EMMAA modules reference¶
- EMMAA Statement (
emmaa.statements
) - 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
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
ScopeTestConnector
StatementCheckingTest
TestConnector
TestManager
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
StatsGenerator
TestRound
TestStatsGenerator
generate_stats_on_s3()
- Query classes (
emmaa.queries
) - Process model queries (
emmaa.answer_queries
) - Priors (
emmaa.priors
) - Readers (
emmaa.readers
) - EMMAA’s Database (
emmaa.db
)- The Database Schema (
emmaa.db.schema
) - Database Manager (
emmaa.db.manager
)EmmaaDatabaseError
EmmaaDatabaseManager
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()
- The Database Schema (
- AWS model update and testing pipeline (
emmaa.aws_lambda_functions
) - xDD client
- EMMAA’s Subscription Service (
emmaa.subscription
)- Notifications functions (
emmaa.subscription.notifications
)EmailHtmlBody
ModelDeltaEmailHtmlBody
QueryEmailHtmlBody
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
) - Email Utilities (
emmaa.subscription.email_util
)
- Notifications functions (
- Utilities (
emmaa.util
) - Functions for node and edge filtering (
emmaa.filter_functions
)