EMMAA modules reference

• EMMAA Statement (emmaa.statements)
  • EmmaaStatement
  • add_emmaa_annotations()
  • check_stmt()
  • filter_emmaa_stmts_by_metadata()
  • filter_indra_stmts_by_metadata()
  • is_internal()
  • to_emmaa_stmts()
• EMMAA Model (emmaa.model)
  • EmmaaModel
    • EmmaaModel.stmts
    • EmmaaModel.assembly_config
    • EmmaaModel.test_config
    • EmmaaModel.reading_config
    • EmmaaModel.query_config
    • EmmaaModel.search_terms
    • EmmaaModel.ndex_network
    • EmmaaModel.assembled_stmts
    • EmmaaModel.add_paper_ids()
    • EmmaaModel.add_statements()
    • EmmaaModel.assemble_dynamic_pysb()
    • EmmaaModel.assemble_pybel()
    • EmmaaModel.assemble_pysb()
    • EmmaaModel.assemble_signed_graph()
    • EmmaaModel.assemble_unsigned_graph()
    • EmmaaModel.eliminate_copies()
    • EmmaaModel.extend_unique()
    • EmmaaModel.get_assembled_entities()
    • EmmaaModel.get_entities()
    • EmmaaModel.get_indra_stmts()
    • EmmaaModel.get_new_readings()
    • EmmaaModel.get_paper_ids_from_stmts()
    • EmmaaModel.load_from_s3()
    • EmmaaModel.run_assembly()
    • EmmaaModel.save_to_s3()
    • EmmaaModel.search_biorxiv()
    • EmmaaModel.search_elsevier()
    • EmmaaModel.search_literature()
    • EmmaaModel.search_pubmed()
    • EmmaaModel.to_json()
    • EmmaaModel.update_from_disease_map()
    • EmmaaModel.update_from_files()
    • EmmaaModel.update_to_ndex()
    • EmmaaModel.update_with_cord19()
    • EmmaaModel.upload_to_ndex()
  • get_assembled_statements()
  • get_model_stats()
  • get_models()
  • last_updated_date()
  • load_config_from_s3()
  • load_extra_evidence()
  • load_stmts_from_s3()
  • pysb_to_gromet()
  • save_config_to_s3()
• EMMAA Model Test Framework (emmaa.model_tests)
  • EmmaaTest
    • EmmaaTest.get_entities()
  • ModelManager
    • ModelManager.mc_mapping
    • ModelManager.mc_types
    • ModelManager.entities
    • ModelManager.applicable_tests
    • ModelManager.date_str
    • ModelManager.path_stmt_types
    • ModelManager.add_result()
    • ModelManager.add_test()
    • ModelManager.answer_dynamic_query()
    • ModelManager.answer_intervention_query()
    • ModelManager.answer_open_query()
    • ModelManager.answer_path_query()
    • ModelManager.answer_queries()
    • ModelManager.get_updated_mc()
    • ModelManager.hash_response_list()
    • ModelManager.process_response()
    • ModelManager.results_to_json()
    • ModelManager.run_all_tests()
    • ModelManager.run_tests_per_mc()
    • ModelManager.save_assembled_statements()
    • ModelManager.upload_results()
  • RefinementTestConnector
    • RefinementTestConnector.applicable()
  • ScopeTestConnector
    • ScopeTestConnector.applicable()
  • StatementCheckingTest
    • StatementCheckingTest.check()
    • StatementCheckingTest.get_entities()
  • TestConnector
    • TestConnector.applicable()
  • TestManager
    • TestManager.make_tests()
    • TestManager.run_tests()
  • load_tests_from_s3()
  • model_to_tests()
  • run_model_tests_from_s3()
  • save_tests_to_s3()
• Analyze model test results (emmaa.analyze_tests_results)
  • ModelRound
    • ModelRound.stmts_by_papers
    • ModelRound.get_agent_distribution()
    • ModelRound.get_all_raw_paper_ids()
    • ModelRound.get_assembled_stmts_by_paper()
    • ModelRound.get_english_statements_by_hash()
    • ModelRound.get_number_raw_papers()
    • ModelRound.get_paper_titles_and_links()
    • ModelRound.get_papers_distribution()
    • ModelRound.get_statement_types()
    • ModelRound.get_statements_by_evidence()
    • ModelRound.get_stmt_hashes()
    • ModelRound.get_total_statements()
  • ModelStatsGenerator
    • ModelStatsGenerator.json_stats
    • ModelStatsGenerator.make_changes_over_time()
    • ModelStatsGenerator.make_curation_summary()
    • ModelStatsGenerator.make_model_delta()
    • ModelStatsGenerator.make_model_summary()
    • ModelStatsGenerator.make_paper_delta()
    • ModelStatsGenerator.make_paper_summary()
    • ModelStatsGenerator.make_stats()
  • Round
    • Round.function_mapping
    • Round.find_delta_hashes()
  • StatsGenerator
    • StatsGenerator.json_stats
    • StatsGenerator.make_changes_over_time()
  • TestRound
    • TestRound.mc_types_results
    • TestRound.tests
    • TestRound.english_test_results
    • TestRound.get_applied_test_hashes()
    • TestRound.get_number_passed_tests()
    • TestRound.get_passed_test_hashes()
    • TestRound.get_total_applied_tests()
    • TestRound.passed_over_total()
  • TestStatsGenerator
    • TestStatsGenerator.json_stats
    • TestStatsGenerator.make_changes_over_time()
    • TestStatsGenerator.make_stats()
    • TestStatsGenerator.make_test_summary()
    • TestStatsGenerator.make_tests_delta()
  • generate_stats_on_s3()
• Query classes (emmaa.queries)
  • ComparativeInterventionProperty
  • DynamicProperty
    • DynamicProperty.get_temporal_pattern()
  • GroundingError
  • OpenSearchQuery
    • OpenSearchQuery.path_stmt
  • PathProperty
    • PathProperty.get_entities()
  • Query
  • SimpleInterventionProperty
  • StructuralProperty
  • get_agent_from_gilda()
  • get_agent_from_text()
  • get_agent_from_trips()
• Process model queries (emmaa.answer_queries)
  • QueryManager
    • QueryManager.answer_immediate_query()
    • QueryManager.answer_registered_queries()
    • QueryManager.get_registered_queries()
    • QueryManager.retrieve_results_from_hashes()
  • answer_queries_from_s3()
  • format_results()
• Priors (emmaa.priors)
  • SearchTerm
    • SearchTerm.from_json()
    • SearchTerm.to_json()
  • get_drugs_for_gene()
  • Literature Prior (emmaa.priors.literature_prior)
    • get_raw_statements_for_pmids()
    • make_search_terms()
  • TCGA Cancer Prior (emmaa.priors.cancer_prior)
    • TcgaCancerPrior
      • TcgaCancerPrior.find_drugs_for_genes()
      • TcgaCancerPrior.get_mutated_genes()
      • TcgaCancerPrior.get_relevant_nodes()
      • TcgaCancerPrior.load_sif_prior()
      • TcgaCancerPrior.make_prior()
      • TcgaCancerPrior.search_terms_from_nodes()
  • Gene List Prior (emmaa.priors.gene_list_prior)
    • GeneListPrior
      • GeneListPrior.make_config()
      • GeneListPrior.make_gene_statements()
      • GeneListPrior.make_model()
      • GeneListPrior.make_search_terms()
    • agent_from_gene_name()
  • Reactome Prior (emmaa.priors.reactome_prior)
    • find_drugs_for_genes()
    • get_genes_contained_in_pathway()
    • get_pathways_containing_gene()
    • make_prior_from_genes()
    • rx_id_from_up_id()
    • up_id_from_rx_id()
  • Querying Prior Statements (emmaa.priors.prior_stmts)
    • get_stmts_for_gene()
    • get_stmts_for_gene_list()
• Readers (emmaa.readers)
  • AWS reader (emmaa.readers.aws_reader)
    • read_pmid_search_terms()
    • read_pmids()
  • INDRA DB client reader (emmaa.readers.db_client_reader)
    • read_db_doi_search_terms()
    • read_db_ids_search_terms()
    • read_db_pmid_search_terms()
• EMMAA’s Database (emmaa.db)
  • The Database Schema (emmaa.db.schema)
    • Query
    • Result
    • Statement
    • User
    • UserModel
    • UserQuery
  • Database Manager (emmaa.db.manager)
    • EmmaaDatabaseError
    • EmmaaDatabaseManager
      • EmmaaDatabaseManager.create_tables()
      • EmmaaDatabaseManager.drop_tables()
    • QueryDatabaseManager
      • QueryDatabaseManager.add_user()
      • QueryDatabaseManager.get_all_result_hashes()
      • QueryDatabaseManager.get_model_users()
      • QueryDatabaseManager.get_queries()
      • QueryDatabaseManager.get_results()
      • QueryDatabaseManager.get_subscribed_queries()
      • QueryDatabaseManager.get_subscribed_users()
      • QueryDatabaseManager.get_user_models()
      • QueryDatabaseManager.put_queries()
      • QueryDatabaseManager.put_results()
      • QueryDatabaseManager.subscribe_to_model()
      • QueryDatabaseManager.update_email_subscription()
    • StatementDatabaseManager
      • StatementDatabaseManager.add_model_from_s3()
      • StatementDatabaseManager.add_statements()
      • StatementDatabaseManager.build_from_s3()
      • StatementDatabaseManager.delete_statements()
      • StatementDatabaseManager.get_latest_date()
      • StatementDatabaseManager.get_number_of_dates()
      • StatementDatabaseManager.get_number_of_statements()
      • StatementDatabaseManager.get_oldest_date()
      • StatementDatabaseManager.get_path_counts()
      • StatementDatabaseManager.get_statements()
      • StatementDatabaseManager.get_statements_by_hash()
      • StatementDatabaseManager.update_statements_path_counts()
• AWS model update and testing pipeline (emmaa.aws_lambda_functions)
  • lambda_handler()
  • lambda_handler()
  • lambda_handler()
  • lambda_handler()
  • upload_function()
• xDD client
  • get_document_figures()
  • get_document_objects()
  • get_figures_from_objects()
  • get_figures_from_query()
  • send_document_search_request()
  • send_query_search_request()
  • send_request()
• EMMAA’s Subscription Service (emmaa.subscription)
  • Notifications functions (emmaa.subscription.notifications)
    • EmailHtmlBody
    • ModelDeltaEmailHtmlBody
      • ModelDeltaEmailHtmlBody.render()
    • QueryEmailHtmlBody
      • QueryEmailHtmlBody.render()
    • get_all_stats()
    • get_all_update_messages()
    • get_model_deltas()
    • get_user_query_delta()
    • make_html_report_per_user()
    • make_model_html_email()
    • make_reports_from_results()
    • make_str_report_per_user()
    • model_update_notify()
    • tweet_deltas()
    • update_path_counts()
  • Email Service (emmaa.subscription.email_service)
    • close_to_quota_max()
    • get_send_statistics()
    • send_email()
  • Email Utilities (emmaa.subscription.email_util)
    • generate_signature()
    • generate_unsubscribe_link()
    • generate_unsubscribe_qs()
    • get_email_subscriptions()
    • register_email_unsubscribe()
    • verify_email_signature()
• Utilities (emmaa.util)
  • NotAClassName
  • does_exist()
  • find_latest_emails()
  • find_latest_s3_file()
  • find_latest_s3_files()
  • find_nth_latest_s3_file()
  • get_credentials()
  • get_s3_client()
  • make_date_str()
  • s3_put()
  • sort_s3_files_by_date_str()
  • sort_s3_files_by_last_mod()
  • strip_out_date()
• Functions for node and edge filtering (emmaa.filter_functions)
  • filter_chem_mesh_go()
  • filter_to_internal_edges()
  • register_filter()