def test_multiple_mappings(self): trait1 = trait.Trait("barrett esophagus/esophageal adenocarcinoma", "http://www.ebi.ac.uk/efo/EFO_0000478", "esophageal adenocarcinoma", 1) trait2 = trait.Trait("barrett esophagus/esophageal adenocarcinoma", "http://www.ebi.ac.uk/efo/EFO_0000280", "Barrett's esophagus", 1) test_trait_list = clinvar_to_evidence_strings.create_trait_list( ["barrett esophagus/esophageal adenocarcinoma"], MAPPINGS.trait_2_efo, 1) self.assertEqual([trait1, trait2], test_trait_list)
def create_trait_list(name_list, trait_2_efo_dict, trait_counter): trait_string, mappings = trait.map_efo(trait_2_efo_dict, name_list) if mappings is None: return None new_trait_list = [] for mapping in mappings: new_trait_list.append( trait.Trait(trait_string, mapping[0], mapping[1], trait_counter)) # Only ClinVar records associated to a # trait with mapped EFO term will generate evidence_strings if not new_trait_list: return None return new_trait_list