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value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | bowshock_logger | creates a logger obj | bowshock/helpers.py | def bowshock_logger():
'''creates a logger obj'''
FORMAT = '%(asctime)-15s %(message)s'
logging.basicConfig(format=FORMAT, level=logging.INFO)
logger = logging.getLogger('bowshock_logger')
return logger | def bowshock_logger():
'''creates a logger obj'''
FORMAT = '%(asctime)-15s %(message)s'
logging.basicConfig(format=FORMAT, level=logging.INFO)
logger = logging.getLogger('bowshock_logger')
return logger | [
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train | TreeCollectionsGitAction.remove_collection | Remove a collection
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and attribute the commit to author.
Returns the SHA of the commit on branch. | peyotl/collections_store/git_actions.py | def remove_collection(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None):
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train | TreeCollectionsGitAction.write_collection | Given a collection_id, temporary filename of content, branch and auth_info
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"""Given a collection_id, temporary filename of content, branch and auth_info
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"""
gh_user = branch.split('_collection_')[0]
msg = "Update Col... | def write_collection(self, collection_id, file_content, branch, author):
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train | TreeCollectionsGitAction.write_collection_from_tmpfile | Given a collection_id, temporary filename of content, branch and auth_info | peyotl/collections_store/git_actions.py | def write_collection_from_tmpfile(self, collection_id, tmpfi, parent_sha, auth_info, commit_msg=''):
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train | Verifier.load_cache | Load caches and archive enough to go offline and be able to verify proof
on content marked of interest in configuration.
Return timestamp (epoch seconds) of cache load event, also used as subdirectory
for cache archives.
:param archive: whether to archive caches to disk
:return... | von_agent/agent/verifier.py | async def load_cache(self, archive: bool = False) -> int:
"""
Load caches and archive enough to go offline and be able to verify proof
on content marked of interest in configuration.
Return timestamp (epoch seconds) of cache load event, also used as subdirectory
for cache archiv... | async def load_cache(self, archive: bool = False) -> int:
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Load caches and archive enough to go offline and be able to verify proof
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train | Verifier.open | Explicit entry. Perform ancestor opening operations,
then parse cache from archive if so configured, and
synchronize revocation registry to tails tree content.
:return: current object | von_agent/agent/verifier.py | async def open(self) -> 'HolderProver':
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Explicit entry. Perform ancestor opening operations,
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train | Verifier.close | Explicit exit. If so configured, populate cache to prove for any creds on schemata,
cred defs, and rev regs marked of interest in configuration at initialization,
archive cache, and purge prior cache archives.
:return: current object | von_agent/agent/verifier.py | async def close(self) -> None:
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Explicit exit. If so configured, populate cache to prove for any creds on schemata,
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archive cache, and purge prior cache archives.
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"""
Explicit exit. If so configured, populate cache to prove for any creds on schemata,
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train | Verifier.verify_proof | Verify proof as Verifier. Raise AbsentRevReg if a proof cites a revocation registry
that does not exist on the distributed ledger.
:param proof_req: proof request as Verifier creates, as per proof_req_json above
:param proof: proof as HolderProver creates
:return: json encoded True if p... | von_agent/agent/verifier.py | async def verify_proof(self, proof_req: dict, proof: dict) -> str:
"""
Verify proof as Verifier. Raise AbsentRevReg if a proof cites a revocation registry
that does not exist on the distributed ledger.
:param proof_req: proof request as Verifier creates, as per proof_req_json above
... | async def verify_proof(self, proof_req: dict, proof: dict) -> str:
"""
Verify proof as Verifier. Raise AbsentRevReg if a proof cites a revocation registry
that does not exist on the distributed ledger.
:param proof_req: proof request as Verifier creates, as per proof_req_json above
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train | _Permission.can | Grant permission if owner or admin. | invenio_communities/permissions.py | 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() | 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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train | tabular2html | Creates an html representation of tabular data, either from a tabarray or
an externa file (`including ``.hsv``, ``.csv``, ``.tsv``). If no data is
directly provided by passing a tabarray to `X`, then a tabarray is
constructed using :func:`tabular.tabarray.tabarray.__new__`.
**Parameters**
... | tabular/web.py | def tabular2html(fname=None, X=None, fin=None, title=None, printheader=False,
split=True, usecss=None, writecss=None, SERVERNAME=None,
SERVER_FROM_CURDIR='../', ROWS_PER_PAGE=1000,
returnstring = False, **kwargs):
"""
Creates an html representation of tabula... | def tabular2html(fname=None, X=None, fin=None, title=None, printheader=False,
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train | space_events | lat & lon expect decimal latitude and longitude values. (Required)
elevation assumes meters. (Optional)
limit assumes an integer. Default is 5. (Optional)
date expects an ISO 8601 formatted date. (Optional) | bowshock/predictthesky.py | def space_events(lon=None, lat=None, limit=None, date=None):
'''
lat & lon expect decimal latitude and longitude values. (Required)
elevation assumes meters. (Optional)
limit assumes an integer. Default is 5. (Optional)
date expects an ISO 8601 formatted date. (Optional)
'''
base_url =... | def space_events(lon=None, lat=None, limit=None, date=None):
'''
lat & lon expect decimal latitude and longitude values. (Required)
elevation assumes meters. (Optional)
limit assumes an integer. Default is 5. (Optional)
date expects an ISO 8601 formatted date. (Optional)
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train | listunion | Take the union of a list of lists.
Take a Python list of Python lists::
[[l11,l12, ...], [l21,l22, ...], ... , [ln1, ln2, ...]]
and return the aggregated list::
[l11,l12, ..., l21, l22 , ...]
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**... | tabular/utils.py | def listunion(ListOfLists):
"""
Take the union of a list of lists.
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train | perminverse | Fast inverse of a (numpy) permutation.
**Paramters**
**s** : sequence
Sequence of indices giving a permutation.
**Returns**
**inv** : numpy array
Sequence of indices giving the inverse of permutation `s`. | tabular/utils.py | def perminverse(s):
'''
Fast inverse of a (numpy) permutation.
**Paramters**
**s** : sequence
Sequence of indices giving a permutation.
**Returns**
**inv** : numpy array
Sequence of indices giving the inverse of permutation `s`.
... | def perminverse(s):
'''
Fast inverse of a (numpy) permutation.
**Paramters**
**s** : sequence
Sequence of indices giving a permutation.
**Returns**
**inv** : numpy array
Sequence of indices giving the inverse of permutation `s`.
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train | listarraytranspose | Tranposes the simple array presentation of a list of lists (of equal length).
Argument:
L = [row1, row2, ...., rowN]
where the rowi are python lists of equal length.
Returns:
LT, a list of python lists such that LT[j][i] = L[i][j]. | tabular/utils.py | def listarraytranspose(L):
'''
Tranposes the simple array presentation of a list of lists (of equal length).
Argument:
L = [row1, row2, ...., rowN]
where the rowi are python lists of equal length.
Returns:
LT, a list of python lists such that LT[j][i] = L[i][j].
'''
retur... | def listarraytranspose(L):
'''
Tranposes the simple array presentation of a list of lists (of equal length).
Argument:
L = [row1, row2, ...., rowN]
where the rowi are python lists of equal length.
Returns:
LT, a list of python lists such that LT[j][i] = L[i][j].
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Take a list of strings, and attempts to infer a numeric data type that fits
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If the strings are all integers, returns a NumPy array of integers.
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Returns a null value for each of various kinds of test values.
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**test** : bool, int, float or string
Value to test.
**Returns**
**null** : element in `[False, 0, 0.0, '']`
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train | JSGObjectExpr.as_python | Return the python representation of the class represented by this object | pyjsg/parser_impl/jsg_objectexpr_parser.py | 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:
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train | JSGObjectExpr.members_entries | Return an ordered list of elements for the _members section
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:return: | pyjsg/parser_impl/jsg_objectexpr_parser.py | 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 = []
if self._mem... | def members_entries(self, all_are_optional: bool=False) -> List[Tuple[str, str]]:
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train | JSGObjectExpr.visitObjectExpr | objectExpr: OBRACE membersDef? CBRACE
OBRACE (LEXER_ID_REF | ANY)? MAPSTO valueType ebnfSuffix? CBRACE | pyjsg/parser_impl/jsg_objectexpr_parser.py | def visitObjectExpr(self, ctx: jsgParser.ObjectExprContext):
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OBRACE (LEXER_ID_REF | ANY)? MAPSTO valueType ebnfSuffix? CBRACE
"""
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member: pairDef COMMA?
lastComma: COMMA ; | pyjsg/parser_impl/jsg_objectexpr_parser.py | def visitMembersDef(self, ctx: jsgParser.MembersDefContext):
""" membersDef: COMMA | member+ (BAR altMemberDef)* (BAR lastComma)? ;
altMemberDef: member* ;
member: pairDef COMMA?
lastComma: COMMA ;
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train | JSGObjectExpr.visitMember | member: pairDef COMMA? | pyjsg/parser_impl/jsg_objectexpr_parser.py | def visitMember(self, ctx: jsgParser.MemberContext):
""" member: pairDef COMMA? """
self._strict = ctx.COMMA() is None
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train | _get_filtered_study_ids | Optionally filters out aliases from standard doc-id list | peyotl/phylesystem/phylesystem_shard.py | 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... | 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 | python | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L18-L29 | [
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train | diagnose_repo_nexml2json | Optimistic test for Nexson version in a shard (tests first study found) | peyotl/phylesystem/phylesystem_shard.py | def diagnose_repo_nexml2json(shard):
"""Optimistic test for Nexson version in a shard (tests first study found)"""
with shard._index_lock:
fp = next(iter(shard.study_index.values()))[2]
with codecs.open(fp, mode='r', encoding='utf-8') as fo:
fj = json.load(fo)
from peyotl.nexson_synt... | def diagnose_repo_nexml2json(shard):
"""Optimistic test for Nexson version in a shard (tests first study found)"""
with shard._index_lock:
fp = next(iter(shard.study_index.values()))[2]
with codecs.open(fp, mode='r', encoding='utf-8') as fo:
fj = json.load(fo)
from peyotl.nexson_synt... | [
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train | PhylesystemShard._determine_next_study_id | Return the numeric part of the newest study_id
Checks out master branch as a side effect! | peyotl/phylesystem/phylesystem_shard.py | 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 ... | 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)
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train | PhylesystemShard._advance_new_study_id | ASSUMES the caller holds the _doc_counter_lock !
Returns the current numeric part of the next study ID, advances
the counter to the next value, and stores that value in the
file in case the server is restarted. | peyotl/phylesystem/phylesystem_shard.py | def _advance_new_study_id(self):
""" ASSUMES the caller holds the _doc_counter_lock !
Returns the current numeric part of the next study ID, advances
the counter to the next value, and stores that value in the
file in case the server is restarted.
"""
c = self._next_study... | def _advance_new_study_id(self):
""" ASSUMES the caller holds the _doc_counter_lock !
Returns the current numeric part of the next study ID, advances
the counter to the next value, and stores that value in the
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train | PhylesystemShard._diagnose_prefixes | Returns a set of all of the prefixes seen in the main document dir | peyotl/phylesystem/phylesystem_shard.py | def _diagnose_prefixes(self):
"""Returns a set of all of the prefixes seen in the main document dir
"""
from peyotl.phylesystem import STUDY_ID_PATTERN
p = set()
for name in os.listdir(self.doc_dir):
if STUDY_ID_PATTERN.match(name):
p.add(name[:3])
... | def _diagnose_prefixes(self):
"""Returns a set of all of the prefixes seen in the main document dir
"""
from peyotl.phylesystem import STUDY_ID_PATTERN
p = set()
for name in os.listdir(self.doc_dir):
if STUDY_ID_PATTERN.match(name):
p.add(name[:3])
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train | PhylesystemShard._mint_new_study_id | Checks out master branch as a side effect | peyotl/phylesystem/phylesystem_shard.py | def _mint_new_study_id(self):
"""Checks out master branch as a side effect"""
# studies created by the OpenTree API start with ot_,
# so they don't conflict with new study id's from other sources
with self._doc_counter_lock:
c = self._advance_new_study_id()
# @TODO. T... | def _mint_new_study_id(self):
"""Checks out master branch as a side effect"""
# studies created by the OpenTree API start with ot_,
# so they don't conflict with new study id's from other sources
with self._doc_counter_lock:
c = self._advance_new_study_id()
# @TODO. T... | [
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train | PhylesystemShard.create_git_action_for_new_study | Checks out master branch as a side effect | peyotl/phylesystem/phylesystem_shard.py | def create_git_action_for_new_study(self, new_study_id=None):
"""Checks out master branch as a side effect"""
ga = self.create_git_action()
if new_study_id is None:
new_study_id = self._mint_new_study_id()
self.register_doc_id(ga, new_study_id)
return ga, new_study_id | def create_git_action_for_new_study(self, new_study_id=None):
"""Checks out master branch as a side effect"""
ga = self.create_git_action()
if new_study_id is None:
new_study_id = self._mint_new_study_id()
self.register_doc_id(ga, new_study_id)
return ga, new_study_id | [
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train | flatten | Return a list of all non-list items in l
:param l: list to be flattened
:return: | pyjsg/parser_impl/parser_utils.py | def flatten(l: Iterable) -> List:
"""Return a list of all non-list items in l
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"""
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train | flatten_unique | Return a list of UNIQUE non-list items in l | pyjsg/parser_impl/parser_utils.py | def flatten_unique(l: Iterable) -> List:
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* idref -- A reference to an existing JSG definition
* LEXER_ID - The name of a match pattern definition
* LEXER_ID_REF - A reference to an existing match pattern definition
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* ID - The name of a JSG definition
* idref -- A reference to an existing JSG definition
* LEXER_ID - The name of a match pattern definition
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""" Extract the token for an identifier from the context. Tokens can be:
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* idref -- A reference to an existing JSG definition
* LEXER_ID - The name of a match pattern definition
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train | as_tokens | Return a stringified list of identifiers in ctx
:param ctx: JSG parser item with a set of identifiers
:return: | pyjsg/parser_impl/parser_utils.py | 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:
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return [as_token(e) for e in ctx] | def as_tokens(ctx: List[ParserRuleContext]) -> List[str]:
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train | is_valid_python | Determine whether tkn is a valid python identifier
:param tkn:
:return: | pyjsg/parser_impl/parser_utils.py | 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... | def is_valid_python(tkn: str) -> bool:
"""Determine whether tkn is a valid python identifier
:param tkn:
:return:
"""
try:
root = ast.parse(tkn)
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train | PhylesystemGitAction.remove_study | 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. | peyotl/phylesystem/git_actions.py | 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.
""... | 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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train | PhylesystemGitAction.write_study | Given a study_id, temporary filename of content, branch and auth_info
Deprecated but needed until we merge api local-dep to master... | peyotl/phylesystem/git_actions.py | def write_study(self, study_id, file_content, branch, author):
"""Given a study_id, temporary filename of content, branch and auth_info
Deprecated but needed until we merge api local-dep to master...
"""
gh_user = branch.split('_study_')[0]
msg = "Update Study #%s via OpenTree ... | def write_study(self, study_id, file_content, branch, author):
"""Given a study_id, temporary filename of content, branch and auth_info
Deprecated but needed until we merge api local-dep to master...
"""
gh_user = branch.split('_study_')[0]
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train | PhylesystemGitAction.write_study_from_tmpfile | Given a study_id, temporary filename of content, branch and auth_info | peyotl/phylesystem/git_actions.py | def write_study_from_tmpfile(self, study_id, tmpfi, parent_sha, auth_info, commit_msg=''):
"""Given a study_id, temporary filename of content, branch and auth_info
"""
return self.write_doc_from_tmpfile(study_id,
tmpfi,
... | def write_study_from_tmpfile(self, study_id, tmpfi, parent_sha, auth_info, commit_msg=''):
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"""
return self.write_doc_from_tmpfile(study_id,
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train | init | Initialize the communities file storage. | invenio_communities/cli.py | 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') | 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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train | addlogo | Add logo to the community. | invenio_communities/cli.py | 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)
... | 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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train | request | Request a record acceptance to a community. | invenio_communities/cli.py | 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... | 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)
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train | remove | Remove a record from community. | invenio_communities/cli.py | 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) | 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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train | sets_are_rooted_compat | treats the 2 sets are sets of taxon IDs on the same (unstated)
universe of taxon ids.
Returns True clades implied by each are compatible and False otherwise | peyotl/phylo/compat.py | def sets_are_rooted_compat(one_set, other):
"""treats the 2 sets are sets of taxon IDs on the same (unstated)
universe of taxon ids.
Returns True clades implied by each are compatible and False otherwise
"""
if one_set.issubset(other) or other.issubset(one_set):
return True
return not in... | def sets_are_rooted_compat(one_set, other):
"""treats the 2 sets are sets of taxon IDs on the same (unstated)
universe of taxon ids.
Returns True clades implied by each are compatible and False otherwise
"""
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train | gen_otu_dict | Takes a NexSON object and returns a dict of
otu_id -> otu_obj | peyotl/__init__.py | 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) >... | 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']
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train | NodePool.open | Explicit entry. Opens pool as configured, for later closure via close().
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Raise any IndyError causing failure to create ledger configuration.
:return: current object | von_agent/nodepool.py | async def open(self) -> 'NodePool':
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train | acquire_lock_raise | Adapts LockError to HTTP. If an exception is not thrown, the git_action has the lock (and must release it!) | peyotl/git_storage/git_workflow.py | def acquire_lock_raise(git_action, fail_msg=''):
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train | merge_from_master | merge from master into the WIP for this document/author
this is needed to allow a worker's future saves to
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this is needed to allow a worker's future saves to
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acquire_lo... | def merge_from_master(git_action, doc_id, auth_info, parent_sha, doctype_display_name="document"):
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train | generic_commit_and_try_merge2master_wf | Actually make a local Git commit and push it to our remote | peyotl/git_storage/git_workflow.py | def generic_commit_and_try_merge2master_wf(git_action,
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train | set_country | Sets the chosen country in the session or cookie.
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"""
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'))
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Sets the chosen country in the session or cookie.
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train | JSGDocContext.reference | Return the element that tkn represents | pyjsg/parser_impl/jsg_doc_context.py | def reference(self, tkn: str):
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return self.grammarelts[tkn] if tkn in self.grammarelts else UndefinedElement(tkn) | def reference(self, tkn: str):
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train | JSGDocContext.dependency_list | Return a list all of the grammarelts that depend on tkn
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:return: | pyjsg/parser_impl/jsg_doc_context.py | def dependency_list(self, tkn: str) -> List[str]:
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:param tkn:
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"""
if tkn not in self.dependency_map:
self.dependency_map[tkn] = [tkn] # Force a circular reference
self.dependency_... | def dependency_list(self, tkn: str) -> List[str]:
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train | JSGDocContext.dependencies | Return all the items that tkn depends on as a set
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return set(self.dependency_list(tkn)) | def dependencies(self, tkn: str) -> Set[str]:
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train | JSGDocContext.undefined_entries | Return the set of tokens that are referenced but not defined. | pyjsg/parser_impl/jsg_doc_context.py | def undefined_entries(self) -> Set[str]:
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train | JSGDocContext.dependency_closure | Determine the transitive closure of tkn's dependencies
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train | JSGDocContext.circular_references | Return the set of recursive (circular) references
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"""
Return the set of recursive (circular) references
:return:
"""
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Return the set of recursive (circular) references
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train | JSGDocContext.resolve_circular_references | Create forward references for all circular references
:return: | pyjsg/parser_impl/jsg_doc_context.py | def resolve_circular_references(self) -> None:
"""
Create forward references for all circular references
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"""
circulars = self.circular_references()
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Create forward references for all circular references
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Within each category, items are returned alphabetically | pyjsg/parser_impl/jsg_doc_context.py | def ordered_elements(self) -> str:
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train | new_request | New request for inclusion. | invenio_communities/receivers.py | def new_request(sender, request=None, notify=True, **kwargs):
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train | inject_provisional_community | Inject 'provisional_communities' key to ES index. | invenio_communities/receivers.py | 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... | 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... | [
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train | create_oaipmh_set | Signal for creating OAI-PMH sets during community creation. | invenio_communities/receivers.py | def create_oaipmh_set(mapper, connection, community):
"""Signal for creating OAI-PMH sets during community creation."""
from invenio_oaiserver.models import OAISet
with db.session.begin_nested():
obj = OAISet(spec=community.oaiset_spec,
name=community.title,
... | def create_oaipmh_set(mapper, connection, community):
"""Signal for creating OAI-PMH sets during community creation."""
from invenio_oaiserver.models import OAISet
with db.session.begin_nested():
obj = OAISet(spec=community.oaiset_spec,
name=community.title,
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train | destroy_oaipmh_set | Signal for creating OAI-PMH sets during community creation. | invenio_communities/receivers.py | def destroy_oaipmh_set(mapper, connection, community):
"""Signal for creating OAI-PMH sets during community creation."""
from invenio_oaiserver.models import OAISet
with db.session.begin_nested():
oaiset = OAISet.query.filter_by(
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if oaise... | def destroy_oaipmh_set(mapper, connection, community):
"""Signal for creating OAI-PMH sets during community creation."""
from invenio_oaiserver.models import OAISet
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oaiset = OAISet.query.filter_by(
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train | _OTIWrapper.find_nodes | Query on node properties. See documentation for _OTIWrapper class. | peyotl/api/oti.py | 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... | 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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train | _OTIWrapper.find_trees | Query on tree properties. See documentation for _OTIWrapper class. | peyotl/api/oti.py | 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}... | 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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train | _OTIWrapper.find_studies | Query on study properties. See documentation for _OTIWrapper class. | peyotl/api/oti.py | 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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"""Query on study properties. See documentation for _OTIWrapper class."""
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uri = '{p}/singlePropertySearchForStudies'.format(p=self.query_prefix)
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train | _OTIWrapper.find_all_studies | Returns a list of dicts for the entire set of studies indexed by oti.
If verbose and include_trees are False, each dict will just have the ot:studyId
If verbose is True, then the keys could also include:
ot:curatorName
ot:dataDeposit
ot:focalClade
ot:foca... | peyotl/api/oti.py | def find_all_studies(self, include_trees=False, verbose=False):
"""Returns a list of dicts for the entire set of studies indexed by oti.
If verbose and include_trees are False, each dict will just have the ot:studyId
If verbose is True, then the keys could also include:
ot:curatorNa... | def find_all_studies(self, include_trees=False, verbose=False):
"""Returns a list of dicts for the entire set of studies indexed by oti.
If verbose and include_trees are False, each dict will just have the ot:studyId
If verbose is True, then the keys could also include:
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train | get_requirements | returns requirements array for package | setup.py | 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 | 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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train | TaxonomicAmendmentStore | Factory function for a _TaxonomicAmendmentStore object.
A wrapper around the _TaxonomicAmendmentStore class instantiation for
the most common use case: a singleton _TaxonomicAmendmentStore.
If you need distinct _TaxonomicAmendmentStore objects, you'll need to
call that class directly. | peyotl/amendments/amendments_umbrella.py | def TaxonomicAmendmentStore(repos_dict=None,
repos_par=None,
with_caching=True,
assumed_doc_version=None,
git_ssh=None,
pkey=None,
git_action_class=Taxo... | 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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train | _TaxonomicAmendmentStore.add_new_amendment | Validate and save this JSON. Ensure (and return) a unique amendment id | peyotl/amendments/amendments_umbrella.py | def add_new_amendment(self,
json_repr,
auth_info,
commit_msg=''):
"""Validate and save this JSON. Ensure (and return) a unique amendment id"""
amendment = self._coerce_json_to_amendment(json_repr)
if amendment is None:... | def add_new_amendment(self,
json_repr,
auth_info,
commit_msg=''):
"""Validate and save this JSON. Ensure (and return) a unique amendment id"""
amendment = self._coerce_json_to_amendment(json_repr)
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train | _TaxonomicAmendmentStore.update_existing_amendment | Validate and save this JSON. Ensure (and return) a unique amendment id | peyotl/amendments/amendments_umbrella.py | def update_existing_amendment(self,
amendment_id=None,
json_repr=None,
auth_info=None,
parent_sha=None,
merged_sha=None,
... | def update_existing_amendment(self,
amendment_id=None,
json_repr=None,
auth_info=None,
parent_sha=None,
merged_sha=None,
... | [
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train | _TaxonomicAmendmentStore._build_amendment_id | Parse the JSON, return a slug in the form '{subtype}-{first ottid}-{last-ottid}'. | peyotl/amendments/amendments_umbrella.py | def _build_amendment_id(self, json_repr):
"""Parse the JSON, return a slug in the form '{subtype}-{first ottid}-{last-ottid}'."""
amendment = self._coerce_json_to_amendment(json_repr)
if amendment is None:
return None
amendment_subtype = 'additions'
# TODO: Look more ... | def _build_amendment_id(self, json_repr):
"""Parse the JSON, return a slug in the form '{subtype}-{first ottid}-{last-ottid}'."""
amendment = self._coerce_json_to_amendment(json_repr)
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return None
amendment_subtype = 'additions'
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train | _TaxonomicAmendmentStore._is_valid_amendment_json | Call the primary validator for a quick test | peyotl/amendments/amendments_umbrella.py | def _is_valid_amendment_json(self, json_repr):
"""Call the primary validator for a quick test"""
amendment = self._coerce_json_to_amendment(json_repr)
if amendment is None:
# invalid JSON, definitely broken
return False
aa = validate_amendment(amendment)
e... | def _is_valid_amendment_json(self, json_repr):
"""Call the primary validator for a quick test"""
amendment = self._coerce_json_to_amendment(json_repr)
if amendment is None:
# invalid JSON, definitely broken
return False
aa = validate_amendment(amendment)
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train | _TaxonomicAmendmentStore._coerce_json_to_amendment | Use to ensure that a JSON string (if found) is parsed to the equivalent dict in python.
If the incoming value is already parsed, do nothing. If a string fails to parse, return None. | peyotl/amendments/amendments_umbrella.py | def _coerce_json_to_amendment(self, json_repr):
"""Use to ensure that a JSON string (if found) is parsed to the equivalent dict in python.
If the incoming value is already parsed, do nothing. If a string fails to parse, return None."""
if isinstance(json_repr, dict):
amendment = json... | def _coerce_json_to_amendment(self, json_repr):
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train | delete_marked_communities | Delete communities after holdout time. | invenio_communities/tasks.py | 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() | 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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train | delete_expired_requests | Delete expired inclusion requests. | invenio_communities/tasks.py | def delete_expired_requests():
"""Delete expired inclusion requests."""
InclusionRequest.query.filter_by(
InclusionRequest.expiry_date > datetime.utcnow()).delete()
db.session.commit() | def delete_expired_requests():
"""Delete expired inclusion requests."""
InclusionRequest.query.filter_by(
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PhyloSchema.__init__ does not have to be soo rich | peyotl/nexson_syntax/__init__.py | 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')
... | def create_content_spec(**kwargs):
"""Sugar. factory for a PhyloSchema object.
Repackages the kwargs to kwargs for PhyloSchema so that our
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"""
format_str = kwargs.get('format', 'nexson')
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train | get_ot_study_info_from_nexml | Converts an XML doc to JSON using the honeybadgerfish convention (see to_honeybadgerfish_dict)
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If nexml_content is provided, it is interpreted as the contents
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encoding=u'utf8',
nexson_syntax_version=DEFAULT_NEXSON_VERSION):
"""Converts an XML doc to JSON using the honeybadgerfish convention (see to_honeybadgerfi... | def get_ot_study_info_from_nexml(src=None,
nexml_content=None,
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train | convert_nexson_format | Take a dict form of NexSON and converts its datastructures to
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If current_format is not specified, it will be inferred.
If `remove_old_structs` is False and different honeybadgerfish varieties
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current_format=None,
remove_old_structs=True,
pristine_if_invalid=False,
sort_arbitrary=False):
"""Take a dict form of NexSON and conve... | def convert_nexson_format(blob,
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train | sort_meta_elements | For v0.0 (which has meta values in a list), this
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and sorts each meta by @property or @rel values. | peyotl/nexson_syntax/__init__.py | def sort_meta_elements(blob):
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and sorts each meta by @property or @rel values.
"""
v = detect_nexson_version(blob)
if _is_badgerfish_version(v):
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"""For v0.0 (which has meta values in a list), this
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sorts the elements in the list by the value of the @id key.
Assumes that @id is unique or the dicts have a meaningul < operator | peyotl/nexson_syntax/__init__.py | def _inplace_sort_by_id(unsorted_list):
"""Takes a list of dicts each of which has an '@id' key,
sorts the elements in the list by the value of the @id key.
Assumes that @id is unique or the dicts have a meaningul < operator
"""
if not isinstance(unsorted_list, list):
return
sorted_list ... | def _inplace_sort_by_id(unsorted_list):
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Assumes that @id is unique or the dicts have a meaningul < operator
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train | sort_arbitrarily_ordered_nexson | Primarily used for testing (getting nice diffs). Calls
sort_meta_elements and then sorts otu, node and edge list by id | peyotl/nexson_syntax/__init__.py | def sort_arbitrarily_ordered_nexson(blob):
"""Primarily used for testing (getting nice diffs). Calls
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"""
# otu, node and edge elements have no necessary orger in v0.0 or v1.0
v = detect_nexson_version(blob)
nex = get_nexml_el(blob)
... | def sort_arbitrarily_ordered_nexson(blob):
"""Primarily used for testing (getting nice diffs). Calls
sort_meta_elements and then sorts otu, node and edge list by id
"""
# otu, node and edge elements have no necessary orger in v0.0 or v1.0
v = detect_nexson_version(blob)
nex = get_nexml_el(blob)
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train | _write_newick_leaf_label | `label_key` is a string (a key in the otu object) or a callable that takes two arguments: the node, and the otu
If `leaf_labels` is not None, it shoulr be a (list, dict) pair which will be filled. The list will
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and the dict will map name to index in the list | peyotl/nexson_syntax/__init__.py | def _write_newick_leaf_label(out, node_id, node, otu_group, label_key, leaf_labels, unlabeled_counter, needs_quotes_pattern):
"""
`label_key` is a string (a key in the otu object) or a callable that takes two arguments: the node, and the otu
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"""
`label_key` is a string (a key in the otu object) or a callable that takes two arguments: the node, and the otu
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label_key,
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needs_quotes_pattern=NEWICK_NEEDING_QUOTING,
subtree_id=None,
bracket_ingroup=False):
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otu_group,
label_key,
leaf_labels,
needs_quotes_pattern=NEWICK_NEEDING_QUOTING,
subtree_id=None,
bracket_ingroup=False):
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train | nexson_frag_write_newick | `label_key` is a string (a key in the otu object) or a callable that takes two arguments:
the node, and the otu (which may be None for an internal node)
If `leaf_labels` is not None, it shoulr be a (list, dict) pair which will be filled. The list will
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edges,
nodes,
otu_group,
label_key,
leaf_labels,
root_id,
needs_quotes_pattern=NEWI... | def nexson_frag_write_newick(out,
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train | cull_nonmatching_trees | Modifies `nexson` and returns it in version 1.2.1
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Note that this does not search through the NexSON for
every node, edge, tree that was deleted. So the resulting
NexSON may have broken references ! | peyotl/nexson_syntax/__init__.py | def cull_nonmatching_trees(nexson, tree_id, curr_version=None):
"""Modifies `nexson` and returns it in version 1.2.1
with any tree that does not match the ID removed.
Note that this does not search through the NexSON for
every node, edge, tree that was deleted. So the resulting
NexSON may have brok... | def cull_nonmatching_trees(nexson, tree_id, curr_version=None):
"""Modifies `nexson` and returns it in version 1.2.1
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train | extract_tree_nexson | Returns a list of (id, tree, otus_group) tuples for the
specified tree_id (all trees if tree_id is None) | peyotl/nexson_syntax/__init__.py | def extract_tree_nexson(nexson, tree_id, curr_version=None):
"""Returns a list of (id, tree, otus_group) tuples for the
specified tree_id (all trees if tree_id is None)
"""
if curr_version is None:
curr_version = detect_nexson_version(nexson)
if not _is_by_id_hbf(curr_version):
nexso... | def extract_tree_nexson(nexson, tree_id, curr_version=None):
"""Returns a list of (id, tree, otus_group) tuples for the
specified tree_id (all trees if tree_id is None)
"""
if curr_version is None:
curr_version = detect_nexson_version(nexson)
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train | PhyloSchema.phylesystem_api_url | Returns URL and param dict for a GET call to phylesystem_api | peyotl/nexson_syntax/__init__.py | def phylesystem_api_url(self, base_url, study_id):
"""Returns URL and param dict for a GET call to phylesystem_api
"""
p = self._phylesystem_api_params()
e = self._phylesystem_api_ext()
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train | JSGArray._is_valid | Determine whether the current contents are valid | pyjsg/jsglib/jsg_array.py | def _is_valid(self, log: Optional[Logger] = None) -> bool:
""" Determine whether the current contents are valid """
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train | Direct2BadgerfishNexson.convert | Takes a dict corresponding to the honeybadgerfish JSON blob of the 1.0.* type and
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train | Optimal2DirectNexson.convert | Takes a dict corresponding to the honeybadgerfish JSON blob of the 1.2.* type and
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train | otu_iter_nexson_proxy | otu_sort can be None (not sorted or stable), True (sorted by ID lexigraphically)
or a key function for a sort function on list of otuIDs
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or a key function for a sort function on list of otuIDs
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train | tree_iter_nexson_proxy | Iterates over NexsonTreeProxy objects in order determined by the nexson blob | peyotl/nexson_proxy.py | def tree_iter_nexson_proxy(nexson_proxy):
"""Iterates over NexsonTreeProxy objects in order determined by the nexson blob"""
nexml_el = nexson_proxy._nexml_el
tg_order = nexml_el['^ot:treesElementOrder']
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for tg_id in tg_order:
tg = tgd[tg_id]
tree_order = ... | def tree_iter_nexson_proxy(nexson_proxy):
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nexml_el = nexson_proxy._nexml_el
tg_order = nexml_el['^ot:treesElementOrder']
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NexsonNodeProxy object
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The first node will be the root and will have None as it's edge | peyotl/nexson_proxy.py | def nexson_tree_preorder_iter(tree_proxy, node_id=None, node=None, edge_id=None, edge=None):
"""Takes a tree in "By ID" NexSON (v1.2). provides and iterator over:
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train | NexsonTreeProxy.edge_by_target | Returns a reference to the dict of target node id to (edge_id, edge) | peyotl/nexson_proxy.py | def edge_by_target(self):
"""Returns a reference to the dict of target node id to (edge_id, edge)"""
if self._edge_by_target is None:
self._edge_by_target = reverse_edge_by_source_dict(self._edge_by_source_id,
self._nexson_tree['... | def edge_by_target(self):
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train | main | Get status from APC NIS and print output on stdout. | apcaccess/__main__.py | def main():
"""Get status from APC NIS and print output on stdout."""
# No need to use "proper" names on such simple code.
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p.add_argument("--host", default="localhost")
p.add_argument("--port", type=int, default=3551)
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train | Server.run | For debugging purposes, you can run this as a standalone server.
.. WARNING:: **Security vulnerability**
This uses :class:`DebuggedJsonRpcApplication` to assist debugging. If you want to use
this in production, you should run :class:`Server` as a standard WSGI app with
`uWS... | typedjsonrpc/server.py | def run(self, host, port, **options):
"""For debugging purposes, you can run this as a standalone server.
.. WARNING:: **Security vulnerability**
This uses :class:`DebuggedJsonRpcApplication` to assist debugging. If you want to use
this in production, you should run :class:`Ser... | def run(self, host, port, **options):
"""For debugging purposes, you can run this as a standalone server.
.. WARNING:: **Security vulnerability**
This uses :class:`DebuggedJsonRpcApplication` to assist debugging. If you want to use
this in production, you should run :class:`Ser... | [
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] | palantir/typedjsonrpc | python | https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/server.py#L114-L127 | [
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train | Server._try_trigger_before_first_request_funcs | Runs each function from ``self.before_first_request_funcs`` once and only once. | typedjsonrpc/server.py | def _try_trigger_before_first_request_funcs(self): # pylint: disable=C0103
"""Runs each function from ``self.before_first_request_funcs`` once and only once."""
if self._after_first_request_handled:
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with self._before_first_request_lock:
if se... | def _try_trigger_before_first_request_funcs(self): # pylint: disable=C0103
"""Runs each function from ``self.before_first_request_funcs`` once and only once."""
if self._after_first_request_handled:
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train | DebuggedJsonRpcApplication.debug_application | Run the application and preserve the traceback frames.
:param environ: The environment which is passed into the wsgi application
:type environ: dict[str, object]
:param start_response: The start_response function of the wsgi application
:type start_response: (str, list[(str, str)]) -> N... | typedjsonrpc/server.py | def debug_application(self, environ, start_response):
"""Run the application and preserve the traceback frames.
:param environ: The environment which is passed into the wsgi application
:type environ: dict[str, object]
:param start_response: The start_response function of the wsgi appli... | def debug_application(self, environ, start_response):
"""Run the application and preserve the traceback frames.
:param environ: The environment which is passed into the wsgi application
:type environ: dict[str, object]
:param start_response: The start_response function of the wsgi appli... | [
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train | DebuggedJsonRpcApplication.handle_debug | Handles the debug endpoint for inspecting previous errors.
:param environ: The environment which is passed into the wsgi application
:type environ: dict[str, object]
:param start_response: The start_response function of the wsgi application
:type start_response: (str, list[(str, str)]) ... | typedjsonrpc/server.py | def handle_debug(self, environ, start_response, traceback_id):
"""Handles the debug endpoint for inspecting previous errors.
:param environ: The environment which is passed into the wsgi application
:type environ: dict[str, object]
:param start_response: The start_response function of t... | def handle_debug(self, environ, start_response, traceback_id):
"""Handles the debug endpoint for inspecting previous errors.
:param environ: The environment which is passed into the wsgi application
:type environ: dict[str, object]
:param start_response: The start_response function of t... | [
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"_copy_over_tra... | 274218fcd236ff9643506caa629029c9ba25a0fb |
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