resolved conficts

Merge branch 'master' of https://gitlab.isb-sib.ch/bgao/arraymapVariant-callsMapping

arraymap2ga4gh.py

@@ -201,7 +201,6 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
                     continue
                 else:
 
-
                     # new biosample_id, create new biosample
                     icdmcode = get_attribute('ICDMORPHOLOGYCODE', sample)
                     icdmcode_termid = 'PGX:ICDOM:'+re.sub('/', '_', icdmcode)
@@ -296,21 +295,21 @@ def cli(input_db, input_collection, output_db, output_collection_individuals, ou
                     # if same individual_id exists, report an error
                     if log is not None:
                         click.echo('Duplicate individual_id: '+individual_id, file=log)
-                else:
-                    individuals[individual_id] = { 'id': individual_id, 'species': {'term_id': 'NCBITaxon:9606', 'term_label': 'Homo sapiens' }, 'sex': {'term_id': 'PATO:0020000', 'term_label': 'genotypic sex' }, 'updated': datetime.datetime.utcnow() }
-                    no_individuals +=1
 
+                else:
                     # processing specific attributes
+
+                    # sex
+                    sex = {'term_id': 'PATO:0020000', 'term_label': 'genotypic sex' }
                     FemaleMatchObj = re.search('^f', sample['SEX'])
                     MaleMatchObj = re.search('^m', sample['SEX'])
                     if MaleMatchObj:
-                    individuals[individual_id]['sex'] = {'term_id': 'PATO:0020001', 'term_label': 'male genotypic sex' }
+                        sex = {'term_id': 'PATO:0020001', 'term_label': 'male genotypic sex' }
                     elif FemaleMatchObj:
-                    individuals[individual_id]['sex'] = {'term_id': 'PATO:0020002', 'term_label': 'female genotypic sex' }
-
-                # adding external identifiers
-                individuals[individual_id]['external_identifiers'] = external_ids
+                        sex = {'term_id': 'PATO:0020002', 'term_label': 'female genotypic sex' }
 
+                    individuals[individual_id] = { 'id': individual_id, 'species': {'term_id': 'NCBITaxon:9606', 'term_label': 'Homo sapiens' }, 'sex': sex, 'external_identifiers': external_ids, 'updated': datetime.datetime.utcnow() }
+                    no_individuals +=1
 
 
                 ################################################################