mars-cli --development submit          --credential-service-name biosamples          --credentials-file /home/bedro/Documents/MARS/mars-cli/tests/test_credentials_example.json          --file-transfer ftp          --data-files /home/bedro/Documents/MARS/test-data/ENA_TEST2.R2.fastq.gz   --submit-to-metabolights False      --output final-isa          /home/bedro/Documents/MARS/test-data/biosamples-input-isa.json
/home/bedro/.config/python_keyring
keyring.backends.SecretService.Keyring (priority: 5)
############# Welcome to the MARS CLI. #############
Running in Development environment
Starting submission of the ISA JSON to the target repositories: biosamples, ena.
ISA JSON with investigation 'Bob's investigation' is valid.
Submission to TargetRepository.BIOSAMPLES was successful. Result:
{'targetRepository': 'biosamples', 'errors': [], 'info': [], 'accessions': [{'value': 'SAMEA131504279', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'materials'}, {'key': 'samples', 'where': {'key': 'name', 'value': 'leaf 1'}}]}, {'value': 'SAMEA131504278', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'materials'}, {'key': 'sources', 'where': {'key': 'name', 'value': 'plant 1'}}]}]}
#sample/331: comments=[] id='#ontology_annotation/accession_#sample/331' annotationValue='SAMEA131504279' termAccession=None termSource=None.
#source/330: comments=[] id='#ontology_annotation/accession_#source/330' annotationValue='SAMEA131504278' termAccession=None termSource=None.
ENA_TEST2.R2.fastq.gz already exists and has the same size on the FTP, skipping
Start submitting to TargetRepository.ENA.
Submission to TargetRepository.ENA was successful. Result:
{'targetRepository': 'ena', 'errors': [{'type': 'INVALID_METADATA', 'message': 'ENA receipt: Accession number of Arabidopsis thaliana-0.7403975790744531 is NULL'}, {'type': 'INVALID_METADATA', 'message': 'ENA receipt: Accession number of #other_material/332-0.7403975790744531 is NULL'}, {'type': 'INVALID_METADATA', 'message': 'ENA receipt: Accession number of #other_material/333-0.7403975790744531 is NULL'}, {'type': 'INVALID_METADATA', 'message': 'ENA receipt: Accession number of #assay/18_20_21-0.7403975790744531 is NULL'}, {'type': 'INVALID_METADATA', 'message': 'File ENA_TEST2.R2.fastq.gz has already been submitted in ERR14097866 and is waiting to be processed'}], 'info': [{'message': 'This submission is a TEST submission and will be discarded within 24 hours'}], 'accessions': []}
Update ISA-JSON based on receipt from TargetRepository.ENA.