The Portal API has replaced session cookie-based authentication with Bearer token authentication. These changes update NmdcPortalApiClient to reflect that.
In testing I also found that the SubmissionPortalTranslator has drifted away from the Portal a bit. In particular, samp_name is now the unique key slot on Biosample instances instead of source_mat_id. These changes also correct that.
Fixes #571
Type of change
[x] Bug fix (non-breaking change which fixes an issue)
How Has This Been Tested?
[x] Unit test suite
These changes update tests/test_ops/test_data_api_ops.py to reflect the new behavior of NmdcPortalApiClient.
These changes fix the test configuration of tests/test_graphs/test_submission_portal_graphs.py and remove the xfail mark.
[x] Manually ran the translate_metadata_submission_to_nmdc_schema_database job in the Dagit interface
Configuration Details: none
Checklist:
[x] My code follows the style guidelines of this project (have you run black nmdc_runtime/?)
[x] I have performed a self-review of my code
[x] I have commented my code, particularly in hard-to-understand areas
Description
The Portal API has replaced session cookie-based authentication with Bearer token authentication. These changes update
NmdcPortalApiClient
to reflect that.In testing I also found that the
SubmissionPortalTranslator
has drifted away from the Portal a bit. In particular,samp_name
is now the unique key slot onBiosample
instances instead ofsource_mat_id
. These changes also correct that.Fixes #571
Type of change
How Has This Been Tested?
tests/test_ops/test_data_api_ops.py
to reflect the new behavior ofNmdcPortalApiClient
.tests/test_graphs/test_submission_portal_graphs.py
and remove thexfail
mark.translate_metadata_submission_to_nmdc_schema_database
job in the Dagit interfaceConfiguration Details: none
Checklist:
black nmdc_runtime/
?)docs/
and in https://github.com/microbiomedata/NMDC_documentation/?)make up-test && make test-run
)