Cleanup and fix datafile accessions

[kdp-cloud]

• Cleaning up of mars_cli.py
• Better logging:
  • extra handler for stdout, with color-coded formatting for different logging levels, instead of printing to stdout.
  • logs in stdout are identical to the ones in the logfiles
  • logs from external libraries are also logged

• Adds Study related accessions as a study comment. E.g. If ENA returns the Study accession 'ERP167466' in the receipt. it will add the following comment:

          {
            "name": "ena_study_accession",
            "value": "ERP167466"
          }

• Add it as a comment in the assay as well
• Add datafile accessions to the updated ISA-JSON

[kdp-cloud]

Test submission to BioSamples and ENA

2025-01-06 10:49:00,067 - MARS-CLI - INFO - ############# Welcome to the MARS CLI. #############
2025-01-06 10:49:00,067 - MARS-CLI - INFO - Running in Development environment
2025-01-06 10:49:00,068 - MARS-CLI - INFO - Starting submission of the ISA JSON to the target repositories: biosamples, ena.
2025-01-06 10:49:00,069 - MARS-CLI - INFO - ISA JSON with investigation 'Bob's investigation' is valid.
2025-01-06 10:49:01,857 - MARS-CLI - INFO - Submission to biosamples was successful. Result:
{'targetRepository': 'biosamples', 'errors': [], 'info': [], 'accessions': [{'value': 'SAMEA131505508', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'materials'}, {'key': 'samples', 'where': {'key': 'name', 'value': 'leaf 1'}}]}, {'value': 'SAMEA131505507', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'materials'}, {'key': 'sources', 'where': {'key': 'name', 'value': 'plant 1'}}]}]}
2025-01-06 10:49:02,517 - MARS-CLI - INFO - Uploading ENA_TEST2.R2.fastq.gz to FTP
2025-01-06 10:49:07,722 - MARS-CLI - INFO - Submission to ena was successful. Result:
{'targetRepository': 'ena', 'errors': [], 'info': [{'message': 'This submission is a TEST submission and will be discarded within 24 hours'}], 'accessions': [{'value': 'ERP167530', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}]}, {'value': 'ERX13507164', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'assays', 'where': {'key': '@id', 'value': '#assay/18_20_21'}}, {'key': 'materials'}, {'key': 'otherMaterials', 'where': {'key': '@id', 'value': '#other_material/332'}}]}, {'value': 'ERX13507165', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'assays', 'where': {'key': '@id', 'value': '#assay/18_20_21'}}, {'key': 'materials'}, {'key': 'otherMaterials', 'where': {'key': '@id', 'value': '#other_material/333'}}]}]}

Repository study accession is dumped as a study comment and an assay comment:

DataFile accessions SHOULD be present as a comment in dataFiles in the updated ISA-JSON. They are not present in this example because the receipt did not include the accessions. However, there are some tests written to simulate this behavior.