Readers (emmaa.readers)

AWS reader (emmaa.readers.aws_reader)

emmaa.readers.aws_reader.read_pmid_search_terms(pmid_search_terms)[source]

Return extracted EmmaaStatements given a PMID-search term dict.

Parameters:pmid_search_terms (dict) – A dict representing a set of PMIDs pointing to search terms that produced them.
Returns:A list of EmmaaStatements extracted from the given PMIDs.
Return type:list[emmaa.model.EmmaaStatement]
emmaa.readers.aws_reader.read_pmids(pmids, date)[source]

Return extracted INDRA Statements per PMID after running reading on AWS.

Parameters:
  • pmids (list[str]) – A list of PMIDs to read.
  • date (datetime) – The date and time associated with the reading, typically the current time.
Returns:

A dict of PMIDs and the list of Statements extracted for the given PMID by reading.
Return type:

dict[str, list[indra.statements.Statement]

INDRA DB client reader (emmaa.readers.db_client_reader)

emmaa.readers.db_client_reader.read_db_doi_search_terms(doi_search_terms)[source]

Return extracted EmmaaStatements from INDRA database given a DOI-search term dict.

Parameters:doi_search_terms (dict) – A dict representing a set of DOIs pointing to search terms that produced them.
Returns:A list of EmmaaStatements extracted from the given DOIs.
Return type:list[emmaa.model.EmmaaStatement]
emmaa.readers.db_client_reader.read_db_ids_search_terms(id_search_terms, id_type)[source]

Return extracted EmmaaStatements from INDRA database given an ID-search term dict.

Parameters:id_search_terms (dict) – A dict representing a set of IDs pointing to search terms that produced them.
Returns:A list of EmmaaStatements extracted from the given IDs.
Return type:list[emmaa.model.EmmaaStatement]
emmaa.readers.db_client_reader.read_db_pmid_search_terms(pmid_search_terms)[source]

Return extracted EmmaaStatements from INDRA database given a PMID-search term dict.

Parameters:pmid_search_terms (dict) – A dict representing a set of PMIDs pointing to search terms that produced them.
Returns:A list of EmmaaStatements extracted from the given PMIDs.
Return type:list[emmaa.model.EmmaaStatement]