diff --git a/isatools/isajson.py b/isatools/isajson.py index 79616a52..7797bf82 100644 --- a/isatools/isajson.py +++ b/isatools/isajson.py @@ -68,7 +68,7 @@ def _build_assay_graph(process_sequence=list()): status=OntologyAnnotation( name=publication_json['status']['annotationValue'], term_accession=publication_json['status']['termAccession'], - term_source=publication_json['status']['termSource'] + term_source=term_source_dict[publication_json['status']['termSource']] ) ) try: @@ -122,13 +122,13 @@ def _build_assay_graph(process_sequence=list()): for assay_json in study_json['assays']: for assay_characteristics_category_json in assay_json['characteristicCategories']: characteristic_category = OntologyAnnotation( + id_=assay_characteristics_category_json['@id'], name=assay_characteristics_category_json['characteristicType']['annotationValue'], term_source=term_source_dict[assay_characteristics_category_json['characteristicType']['termSource']], term_accession=assay_characteristics_category_json['characteristicType']['termAccession'], ) # study.characteristic_categories.append(characteristic_category) categories_dict[characteristic_category.id] = characteristic_category - for study_json in isajson['studies']: logger.debug('Start building Study object') study = Study(