For re-demux: keep PDC archive date if exists #433
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #433 +/- ##
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- Coverage 26.63% 26.57% -0.07%
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Files 28 28
Lines 3949 3959 +10
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Hits 1052 1052
- Misses 2897 2907 +10 ☔ View full report in Codecov by Sentry. |
taca/analysis/analysis.py
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| @@ -155,6 +155,19 @@ def _upload_to_statusdb(run): | |||
| parser.obj["DemultiplexConfig"] = { | |||
| "Setup": {"Software": run.CONFIG.get("bcl2fastq", {})} | |||
| } | |||
| # Keep PDC archive date if there is one already | |||
| run_vals = run.split("_") | |||
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Does this work? run is a run object and not a string right?
taca/analysis/analysis.py
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| else: | ||
| run_date = run_vals[0] | ||
| run_fc = f"{run_date}_{run_vals[-1]}" | ||
| fc_names = {e.key: e.id for e in db.view("names/name", reduce=False)} |
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This would fetch all flowcell IDs in the database. I think you can fetch the document you want directly with the key in just one call. I would have to look up the specific syntax though.
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Hi, I'm re-using the code here:
Line 258 in c08d3f3
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doc = db.view("names/name", reduce=False, include_docs=True)[run_fc].rows[0].doc
should do the trick, but one would need to wrap it in try except to catch the case when the flowcell is not present in the view. Alternatively one could have multiple lines and check that the rows are not empty after fetching.
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