schema.MetaData.drop_all` | src/bio2bel/manager/abstract_manager.py | def drop_all(self, check_first: bool = True):
"""Drop all tables from the database.
:param bool check_first: Defaults to True, only issue DROPs for tables confirmed to be
present in the target database. Defers to :meth:`sqlalchemy.sql.schema.MetaData.drop_all`
"""
self._metada... | def drop_all(self, check_first: bool = True):
"""Drop all tables from the database.
:param bool check_first: Defaults to True, only issue DROPs for tables confirmed to be
present in the target database. Defers to :meth:`sqlalchemy.sql.schema.MetaData.drop_all`
"""
self._metada... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/abstract_manager.py#L237-L244 | [
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valid | AbstractManager.get_cli | Get the :mod:`click` main function to use as a command line interface. | src/bio2bel/manager/abstract_manager.py | def get_cli(cls) -> click.Group:
"""Get the :mod:`click` main function to use as a command line interface."""
main = super().get_cli()
cls._cli_add_populate(main)
cls._cli_add_drop(main)
cls._cli_add_cache(main)
cls._cli_add_summarize(main)
return main | def get_cli(cls) -> click.Group:
"""Get the :mod:`click` main function to use as a command line interface."""
main = super().get_cli()
cls._cli_add_populate(main)
cls._cli_add_drop(main)
cls._cli_add_cache(main)
cls._cli_add_summarize(main)
return main | [
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valid | label | Provide a label for a list of labels.
The items in the list of labels are assumed to be either instances of
:class:`Label`, or dicts with at least the key `label` in them. These will
be passed to the :func:`dict_to_label` function.
This method tries to find a label by looking if there's
a pref lab... | skosprovider/skos.py | def label(labels=[], language='any', sortLabel=False):
'''
Provide a label for a list of labels.
The items in the list of labels are assumed to be either instances of
:class:`Label`, or dicts with at least the key `label` in them. These will
be passed to the :func:`dict_to_label` function.
Thi... | def label(labels=[], language='any', sortLabel=False):
'''
Provide a label for a list of labels.
The items in the list of labels are assumed to be either instances of
:class:`Label`, or dicts with at least the key `label` in them. These will
be passed to the :func:`dict_to_label` function.
Thi... | [
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valid | find_best_label_for_type | Find the best label for a certain labeltype.
:param list labels: A list of :class:`Label`.
:param str language: An IANA language string, eg. `nl` or `nl-BE`.
:param str labeltype: Type of label to look for, eg. `prefLabel`. | skosprovider/skos.py | def find_best_label_for_type(labels, language, labeltype):
'''
Find the best label for a certain labeltype.
:param list labels: A list of :class:`Label`.
:param str language: An IANA language string, eg. `nl` or `nl-BE`.
:param str labeltype: Type of label to look for, eg. `prefLabel`.
'''
... | def find_best_label_for_type(labels, language, labeltype):
'''
Find the best label for a certain labeltype.
:param list labels: A list of :class:`Label`.
:param str language: An IANA language string, eg. `nl` or `nl-BE`.
:param str labeltype: Type of label to look for, eg. `prefLabel`.
'''
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valid | filter_labels_by_language | Filter a list of labels, leaving only labels of a certain language.
:param list labels: A list of :class:`Label`.
:param str language: An IANA language string, eg. `nl` or `nl-BE`.
:param boolean broader: When true, will also match `nl-BE` when filtering
on `nl`. When false, only exact matches are ... | skosprovider/skos.py | def filter_labels_by_language(labels, language, broader=False):
'''
Filter a list of labels, leaving only labels of a certain language.
:param list labels: A list of :class:`Label`.
:param str language: An IANA language string, eg. `nl` or `nl-BE`.
:param boolean broader: When true, will also match... | def filter_labels_by_language(labels, language, broader=False):
'''
Filter a list of labels, leaving only labels of a certain language.
:param list labels: A list of :class:`Label`.
:param str language: An IANA language string, eg. `nl` or `nl-BE`.
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valid | dict_to_label | Transform a dict with keys `label`, `type` and `language` into a
:class:`Label`.
Only the `label` key is mandatory. If `type` is not present, it will
default to `prefLabel`. If `language` is not present, it will default
to `und`.
If the argument passed is not a dict, this method just
returns t... | skosprovider/skos.py | def dict_to_label(dict):
'''
Transform a dict with keys `label`, `type` and `language` into a
:class:`Label`.
Only the `label` key is mandatory. If `type` is not present, it will
default to `prefLabel`. If `language` is not present, it will default
to `und`.
If the argument passed is not a... | def dict_to_label(dict):
'''
Transform a dict with keys `label`, `type` and `language` into a
:class:`Label`.
Only the `label` key is mandatory. If `type` is not present, it will
default to `prefLabel`. If `language` is not present, it will default
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"'language'",
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"'und'",
")",
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"ex... | 7304a37953978ca8227febc2d3cc2b2be178f215 |
valid | dict_to_note | Transform a dict with keys `note`, `type` and `language` into a
:class:`Note`.
Only the `note` key is mandatory. If `type` is not present, it will
default to `note`. If `language` is not present, it will default to `und`.
If `markup` is not present it will default to `None`.
If the argument passed... | skosprovider/skos.py | def dict_to_note(dict):
'''
Transform a dict with keys `note`, `type` and `language` into a
:class:`Note`.
Only the `note` key is mandatory. If `type` is not present, it will
default to `note`. If `language` is not present, it will default to `und`.
If `markup` is not present it will default to... | def dict_to_note(dict):
'''
Transform a dict with keys `note`, `type` and `language` into a
:class:`Note`.
Only the `note` key is mandatory. If `type` is not present, it will
default to `note`. If `language` is not present, it will default to `und`.
If `markup` is not present it will default to... | [
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"Note",
"."
] | koenedaele/skosprovider | python | https://github.com/koenedaele/skosprovider/blob/7304a37953978ca8227febc2d3cc2b2be178f215/skosprovider/skos.py#L596-L615 | [
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".",... | 7304a37953978ca8227febc2d3cc2b2be178f215 |
valid | dict_to_source | Transform a dict with key 'citation' into a :class:`Source`.
If the argument passed is already a :class:`Source`, this method just
returns the argument. | skosprovider/skos.py | def dict_to_source(dict):
'''
Transform a dict with key 'citation' into a :class:`Source`.
If the argument passed is already a :class:`Source`, this method just
returns the argument.
'''
if isinstance(dict, Source):
return dict
return Source(
dict['citation'],
dict.... | def dict_to_source(dict):
'''
Transform a dict with key 'citation' into a :class:`Source`.
If the argument passed is already a :class:`Source`, this method just
returns the argument.
'''
if isinstance(dict, Source):
return dict
return Source(
dict['citation'],
dict.... | [
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"."
] | koenedaele/skosprovider | python | https://github.com/koenedaele/skosprovider/blob/7304a37953978ca8227febc2d3cc2b2be178f215/skosprovider/skos.py#L618-L631 | [
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")",
")"
] | 7304a37953978ca8227febc2d3cc2b2be178f215 |
valid | ConceptScheme._sortkey | Provide a single sortkey for this conceptscheme.
:param string key: Either `uri`, `label` or `sortlabel`.
:param string language: The preferred language to receive the label in
if key is `label` or `sortlabel`. This should be a valid IANA language tag.
:rtype: :class:`str` | skosprovider/skos.py | def _sortkey(self, key='uri', language='any'):
'''
Provide a single sortkey for this conceptscheme.
:param string key: Either `uri`, `label` or `sortlabel`.
:param string language: The preferred language to receive the label in
if key is `label` or `sortlabel`. This should b... | def _sortkey(self, key='uri', language='any'):
'''
Provide a single sortkey for this conceptscheme.
:param string key: Either `uri`, `label` or `sortlabel`.
:param string language: The preferred language to receive the label in
if key is `label` or `sortlabel`. This should b... | [
"Provide",
"a",
"single",
"sortkey",
"for",
"this",
"conceptscheme",
"."
] | koenedaele/skosprovider | python | https://github.com/koenedaele/skosprovider/blob/7304a37953978ca8227febc2d3cc2b2be178f215/skosprovider/skos.py#L249-L262 | [
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valid | _iterate_managers | Iterate over instantiated managers. | src/bio2bel/cli.py | def _iterate_managers(connection, skip):
"""Iterate over instantiated managers."""
for idx, name, manager_cls in _iterate_manage_classes(skip):
if name in skip:
continue
try:
manager = manager_cls(connection=connection)
except TypeError as e:
click.se... | def _iterate_managers(connection, skip):
"""Iterate over instantiated managers."""
for idx, name, manager_cls in _iterate_manage_classes(skip):
if name in skip:
continue
try:
manager = manager_cls(connection=connection)
except TypeError as e:
click.se... | [
"Iterate",
"over",
"instantiated",
"managers",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L45-L56 | [
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"manager_c... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | populate | Populate all. | src/bio2bel/cli.py | def populate(connection, reset, force, skip):
"""Populate all."""
for idx, name, manager in _iterate_managers(connection, skip):
click.echo(
click.style(f'[{idx}/{len(MANAGERS)}] ', fg='blue', bold=True) +
click.style(f'populating {name}', fg='cyan', bold=True)
)
... | def populate(connection, reset, force, skip):
"""Populate all."""
for idx, name, manager in _iterate_managers(connection, skip):
click.echo(
click.style(f'[{idx}/{len(MANAGERS)}] ', fg='blue', bold=True) +
click.style(f'populating {name}', fg='cyan', bold=True)
)
... | [
"Populate",
"all",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L71-L93 | [
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | drop | Drop all. | src/bio2bel/cli.py | def drop(connection, skip):
"""Drop all."""
for idx, name, manager in _iterate_managers(connection, skip):
click.secho(f'dropping {name}', fg='cyan', bold=True)
manager.drop_all() | def drop(connection, skip):
"""Drop all."""
for idx, name, manager in _iterate_managers(connection, skip):
click.secho(f'dropping {name}', fg='cyan', bold=True)
manager.drop_all() | [
"Drop",
"all",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L100-L104 | [
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",",
"fg",
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"'cyan'",
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"b... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | clear | Clear all caches. | src/bio2bel/cli.py | def clear(skip):
"""Clear all caches."""
for name in sorted(MODULES):
if name in skip:
continue
click.secho(f'clearing cache for {name}', fg='cyan', bold=True)
clear_cache(name) | def clear(skip):
"""Clear all caches."""
for name in sorted(MODULES):
if name in skip:
continue
click.secho(f'clearing cache for {name}', fg='cyan', bold=True)
clear_cache(name) | [
"Clear",
"all",
"caches",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L114-L120 | [
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"True",... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | summarize | Summarize all. | src/bio2bel/cli.py | def summarize(connection, skip):
"""Summarize all."""
for idx, name, manager in _iterate_managers(connection, skip):
click.secho(name, fg='cyan', bold=True)
if not manager.is_populated():
click.echo('👎 unpopulated')
continue
if isinstance(manager, BELNamespaceMa... | def summarize(connection, skip):
"""Summarize all."""
for idx, name, manager in _iterate_managers(connection, skip):
click.secho(name, fg='cyan', bold=True)
if not manager.is_populated():
click.echo('👎 unpopulated')
continue
if isinstance(manager, BELNamespaceMa... | [
"Summarize",
"all",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L126-L145 | [
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"... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | sheet | Generate a summary sheet. | src/bio2bel/cli.py | def sheet(connection, skip, file: TextIO):
"""Generate a summary sheet."""
from tabulate import tabulate
header = ['', 'Name', 'Description', 'Terms', 'Relations']
rows = []
for i, (idx, name, manager) in enumerate(_iterate_managers(connection, skip), start=1):
try:
if not manag... | def sheet(connection, skip, file: TextIO):
"""Generate a summary sheet."""
from tabulate import tabulate
header = ['', 'Name', 'Description', 'Terms', 'Relations']
rows = []
for i, (idx, name, manager) in enumerate(_iterate_managers(connection, skip), start=1):
try:
if not manag... | [
"Generate",
"a",
"summary",
"sheet",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L152-L182 | [
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"]",
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"]... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | write | Write a BEL namespace names/identifiers to terminology store. | src/bio2bel/cli.py | def write(connection, skip, directory, force):
"""Write a BEL namespace names/identifiers to terminology store."""
os.makedirs(directory, exist_ok=True)
from .manager.namespace_manager import BELNamespaceManagerMixin
for idx, name, manager in _iterate_managers(connection, skip):
if not (isinstan... | def write(connection, skip, directory, force):
"""Write a BEL namespace names/identifiers to terminology store."""
os.makedirs(directory, exist_ok=True)
from .manager.namespace_manager import BELNamespaceManagerMixin
for idx, name, manager in _iterate_managers(connection, skip):
if not (isinstan... | [
"Write",
"a",
"BEL",
"namespace",
"names",
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"identifiers",
"to",
"terminology",
"store",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L196-L222 | [
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"for... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | write | Write all as BEL. | src/bio2bel/cli.py | def write(connection, skip, directory, force):
"""Write all as BEL."""
os.makedirs(directory, exist_ok=True)
from .manager.bel_manager import BELManagerMixin
import pybel
for idx, name, manager in _iterate_managers(connection, skip):
if not isinstance(manager, BELManagerMixin):
c... | def write(connection, skip, directory, force):
"""Write all as BEL."""
os.makedirs(directory, exist_ok=True)
from .manager.bel_manager import BELManagerMixin
import pybel
for idx, name, manager in _iterate_managers(connection, skip):
if not isinstance(manager, BELManagerMixin):
c... | [
"Write",
"all",
"as",
"BEL",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L236-L255 | [
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"import",
"pybel"... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | web | Run a combine web interface. | src/bio2bel/cli.py | def web(connection, host, port):
"""Run a combine web interface."""
from bio2bel.web.application import create_application
app = create_application(connection=connection)
app.run(host=host, port=port) | def web(connection, host, port):
"""Run a combine web interface."""
from bio2bel.web.application import create_application
app = create_application(connection=connection)
app.run(host=host, port=port) | [
"Run",
"a",
"combine",
"web",
"interface",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L262-L266 | [
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"ho... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | actions | List all actions. | src/bio2bel/cli.py | def actions(connection):
"""List all actions."""
session = _make_session(connection=connection)
for action in Action.ls(session=session):
click.echo(f'{action.created} {action.action} {action.resource}') | def actions(connection):
"""List all actions."""
session = _make_session(connection=connection)
for action in Action.ls(session=session):
click.echo(f'{action.created} {action.action} {action.resource}') | [
"List",
"all",
"actions",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/cli.py#L271-L275 | [
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"f'{action.created} ... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | add_cli_to_bel | Add several command to main :mod:`click` function related to export to BEL. | src/bio2bel/manager/bel_manager.py | def add_cli_to_bel(main: click.Group) -> click.Group: # noqa: D202
"""Add several command to main :mod:`click` function related to export to BEL."""
@main.command()
@click.option('-o', '--output', type=click.File('w'), default=sys.stdout)
@click.option('-f', '--fmt', default='bel', show_default=True, ... | def add_cli_to_bel(main: click.Group) -> click.Group: # noqa: D202
"""Add several command to main :mod:`click` function related to export to BEL."""
@main.command()
@click.option('-o', '--output', type=click.File('w'), default=sys.stdout)
@click.option('-f', '--fmt', default='bel', show_default=True, ... | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/bel_manager.py#L128-L141 | [
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".... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | add_cli_upload_bel | Add several command to main :mod:`click` function related to export to BEL. | src/bio2bel/manager/bel_manager.py | def add_cli_upload_bel(main: click.Group) -> click.Group: # noqa: D202
"""Add several command to main :mod:`click` function related to export to BEL."""
@main.command()
@host_option
@click.pass_obj
def upload(manager: BELManagerMixin, host: str):
"""Upload BEL to BEL Commons."""
gr... | def add_cli_upload_bel(main: click.Group) -> click.Group: # noqa: D202
"""Add several command to main :mod:`click` function related to export to BEL."""
@main.command()
@host_option
@click.pass_obj
def upload(manager: BELManagerMixin, host: str):
"""Upload BEL to BEL Commons."""
gr... | [
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"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/bel_manager.py#L144-L155 | [
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... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | BELManagerMixin.count_relations | Count the number of BEL relations generated. | src/bio2bel/manager/bel_manager.py | def count_relations(self) -> int:
"""Count the number of BEL relations generated."""
if self.edge_model is ...:
raise Bio2BELMissingEdgeModelError('edge_edge model is undefined/count_bel_relations is not overridden')
elif isinstance(self.edge_model, list):
return sum(self... | def count_relations(self) -> int:
"""Count the number of BEL relations generated."""
if self.edge_model is ...:
raise Bio2BELMissingEdgeModelError('edge_edge model is undefined/count_bel_relations is not overridden')
elif isinstance(self.edge_model, list):
return sum(self... | [
"Count",
"the",
"number",
"of",
"BEL",
"relations",
"generated",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/bel_manager.py#L51-L58 | [
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"self",... | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | BELManagerMixin.to_indra_statements | Dump as a list of INDRA statements.
:rtype: List[indra.Statement] | src/bio2bel/manager/bel_manager.py | def to_indra_statements(self, *args, **kwargs):
"""Dump as a list of INDRA statements.
:rtype: List[indra.Statement]
"""
graph = self.to_bel(*args, **kwargs)
return to_indra_statements(graph) | def to_indra_statements(self, *args, **kwargs):
"""Dump as a list of INDRA statements.
:rtype: List[indra.Statement]
"""
graph = self.to_bel(*args, **kwargs)
return to_indra_statements(graph) | [
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"statements",
"."
] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/bel_manager.py#L95-L101 | [
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] | d80762d891fa18b248709ff0b0f97ebb65ec64c2 |
valid | BELManagerMixin.get_cli | Get a :mod:`click` main function with added BEL commands. | src/bio2bel/manager/bel_manager.py | def get_cli(cls) -> click.Group:
"""Get a :mod:`click` main function with added BEL commands."""
main = super().get_cli()
@main.group()
def bel():
"""Manage BEL."""
cls._cli_add_to_bel(bel)
cls._cli_add_upload_bel(bel)
return main | def get_cli(cls) -> click.Group:
"""Get a :mod:`click` main function with added BEL commands."""
main = super().get_cli()
@main.group()
def bel():
"""Manage BEL."""
cls._cli_add_to_bel(bel)
cls._cli_add_upload_bel(bel)
return main | [
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] | bio2bel/bio2bel | python | https://github.com/bio2bel/bio2bel/blob/d80762d891fa18b248709ff0b0f97ebb65ec64c2/src/bio2bel/manager/bel_manager.py#L114-L125 | [
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valid | exebench | benchorg.jpg is
'http://upload.wikimedia.org/wikipedia/commons/d/df/SAND_LUE.jpg' | benchmark/imagescale_benchmark.py | def exebench(width):
"""
benchorg.jpg is
'http://upload.wikimedia.org/wikipedia/commons/d/df/SAND_LUE.jpg'
"""
height = width * 2 / 3
with Benchmarker(width=30, loop=N) as bm:
for i in bm('kaa.imlib2'):
imlib2_scale('benchorg.jpg', width, height)
for i in bm("PIL"):
... | def exebench(width):
"""
benchorg.jpg is
'http://upload.wikimedia.org/wikipedia/commons/d/df/SAND_LUE.jpg'
"""
height = width * 2 / 3
with Benchmarker(width=30, loop=N) as bm:
for i in bm('kaa.imlib2'):
imlib2_scale('benchorg.jpg', width, height)
for i in bm("PIL"):
... | [
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valid | _convert_coordinatelist | convert from 'list' or 'tuple' object to pgmagick.CoordinateList.
:type input_obj: list or tuple | pgmagick/api.py | def _convert_coordinatelist(input_obj):
"""convert from 'list' or 'tuple' object to pgmagick.CoordinateList.
:type input_obj: list or tuple
"""
cdl = pgmagick.CoordinateList()
for obj in input_obj:
cdl.append(pgmagick.Coordinate(obj[0], obj[1]))
return cdl | def _convert_coordinatelist(input_obj):
"""convert from 'list' or 'tuple' object to pgmagick.CoordinateList.
:type input_obj: list or tuple
"""
cdl = pgmagick.CoordinateList()
for obj in input_obj:
cdl.append(pgmagick.Coordinate(obj[0], obj[1]))
return cdl | [
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] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L478-L486 | [
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valid | _convert_vpathlist | convert from 'list' or 'tuple' object to pgmagick.VPathList.
:type input_obj: list or tuple | pgmagick/api.py | def _convert_vpathlist(input_obj):
"""convert from 'list' or 'tuple' object to pgmagick.VPathList.
:type input_obj: list or tuple
"""
vpl = pgmagick.VPathList()
for obj in input_obj:
# FIXME
obj = pgmagick.PathMovetoAbs(pgmagick.Coordinate(obj[0], obj[1]))
vpl.append(obj)
... | def _convert_vpathlist(input_obj):
"""convert from 'list' or 'tuple' object to pgmagick.VPathList.
:type input_obj: list or tuple
"""
vpl = pgmagick.VPathList()
for obj in input_obj:
# FIXME
obj = pgmagick.PathMovetoAbs(pgmagick.Coordinate(obj[0], obj[1]))
vpl.append(obj)
... | [
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] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L500-L510 | [
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valid | Image.get_exif_info | return exif-tag dict | pgmagick/api.py | def get_exif_info(self):
"""return exif-tag dict
"""
_dict = {}
for tag in _EXIF_TAGS:
ret = self.img.attribute("EXIF:%s" % tag)
if ret and ret != 'unknown':
_dict[tag] = ret
return _dict | def get_exif_info(self):
"""return exif-tag dict
"""
_dict = {}
for tag in _EXIF_TAGS:
ret = self.img.attribute("EXIF:%s" % tag)
if ret and ret != 'unknown':
_dict[tag] = ret
return _dict | [
"return",
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"-",
"tag",
"dict"
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L733-L741 | [
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... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | Draw.bezier | Draw a Bezier-curve.
:param points: ex.) ((5, 5), (6, 6), (7, 7))
:type points: list | pgmagick/api.py | def bezier(self, points):
"""Draw a Bezier-curve.
:param points: ex.) ((5, 5), (6, 6), (7, 7))
:type points: list
"""
coordinates = pgmagick.CoordinateList()
for point in points:
x, y = float(point[0]), float(point[1])
coordinates.append(pgmagick.... | def bezier(self, points):
"""Draw a Bezier-curve.
:param points: ex.) ((5, 5), (6, 6), (7, 7))
:type points: list
"""
coordinates = pgmagick.CoordinateList()
for point in points:
x, y = float(point[0]), float(point[1])
coordinates.append(pgmagick.... | [
"Draw",
"a",
"Bezier",
"-",
"curve",
"."
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L761-L771 | [
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valid | Draw.color | :param paint_method: 'point' or 'replace' or 'floodfill' or
'filltoborder' or 'reset'
:type paint_method: str or pgmagick.PaintMethod | pgmagick/api.py | def color(self, x, y, paint_method):
"""
:param paint_method: 'point' or 'replace' or 'floodfill' or
'filltoborder' or 'reset'
:type paint_method: str or pgmagick.PaintMethod
"""
paint_method = _convert_paintmethod(paint_method)
color = pgmagi... | def color(self, x, y, paint_method):
"""
:param paint_method: 'point' or 'replace' or 'floodfill' or
'filltoborder' or 'reset'
:type paint_method: str or pgmagick.PaintMethod
"""
paint_method = _convert_paintmethod(paint_method)
color = pgmagi... | [
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"... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | Draw.ellipse | :param org_x: origination x axis
:param org_y: origination y axis
:param radius_x: radius x axis
:param radius_y: radius y axis
:param arc_start: arc start angle
:param arc_end: arc end angle | pgmagick/api.py | def ellipse(self, org_x, org_y, radius_x, radius_y, arc_start, arc_end):
"""
:param org_x: origination x axis
:param org_y: origination y axis
:param radius_x: radius x axis
:param radius_y: radius y axis
:param arc_start: arc start angle
:param arc_end: arc end a... | def ellipse(self, org_x, org_y, radius_x, radius_y, arc_start, arc_end):
"""
:param org_x: origination x axis
:param org_y: origination y axis
:param radius_x: radius x axis
:param radius_y: radius y axis
:param arc_start: arc start angle
:param arc_end: arc end a... | [
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valid | Draw.fill_opacity | :param opacity: 0.0 ~ 1.0 | pgmagick/api.py | def fill_opacity(self, opacity):
"""
:param opacity: 0.0 ~ 1.0
"""
opacity = pgmagick.DrawableFillOpacity(float(opacity))
self.drawer.append(opacity) | def fill_opacity(self, opacity):
"""
:param opacity: 0.0 ~ 1.0
"""
opacity = pgmagick.DrawableFillOpacity(float(opacity))
self.drawer.append(opacity) | [
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valid | Draw.matte | :param paint_method: 'point' or 'replace' or 'floodfill' or
'filltoborder' or 'reset'
:type paint_method: str or pgmagick.PaintMethod | pgmagick/api.py | def matte(self, x, y, paint_method):
"""
:param paint_method: 'point' or 'replace' or 'floodfill' or
'filltoborder' or 'reset'
:type paint_method: str or pgmagick.PaintMethod
"""
paint_method = _convert_paintmethod(paint_method)
self.drawer.ap... | def matte(self, x, y, paint_method):
"""
:param paint_method: 'point' or 'replace' or 'floodfill' or
'filltoborder' or 'reset'
:type paint_method: str or pgmagick.PaintMethod
"""
paint_method = _convert_paintmethod(paint_method)
self.drawer.ap... | [
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valid | Draw.scaling | Scaling Draw Object
:param x: 0.0 ~ 1.0
:param y: 0.0 ~ 1.0 | pgmagick/api.py | def scaling(self, x, y):
"""Scaling Draw Object
:param x: 0.0 ~ 1.0
:param y: 0.0 ~ 1.0
"""
self.drawer.append(pgmagick.DrawableScaling(float(x), float(y))) | def scaling(self, x, y):
"""Scaling Draw Object
:param x: 0.0 ~ 1.0
:param y: 0.0 ~ 1.0
"""
self.drawer.append(pgmagick.DrawableScaling(float(x), float(y))) | [
"Scaling",
"Draw",
"Object"
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L925-L931 | [
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valid | Draw.stroke_antialias | stroke antialias
:param flag: True or False. (default is True)
:type flag: bool | pgmagick/api.py | def stroke_antialias(self, flag=True):
"""stroke antialias
:param flag: True or False. (default is True)
:type flag: bool
"""
antialias = pgmagick.DrawableStrokeAntialias(flag)
self.drawer.append(antialias) | def stroke_antialias(self, flag=True):
"""stroke antialias
:param flag: True or False. (default is True)
:type flag: bool
"""
antialias = pgmagick.DrawableStrokeAntialias(flag)
self.drawer.append(antialias) | [
"stroke",
"antialias"
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L939-L946 | [
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valid | Draw.stroke_linecap | set to stroke linecap.
:param linecap: 'undefined', 'butt', 'round', 'square'
:type linecap: str | pgmagick/api.py | def stroke_linecap(self, linecap):
"""set to stroke linecap.
:param linecap: 'undefined', 'butt', 'round', 'square'
:type linecap: str
"""
linecap = getattr(pgmagick.LineCap, "%sCap" % linecap.title())
linecap = pgmagick.DrawableStrokeLineCap(linecap)
self.drawer... | def stroke_linecap(self, linecap):
"""set to stroke linecap.
:param linecap: 'undefined', 'butt', 'round', 'square'
:type linecap: str
"""
linecap = getattr(pgmagick.LineCap, "%sCap" % linecap.title())
linecap = pgmagick.DrawableStrokeLineCap(linecap)
self.drawer... | [
"set",
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"linec... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | Draw.stroke_linejoin | set to stroke linejoin.
:param linejoin: 'undefined', 'miter', 'round', 'bevel'
:type linejoin: str | pgmagick/api.py | def stroke_linejoin(self, linejoin):
"""set to stroke linejoin.
:param linejoin: 'undefined', 'miter', 'round', 'bevel'
:type linejoin: str
"""
linejoin = getattr(pgmagick.LineJoin, "%sJoin" % linejoin.title())
linejoin = pgmagick.DrawableStrokeLineJoin(linejoin)
... | def stroke_linejoin(self, linejoin):
"""set to stroke linejoin.
:param linejoin: 'undefined', 'miter', 'round', 'bevel'
:type linejoin: str
"""
linejoin = getattr(pgmagick.LineJoin, "%sJoin" % linejoin.title())
linejoin = pgmagick.DrawableStrokeLineJoin(linejoin)
... | [
"set",
"to",
"stroke",
"linejoin",
"."
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L963-L971 | [
"def",
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"=",
"pgmagick",
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"DrawableStrokeLineJoin",
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... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | Draw.text_antialias | text antialias
:param flag: True or False. (default is True)
:type flag: bool | pgmagick/api.py | def text_antialias(self, flag=True):
"""text antialias
:param flag: True or False. (default is True)
:type flag: bool
"""
antialias = pgmagick.DrawableTextAntialias(flag)
self.drawer.append(antialias) | def text_antialias(self, flag=True):
"""text antialias
:param flag: True or False. (default is True)
:type flag: bool
"""
antialias = pgmagick.DrawableTextAntialias(flag)
self.drawer.append(antialias) | [
"text",
"antialias"
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L986-L993 | [
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"drawer",
".",
"append",
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"antialias",
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] | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | Draw.text_decoration | text decoration
:param decoration: 'no', 'underline', 'overline', 'linethrough'
:type decoration: str | pgmagick/api.py | def text_decoration(self, decoration):
"""text decoration
:param decoration: 'no', 'underline', 'overline', 'linethrough'
:type decoration: str
"""
if decoration.lower() == 'linethrough':
d = pgmagick.DecorationType.LineThroughDecoration
else:
dec... | def text_decoration(self, decoration):
"""text decoration
:param decoration: 'no', 'underline', 'overline', 'linethrough'
:type decoration: str
"""
if decoration.lower() == 'linethrough':
d = pgmagick.DecorationType.LineThroughDecoration
else:
dec... | [
"text",
"decoration"
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/pgmagick/api.py#L995-L1007 | [
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"... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | get_version_from_pc | similar to 'pkg-config --modversion GraphicsMagick++ | setup.py | def get_version_from_pc(search_dirs, target):
"""similar to 'pkg-config --modversion GraphicsMagick++'"""
for dirname in search_dirs:
for root, dirs, files in os.walk(dirname):
for f in files:
if f == target:
file_path = os.path.join(root, target)
... | def get_version_from_pc(search_dirs, target):
"""similar to 'pkg-config --modversion GraphicsMagick++'"""
for dirname in search_dirs:
for root, dirs, files in os.walk(dirname):
for f in files:
if f == target:
file_path = os.path.join(root, target)
... | [
"similar",
"to",
"pkg",
"-",
"config",
"--",
"modversion",
"GraphicsMagick",
"++"
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/setup.py#L79-L89 | [
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... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | library_supports_api | Returns whether api_version is supported by given library version.
E. g. library_version (1,3,21) returns True for api_version (1,3,21), (1,3,19), (1,3,'x'), (1,2,'x'), (1, 'x')
False for (1,3,24), (1,4,'x'), (2,'x')
different_major_breaks_support - if enabled and library and api major versions are... | setup.py | def library_supports_api(library_version, api_version, different_major_breaks_support=True):
"""
Returns whether api_version is supported by given library version.
E. g. library_version (1,3,21) returns True for api_version (1,3,21), (1,3,19), (1,3,'x'), (1,2,'x'), (1, 'x')
False for (1,3,24), (... | def library_supports_api(library_version, api_version, different_major_breaks_support=True):
"""
Returns whether api_version is supported by given library version.
E. g. library_version (1,3,21) returns True for api_version (1,3,21), (1,3,19), (1,3,'x'), (1,2,'x'), (1, 'x')
False for (1,3,24), (... | [
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... | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/setup.py#L106-L122 | [
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"ass... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | version | Return version string. | setup.py | def version():
"""Return version string."""
with io.open('pgmagick/_version.py') as input_file:
for line in input_file:
if line.startswith('__version__'):
return ast.parse(line).body[0].value.s | def version():
"""Return version string."""
with io.open('pgmagick/_version.py') as input_file:
for line in input_file:
if line.startswith('__version__'):
return ast.parse(line).body[0].value.s | [
"Return",
"version",
"string",
"."
] | hhatto/pgmagick | python | https://github.com/hhatto/pgmagick/blob/5dce5fa4681400b4c059431ad69233e6a3e5799a/setup.py#L202-L207 | [
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"parse... | 5dce5fa4681400b4c059431ad69233e6a3e5799a |
valid | post_license_request | Submission to create a license acceptance request. | cnxpublishing/views/user_actions.py | def post_license_request(request):
"""Submission to create a license acceptance request."""
uuid_ = request.matchdict['uuid']
posted_data = request.json
license_url = posted_data.get('license_url')
licensors = posted_data.get('licensors', [])
with db_connect() as db_conn:
with db_conn.c... | def post_license_request(request):
"""Submission to create a license acceptance request."""
uuid_ = request.matchdict['uuid']
posted_data = request.json
license_url = posted_data.get('license_url')
licensors = posted_data.get('licensors', [])
with db_connect() as db_conn:
with db_conn.c... | [
"Submission",
"to",
"create",
"a",
"license",
"acceptance",
"request",
"."
] | openstax/cnx-publishing | python | https://github.com/openstax/cnx-publishing/blob/f55b4a2c45d8618737288f1b74b4139d5ac74154/cnxpublishing/views/user_actions.py#L77-L120 | [
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"license_url",
"=",
"posted_data",
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"get",
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"'license_url'",
")",
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"=",
"p... | f55b4a2c45d8618737288f1b74b4139d5ac74154 |
valid | delete_license_request | Submission to remove a license acceptance request. | cnxpublishing/views/user_actions.py | def delete_license_request(request):
"""Submission to remove a license acceptance request."""
uuid_ = request.matchdict['uuid']
posted_uids = [x['uid'] for x in request.json.get('licensors', [])]
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
remove_license_requests(... | def delete_license_request(request):
"""Submission to remove a license acceptance request."""
uuid_ = request.matchdict['uuid']
posted_uids = [x['uid'] for x in request.json.get('licensors', [])]
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
remove_license_requests(... | [
"Submission",
"to",
"remove",
"a",
"license",
"acceptance",
"request",
"."
] | openstax/cnx-publishing | python | https://github.com/openstax/cnx-publishing/blob/f55b4a2c45d8618737288f1b74b4139d5ac74154/cnxpublishing/views/user_actions.py#L126-L137 | [
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"[... | f55b4a2c45d8618737288f1b74b4139d5ac74154 |
valid | get_roles_request | Returns a list of accepting roles. | cnxpublishing/views/user_actions.py | def get_roles_request(request):
"""Returns a list of accepting roles."""
uuid_ = request.matchdict['uuid']
user_id = request.matchdict.get('uid')
args = [uuid_]
if user_id is not None:
fmt_conditional = "AND user_id = %s"
args.append(user_id)
else:
fmt_conditional = ""
... | def get_roles_request(request):
"""Returns a list of accepting roles."""
uuid_ = request.matchdict['uuid']
user_id = request.matchdict.get('uid')
args = [uuid_]
if user_id is not None:
fmt_conditional = "AND user_id = %s"
args.append(user_id)
else:
fmt_conditional = ""
... | [
"Returns",
"a",
"list",
"of",
"accepting",
"roles",
"."
] | openstax/cnx-publishing | python | https://github.com/openstax/cnx-publishing/blob/f55b4a2c45d8618737288f1b74b4139d5ac74154/cnxpublishing/views/user_actions.py#L143-L180 | [
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"not... | f55b4a2c45d8618737288f1b74b4139d5ac74154 |
valid | post_roles_request | Submission to create a role acceptance request. | cnxpublishing/views/user_actions.py | def post_roles_request(request):
"""Submission to create a role acceptance request."""
uuid_ = request.matchdict['uuid']
posted_roles = request.json
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute("""\
SELECT TRUE FROM document_controls WHERE uuid = %s:... | def post_roles_request(request):
"""Submission to create a role acceptance request."""
uuid_ = request.matchdict['uuid']
posted_roles = request.json
with db_connect() as db_conn:
with db_conn.cursor() as cursor:
cursor.execute("""\
SELECT TRUE FROM document_controls WHERE uuid = %s:... | [
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"role",
"acceptance",
"request",
"."
] | openstax/cnx-publishing | python | https://github.com/openstax/cnx-publishing/blob/f55b4a2c45d8618737288f1b74b4139d5ac74154/cnxpublishing/views/user_actions.py#L186-L212 | [
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... | f55b4a2c45d8618737288f1b74b4139d5ac74154 |
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