DATS to JSON convertor output is not valid
The JSON output of DATS to JSON is not validated by dats-validator. For replicating error, please use the following actions:
- Download the Excel file of DATS
- Convert the DATS Excel file to a JSON file using the script available in the ng-dats-to-json branch of this repository.
- Use dats-validator script to validate the output JSON file of the previous step.
You will see following error:
Validating 2025 04 29DATS-sheet-template_202501_ITMP-mRNA data_project.json against ./schemas/project_schema.json {'name': 'IL-2 Hepatotox-Cohort', 'type': 'array', 'identifier': {'identifier': nan, '@type': 'Identifier', '@context': 'https://w3id.org/dats/context/sdo/identifier_info_sdo_context.jsonld'}, '@type': 'Study', '@context': 'https://w3id.org/dats/context/sdo/study_sdo_context.jsonld', 'description': 'In vitro assays to identify IL-2 mediated hepatotoxicity', 'types': [{'value': 'Clinical trial NCIT:C71104', '@type': 'Annotation', '@context': 'https://w3id.org/dats/context/sdo/annotation_sdo_context.jsonld'}], 'studyGroups': [{'@type': 'StudyGroup', '@context': 'https://w3id.org/dats/context/sdo/studygroup_sdo_context.jsonld', 'name': 'healthy donors for CD8+ T cells; patients with unknwon disease for primary hepatocytes', 'size': '3 donors of CD8+ Tcells and 3 donors of hepatocytes', 'consentInformation': [{'name': {'value': 'informed consent', 'valueIRI': 'NCIT:C16735', '@type': 'Annotation', '@context': 'https://w3id.org/dats/context/sdo/annotation_sdo_context.jsonld'}, '@type': 'ConsentInfo', '@context': 'https://w3id.org/dats/context/sdo/consent_info_obo_context.jsonld'}]}], 'input': [{'@type': 'Material', '@context': 'https://w3id.org/dats/context/sdo/material_sdo_context.jsonld', 'name': 'input material', 'types': [{'value': 'blood, tissue samples', '@type': 'Annotation', '@context': 'https://w3id.org/dats/context/sdo/annotation_sdo_context.jsonld'}], 'taxonomy': [{'@type': 'TaxonomicInformation', '@context': 'https://w3id.org/dats/context/sdo/taxonomic_info_sdo_context.jsonld', 'name': 'Homo sapiens'}], 'derivesFrom': [{'name': 'blood, liver samples', '@type': 'AnatomicalPart', '@context': 'https://w3id.org/dats/context/sdo/anatomical_part_sdo_context.jsonld'}], 'bearerOfDisease': [{'name': 'not relevant', '@type': 'Disease', '@context': 'https://w3id.org/dats/context/sdo/disease_sdo_context.jsonld', 'identifier': {'@type': 'Identifier', '@context': 'https://w3id.org/dats/context/sdo/identifier_info_sdo_context.jsonld'}}]}], 'output': [], 'acronym': nan, 'characteristics': [{'name': {'value': 'Multi-institution Indicator', 'valueIRI': 'NCIT:C93599', '@type': 'Annotation', '@context': 'https://w3id.org/dats/context/sdo/annotation_sdo_context.jsonld'}, 'values': [{'value': 'no', '@type': 'Annotation', '@context': 'https://w3id.org/dats/context/sdo/annotation_sdo_context.jsonld'}], '@type': 'Dimension', '@context': 'https://w3id.org/dats/context/sdo/dimension_sdo_context.jsonld'}]} is not valid under any of the given schemas [0, 'additionalProperties'] Additional properties are not allowed ('type' was unexpected) [0, 'properties', 'acronym', 'type'] nan is not of type 'string' [0, 'properties', 'identifier', 'properties', 'identifier', 'type'] nan is not of type 'string' [1, 'additionalProperties'] Additional properties are not allowed ('acronym', 'studyGroups', 'name', 'characteristics', 'input', 'output', 'type' were unexpected) [1, 'properties', '@type', 'const'] 'Dataset' was expected [1, 'properties', 'identifier', 'properties', 'identifier', 'type'] nan is not of type 'string' [1, 'required'] 'title' is a required property [1, 'required'] 'creators' is a required property The following files are not valid. ['2025 04 29DATS-sheet-template_202501_ITMP-mRNA data_project.json']