def load_ontology(ontology_file): nex_session = get_session() source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()]) obiid_to_obi = dict([(x.obiid, x) for x in nex_session.query(Obi).all()]) term_to_ro_id = dict([(x.display_name, x.ro_id) for x in nex_session.query(Ro).all()]) obi_id_to_parent = {} for x in nex_session.query(ObiRelation).all(): parents = [] if x.child_id in obi_id_to_parent: parents = obi_id_to_parent[x.child_id] parents.append(x.parent_id) obi_id_to_parent[x.child_id] = parents #################################### fw = open(log_file, "w") is_sgd_term = {} data = read_owl(ontology_file, ontology) [update_log, to_delete_list] = load_new_data(nex_session, data, source_to_id, obiid_to_obi, term_to_ro_id['is a'], obi_id_to_parent, fw) write_summary_and_send_email(fw, update_log, to_delete_list) nex_session.close() fw.close()
def load_ontology(ontology_file): nex_session = get_session() log.info(str(datetime.now())) log.info("Getting data from database...") source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()]) chebiid_to_chebi = dict([(x.chebiid, x) for x in nex_session.query(Chebi).all()]) chebi_id_to_alias = {} for x in nex_session.query(ChebiAlia).all(): if x.alias_type in ['PharmGKB ID', 'YeastPathway ID']: continue aliases = [] if x.chebi_id in chebi_id_to_alias: aliases = chebi_id_to_alias[x.chebi_id] aliases.append((x.display_name, x.alias_type)) chebi_id_to_alias[x.chebi_id] = aliases #################################### fw = open(log_file, "w") log.info("Reading data from ontology file...") is_3_star_term = {} data = read_owl(ontology_file, ontology, is_3_star_term) log.info("Updating chebi ontology data in the database...") [update_log, to_delete_list, term_name_changed] = load_new_data(nex_session, data, source_to_id, chebiid_to_chebi, chebi_id_to_alias, is_3_star_term, fw) log.info("Writing loading summary...") write_summary_and_send_email(fw, update_log, to_delete_list, term_name_changed) nex_session.close() fw.close() log.info(str(datetime.now())) log.info("Done!\n\n")
def load_ontology(ontology_file): nex_session = get_session() source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()]) taxid_to_taxonomy = dict([(x.taxid, x) for x in nex_session.query(Taxonomy).all()]) term_to_ro_id = dict([(x.display_name, x.ro_id) for x in nex_session.query(Ro).all()]) taxonomy_id_to_alias = {} for x in nex_session.query(TaxonomyAlia).all(): aliases = [] if x.taxonomy_id in taxonomy_id_to_alias: aliases = taxonomy_id_to_alias[x.taxonomy_id] aliases.append((x.display_name, x.alias_type)) taxonomy_id_to_alias[x.taxonomy_id] = aliases taxonomy_id_to_parent = {} for x in nex_session.query(TaxonomyRelation).all(): parents = [] if x.child_id in taxonomy_id_to_parent: parents = taxonomy_id_to_parent[x.child_id] parents.append(x.parent_id) taxonomy_id_to_parent[x.child_id] = parents #################################### fw = open(log_file, "w") [filtered_set, id_to_rank] = children_for_taxonomy_ancestor(ontology_file, ancestor) ## total 1037 in the filtered set ## print "COUNT=", len(filtered_set) data = read_owl(ontology_file, ontology) [update_log, to_delete_list ] = load_new_data(nex_session, data, source_to_id, taxid_to_taxonomy, term_to_ro_id['is a'], taxonomy_id_to_alias, taxonomy_id_to_parent, filtered_set, id_to_rank, fw) write_summary_and_send_email(fw, update_log, to_delete_list) nex_session.close() fw.close()
def load_ontology(ontology_file): nex_session = get_session() source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()]) soid_to_so = dict([(x.soid, x) for x in nex_session.query(So).all()]) term_to_ro_id = dict([(x.display_name, x.ro_id) for x in nex_session.query(Ro).all()]) so_id_to_alias = {} for x in nex_session.query(SoAlia).all(): aliases = [] if x.so_id in so_id_to_alias: aliases = so_id_to_alias[x.so_id] aliases.append((x.display_name, x.alias_type)) so_id_to_alias[x.so_id] = aliases so_id_to_parent = {} for x in nex_session.query(SoRelation).all(): parents = [] if x.child_id in so_id_to_parent: parents = so_id_to_parent[x.child_id] parents.append(x.parent_id) so_id_to_parent[x.child_id] = parents #################################### fw = open(log_file, "w") is_sgd_term = {} data = read_owl(ontology_file, ontology) [update_log, to_delete_list] = load_new_data(nex_session, data, source_to_id, soid_to_so, term_to_ro_id['is a'], so_id_to_alias, so_id_to_parent, fw) write_summary_and_send_email(fw, update_log, to_delete_list) nex_session.close() fw.close()
def load_ontology(ontology_file): nex_session = get_session() source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()]) roid_to_ro = dict([(x.roid, x) for x in nex_session.query(Ro).all()]) fw = open(log_file, "w") data = read_owl(ontology_file, ontology) [update_log, to_delete_list] = load_new_data(nex_session, data, source_to_id[src], roid_to_ro, fw) write_summary_and_send_email(fw, update_log, to_delete_list) nex_session.close() fw.close()
def load_ontology(ontology_file): nex_session = get_session() log.info(str(datetime.now())) log.info("Getting data from database...") source_to_id = dict([(x.display_name, x.source_id) for x in nex_session.query(Source).all()]) doid_to_disease = dict([(x.doid, x) for x in nex_session.query(Disease).all()]) term_to_ro_id = dict([(x.display_name, x.ro_id) for x in nex_session.query(Ro).all()]) edam_to_id = dict([(x.format_name, x.edam_id) for x in nex_session.query(Edam).all()]) disease_id_to_alias = {} for x in nex_session.query(DiseaseAlias).all(): aliases = [] if x.disease_id in disease_id_to_alias: aliases = disease_id_to_alias[x.disease_id] aliases.append((x.display_name, x.alias_type)) disease_id_to_alias[x.disease_id] = aliases disease_id_to_parent = {} for x in nex_session.query(DiseaseRelation).all(): parents = [] if x.child_id in disease_id_to_parent: parents = disease_id_to_parent[x.child_id] parents.append(x.parent_id) disease_id_to_parent[x.child_id] = parents #################################### fw = open(log_file, "w") log.info(str(datetime.now())) log.info("Reading data from owl file...") is_sgd_term = {} data = read_owl(ontology_file, ontology) log.info(str(datetime.now())) log.info("Loading data into database...") [update_log, to_delete_list] = load_new_data(nex_session, data, source_to_id, doid_to_disease, term_to_ro_id['is a'], disease_id_to_alias, disease_id_to_parent, fw) # log.info("Uploading file to S3...") # update_database_load_file_to_s3(nex_session, ontology_file, source_to_id, edam_to_id) log.info("Writing loading summary...") write_summary_and_send_email(fw, update_log, to_delete_list) nex_session.close() fw.close() log.info(str(datetime.now())) log.info("Done!\n\n")