Multi auth provider credentials

[kdp-cloud]

• Changes the authentication to incorporate multiple sets of credentials, which are repository specific.
• Makes the file-transfer protocol mandatory

[kdp-cloud]

Test towards BioSamples and ENA:

############# 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 biosamples was successful. Result:
{'targetRepository': 'biosamples', 'errors': [], 'info': [], 'accessions': [{'value': 'SAMEA131504475', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}, {'key': 'materials'}, {'key': 'samples', 'where': {'key': 'name', 'value': 'leaf 1'}}]}, {'value': 'SAMEA131504474', '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='SAMEA131504475' termAccession=None termSource=None.
#source/330: comments=[] id='#ontology_annotation/accession_#source/330' annotationValue='SAMEA131504474' termAccession=None termSource=None.
ENA_TEST2.R2.fastq.gz already exists and has the same size on the FTP, skipping
Start submitting to ena.
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': 'ERP167451', 'path': [{'key': 'investigation'}, {'key': 'studies', 'where': {'key': 'title', 'value': 'Arabidopsis thaliana'}}]}, {'value': 'ERX13505762', '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': 'ERX13505763', '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'}}]}]}
Update ISA-JSON based on receipt from ena.
#other_material/332: comments=[] id='#ontology_annotation/accession_#other_material/332' annotationValue='ERX13505762' termAccession=None termSource=None.
#other_material/333: comments=[] id='#ontology_annotation/accession_#other_material/333' annotationValue='ERX13505763' termAccession=None termSource=None.

[bedroesb]

We get pie!

🥳

[bedroesb]

I managed to do a successful submission to ENA, but a failed submission to ENA would still print it as successful. Don't know if we want to fix that in this PR

[kdp-cloud]

I managed to do a successful submission to ENA, but a failed submission to ENA would still print it as successful. Don't know if we want to fix that in this PR

No I think this PR is old enough as it is. We can fix it later.

[bedroesb]

Thanks a lot!