'raw' gather report should output all PU repeats #884
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Thanks @frannerin - just a couple of things.
I think there's that one test that will fail and will require manually adding in the repeats to the stored table string.
| return [(pu['outputs']['unit_estimate'], | ||
| pu['outputs']['unit_estimate_error']) | ||
| # could add to each tuple pu[0]["source_key"] for repeat ID | ||
| return [(pu[0]['outputs']['unit_estimate'], |
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Could you maybe provide some context for this change?
As far as I remember, the zero list index on line 134 is to deal with avoiding to do it here twice - that being said I could be convinced that this is a better approach with the right context.
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list(results['protocol_result']['data'].values()) in line 134 contains an item for each ProtocolUnit, so by taking the zero list index there only the first PU is further processed. Each item in list(results['protocol_result']['data'].values()) is a list itself, with length 1 (afaik), so that's why pu[0] must be done to access the single dictionary within.
openfecli/commands/gather.py
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| for ligpair, vals in sorted(legs.items()): | ||
| for simtype, repeats in sorted(vals.items()): | ||
| for m, u in repeats: | ||
| for rep, (m, u) in enumerate(repeats, 1): |
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I think we'd want this to be zero indexed - I'll have a poke around our other outputs later, but at least on the Python layer, we keep everything zero indexed.
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I did the zero-indexed repeats thing and updated the test_gather.py. I ran pytest -k test_gather and got: 23 passed, 3 skipped, 840 deselected, 1 xfailed, 2 xpassed, 25 warnings |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #884 +/- ##
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- Coverage 94.59% 91.64% -2.95%
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Files 134 134
Lines 9935 9935
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- Hits 9398 9105 -293
- Misses 537 830 +293
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Function
_parse_raw_unitsin openfecli/commands/gather.py only processed first ProtocolUnit repeat and then_write_rawdid not distinguish between repeats if there were any._write_dg_rawis left unchanged because it seems to be unused.Example output (openfe gather --report raw ) before fix for a RBFE protocol with 3 PU repeats for the solvent legs, and 1 repeat for the complex legs:
Example output after fix:
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