Refseq annotation #71
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| if identifier.startswith("GCF_"): | ||
| return f"insdc.gcf:{identifier}" |
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let's also add in
if identifier.startswith("GCA_"):
return f"insdc.gca:{identifier}"| @@ -0,0 +1,710 @@ | |||
| import json | |||
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Before you start doing any refactoring, can you add in an integration test that checks the results of parsing the JSON data into all 8 CDM tables? Let me know when you have done that so I can take a look.
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| expected_tables = [ | ||
| "contig", | ||
| "contig_x_contigcollection", | ||
| "contigcollection_x_feature", | ||
| "contigcollection_x_protein", | ||
| "feature", | ||
| "feature_x_protein", | ||
| "identifier", | ||
| "name", | ||
| ] |
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You also need the protein table -- it looks like the parser is not capturing the protein information any more.
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| # Load NCBI dataset from NCBI API | ||
| sample_api_response = test_data_dir / "refseq" / "annotation_report.json" | ||
| dataset = json.load(sample_api_response.open()) | ||
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| # Run parse function | ||
| parse_annotation_data(spark, [dataset], TEST_NS) |
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You need to load the annotation_report.parsed.json file here and use that to populated expected_df.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #71 +/- ##
===========================================
- Coverage 52.69% 6.43% -46.27%
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Files 63 64 +1
Lines 3241 3403 +162
===========================================
- Hits 1708 219 -1489
- Misses 1533 3184 +1651
... and 36 files with indirect coverage changes Continue to review full report in Codecov by Sentry.
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