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OpenTreeOfLife/peyotl | peyotl/nexson_syntax/helper.py | _add_uniq_value_to_dict_bf | def _add_uniq_value_to_dict_bf(d, k, v):
"""Like _add_value_to_dict_bf but will not add v if another
element in under key `k` has the same value.
"""
prev = d.get(k)
if prev is None:
d[k] = v
elif isinstance(prev, list):
if not isinstance(v, list):
v = [v]
for... | python | def _add_uniq_value_to_dict_bf(d, k, v):
"""Like _add_value_to_dict_bf but will not add v if another
element in under key `k` has the same value.
"""
prev = d.get(k)
if prev is None:
d[k] = v
elif isinstance(prev, list):
if not isinstance(v, list):
v = [v]
for... | [
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OpenTreeOfLife/peyotl | peyotl/nexson_syntax/helper.py | _debug_dump_dom | def _debug_dump_dom(el):
"""Debugging helper. Prints out `el` contents."""
import xml.dom.minidom
s = [el.nodeName]
att_container = el.attributes
for i in range(att_container.length):
attr = att_container.item(i)
s.append(' @{a}="{v}"'.format(a=attr.name, v=attr.value))
for c in... | python | def _debug_dump_dom(el):
"""Debugging helper. Prints out `el` contents."""
import xml.dom.minidom
s = [el.nodeName]
att_container = el.attributes
for i in range(att_container.length):
attr = att_container.item(i)
s.append(' @{a}="{v}"'.format(a=attr.name, v=attr.value))
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OpenTreeOfLife/peyotl | peyotl/nexson_syntax/helper.py | _convert_hbf_meta_val_for_xml | def _convert_hbf_meta_val_for_xml(key, val):
"""Convert to a BadgerFish-style dict for addition to a dict suitable for
addition to XML tree or for v1.0 to v0.0 conversion."""
if isinstance(val, list):
return [_convert_hbf_meta_val_for_xml(key, i) for i in val]
is_literal = True
content = Non... | python | def _convert_hbf_meta_val_for_xml(key, val):
"""Convert to a BadgerFish-style dict for addition to a dict suitable for
addition to XML tree or for v1.0 to v0.0 conversion."""
if isinstance(val, list):
return [_convert_hbf_meta_val_for_xml(key, i) for i in val]
is_literal = True
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OpenTreeOfLife/peyotl | peyotl/nexson_syntax/helper.py | find_nested_meta_first | def find_nested_meta_first(d, prop_name, version):
"""Returns obj. for badgerfish and val for hbf. Appropriate for nested literals"""
if _is_badgerfish_version(version):
return find_nested_meta_first_bf(d, prop_name)
p = '^' + prop_name
return d.get(p) | python | def find_nested_meta_first(d, prop_name, version):
"""Returns obj. for badgerfish and val for hbf. Appropriate for nested literals"""
if _is_badgerfish_version(version):
return find_nested_meta_first_bf(d, prop_name)
p = '^' + prop_name
return d.get(p) | [
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PSPC-SPAC-buyandsell/von_agent | von_agent/codec.py | decode | def decode(value: str) -> Union[str, None, bool, int, float]:
"""
Decode encoded credential attribute value.
:param value: numeric string to decode
:return: decoded value, stringified if original was neither str, bool, int, nor float
"""
assert value.isdigit() or value[0] == '-' and value[1:].... | python | def decode(value: str) -> Union[str, None, bool, int, float]:
"""
Decode encoded credential attribute value.
:param value: numeric string to decode
:return: decoded value, stringified if original was neither str, bool, int, nor float
"""
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palantir/typedjsonrpc | typedjsonrpc/parameter_checker.py | validate_params_match | def validate_params_match(method, parameters):
"""Validates that the given parameters are exactly the method's declared parameters.
:param method: The method to be called
:type method: function
:param parameters: The parameters to use in the call
:type parameters: dict[str, object] | list[object]
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"""Validates that the given parameters are exactly the method's declared parameters.
:param method: The method to be called
:type method: function
:param parameters: The parameters to use in the call
:type parameters: dict[str, object] | list[object]
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palantir/typedjsonrpc | typedjsonrpc/parameter_checker.py | check_types | def check_types(parameters, parameter_types, strict_floats):
"""Checks that the given parameters have the correct types.
:param parameters: List of (name, value) pairs of the given parameters
:type parameters: dict[str, object]
:param parameter_types: Parameter type by name.
:type parameter_types: ... | python | def check_types(parameters, parameter_types, strict_floats):
"""Checks that the given parameters have the correct types.
:param parameters: List of (name, value) pairs of the given parameters
:type parameters: dict[str, object]
:param parameter_types: Parameter type by name.
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palantir/typedjsonrpc | typedjsonrpc/parameter_checker.py | check_type_declaration | def check_type_declaration(parameter_names, parameter_types):
"""Checks that exactly the given parameter names have declared types.
:param parameter_names: The names of the parameters in the method declaration
:type parameter_names: list[str]
:param parameter_types: Parameter type by name
:type par... | python | def check_type_declaration(parameter_names, parameter_types):
"""Checks that exactly the given parameter names have declared types.
:param parameter_names: The names of the parameters in the method declaration
:type parameter_names: list[str]
:param parameter_types: Parameter type by name
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palantir/typedjsonrpc | typedjsonrpc/parameter_checker.py | check_return_type | def check_return_type(value, expected_type, strict_floats):
"""Checks that the given return value has the correct type.
:param value: Value returned by the method
:type value: object
:param expected_type: Expected return type
:type expected_type: type
:param strict_floats: If False, treat integ... | python | def check_return_type(value, expected_type, strict_floats):
"""Checks that the given return value has the correct type.
:param value: Value returned by the method
:type value: object
:param expected_type: Expected return type
:type expected_type: type
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OpenTreeOfLife/peyotl | peyotl/phylesystem/helper.py | _make_phylesystem_cache_region | def _make_phylesystem_cache_region(**kwargs):
"""Only intended to be called by the Phylesystem singleton.
"""
global _CACHE_REGION_CONFIGURED, _REGION
if _CACHE_REGION_CONFIGURED:
return _REGION
_CACHE_REGION_CONFIGURED = True
try:
# noinspection PyPackageRequirements
fro... | python | def _make_phylesystem_cache_region(**kwargs):
"""Only intended to be called by the Phylesystem singleton.
"""
global _CACHE_REGION_CONFIGURED, _REGION
if _CACHE_REGION_CONFIGURED:
return _REGION
_CACHE_REGION_CONFIGURED = True
try:
# noinspection PyPackageRequirements
fro... | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.path_for_doc | def path_for_doc(self, doc_id):
"""Returns doc_dir and doc_filepath for doc_id.
"""
full_path = self.path_for_doc_fn(self.repo, doc_id)
# _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc_fn: {}'.format(self.path_for_doc_fn))
# _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc re... | python | def path_for_doc(self, doc_id):
"""Returns doc_dir and doc_filepath for doc_id.
"""
full_path = self.path_for_doc_fn(self.repo, doc_id)
# _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc_fn: {}'.format(self.path_for_doc_fn))
# _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc re... | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.current_branch | def current_branch(self):
"""Return the current branch name"""
branch_name = git(self.gitdir, self.gitwd, "symbolic-ref", "HEAD")
return branch_name.replace('refs/heads/', '').strip() | python | def current_branch(self):
"""Return the current branch name"""
branch_name = git(self.gitdir, self.gitwd, "symbolic-ref", "HEAD")
return branch_name.replace('refs/heads/', '').strip() | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.branch_exists | def branch_exists(self, branch):
"""Returns true or false depending on if a branch exists"""
try:
git(self.gitdir, self.gitwd, "rev-parse", branch)
except sh.ErrorReturnCode:
return False
return True | python | def branch_exists(self, branch):
"""Returns true or false depending on if a branch exists"""
try:
git(self.gitdir, self.gitwd, "rev-parse", branch)
except sh.ErrorReturnCode:
return False
return True | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.fetch | def fetch(self, remote='origin'):
"""fetch from a remote"""
git(self.gitdir, "fetch", remote, _env=self.env()) | python | def fetch(self, remote='origin'):
"""fetch from a remote"""
git(self.gitdir, "fetch", remote, _env=self.env()) | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.get_version_history_for_file | def get_version_history_for_file(self, filepath):
""" Return a dict representation of this file's commit history
This uses specially formatted git-log output for easy parsing, as described here:
http://blog.lost-theory.org/post/how-to-parse-git-log-output/
For a full list of availab... | python | def get_version_history_for_file(self, filepath):
""" Return a dict representation of this file's commit history
This uses specially formatted git-log output for easy parsing, as described here:
http://blog.lost-theory.org/post/how-to-parse-git-log-output/
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase._add_and_commit | def _add_and_commit(self, doc_filepath, author, commit_msg):
"""Low level function used internally when you have an absolute filepath to add and commit"""
try:
git(self.gitdir, self.gitwd, "add", doc_filepath)
git(self.gitdir, self.gitwd, "commit", author=author, message=commit_m... | python | def _add_and_commit(self, doc_filepath, author, commit_msg):
"""Low level function used internally when you have an absolute filepath to add and commit"""
try:
git(self.gitdir, self.gitwd, "add", doc_filepath)
git(self.gitdir, self.gitwd, "commit", author=author, message=commit_m... | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase._remove_document | def _remove_document(self, gh_user, doc_id, parent_sha, author, commit_msg=None):
"""Remove a document
Remove a document on the given branch and attribute the commit to author.
Returns the SHA of the commit on branch.
"""
# _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc... | python | def _remove_document(self, gh_user, doc_id, parent_sha, author, commit_msg=None):
"""Remove a document
Remove a document on the given branch and attribute the commit to author.
Returns the SHA of the commit on branch.
"""
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.write_document | def write_document(self, gh_user, doc_id, file_content, branch, author, commit_msg=None):
"""Given a document id, temporary filename of content, branch and auth_info
Deprecated but needed until we merge api local-dep to master...
"""
parent_sha = None
fc = tempfile.NamedTempora... | python | def write_document(self, gh_user, doc_id, file_content, branch, author, commit_msg=None):
"""Given a document id, temporary filename of content, branch and auth_info
Deprecated but needed until we merge api local-dep to master...
"""
parent_sha = None
fc = tempfile.NamedTempora... | [
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OpenTreeOfLife/peyotl | peyotl/git_storage/git_action.py | GitActionBase.write_doc_from_tmpfile | def write_doc_from_tmpfile(self,
doc_id,
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OpenTreeOfLife/peyotl | peyotl/amendments/git_actions.py | TaxonomicAmendmentsGitAction.remove_amendment | def remove_amendment(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None):
"""Remove an amendment
Given a amendment_id, branch and optionally an
author, remove an amendment on the given branch
and attribute the commit to author.
Returns the SHA of the commit on ... | python | def remove_amendment(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None):
"""Remove an amendment
Given a amendment_id, branch and optionally an
author, remove an amendment on the given branch
and attribute the commit to author.
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inveniosoftware/invenio-communities | invenio_communities/models.py | InclusionRequest.create | def create(cls, community, record, user=None, expires_at=None,
notify=True):
"""Create a record inclusion request to a community.
:param community: Community object.
:param record: Record API object.
:param expires_at: Time after which the request expires and shouldn't
... | python | def create(cls, community, record, user=None, expires_at=None,
notify=True):
"""Create a record inclusion request to a community.
:param community: Community object.
:param record: Record API object.
:param expires_at: Time after which the request expires and shouldn't
... | [
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inveniosoftware/invenio-communities | invenio_communities/models.py | InclusionRequest.get | def get(cls, community_id, record_uuid):
"""Get an inclusion request."""
return cls.query.filter_by(
id_record=record_uuid, id_community=community_id
).one_or_none() | python | def get(cls, community_id, record_uuid):
"""Get an inclusion request."""
return cls.query.filter_by(
id_record=record_uuid, id_community=community_id
).one_or_none() | [
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.filter_communities | def filter_communities(cls, p, so, with_deleted=False):
"""Search for communities.
Helper function which takes from database only those communities which
match search criteria. Uses parameter 'so' to set communities in the
correct order.
Parameter 'page' is introduced to restri... | python | def filter_communities(cls, p, so, with_deleted=False):
"""Search for communities.
Helper function which takes from database only those communities which
match search criteria. Uses parameter 'so' to set communities in the
correct order.
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.add_record | def add_record(self, record):
"""Add a record to the community.
:param record: Record object.
:type record: `invenio_records.api.Record`
"""
key = current_app.config['COMMUNITIES_RECORD_KEY']
record.setdefault(key, [])
if self.has_record(record):
cur... | python | def add_record(self, record):
"""Add a record to the community.
:param record: Record object.
:type record: `invenio_records.api.Record`
"""
key = current_app.config['COMMUNITIES_RECORD_KEY']
record.setdefault(key, [])
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.remove_record | def remove_record(self, record):
"""Remove an already accepted record from the community.
:param record: Record object.
:type record: `invenio_records.api.Record`
"""
if not self.has_record(record):
current_app.logger.warning(
'Community removal: reco... | python | def remove_record(self, record):
"""Remove an already accepted record from the community.
:param record: Record object.
:type record: `invenio_records.api.Record`
"""
if not self.has_record(record):
current_app.logger.warning(
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.accept_record | def accept_record(self, record):
"""Accept a record for inclusion in the community.
:param record: Record object.
"""
with db.session.begin_nested():
req = InclusionRequest.get(self.id, record.id)
if req is None:
raise InclusionRequestMissingError... | python | def accept_record(self, record):
"""Accept a record for inclusion in the community.
:param record: Record object.
"""
with db.session.begin_nested():
req = InclusionRequest.get(self.id, record.id)
if req is None:
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.reject_record | def reject_record(self, record):
"""Reject a record for inclusion in the community.
:param record: Record object.
"""
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req = InclusionRequest.get(self.id, record.id)
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"""Reject a record for inclusion in the community.
:param record: Record object.
"""
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.delete | def delete(self):
"""Mark the community for deletion.
:param delete_time: DateTime after which to delete the community.
:type delete_time: datetime.datetime
:raises: CommunitiesError
"""
if self.deleted_at is not None:
raise CommunitiesError(community=self)
... | python | def delete(self):
"""Mark the community for deletion.
:param delete_time: DateTime after which to delete the community.
:type delete_time: datetime.datetime
:raises: CommunitiesError
"""
if self.deleted_at is not None:
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.logo_url | def logo_url(self):
"""Get URL to collection logo.
:returns: Path to community logo.
:rtype: str
"""
if self.logo_ext:
return '/api/files/{bucket}/{key}'.format(
bucket=current_app.config['COMMUNITIES_BUCKET_UUID'],
key='{0}/logo.{1}'.... | python | def logo_url(self):
"""Get URL to collection logo.
:returns: Path to community logo.
:rtype: str
"""
if self.logo_ext:
return '/api/files/{bucket}/{key}'.format(
bucket=current_app.config['COMMUNITIES_BUCKET_UUID'],
key='{0}/logo.{1}'.... | [
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.oaiset | def oaiset(self):
"""Return the corresponding OAISet for given community.
If OAIServer is not installed this property will return None.
:returns: returns OAISet object corresponding to this community.
:rtype: `invenio_oaiserver.models.OAISet` or None
"""
if current_app.... | python | def oaiset(self):
"""Return the corresponding OAISet for given community.
If OAIServer is not installed this property will return None.
:returns: returns OAISet object corresponding to this community.
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.oaiset_url | def oaiset_url(self):
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:rtype: str
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:returns: URL of corresponding OAISet.
:rtype: str
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inveniosoftware/invenio-communities | invenio_communities/models.py | Community.version_id | def version_id(self):
"""Return the version of the community.
:returns: hash which encodes the community id and its las update.
:rtype: str
"""
return hashlib.sha1('{0}__{1}'.format(
self.id, self.updated).encode('utf-8')).hexdigest() | python | def version_id(self):
"""Return the version of the community.
:returns: hash which encodes the community id and its las update.
:rtype: str
"""
return hashlib.sha1('{0}__{1}'.format(
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inveniosoftware/invenio-communities | invenio_communities/models.py | FeaturedCommunity.get_featured_or_none | def get_featured_or_none(cls, start_date=None):
"""Get the latest featured community.
:param start_date: Date after which the featuring starts
:returns: Community object or None
:rtype: `invenio_communities.models.Community` or None
"""
start_date = start_date or datetim... | python | def get_featured_or_none(cls, start_date=None):
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ARMmbed/mbed-connector-api-python | mbed_connector_api/mbed_connector_api.py | connector.getConnectorVersion | def getConnectorVersion(self):
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"""
GET the current Connector version.
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'''
Register a handler for a particular notification type.
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_doc_parser.py | JSGDocParser.as_python | def as_python(self, infile, include_original_shex: bool=False):
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emirozer/bowshock | bowshock/modis.py | __getDummyDateList | def __getDummyDateList():
"""
Generate a dummy date list for testing without
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"""
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return D | python | def __getDummyDateList():
"""
Generate a dummy date list for testing without
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CybOXProject/mixbox | mixbox/idgen.py | IDGenerator.create_id | def create_id(self, prefix="guid"):
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yamins81/tabular | tabular/spreadsheet.py | grayspec | def grayspec(k):
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List of gray-scale colors in HSV space as web hex triplets.
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List of gray-scale colors in HSV space as web hex triplets.
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Rename column of a numpy ndarray with structured dtype, in-place.
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yamins81/tabular | tabular/spreadsheet.py | replace | def replace(X, old, new, strict=True, cols=None, rows=None):
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Implemented by the tabarray method
:func:`tabular.tab.tabarray.replace`.
**Parameters**
**X** : numpy ndarray with structured dtype
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yamins81/tabular | tabular/spreadsheet.py | rowstack | def rowstack(seq, mode='nulls', nullvals=None):
'''
Vertically stack a sequence of numpy ndarrays with structured dtype
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Implemented by the tabarray method
:func:`tabular.tab.tabarray.rowstack` which uses
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... | python | def rowstack(seq, mode='nulls', nullvals=None):
'''
Vertically stack a sequence of numpy ndarrays with structured dtype
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yamins81/tabular | tabular/spreadsheet.py | colstack | def colstack(seq, mode='abort',returnnaming=False):
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yamins81/tabular | tabular/spreadsheet.py | DEFAULT_RENAMER | def DEFAULT_RENAMER(L, Names=None):
"""
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* If `L` is a list, it will append the number in the list to the key
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emirozer/bowshock | bowshock/helioviewer.py | getjp2image | def getjp2image(date,
sourceId=None,
observatory=None,
instrument=None,
detector=None,
measurement=None):
'''
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sourceId=None,
observatory=None,
instrument=None,
detector=None,
measurement=None):
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Download a JP2 image for the specified datasource that is the closest match in time to the `date` requested.
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hsolbrig/pyjsg | pyjsg/jsglib/loader.py | loads_loader | def loads_loader(load_module: types.ModuleType, pairs: Dict[str, str]) -> Optional[JSGValidateable]:
"""json loader objecthook
:param load_module: Module that contains the various types
:param pairs: key/value tuples (In our case, they are str/str)
:return:
"""
cntxt = load_module._CONTEXT
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:param pairs: key/value tuples (In our case, they are str/str)
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hsolbrig/pyjsg | pyjsg/jsglib/loader.py | isinstance_ | def isinstance_(x, A_tuple):
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hsolbrig/pyjsg | pyjsg/jsglib/loader.py | is_valid | def is_valid(obj: JSGValidateable, log: Optional[Union[TextIO, Logger]] = None) -> bool:
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:param obj: Object to validate
:param log: Logger to record validation failures. If absent, no information is recorded
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return obj._is_valid(log) | python | def is_valid(obj: JSGValidateable, log: Optional[Union[TextIO, Logger]] = None) -> bool:
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cydrobolt/pifx | pifx/util.py | arg_tup_to_dict | def arg_tup_to_dict(argument_tuples):
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data = dict()
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cydrobolt/pifx | pifx/util.py | handle_error | def handle_error(response):
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status_code = response.status_code
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error_explanation = A_ERROR_HTTP_CODES.get(status_code)
raise_error = "{}: {}".format(status_code, error_explanation)
raise Exceptio... | python | def handle_error(response):
"""Raise appropriate exceptions if necessary."""
status_code = response.status_code
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PSPC-SPAC-buyandsell/von_agent | von_agent/agent/base.py | _BaseAgent.open | async def open(self) -> '_BaseAgent':
"""
Context manager entry; open wallet.
For use when keeping agent open across multiple calls.
:return: current object
"""
LOGGER.debug('_BaseAgent.open >>>')
# Do not open pool independently: let relying party decide when ... | python | async def open(self) -> '_BaseAgent':
"""
Context manager entry; open wallet.
For use when keeping agent open across multiple calls.
:return: current object
"""
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PSPC-SPAC-buyandsell/von_agent | von_agent/agent/base.py | _BaseAgent._get_rev_reg_def | async def _get_rev_reg_def(self, rr_id: str) -> str:
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Get revocation registry definition from ledger by its identifier. Raise AbsentRevReg
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Get revocation registry definition from ledger by its identifier. Raise AbsentRevReg
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hsolbrig/pyjsg | pyjsg/jsglib/typing_patch_37.py | is_union | def is_union(etype) -> bool:
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OpenTreeOfLife/peyotl | peyotl/collections_store/git_actions.py | TreeCollectionsGitAction.remove_collection | def remove_collection(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None):
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PSPC-SPAC-buyandsell/von_agent | von_agent/agent/verifier.py | Verifier.load_cache | async def load_cache(self, archive: bool = False) -> int:
"""
Load caches and archive enough to go offline and be able to verify proof
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Return timestamp (epoch seconds) of cache load event, also used as subdirectory
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inveniosoftware/invenio-communities | invenio_communities/permissions.py | _Permission.can | def can(self):
"""Grant permission if owner or admin."""
return str(current_user.get_id()) == str(self.community.id_user) or \
DynamicPermission(ActionNeed('admin-access')).can() | python | def can(self):
"""Grant permission if owner or admin."""
return str(current_user.get_id()) == str(self.community.id_user) or \
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yamins81/tabular | tabular/utils.py | listunion | def listunion(ListOfLists):
"""
Take the union of a list of lists.
Take a Python list of Python lists::
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"""
Take the union of a list of lists.
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yamins81/tabular | tabular/utils.py | DEFAULT_NULLVALUE | def DEFAULT_NULLVALUE(test):
"""
Returns a null value for each of various kinds of test values.
**Parameters**
**test** : bool, int, float or string
Value to test.
**Returns**
**null** : element in `[False, 0, 0.0, '']`
Null value c... | python | def DEFAULT_NULLVALUE(test):
"""
Returns a null value for each of various kinds of test values.
**Parameters**
**test** : bool, int, float or string
Value to test.
**Returns**
**null** : element in `[False, 0, 0.0, '']`
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_objectexpr_parser.py | JSGObjectExpr.as_python | def as_python(self, name: str) -> str:
""" Return the python representation of the class represented by this object """
if self._map_valuetype:
return self.map_as_python(name)
else:
return self.obj_as_python(name) | python | def as_python(self, name: str) -> str:
""" Return the python representation of the class represented by this object """
if self._map_valuetype:
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_objectexpr_parser.py | JSGObjectExpr.members_entries | def members_entries(self, all_are_optional: bool=False) -> List[Tuple[str, str]]:
""" Return an ordered list of elements for the _members section
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"""
rval = []
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""" Return an ordered list of elements for the _members section
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OpenTreeOfLife/peyotl | peyotl/phylesystem/phylesystem_shard.py | _get_filtered_study_ids | def _get_filtered_study_ids(shard, include_aliases=False):
"""Optionally filters out aliases from standard doc-id list"""
from peyotl.phylesystem.helper import DIGIT_PATTERN
k = shard.get_doc_ids()
if shard.has_aliases and (not include_aliases):
x = []
for i in k:
if DIGIT_PA... | python | def _get_filtered_study_ids(shard, include_aliases=False):
"""Optionally filters out aliases from standard doc-id list"""
from peyotl.phylesystem.helper import DIGIT_PATTERN
k = shard.get_doc_ids()
if shard.has_aliases and (not include_aliases):
x = []
for i in k:
if DIGIT_PA... | [
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OpenTreeOfLife/peyotl | peyotl/phylesystem/phylesystem_shard.py | PhylesystemShard._determine_next_study_id | def _determine_next_study_id(self):
"""Return the numeric part of the newest study_id
Checks out master branch as a side effect!
"""
if self._doc_counter_lock is None:
self._doc_counter_lock = Lock()
prefix = self._new_study_prefix
lp = len(prefix)
n ... | python | def _determine_next_study_id(self):
"""Return the numeric part of the newest study_id
Checks out master branch as a side effect!
"""
if self._doc_counter_lock is None:
self._doc_counter_lock = Lock()
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lp = len(prefix)
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OpenTreeOfLife/peyotl | peyotl/phylesystem/phylesystem_shard.py | PhylesystemShard._advance_new_study_id | def _advance_new_study_id(self):
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Returns the current numeric part of the next study ID, advances
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hsolbrig/pyjsg | pyjsg/parser_impl/parser_utils.py | flatten | def flatten(l: Iterable) -> List:
"""Return a list of all non-list items in l
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"""
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hsolbrig/pyjsg | pyjsg/parser_impl/parser_utils.py | flatten_unique | def flatten_unique(l: Iterable) -> List:
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""" Return a list of UNIQUE non-list items in l """
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hsolbrig/pyjsg | pyjsg/parser_impl/parser_utils.py | as_tokens | def as_tokens(ctx: List[ParserRuleContext]) -> List[str]:
"""Return a stringified list of identifiers in ctx
:param ctx: JSG parser item with a set of identifiers
:return:
"""
return [as_token(e) for e in ctx] | python | def as_tokens(ctx: List[ParserRuleContext]) -> List[str]:
"""Return a stringified list of identifiers in ctx
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:return:
"""
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hsolbrig/pyjsg | pyjsg/parser_impl/parser_utils.py | is_valid_python | def is_valid_python(tkn: str) -> bool:
"""Determine whether tkn is a valid python identifier
:param tkn:
:return:
"""
try:
root = ast.parse(tkn)
except SyntaxError:
return False
return len(root.body) == 1 and isinstance(root.body[0], ast.Expr) and isinstance(root.body[0].val... | python | def is_valid_python(tkn: str) -> bool:
"""Determine whether tkn is a valid python identifier
:param tkn:
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"""
try:
root = ast.parse(tkn)
except SyntaxError:
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OpenTreeOfLife/peyotl | peyotl/phylesystem/git_actions.py | PhylesystemGitAction.remove_study | def remove_study(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None):
"""Remove a study
Given a study_id, branch and optionally an
author, remove a study on the given branch
and attribute the commit to author.
Returns the SHA of the commit on branch.
""... | python | def remove_study(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None):
"""Remove a study
Given a study_id, branch and optionally an
author, remove a study on the given branch
and attribute the commit to author.
Returns the SHA of the commit on branch.
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inveniosoftware/invenio-communities | invenio_communities/cli.py | init | def init():
"""Initialize the communities file storage."""
try:
initialize_communities_bucket()
click.secho('Community init successful.', fg='green')
except FilesException as e:
click.secho(e.message, fg='red') | python | def init():
"""Initialize the communities file storage."""
try:
initialize_communities_bucket()
click.secho('Community init successful.', fg='green')
except FilesException as e:
click.secho(e.message, fg='red') | [
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inveniosoftware/invenio-communities | invenio_communities/cli.py | addlogo | def addlogo(community_id, logo):
"""Add logo to the community."""
# Create the bucket
c = Community.get(community_id)
if not c:
click.secho('Community {0} does not exist.'.format(community_id),
fg='red')
return
ext = save_and_validate_logo(logo, logo.name, c.id)
... | python | def addlogo(community_id, logo):
"""Add logo to the community."""
# Create the bucket
c = Community.get(community_id)
if not c:
click.secho('Community {0} does not exist.'.format(community_id),
fg='red')
return
ext = save_and_validate_logo(logo, logo.name, c.id)
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inveniosoftware/invenio-communities | invenio_communities/cli.py | request | def request(community_id, record_id, accept):
"""Request a record acceptance to a community."""
c = Community.get(community_id)
assert c is not None
record = Record.get_record(record_id)
if accept:
c.add_record(record)
record.commit()
else:
InclusionRequest.create(communi... | python | def request(community_id, record_id, accept):
"""Request a record acceptance to a community."""
c = Community.get(community_id)
assert c is not None
record = Record.get_record(record_id)
if accept:
c.add_record(record)
record.commit()
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inveniosoftware/invenio-communities | invenio_communities/cli.py | remove | def remove(community_id, record_id):
"""Remove a record from community."""
c = Community.get(community_id)
assert c is not None
c.remove_record(record_id)
db.session.commit()
RecordIndexer().index_by_id(record_id) | python | def remove(community_id, record_id):
"""Remove a record from community."""
c = Community.get(community_id)
assert c is not None
c.remove_record(record_id)
db.session.commit()
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OpenTreeOfLife/peyotl | peyotl/__init__.py | gen_otu_dict | def gen_otu_dict(nex_obj, nexson_version=None):
"""Takes a NexSON object and returns a dict of
otu_id -> otu_obj
"""
if nexson_version is None:
nexson_version = detect_nexson_version(nex_obj)
if _is_by_id_hbf(nexson_version):
otus = nex_obj['nexml']['otusById']
if len(otus) >... | python | def gen_otu_dict(nex_obj, nexson_version=None):
"""Takes a NexSON object and returns a dict of
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"""
if nexson_version is None:
nexson_version = detect_nexson_version(nex_obj)
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color/django-country | django_country/views.py | set_country | def set_country(request):
"""
Sets the chosen country in the session or cookie.
If `next' query param is present, it redirects to a given url.
"""
if request.method == 'POST':
next = request.POST.get('next', request.GET.get('next'))
if is_safe_url(url=next, host=request.get_host()):... | python | def set_country(request):
"""
Sets the chosen country in the session or cookie.
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"""
if request.method == 'POST':
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_doc_context.py | JSGDocContext.reference | def reference(self, tkn: str):
""" Return the element that tkn represents"""
return self.grammarelts[tkn] if tkn in self.grammarelts else UndefinedElement(tkn) | python | def reference(self, tkn: str):
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_doc_context.py | JSGDocContext.dependency_list | def dependency_list(self, tkn: str) -> List[str]:
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_doc_context.py | JSGDocContext.dependencies | def dependencies(self, tkn: str) -> Set[str]:
"""Return all the items that tkn depends on as a set
:param tkn:
:return:
"""
return set(self.dependency_list(tkn)) | python | def dependencies(self, tkn: str) -> Set[str]:
"""Return all the items that tkn depends on as a set
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hsolbrig/pyjsg | pyjsg/parser_impl/jsg_doc_context.py | JSGDocContext.undefined_entries | def undefined_entries(self) -> Set[str]:
""" Return the set of tokens that are referenced but not defined. """
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for k in self.grammarelts.keys()]) | python | def undefined_entries(self) -> Set[str]:
""" Return the set of tokens that are referenced but not defined. """
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inveniosoftware/invenio-communities | invenio_communities/receivers.py | new_request | def new_request(sender, request=None, notify=True, **kwargs):
"""New request for inclusion."""
if current_app.config['COMMUNITIES_MAIL_ENABLED'] and notify:
send_community_request_email(request) | python | def new_request(sender, request=None, notify=True, **kwargs):
"""New request for inclusion."""
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inveniosoftware/invenio-communities | invenio_communities/receivers.py | inject_provisional_community | def inject_provisional_community(sender, json=None, record=None, index=None,
**kwargs):
"""Inject 'provisional_communities' key to ES index."""
if index and not index.startswith(
current_app.config['COMMUNITIES_INDEX_PREFIX']):
return
json['provisional_c... | python | def inject_provisional_community(sender, json=None, record=None, index=None,
**kwargs):
"""Inject 'provisional_communities' key to ES index."""
if index and not index.startswith(
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OpenTreeOfLife/peyotl | peyotl/api/oti.py | _OTIWrapper.find_nodes | def find_nodes(self, query_dict=None, exact=False, verbose=False, **kwargs):
"""Query on node properties. See documentation for _OTIWrapper class."""
assert self.use_v1
return self._do_query('{p}/singlePropertySearchForTreeNodes'.format(p=self.query_prefix),
query_d... | python | def find_nodes(self, query_dict=None, exact=False, verbose=False, **kwargs):
"""Query on node properties. See documentation for _OTIWrapper class."""
assert self.use_v1
return self._do_query('{p}/singlePropertySearchForTreeNodes'.format(p=self.query_prefix),
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OpenTreeOfLife/peyotl | peyotl/api/oti.py | _OTIWrapper.find_trees | def find_trees(self, query_dict=None, exact=False, verbose=False, wrap_response=False, **kwargs):
"""Query on tree properties. See documentation for _OTIWrapper class."""
if self.use_v1:
uri = '{p}/singlePropertySearchForTrees'.format(p=self.query_prefix)
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uri = '{p}... | python | def find_trees(self, query_dict=None, exact=False, verbose=False, wrap_response=False, **kwargs):
"""Query on tree properties. See documentation for _OTIWrapper class."""
if self.use_v1:
uri = '{p}/singlePropertySearchForTrees'.format(p=self.query_prefix)
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OpenTreeOfLife/peyotl | peyotl/api/oti.py | _OTIWrapper.find_studies | def find_studies(self, query_dict=None, exact=False, verbose=False, **kwargs):
"""Query on study properties. See documentation for _OTIWrapper class."""
if self.use_v1:
uri = '{p}/singlePropertySearchForStudies'.format(p=self.query_prefix)
else:
uri = '{p}/find_studies'.f... | python | def find_studies(self, query_dict=None, exact=False, verbose=False, **kwargs):
"""Query on study properties. See documentation for _OTIWrapper class."""
if self.use_v1:
uri = '{p}/singlePropertySearchForStudies'.format(p=self.query_prefix)
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SpotlightData/preprocessing | setup.py | get_requirements | def get_requirements():
'''returns requirements array for package'''
packages = []
with open("requirements.txt", "r") as req_doc:
for package in req_doc:
packages.append(package.replace("\n", ""))
return packages | python | def get_requirements():
'''returns requirements array for package'''
packages = []
with open("requirements.txt", "r") as req_doc:
for package in req_doc:
packages.append(package.replace("\n", ""))
return packages | [
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OpenTreeOfLife/peyotl | peyotl/amendments/amendments_umbrella.py | TaxonomicAmendmentStore | def TaxonomicAmendmentStore(repos_dict=None,
repos_par=None,
with_caching=True,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=Taxo... | python | def TaxonomicAmendmentStore(repos_dict=None,
repos_par=None,
with_caching=True,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=Taxo... | [
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inveniosoftware/invenio-communities | invenio_communities/tasks.py | delete_marked_communities | def delete_marked_communities():
"""Delete communities after holdout time."""
# TODO: Delete the community ID from all records metadata first
raise NotImplementedError()
Community.query.filter_by(
Community.delete_time > datetime.utcnow()).delete()
db.session.commit() | python | def delete_marked_communities():
"""Delete communities after holdout time."""
# TODO: Delete the community ID from all records metadata first
raise NotImplementedError()
Community.query.filter_by(
Community.delete_time > datetime.utcnow()).delete()
db.session.commit() | [
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inveniosoftware/invenio-communities | invenio_communities/tasks.py | delete_expired_requests | def delete_expired_requests():
"""Delete expired inclusion requests."""
InclusionRequest.query.filter_by(
InclusionRequest.expiry_date > datetime.utcnow()).delete()
db.session.commit() | python | def delete_expired_requests():
"""Delete expired inclusion requests."""
InclusionRequest.query.filter_by(
InclusionRequest.expiry_date > datetime.utcnow()).delete()
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OpenTreeOfLife/peyotl | peyotl/nexson_syntax/__init__.py | create_content_spec | def create_content_spec(**kwargs):
"""Sugar. factory for a PhyloSchema object.
Repackages the kwargs to kwargs for PhyloSchema so that our
PhyloSchema.__init__ does not have to be soo rich
"""
format_str = kwargs.get('format', 'nexson')
nexson_version = kwargs.get('nexson_version', 'native')
... | python | def create_content_spec(**kwargs):
"""Sugar. factory for a PhyloSchema object.
Repackages the kwargs to kwargs for PhyloSchema so that our
PhyloSchema.__init__ does not have to be soo rich
"""
format_str = kwargs.get('format', 'nexson')
nexson_version = kwargs.get('nexson_version', 'native')
... | [
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OpenTreeOfLife/peyotl | peyotl/nexson_syntax/__init__.py | convert_nexson_format | def convert_nexson_format(blob,
out_nexson_format,
current_format=None,
remove_old_structs=True,
pristine_if_invalid=False,
sort_arbitrary=False):
"""Take a dict form of NexSON and conve... | python | def convert_nexson_format(blob,
out_nexson_format,
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pristine_if_invalid=False,
sort_arbitrary=False):
"""Take a dict form of NexSON and conve... | [
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