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Like _add_value_to_dict_bf but will not add v if another element in under key k has the same value . | def _add_uniq_value_to_dict_bf ( d , k , v ) : prev = d . get ( k ) if prev is None : d [ k ] = v elif isinstance ( prev , list ) : if not isinstance ( v , list ) : v = [ v ] for sel in v : found = False for el in prev : if el == sel : found = True break if not found : prev . append ( sel ) else : if isinstance ( v , l... | 400 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L136-L168 | [
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Debugging helper . Prints out el contents . | def _debug_dump_dom ( el ) : 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 el . childNodes : if c . nodeType == xml . do... | 401 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L177-L190 | [
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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 . | def _convert_hbf_meta_val_for_xml ( key , val ) : if isinstance ( val , list ) : return [ _convert_hbf_meta_val_for_xml ( key , i ) for i in val ] is_literal = True content = None if isinstance ( val , dict ) : ret = val if '@href' in val : is_literal = False else : content = val . get ( '$' ) if isinstance ( content ,... | 402 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L249-L277 | [
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Returns obj . for badgerfish and val for hbf . Appropriate for nested literals | def find_nested_meta_first ( d , prop_name , version ) : if _is_badgerfish_version ( version ) : return find_nested_meta_first_bf ( d , prop_name ) p = '^' + prop_name return d . get ( p ) | 403 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L361-L366 | [
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Decode encoded credential attribute value . | def decode ( value : str ) -> Union [ str , None , bool , int , float ] : assert value . isdigit ( ) or value [ 0 ] == '-' and value [ 1 : ] . isdigit ( ) if - I32_BOUND <= int ( value ) < I32_BOUND : # it's an i32: it is its own encoding return int ( value ) elif int ( value ) == I32_BOUND : return None ( prefix , val... | 404 | https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/codec.py#L70-L96 | [
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Validates that the given parameters are exactly the method s declared parameters . | def validate_params_match ( method , parameters ) : argspec = inspect . getargspec ( method ) # pylint: disable=deprecated-method default_length = len ( argspec . defaults ) if argspec . defaults is not None else 0 if isinstance ( parameters , list ) : if len ( parameters ) > len ( argspec . args ) and argspec . vararg... | 405 | https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L27-L55 | [
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Checks that the given parameters have the correct types . | def check_types ( parameters , parameter_types , strict_floats ) : for name , parameter_type in parameter_types . items ( ) : if name not in parameters : raise InvalidParamsError ( "Parameter '{}' is missing." . format ( name ) ) if not _is_instance ( parameters [ name ] , parameter_type , strict_floats ) : raise Inval... | 406 | https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L58-L73 | [
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Checks that exactly the given parameter names have declared types . | def check_type_declaration ( parameter_names , parameter_types ) : if len ( parameter_names ) != len ( parameter_types ) : raise Exception ( "Number of method parameters ({}) does not match number of " "declared types ({})" . format ( len ( parameter_names ) , len ( parameter_types ) ) ) for parameter_name in parameter... | 407 | https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L76-L90 | [
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Checks that the given return value has the correct type . | def check_return_type ( value , expected_type , strict_floats ) : if expected_type is None : if value is not None : raise InvalidReturnTypeError ( "Returned value is '{}' but None was expected" . format ( value ) ) elif not _is_instance ( value , expected_type , strict_floats ) : raise InvalidReturnTypeError ( "Type of... | 408 | https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L93-L109 | [
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Only intended to be called by the Phylesystem singleton . | def _make_phylesystem_cache_region ( * * kwargs ) : global _CACHE_REGION_CONFIGURED , _REGION if _CACHE_REGION_CONFIGURED : return _REGION _CACHE_REGION_CONFIGURED = True try : # noinspection PyPackageRequirements from dogpile . cache import make_region except : _LOG . debug ( 'dogpile.cache not available' ) return reg... | 409 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/helper.py#L125-L187 | [
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Returns doc_dir and doc_filepath for doc_id . | def path_for_doc ( self , 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 returning: [{}]'.format(full_path)) return full_path | 410 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L143-L149 | [
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Return the current branch name | def current_branch ( self ) : branch_name = git ( self . gitdir , self . gitwd , "symbolic-ref" , "HEAD" ) return branch_name . replace ( 'refs/heads/' , '' ) . strip ( ) | 411 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L169-L172 | [
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Returns true or false depending on if a branch exists | def branch_exists ( self , branch ) : try : git ( self . gitdir , self . gitwd , "rev-parse" , branch ) except sh . ErrorReturnCode : return False return True | 412 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L174-L180 | [
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fetch from a remote | def fetch ( self , remote = 'origin' ) : git ( self . gitdir , "fetch" , remote , _env = self . env ( ) ) | 413 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L204-L206 | [
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Return a dict representation of this file s commit history | def get_version_history_for_file ( self , filepath ) : # define the desired fields for logout output, matching the order in these lists! GIT_COMMIT_FIELDS = [ 'id' , 'author_name' , 'author_email' , 'date' , 'date_ISO_8601' , 'relative_date' , 'message_subject' , 'message_body' ] GIT_LOG_FORMAT = [ '%H' , '%an' , '%ae'... | 414 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L235-L273 | [
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Remove a document Remove a document on the given branch and attribute the commit to author . Returns the SHA of the commit on branch . | def _remove_document ( self , gh_user , doc_id , parent_sha , author , commit_msg = None ) : # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_id={}".format(doc_id)) doc_filepath = self . path_for_doc ( doc_id ) # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_filepath={}".format(doc_filepath)) branc... | 416 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L429-L465 | [
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Given a document id temporary filename of content branch and auth_info | def write_document ( self , gh_user , doc_id , file_content , branch , author , commit_msg = None ) : parent_sha = None fc = tempfile . NamedTemporaryFile ( ) # N.B. we currently assume file_content is text/JSON, or should be serialized from a dict if is_str_type ( file_content ) : fc . write ( file_content ) else : wr... | 417 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L467-L516 | [
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Given a doc_id temporary filename of content branch and auth_info | def write_doc_from_tmpfile ( self , doc_id , tmpfi , parent_sha , auth_info , commit_msg = '' , doctype_display_name = "document" ) : gh_user , author = get_user_author ( auth_info ) doc_filepath = self . path_for_doc ( doc_id ) doc_dir = os . path . split ( doc_filepath ) [ 0 ] if parent_sha is None : self . checkout_... | 418 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L518-L559 | [
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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 branch . | def remove_amendment ( self , first_arg , sec_arg , third_arg , fourth_arg = None , commit_msg = None ) : if fourth_arg is None : amendment_id , branch_name , author = first_arg , sec_arg , third_arg gh_user = branch_name . split ( '_amendment_' ) [ 0 ] parent_sha = self . get_master_sha ( ) else : gh_user , amendment_... | 419 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/amendments/git_actions.py#L92-L107 | [
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Create a record inclusion request to a community . | def create ( cls , community , record , user = None , expires_at = None , notify = True ) : if expires_at and expires_at < datetime . utcnow ( ) : raise InclusionRequestExpiryTimeError ( community = community , record = record ) if community . has_record ( record ) : raise InclusionRequestObsoleteError ( community = co... | 420 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L114-L152 | [
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Get an inclusion request . | def get ( cls , community_id , record_uuid ) : return cls . query . filter_by ( id_record = record_uuid , id_community = community_id ) . one_or_none ( ) | 421 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L155-L159 | [
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Add a record to the community . | def add_record ( self , record ) : key = current_app . config [ 'COMMUNITIES_RECORD_KEY' ] record . setdefault ( key , [ ] ) if self . has_record ( record ) : current_app . logger . warning ( 'Community addition: record {uuid} is already in community ' '"{comm}"' . format ( uuid = record . id , comm = self . id ) ) els... | 423 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L286-L304 | [
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Remove an already accepted record from the community . | def remove_record ( self , record ) : if not self . has_record ( record ) : current_app . logger . warning ( 'Community removal: record {uuid} was not in community ' '"{comm}"' . format ( uuid = record . id , comm = self . id ) ) else : key = current_app . config [ 'COMMUNITIES_RECORD_KEY' ] record [ key ] = [ c for c ... | 424 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L306-L322 | [
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Accept a record for inclusion in the community . | def accept_record ( self , record ) : with db . session . begin_nested ( ) : req = InclusionRequest . get ( self . id , record . id ) if req is None : raise InclusionRequestMissingError ( community = self , record = record ) req . delete ( ) self . add_record ( record ) self . last_record_accepted = datetime . utcnow (... | 425 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L329-L341 | [
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Reject a record for inclusion in the community . | def reject_record ( self , record ) : with db . session . begin_nested ( ) : req = InclusionRequest . get ( self . id , record . id ) if req is None : raise InclusionRequestMissingError ( community = self , record = record ) req . delete ( ) | 426 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L343-L353 | [
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Mark the community for deletion . | def delete ( self ) : if self . deleted_at is not None : raise CommunitiesError ( community = self ) else : self . deleted_at = datetime . utcnow ( ) | 427 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L355-L365 | [
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Get URL to collection logo . | def logo_url ( self ) : if self . logo_ext : return '/api/files/{bucket}/{key}' . format ( bucket = current_app . config [ 'COMMUNITIES_BUCKET_UUID' ] , key = '{0}/logo.{1}' . format ( self . id , self . logo_ext ) , ) return None | 428 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L380-L391 | [
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Return the corresponding OAISet for given community . | def oaiset ( self ) : if current_app . config [ 'COMMUNITIES_OAI_ENABLED' ] : from invenio_oaiserver . models import OAISet return OAISet . query . filter_by ( spec = self . oaiset_spec ) . one ( ) else : return None | 429 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L421-L433 | [
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Return the version of the community . | def version_id ( self ) : return hashlib . sha1 ( '{0}__{1}' . format ( self . id , self . updated ) . encode ( 'utf-8' ) ) . hexdigest ( ) | 431 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L448-L455 | [
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Get the latest featured community . | def get_featured_or_none ( cls , start_date = None ) : start_date = start_date or datetime . utcnow ( ) comm = cls . query . filter ( FeaturedCommunity . start_date <= start_date ) . order_by ( cls . start_date . desc ( ) ) . first ( ) return comm if comm is None else comm . community | 432 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L486-L500 | [
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Load caches and archive enough to go offline and be able to verify proof on content marked of interest in configuration . | async def load_cache ( self , archive : bool = False ) -> int : LOGGER . debug ( 'Verifier.load_cache >>> archive: %s' , archive ) rv = int ( time ( ) ) for s_id in self . cfg . get ( 'archive-on-close' , { } ) . get ( 'schema_id' , { } ) : with SCHEMA_CACHE . lock : await self . get_schema ( s_id ) for cd_id in self .... | 465 | https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/verifier.py#L165-L204 | [
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Optionally filters out aliases from standard doc - id list | def _get_filtered_study_ids ( shard , include_aliases = False ) : 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_PATTERN . match ( i ) or ( ( len ( i ) > 1 ) and ( i [ - 2 ] == '_' ) ) : pass else : x... | 471 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L18-L29 | [
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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 . | def _advance_new_study_id ( self ) : c = self . _next_study_id self . _next_study_id = 1 + c content = u'{"next_study_id": %d}\n' % self . _next_study_id # The content is JSON, but we hand-rolled the string above # so that we can use it as a commit_msg self . _write_master_branch_resource ( content , self . _id_m... | 473 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L281-L296 | [
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Return a list of UNIQUE non - list items in l | def flatten_unique ( l : Iterable ) -> List : rval = OrderedDict ( ) for e in l : if not isinstance ( e , str ) and isinstance ( e , Iterable ) : for ev in flatten_unique ( e ) : rval [ ev ] = None else : rval [ e ] = None return list ( rval . keys ( ) ) | 475 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L30-L39 | [
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Return a stringified list of identifiers in ctx | def as_tokens ( ctx : List [ ParserRuleContext ] ) -> List [ str ] : return [ as_token ( e ) for e in ctx ] | 476 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L85-L91 | [
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Determine whether tkn is a valid python identifier | def is_valid_python ( tkn : str ) -> bool : 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 ] . value , ast . Name ) | 477 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L94-L104 | [
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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 ) : if fourth_arg is None : study_id , branch_name , author = first_arg , sec_arg , third_arg gh_user = branch_name . split ( '_study_' ) [ 0 ] parent_sha = self . get_master_sha ( ) else : gh_user , study_id , parent_sha ... | 478 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/git_actions.py#L108-L123 | [
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Initialize the communities file storage . | def init ( ) : try : initialize_communities_bucket ( ) click . secho ( 'Community init successful.' , fg = 'green' ) except FilesException as e : click . secho ( e . message , fg = 'red' ) | 479 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L50-L56 | [
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Add logo to the community . | def addlogo ( community_id , logo ) : # 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 ) c . logo_ext = ext db . session . commit ( ) | 480 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L63-L73 | [
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Request a record acceptance to a community . | def request ( community_id , record_id , accept ) : 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 ( community = c , record = record , notify = False ) db . session . commit (... | 481 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L81-L93 | [
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Remove a record from community . | def remove ( community_id , record_id ) : c = Community . get ( community_id ) assert c is not None c . remove_record ( record_id ) db . session . commit ( ) RecordIndexer ( ) . index_by_id ( record_id ) | 482 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L100-L106 | [
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Takes a NexSON object and returns a dict of otu_id - > otu_obj | def gen_otu_dict ( nex_obj , nexson_version = None ) : 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 ) > 1 : d = { } for v in otus . values ( ) : d . update ( v [ 'otuById' ] ) return d else : ... | 483 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/__init__.py#L33-L53 | [
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Sets the chosen country in the session or cookie . | def set_country ( request ) : if request . method == 'POST' : next = request . POST . get ( 'next' , request . GET . get ( 'next' ) ) if is_safe_url ( url = next , host = request . get_host ( ) ) : response = http . HttpResponseRedirect ( next ) else : response = http . HttpResponse ( ) country_code = request . POST . ... | 484 | https://github.com/color/django-country/blob/1d272a196d998e21bb8d407e2657b88211f35232/django_country/views.py#L8-L34 | [
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Return the element that tkn represents | def reference ( self , tkn : str ) : return self . grammarelts [ tkn ] if tkn in self . grammarelts else UndefinedElement ( tkn ) | 485 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L111-L113 | [
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Return a list all of the grammarelts that depend on tkn | def dependency_list ( self , tkn : str ) -> List [ str ] : if tkn not in self . dependency_map : self . dependency_map [ tkn ] = [ tkn ] # Force a circular reference self . dependency_map [ tkn ] = self . reference ( tkn ) . dependency_list ( ) return self . dependency_map [ tkn ] | 486 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L139-L148 | [
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Return all the items that tkn depends on as a set | def dependencies ( self , tkn : str ) -> Set [ str ] : return set ( self . dependency_list ( tkn ) ) | 487 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L150-L156 | [
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Return the set of tokens that are referenced but not defined . | def undefined_entries ( self ) -> Set [ str ] : return as_set ( [ [ d for d in self . dependencies ( k ) if d not in self . grammarelts ] for k in self . grammarelts . keys ( ) ] ) | 488 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L158-L161 | [
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New request for inclusion . | def new_request ( sender , request = None , notify = True , * * kwargs ) : if current_app . config [ 'COMMUNITIES_MAIL_ENABLED' ] and notify : send_community_request_email ( request ) | 489 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/receivers.py#L36-L39 | [
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Inject provisional_communities key to ES index . | def inject_provisional_community ( sender , json = None , record = None , index = None , * * kwargs ) : if index and not index . startswith ( current_app . config [ 'COMMUNITIES_INDEX_PREFIX' ] ) : return json [ 'provisional_communities' ] = list ( sorted ( [ r . id_community for r in InclusionRequest . get_by_record (... | 490 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/receivers.py#L42-L51 | [
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Query on node properties . See documentation for _OTIWrapper class . | def find_nodes ( self , query_dict = None , exact = False , verbose = False , * * kwargs ) : assert self . use_v1 return self . _do_query ( '{p}/singlePropertySearchForTreeNodes' . format ( p = self . query_prefix ) , query_dict = query_dict , exact = exact , verbose = verbose , valid_keys = self . node_search_term_set... | 491 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/oti.py#L119-L127 | [
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Query on tree properties . See documentation for _OTIWrapper class . | def find_trees ( self , query_dict = None , exact = False , verbose = False , wrap_response = False , * * kwargs ) : if self . use_v1 : uri = '{p}/singlePropertySearchForTrees' . format ( p = self . query_prefix ) else : uri = '{p}/find_trees' . format ( p = self . query_prefix ) resp = self . _do_query ( uri , query_d... | 492 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/oti.py#L129-L143 | [
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Query on study properties . See documentation for _OTIWrapper class . | def find_studies ( self , query_dict = None , exact = False , verbose = False , * * kwargs ) : if self . use_v1 : uri = '{p}/singlePropertySearchForStudies' . format ( p = self . query_prefix ) else : uri = '{p}/find_studies' . format ( p = self . query_prefix ) return self . _do_query ( uri , query_dict = query_dict ,... | 493 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/oti.py#L145-L156 | [
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returns requirements array for package | def get_requirements ( ) : packages = [ ] with open ( "requirements.txt" , "r" ) as req_doc : for package in req_doc : packages . append ( package . replace ( "\n" , "" ) ) return packages | 494 | https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/setup.py#L5-L11 | [
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Factory function for a _TaxonomicAmendmentStore object . | def TaxonomicAmendmentStore ( repos_dict = None , repos_par = None , with_caching = True , assumed_doc_version = None , git_ssh = None , pkey = None , git_action_class = TaxonomicAmendmentsGitAction , mirror_info = None , infrastructure_commit_author = 'OpenTree API <api@opentreeoflife.org>' ) : global _THE_TAXONOMIC_A... | 495 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/amendments/amendments_umbrella.py#L352-L379 | [
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Delete communities after holdout time . | def delete_marked_communities ( ) : # 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 ( ) | 496 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/tasks.py#L38-L44 | [
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Delete expired inclusion requests . | def delete_expired_requests ( ) : InclusionRequest . query . filter_by ( InclusionRequest . expiry_date > datetime . utcnow ( ) ) . delete ( ) db . session . commit ( ) | 497 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/tasks.py#L48-L52 | [
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Sugar . factory for a PhyloSchema object . | def create_content_spec ( * * kwargs ) : format_str = kwargs . get ( 'format' , 'nexson' ) nexson_version = kwargs . get ( 'nexson_version' , 'native' ) otu_label = kwargs . get ( 'otu_label' ) if otu_label is None : otu_label = kwargs . get ( 'tip_label' ) content = kwargs . get ( 'content' ) if content is not None : ... | 498 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/__init__.py#L178-L205 | [
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Take a dict form of NexSON and converts its datastructures to those needed to serialize as out_nexson_format . If current_format is not specified it will be inferred . If remove_old_structs is False and different honeybadgerfish varieties are selected the blob will be fat containing both types of lookup structures . If... | def convert_nexson_format ( blob , out_nexson_format , current_format = None , remove_old_structs = True , pristine_if_invalid = False , sort_arbitrary = False ) : if not current_format : current_format = detect_nexson_version ( blob ) out_nexson_format = resolve_nexson_format ( out_nexson_format ) if current_format ==... | 499 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/__init__.py#L646-L699 | [
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