Unfreeze PyMongo and replace deprecated count() with count_documents() #124
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That's a good idea, I'll fix tomorrow. Thanks for the review! |
Mmm I've changed the automatic tests to run with Mongo 7 and a new version of PyMongo, but I see that there are some deprecated methods in the code that shouldn't be supported in the older versions of pymongo. Perhaps these are not covered by the tests. I'll fix! |
northwestwitch
changed the title
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Ok, now I feel thsi ready for a review @henrikstranneheim, thanks! |
loqusdb/commands/identity.py
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| result = adapter.get_clusters(variant_id) | ||
| if result.count() == 0: | ||
| nr_results = adapter.db.identity.count_documents({"variant_id": variant_id}) | ||
| if nr_results == 0: | ||
| LOG.info("No hits for variant %s", variant_id) |
tests/commands/test_export.py
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| from loqusdb.commands.cli import cli as base_command | ||
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| def test_export_base(real_db_name): |
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| ## THEN it should return success | ||
| result = runner.invoke(base_command, command) | ||
| assert result.exit_code == 0 |
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Can we also test that it actually exported a file?
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If you don't provide the -o param in the cli is not exporting to file, but printing into the terminal:
For the purpose of testing that the are 0 cases with the modified count command I think this is good enough.
But I agree that more and better tests for the cli could have been written!
tests/commands/test_identity.py
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| from loqusdb.commands.cli import cli as base_command | ||
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| def test_identity(real_db_name): |
tests/commands/test_view.py
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| from loqusdb.commands.cli import cli as base_command | ||
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| def test_view_cases_base(real_mongo_adapter, real_db_name): |
Co-authored-by: Henrik Stranneheim <henrik.stranneheim@scilifelab.se>
Co-authored-by: Henrik Stranneheim <henrik.stranneheim@scilifelab.se>
This PR adds | fixes:
.count()function withcount_documents()in code.How to test:
Expected outcome:
Review:
This version is a: