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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 , list ) : prev = [ prev ] for sel in v : found = False for el in prev : if el == sel : found = True break if not found : prev . append ( sel ) if len ( prev ) > 1 : d [ k ] = prev elif prev != v : d [ k ] = [ prev , v ] | 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 . dom . minidom . Node . TEXT_NODE : s . append ( ' {a} type="TEXT" data="{d}"' . format ( a = c . nodeName , d = c . data ) ) else : s . append ( ' {a} child' . format ( a = c . nodeName ) ) return '\n' . join ( s ) | 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 ( '$' ) if isinstance ( content , dict ) and _contains_hbf_meta_keys ( val ) : is_literal = False else : ret = { } content = val if is_literal : ret . setdefault ( '@xsi:type' , 'nex:LiteralMeta' ) ret . setdefault ( '@property' , key ) if content is not None : ret . setdefault ( '@datatype' , _python_instance_to_nexml_meta_datatype ( content ) ) if ret is not val : ret [ '$' ] = content else : ret . setdefault ( '@xsi:type' , 'nex:ResourceMeta' ) ret . setdefault ( '@rel' , key ) return ret | 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 , value ) = ( int ( value [ 0 ] ) , int ( value [ 1 : ] ) ) ival = int ( value ) - I32_BOUND if ival == 0 : return '' # special case: empty string encodes as 2**31 elif ival == 1 : return False # sentinel for bool False elif ival == 2 : return True # sentinel for bool True blen = ceil ( log ( ival , 16 ) / 2 ) ibytes = unhexlify ( ival . to_bytes ( blen , 'big' ) ) return DECODE_PREFIX . get ( prefix , str ) ( ibytes . decode ( ) ) | 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 . varargs is None : raise InvalidParamsError ( "Too many parameters" ) remaining_parameters = len ( argspec . args ) - len ( parameters ) if remaining_parameters > default_length : raise InvalidParamsError ( "Not enough parameters" ) elif isinstance ( parameters , dict ) : missing_parameters = [ key for key in argspec . args if key not in parameters ] default_parameters = set ( argspec . args [ len ( argspec . args ) - default_length : ] ) for key in missing_parameters : if key not in default_parameters : raise InvalidParamsError ( "Parameter {} has not been satisfied" . format ( key ) ) extra_params = [ key for key in parameters if key not in argspec . args ] if len ( extra_params ) > 0 and argspec . keywords is None : raise InvalidParamsError ( "Too many parameters" ) | 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 InvalidParamsError ( "Value '{}' for parameter '{}' is not of expected type {}." . format ( parameters [ name ] , name , parameter_type ) ) | 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_names : if parameter_name not in parameter_types : raise Exception ( "Parameter '{}' does not have a declared type" . format ( parameter_name ) ) | 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 return value '{}' does not match expected type {}" . format ( value , expected_type ) ) | 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 region = None trial_key = 'test_key' trial_val = { 'test_val' : [ 4 , 3 ] } trying_redis = True if trying_redis : try : a = { 'host' : 'localhost' , 'port' : 6379 , 'db' : 0 , # default is 0 'redis_expiration_time' : 60 * 60 * 24 * 2 , # 2 days 'distributed_lock' : False # True if multiple processes will use redis } region = make_region ( ) . configure ( 'dogpile.cache.redis' , arguments = a ) _LOG . debug ( 'cache region set up with cache.redis.' ) _LOG . debug ( 'testing redis caching...' ) region . set ( trial_key , trial_val ) assert trial_val == region . get ( trial_key ) _LOG . debug ( 'redis caching works' ) region . delete ( trial_key ) _REGION = region return region except : _LOG . debug ( 'redis cache set up failed.' ) region = None trying_file_dbm = False if trying_file_dbm : _LOG . debug ( 'Going to try dogpile.cache.dbm ...' ) first_par = _get_phylesystem_parent ( * * kwargs ) [ 0 ] cache_db_dir = os . path . split ( first_par ) [ 0 ] cache_db = os . path . join ( cache_db_dir , 'phylesystem-cachefile.dbm' ) _LOG . debug ( 'dogpile.cache region using "{}"' . format ( cache_db ) ) try : a = { 'filename' : cache_db } region = make_region ( ) . configure ( 'dogpile.cache.dbm' , expiration_time = 36000 , arguments = a ) _LOG . debug ( 'cache region set up with cache.dbm.' ) _LOG . debug ( 'testing anydbm caching...' ) region . set ( trial_key , trial_val ) assert trial_val == region . get ( trial_key ) _LOG . debug ( 'anydbm caching works' ) region . delete ( trial_key ) _REGION = region return region except : _LOG . debug ( 'anydbm cache set up failed' ) _LOG . debug ( 'exception in the configuration of the cache.' ) _LOG . debug ( 'Phylesystem will not use caching' ) return None | 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' , '%aD' , '%ai' , '%ar' , '%s' , '%b' ] # make the final format string, using standard ASCII field/record delimiters GIT_LOG_FORMAT = '%x1f' . join ( GIT_LOG_FORMAT ) + '%x1e' try : log = git ( self . gitdir , self . gitwd , '--no-pager' , 'log' , '--format=%s' % GIT_LOG_FORMAT , '--follow' , # Track file's history when moved/renamed... '--find-renames=100%' , # ... but only if the contents are identical! '--' , filepath ) # _LOG.debug('log said "{}"'.format(log)) log = log . strip ( '\n\x1e' ) . split ( "\x1e" ) log = [ row . strip ( ) . split ( "\x1f" ) for row in log ] log = [ dict ( zip ( GIT_COMMIT_FIELDS , row ) ) for row in log ] except : _LOG . exception ( 'git log failed' ) raise return log | 414 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L235-L273 | [
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Low level function used internally when you have an absolute filepath to add and commit | def _add_and_commit ( self , doc_filepath , author , commit_msg ) : try : git ( self . gitdir , self . gitwd , "add" , doc_filepath ) git ( self . gitdir , self . gitwd , "commit" , author = author , message = commit_msg ) except Exception as e : # We can ignore this if no changes are new, # otherwise raise a 400 if "nothing to commit" in e . message : # @EJM is this dangerous? _LOG . debug ( '"nothing to commit" found in error response' ) else : _LOG . exception ( '"git commit" failed' ) self . reset_hard ( ) raise | 415 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L275-L288 | [
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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)) branch = self . create_or_checkout_branch ( gh_user , doc_id , parent_sha ) prev_file_sha = None if commit_msg is None : msg = "Delete document '%s' via OpenTree API" % doc_id else : msg = commit_msg if os . path . exists ( doc_filepath ) : prev_file_sha = self . get_blob_sha_for_file ( doc_filepath ) if self . doc_type == 'nexson' : # delete the parent directory entirely doc_dir = os . path . split ( doc_filepath ) [ 0 ] # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_dir={}".format(doc_dir)) git ( self . gitdir , self . gitwd , "rm" , "-rf" , doc_dir ) elif self . doc_type in ( 'collection' , 'favorites' , 'amendment' ) : # delete just the target file git ( self . gitdir , self . gitwd , "rm" , doc_filepath ) else : raise NotImplementedError ( "No deletion rules for doc_type '{}'" . format ( self . doc_type ) ) git ( self . gitdir , self . gitwd , "commit" , author = author , message = msg ) new_sha = git ( self . gitdir , self . gitwd , "rev-parse" , "HEAD" ) . strip ( ) return { 'commit_sha' : new_sha , 'branch' : branch , 'prev_file_sha' : prev_file_sha , } | 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 : write_as_json ( file_content , fc ) fc . flush ( ) try : doc_filepath = self . path_for_doc ( doc_id ) doc_dir = os . path . split ( doc_filepath ) [ 0 ] if parent_sha is None : self . checkout_master ( ) parent_sha = self . get_master_sha ( ) branch = self . create_or_checkout_branch ( gh_user , doc_id , parent_sha , force_branch_name = True ) # create a document directory if this is a new doc EJM- what if it isn't? if not os . path . isdir ( doc_dir ) : os . makedirs ( doc_dir ) shutil . copy ( fc . name , doc_filepath ) git ( self . gitdir , self . gitwd , "add" , doc_filepath ) if commit_msg is None : commit_msg = "Update document '%s' via OpenTree API" % doc_id try : git ( self . gitdir , self . gitwd , "commit" , author = author , message = commit_msg ) except Exception as e : # We can ignore this if no changes are new, # otherwise raise a 400 if "nothing to commit" in e . message : # @EJM is this dangerous? pass else : _LOG . exception ( '"git commit" failed' ) self . reset_hard ( ) raise new_sha = git ( self . gitdir , self . gitwd , "rev-parse" , "HEAD" ) except Exception as e : _LOG . exception ( 'write_document exception' ) raise GitWorkflowError ( "Could not write to document #%s ! Details: \n%s" % ( doc_id , e . message ) ) finally : fc . close ( ) return new_sha | 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_master ( ) parent_sha = self . get_master_sha ( ) branch = self . create_or_checkout_branch ( gh_user , doc_id , parent_sha ) # build complete (probably type-specific) commit message default_commit_msg = "Update %s '%s' via OpenTree API" % ( doctype_display_name , doc_id ) if commit_msg : commit_msg = "%s\n\n(%s)" % ( commit_msg , default_commit_msg ) else : commit_msg = default_commit_msg # create a doc directory if this is a new document EJM- what if it isn't? if not os . path . isdir ( doc_dir ) : os . makedirs ( doc_dir ) if os . path . exists ( doc_filepath ) : prev_file_sha = self . get_blob_sha_for_file ( doc_filepath ) else : prev_file_sha = None shutil . copy ( tmpfi . name , doc_filepath ) self . _add_and_commit ( doc_filepath , author , commit_msg ) new_sha = git ( self . gitdir , self . gitwd , "rev-parse" , "HEAD" ) _LOG . debug ( 'Committed document "{i}" to branch "{b}" commit SHA: "{s}"' . format ( i = doc_id , b = branch , s = new_sha . strip ( ) ) ) return { 'commit_sha' : new_sha . strip ( ) , 'branch' : branch , 'prev_file_sha' : prev_file_sha , } | 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_id , parent_sha , author = first_arg , sec_arg , third_arg , fourth_arg if commit_msg is None : commit_msg = "Delete Amendment '%s' via OpenTree API" % amendment_id return self . _remove_document ( gh_user , amendment_id , parent_sha , author , commit_msg ) | 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 = community , record = record ) try : # Create inclusion request with db . session . begin_nested ( ) : obj = cls ( id_community = community . id , id_record = record . id , user = user , expires_at = expires_at ) db . session . add ( obj ) except ( IntegrityError , FlushError ) : raise InclusionRequestExistsError ( community = community , record = record ) # Send signal inclusion_request_created . send ( current_app . _get_current_object ( ) , request = obj , notify = notify ) return obj | 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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Search for communities . | def filter_communities ( cls , p , so , with_deleted = False ) : query = cls . query if with_deleted else cls . query . filter ( cls . deleted_at . is_ ( None ) ) if p : p = p . replace ( ' ' , '%' ) query = query . filter ( db . or_ ( cls . id . ilike ( '%' + p + '%' ) , cls . title . ilike ( '%' + p + '%' ) , cls . description . ilike ( '%' + p + '%' ) , ) ) if so in current_app . config [ 'COMMUNITIES_SORTING_OPTIONS' ] : order = so == 'title' and db . asc or db . desc query = query . order_by ( order ( getattr ( cls , so ) ) ) else : query = query . order_by ( db . desc ( cls . ranking ) ) return query | 422 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L257-L284 | [
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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 ) ) else : record [ key ] . append ( self . id ) record [ key ] = sorted ( record [ key ] ) if current_app . config [ 'COMMUNITIES_OAI_ENABLED' ] : if not self . oaiset . has_record ( record ) : self . oaiset . add_record ( record ) | 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 in record [ key ] if c != self . id ] if current_app . config [ 'COMMUNITIES_OAI_ENABLED' ] : if self . oaiset . has_record ( record ) : self . oaiset . remove_record ( record ) | 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 OAISet URL for given community . | def oaiset_url ( self ) : return url_for ( 'invenio_oaiserver.response' , verb = 'ListRecords' , metadataPrefix = 'oai_dc' , set = self . oaiset_spec , _external = True ) | 430 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L436-L445 | [
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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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GET the current Connector version . | def getConnectorVersion ( self ) : result = asyncResult ( ) data = self . _getURL ( "/" , versioned = False ) result . fill ( data ) if data . status_code == 200 : result . error = False else : result . error = response_codes ( "get_mdc_version" , data . status_code ) result . is_done = True return result | 433 | https://github.com/ARMmbed/mbed-connector-api-python/blob/a5024a01dc67cc192c8bf7a70b251fcf0a3f279b/mbed_connector_api/mbed_connector_api.py#L72-L87 | [
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Register a handler for a particular notification type . These are the types of notifications that are acceptable . | async - responses | registrations - expired | de - registrations | reg - updates | registrations | notifications | def setHandler ( self , handler , cbfn ) : if handler == "async-responses" : self . async_responses_callback = cbfn elif handler == "registrations-expired" : self . registrations_expired_callback = cbfn elif handler == "de-registrations" : self . de_registrations_callback = cbfn elif handler == "reg-updates" : self . reg_updates_callback = cbfn elif handler == "registrations" : self . registrations_callback = cbfn elif handler == "notifications" : self . notifications_callback = cbfn else : self . log . warn ( "'%s' is not a legitimate notification channel option. Please check your spelling." , handler ) | 434 | https://github.com/ARMmbed/mbed-connector-api-python/blob/a5024a01dc67cc192c8bf7a70b251fcf0a3f279b/mbed_connector_api/mbed_connector_api.py#L554-L583 | [
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Append one or more records to the end of a numpy recarray or ndarray . | def addrecords ( X , new ) : if isinstance ( new , np . record ) or isinstance ( new , np . void ) or isinstance ( new , tuple ) : new = [ new ] return np . append ( X , utils . fromrecords ( new , type = np . ndarray , dtype = X . dtype ) , axis = 0 ) | 440 | https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L704-L737 | [
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Rename column of a numpy ndarray with structured dtype in - place . | def renamecol ( X , old , new ) : NewNames = tuple ( [ n if n != old else new for n in X . dtype . names ] ) X . dtype . names = NewNames | 443 | https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L845-L868 | [
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Replace value old with new everywhere it appears in - place . | def replace ( X , old , new , strict = True , cols = None , rows = None ) : if cols == None : cols = X . dtype . names elif isinstance ( cols , str ) : cols = cols . split ( ',' ) if rows == None : rows = np . ones ( ( len ( X ) , ) , bool ) if strict : new = np . array ( new ) for a in cols : if X . dtype [ a ] < new . dtype : print ( 'WARNING: dtype of column' , a , 'is inferior to dtype of ' , new , 'which may cause problems.' ) try : X [ a ] [ ( X [ a ] == old ) [ rows ] ] = new except : print ( 'Replacement not made on column' , a , '.' ) else : for a in cols : QuickRep = True try : colstr = '' . join ( X [ a ] [ rows ] ) except TypeError : print ( 'Not replacing in column' , a , 'due to type mismatch.' ) else : avoid = [ ord ( o ) for o in utils . uniqify ( old + new + colstr ) ] ok = set ( range ( 256 ) ) . difference ( avoid ) if len ( ok ) > 0 : sep = chr ( list ( ok ) [ 0 ] ) else : ok = set ( range ( 65536 ) ) . difference ( avoid ) if len ( ok ) > 0 : sep = unichr ( list ( ok ) [ 0 ] ) else : print ( 'All unicode characters represented in column' , a , ', can\t replace quickly.' ) QuickRep = False if QuickRep : newrows = np . array ( sep . join ( X [ a ] [ rows ] ) . replace ( old , new ) . split ( sep ) ) else : newrows = np . array ( [ aa . replace ( old , new ) for aa in X [ a ] [ rows ] ] ) X [ a ] [ rows ] = np . cast [ X . dtype [ a ] ] ( newrows ) if newrows . dtype > X . dtype [ a ] : print ( 'WARNING: dtype of column' , a , 'is inferior to the ' 'dtype of its replacement which may cause problems ' '(ends of strings might get chopped off).' ) | 444 | https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L871-L964 | [
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Vertically stack a sequence of numpy ndarrays with structured dtype | def rowstack ( seq , mode = 'nulls' , nullvals = None ) : if nullvals == None : nullvals = utils . DEFAULT_NULLVALUEFORMAT #newseq = [ss for ss in seq if len(ss) > 0] if len ( seq ) > 1 : assert mode in [ 'commons' , 'nulls' , 'abort' ] , ( '"mode" argument must either by "commons", "abort", or "nulls".' ) if mode == 'abort' : if not all ( [ set ( l . dtype . names ) == set ( seq [ 0 ] . dtype . names ) for l in seq ] ) : raise ValueError ( 'Some column names are different.' ) else : mode = 'commons' if mode == 'nulls' : names = utils . uniqify ( utils . listunion ( [ list ( s . dtype . names ) for s in seq if s . dtype . names != None ] ) ) formats = [ max ( [ s . dtype [ att ] for s in seq if s . dtype . names != None and att in s . dtype . names ] ) . str for att in names ] dtype = np . dtype ( zip ( names , formats ) ) return utils . fromarrays ( [ utils . listunion ( [ s [ att ] . tolist ( ) if ( s . dtype . names != None and att in s . dtype . names ) else [ nullvals ( format ) ] * len ( s ) for s in seq ] ) for ( att , format ) in zip ( names , formats ) ] , type = np . ndarray , dtype = dtype ) elif mode == 'commons' : names = [ x for x in seq [ 0 ] . dtype . names if all ( [ x in l . dtype . names for l in seq [ 1 : ] ] ) ] formats = [ max ( [ a . dtype [ att ] for a in seq ] ) . str for att in names ] return utils . fromrecords ( utils . listunion ( [ ar . tolist ( ) for ar in seq ] ) , type = np . ndarray , names = names , formats = formats ) else : return seq [ 0 ] | 445 | https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L967-L1044 | [
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Horizontally stack a sequence of numpy ndarrays with structured dtypes | def colstack ( seq , mode = 'abort' , returnnaming = False ) : assert mode in [ 'first' , 'drop' , 'abort' , 'rename' ] , 'mode argument must take on value "first","drop", "rename", or "abort".' AllNames = utils . uniqify ( utils . listunion ( [ list ( l . dtype . names ) for l in seq ] ) ) NameList = [ ( x , [ i for i in range ( len ( seq ) ) if x in seq [ i ] . dtype . names ] ) for x in AllNames ] Commons = [ x [ 0 ] for x in NameList if len ( x [ 1 ] ) > 1 ] if len ( Commons ) > 0 or mode == 'first' : if mode == 'abort' : raise ValueError ( 'There are common column names with differing ' + 'values in the columns' ) elif mode == 'drop' : Names = [ ( L [ 0 ] , x , x ) for ( x , L ) in NameList if x not in Commons ] elif mode == 'rename' : NameDict = dict ( NameList ) Names = utils . listunion ( [ [ ( i , n , n ) if len ( NameDict [ n ] ) == 1 else ( i , n , n + '_' + str ( i ) ) for n in s . dtype . names ] for ( i , s ) in enumerate ( seq ) ] ) else : Names = [ ( L [ 0 ] , x , x ) for ( x , L ) in NameList ] if returnnaming : return utils . fromarrays ( [ seq [ i ] [ x ] for ( i , x , y ) in Names ] , type = np . ndarray , names = zip ( * Names ) [ 2 ] ) , Names else : return utils . fromarrays ( [ seq [ i ] [ x ] for ( i , x , y ) in Names ] , type = np . ndarray , names = zip ( * Names ) [ 2 ] ) | 446 | https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L1047-L1123 | [
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Renames overlapping column names of numpy ndarrays with structured dtypes | def DEFAULT_RENAMER ( L , Names = None ) : if isinstance ( L , dict ) : Names = L . keys ( ) LL = L . values ( ) else : if Names == None : Names = range ( len ( L ) ) else : assert len ( Names ) == len ( L ) LL = L commons = Commons ( [ l . dtype . names for l in LL ] ) D = { } for ( i , l ) in zip ( Names , LL ) : d = { } for c in commons : if c in l . dtype . names : d [ c ] = c + '_' + str ( i ) if d : D [ i ] = d return D | 447 | https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L1520-L1571 | [
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Helioviewer . org and JHelioviewer operate off of JPEG2000 formatted image data generated from science - quality FITS files . Use the APIs below to interact directly with these intermediary JPEG2000 files . Download a JP2 image for the specified datasource that is the closest match in time to the date requested . | def getjp2image ( date , sourceId = None , observatory = None , instrument = None , detector = None , measurement = None ) : base_url = 'http://helioviewer.org/api/v1/getJP2Image/?' req_url = '' try : validate_iso8601 ( date ) if not date [ - 1 : ] == 'Z' : date += 'Z' base_url += 'date=' + date except : raise ValueError ( "Your date input is not in iso8601 format. ex: 2014-01-01T23:59:59" ) if sourceId : if not isinstance ( sourceId , int ) : logger . error ( "The sourceId argument should be an int, ignoring it" ) else : base_url += "sourceId=" + str ( sourceId ) + "&" if observatory : if not isinstance ( observatory , str ) : logger . error ( "The observatory argument should be a str, ignoring it" ) else : base_url += "observatory=" + observatory + "&" if instrument : if not isinstance ( instrument , str ) : logger . error ( "The instrument argument should be a str, ignoring it" ) else : base_url += "instrument=" + instrument + "&" if detector : if not isinstance ( detector , str ) : logger . error ( "The detector argument should be a str, ignoring it" ) else : base_url += "detector=" + detector + "&" if measurement : if not isinstance ( measurement , str ) : logger . error ( "The measurement argument should be a str, ignoring it" ) else : base_url += "measurement=" + detector + "&" req_url += base_url + "jpip=true" return dispatch_http_get ( req_url ) | 448 | https://github.com/emirozer/bowshock/blob/9f5e053f1d54995b833b83616f37c67178c3e840/bowshock/helioviewer.py#L10-L85 | [
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json loader objecthook | def loads_loader ( load_module : types . ModuleType , pairs : Dict [ str , str ] ) -> Optional [ JSGValidateable ] : cntxt = load_module . _CONTEXT # If the type element is a member of the JSON, load it possible_type = pairs [ cntxt . TYPE ] if cntxt . TYPE in pairs else None target_class = getattr ( load_module , possible_type , None ) if isinstance ( possible_type , str ) else None if target_class : return target_class ( * * pairs ) # See whether there are any exception types that are valid for the incoming data for type_exception in cntxt . TYPE_EXCEPTIONS : if not hasattr ( load_module , type_exception ) : raise ValueError ( UNKNOWN_TYPE_EXCEPTION . format ( type_exception ) ) target_class = getattr ( load_module , type_exception ) target_strict = target_class . _strict target_class . _strict = False try : rval = target_class ( * * pairs ) finally : target_class . _strict = target_strict if is_valid ( rval ) : return rval # If there is not a type variable and nothing fits, just load up the first (and perhaps only) exception # It will later fail any is_valid tests if not cntxt . TYPE and cntxt . TYPE_EXCEPTIONS : return getattr ( load_module , cntxt . TYPE_EXCEPTIONS [ 0 ] ) ( * * pairs ) if cntxt . TYPE in pairs : raise ValueError ( f'Unknown reference type: "{cntxt.TYPE}": "{pairs[cntxt.TYPE]}"' ) else : raise ValueError ( f'Missing "{cntxt.TYPE}" element' ) | 449 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L17-L54 | [
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Convert a file name or file - like object containing stringified JSON into a JSGObject | def load ( fp : Union [ TextIO , str ] , load_module : types . ModuleType , * * kwargs ) : if isinstance ( fp , str ) : with open ( fp ) as f : return loads ( f . read ( ) , load_module , * * kwargs ) else : return loads ( fp . read ( ) , load_module , * * kwargs ) | 451 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L68-L80 | [
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native isinstance_ with the test for typing . Union overridden | def isinstance_ ( x , A_tuple ) : if is_union ( A_tuple ) : return any ( isinstance_ ( x , t ) for t in A_tuple . __args__ ) elif getattr ( A_tuple , '__origin__' , None ) is not None : return isinstance ( x , A_tuple . __origin__ ) else : return isinstance ( x , A_tuple ) | 452 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L83-L90 | [
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Get revocation registry definition from ledger by its identifier . Raise AbsentRevReg for no such revocation registry logging any error condition and raising BadLedgerTxn on bad request . | async def _get_rev_reg_def ( self , rr_id : str ) -> str : LOGGER . debug ( '_BaseAgent._get_rev_reg_def >>> rr_id: %s' , rr_id ) rv_json = json . dumps ( { } ) with REVO_CACHE . lock : revo_cache_entry = REVO_CACHE . get ( rr_id , None ) rr_def = revo_cache_entry . rev_reg_def if revo_cache_entry else None if rr_def : LOGGER . info ( '_BaseAgent._get_rev_reg_def: rev reg def for %s from cache' , rr_id ) rv_json = json . dumps ( rr_def ) else : get_rrd_req_json = await ledger . build_get_revoc_reg_def_request ( self . did , rr_id ) resp_json = await self . _submit ( get_rrd_req_json ) try : ( _ , rv_json ) = await ledger . parse_get_revoc_reg_def_response ( resp_json ) rr_def = json . loads ( rv_json ) except IndyError : # ledger replied, but there is no such rev reg LOGGER . debug ( '_BaseAgent._get_rev_reg_def: <!< no rev reg exists on %s' , rr_id ) raise AbsentRevReg ( 'No rev reg exists on {}' . format ( rr_id ) ) if revo_cache_entry is None : REVO_CACHE [ rr_id ] = RevoCacheEntry ( rr_def , None ) else : REVO_CACHE [ rr_id ] . rev_reg_def = rr_def LOGGER . debug ( '_BaseAgent._get_rev_reg_def <<< %s' , rv_json ) return rv_json | 457 | https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/base.py#L289-L329 | [
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Unset the TypedFields on the input entity . | def unset ( entity , * types ) : if not types : types = ( TypedField , ) fields = list ( entity . _fields . keys ( ) ) remove = ( x for x in fields if isinstance ( x , types ) ) for field in remove : del entity . _fields [ field ] | 460 | https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L17-L32 | [
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Return True if the input TypedField field contains instance attributes that match the input parameters . | def _matches ( field , params ) : fieldattrs = six . iteritems ( params ) return all ( getattr ( field , attr ) == val for attr , val in fieldattrs ) | 461 | https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L35-L47 | [
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Validate and clean a candidate value for this field . | def _clean ( self , value ) : if value is None : return None elif self . type_ is None : return value elif self . check_type ( value ) : return value elif self . is_type_castable : # noqa return self . type_ ( value ) error_fmt = "%s must be a %s, not a %s" error = error_fmt % ( self . name , self . type_ , type ( value ) ) raise TypeError ( error ) | 463 | https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L177-L190 | [
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Remove a collection Given a collection_id branch and optionally an author remove a collection on the given branch and attribute the commit to author . Returns the SHA of the commit on branch . | def remove_collection ( self , first_arg , sec_arg , third_arg , fourth_arg = None , commit_msg = None ) : if fourth_arg is None : collection_id , branch_name , author = first_arg , sec_arg , third_arg gh_user = branch_name . split ( '_collection_' ) [ 0 ] parent_sha = self . get_master_sha ( ) else : gh_user , collection_id , parent_sha , author = first_arg , sec_arg , third_arg , fourth_arg if commit_msg is None : commit_msg = "Delete Collection '%s' via OpenTree API" % collection_id return self . _remove_document ( gh_user , collection_id , parent_sha , author , commit_msg ) | 464 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/collections_store/git_actions.py#L92-L107 | [
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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 . cfg . get ( 'archive-on-close' , { } ) . get ( 'cred_def_id' , { } ) : with CRED_DEF_CACHE . lock : await self . get_cred_def ( cd_id ) for rr_id in self . cfg . get ( 'archive-on-close' , { } ) . get ( 'rev_reg_id' , { } ) : await self . _get_rev_reg_def ( rr_id ) with REVO_CACHE . lock : revo_cache_entry = REVO_CACHE . get ( rr_id , None ) if revo_cache_entry : try : await revo_cache_entry . get_state_json ( self . _build_rr_state_json , rv , rv ) except ClosedPool : LOGGER . warning ( 'Verifier %s is offline from pool %s, cannot update revo cache reg state for %s to %s' , self . wallet . name , self . pool . name , rr_id , rv ) if archive : Caches . archive ( self . dir_cache ) LOGGER . debug ( 'Verifier.load_cache <<< %s' , rv ) return rv | 465 | https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/verifier.py#L165-L204 | [
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Grant permission if owner or admin . | def can ( self ) : return str ( current_user . get_id ( ) ) == str ( self . community . id_user ) or DynamicPermission ( ActionNeed ( 'admin-access' ) ) . can ( ) | 466 | https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/permissions.py#L46-L49 | [
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Return the python representation of the class represented by this object | def as_python ( self , name : str ) -> str : if self . _map_valuetype : return self . map_as_python ( name ) else : return self . obj_as_python ( name ) | 469 | https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_objectexpr_parser.py#L87-L92 | [
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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 . append ( i ) return x | 471 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L18-L29 | [
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Return the numeric part of the newest study_id | def _determine_next_study_id ( self ) : if self . _doc_counter_lock is None : self . _doc_counter_lock = Lock ( ) prefix = self . _new_study_prefix lp = len ( prefix ) n = 0 # this function holds the lock for quite awhile, # but it only called on the first instance of # of creating a new study with self . _doc_counter_lock : with self . _index_lock : for k in self . study_index . keys ( ) : if k . startswith ( prefix ) : try : pn = int ( k [ lp : ] ) if pn > n : n = pn except : pass nsi_contents = self . _read_master_branch_resource ( self . _id_minting_file , is_json = True ) if nsi_contents : self . _next_study_id = nsi_contents [ 'next_study_id' ] if self . _next_study_id <= n : m = 'next_study_id in {} is set lower than the ID of an existing study!' m = m . format ( self . _id_minting_file ) raise RuntimeError ( m ) else : # legacy support for repo with no next_study_id.json file self . _next_study_id = n self . _advance_new_study_id ( ) | 472 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L246-L279 | [
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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_minting_file , commit_msg = content , is_json = False ) return c | 473 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L281-L296 | [
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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 , author = first_arg , sec_arg , third_arg , fourth_arg if commit_msg is None : commit_msg = "Delete Study #%s via OpenTree API" % study_id return self . _remove_document ( gh_user , study_id , parent_sha , author , commit_msg ) | 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 ( ) RecordIndexer ( ) . index_by_id ( record . id ) | 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 : return otus . values ( ) [ 0 ] [ 'otuById' ] o_dict = { } for ob in nex_obj . get ( 'otus' , [ ] ) : for o in ob . get ( 'otu' , [ ] ) : oid = o [ '@id' ] o_dict [ oid ] = o return o_dict | 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 . get ( 'country' , '' ) . upper ( ) if country_code != geo . get_supported_country ( country_code ) : return http . HttpResponseBadRequest ( ) if hasattr ( request , 'session' ) : request . session [ geo . COUNTRY_SESSION_KEY ] = country_code else : response . set_cookie ( geo . COUNTRY_COOKIE_NAME , country_code , max_age = geo . COUNTRY_COOKIE_AGE , path = geo . COUNTRY_COOKIE_PATH ) return response else : return http . HttpResponseNotAllowed ( [ '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 ( record . id ) ] ) ) | 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 , kwargs = kwargs ) | 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_dict = query_dict , exact = exact , verbose = verbose , valid_keys = self . tree_search_term_set , kwargs = kwargs ) if wrap_response : return TreeRefList ( resp ) return resp | 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 , exact = exact , verbose = verbose , valid_keys = self . study_search_term_set , kwargs = kwargs ) | 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_AMENDMENT_STORE if _THE_TAXONOMIC_AMENDMENT_STORE is None : _THE_TAXONOMIC_AMENDMENT_STORE = _TaxonomicAmendmentStore ( repos_dict = repos_dict , repos_par = repos_par , with_caching = with_caching , assumed_doc_version = assumed_doc_version , git_ssh = git_ssh , pkey = pkey , git_action_class = git_action_class , mirror_info = mirror_info , infrastructure_commit_author = infrastructure_commit_author ) return _THE_TAXONOMIC_AMENDMENT_STORE | 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 : content_id = kwargs . get ( 'content_id' ) if content_id is None : content_id = _get_content_id_from ( * * kwargs ) else : content , content_id = _sniff_content_from_kwargs ( * * kwargs ) if content is None : content = 'study' return PhyloSchema ( content = content , content_id = content_id , format_str = format_str , version = nexson_version , otu_label = otu_label , repo_nexml2json = kwargs . get ( 'repo_nexml2json' ) , bracket_ingroup = bool ( kwargs . get ( 'bracket_ingroup' , False ) ) , cull_nonmatching = kwargs . get ( 'cull_nonmatching' ) ) | 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 pristine_if_invalid is False then the object may be corrupted if it is an invalid nexson struct . Setting this to False can result in faster translation but if an exception is raised the object may be polluted with partially constructed fields for the out_nexson_format . | 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 == out_nexson_format : if sort_arbitrary : sort_arbitrarily_ordered_nexson ( blob ) return blob two2zero = _is_by_id_hbf ( out_nexson_format ) and _is_badgerfish_version ( current_format ) zero2two = _is_by_id_hbf ( current_format ) and _is_badgerfish_version ( out_nexson_format ) if two2zero or zero2two : # go from 0.0 -> 1.0 then the 1.0->1.2 should succeed without nexml... blob = convert_nexson_format ( blob , DIRECT_HONEY_BADGERFISH , current_format = current_format , remove_old_structs = remove_old_structs , pristine_if_invalid = pristine_if_invalid ) current_format = DIRECT_HONEY_BADGERFISH ccdict = { 'output_format' : out_nexson_format , 'input_format' : current_format , 'remove_old_structs' : remove_old_structs , 'pristine_if_invalid' : pristine_if_invalid } ccfg = ConversionConfig ( ccdict ) if _is_badgerfish_version ( current_format ) : converter = Badgerfish2DirectNexson ( ccfg ) elif _is_badgerfish_version ( out_nexson_format ) : assert _is_direct_hbf ( current_format ) converter = Direct2BadgerfishNexson ( ccfg ) elif _is_direct_hbf ( current_format ) and ( out_nexson_format == BY_ID_HONEY_BADGERFISH ) : converter = Direct2OptimalNexson ( ccfg ) elif _is_direct_hbf ( out_nexson_format ) and ( current_format == BY_ID_HONEY_BADGERFISH ) : converter = Optimal2DirectNexson ( ccfg ) else : raise NotImplementedError ( 'Conversion from {i} to {o}' . format ( i = current_format , o = out_nexson_format ) ) blob = converter . convert ( blob ) if sort_arbitrary : sort_arbitrarily_ordered_nexson ( blob ) return blob | 499 | https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/__init__.py#L646-L699 | [
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