MAINT: Added new files to BuscoDatabaseDirFmt #231
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #231 +/- ##
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- Coverage 95.60% 95.42% -0.19%
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Files 34 34
Lines 1956 1987 +31
Branches 226 232 +6
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+ Hits 1870 1896 +26
- Misses 48 50 +2
- Partials 38 41 +3 ☔ View full report in Codecov by Sentry. |
| @@ -37,6 +38,12 @@ def fetch_busco_db( | |||
| f"Error during BUSCO database download: {e.returncode}" | |||
| ) | |||
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| # There is a symlink in the BUSCO database that needs to be removed | |||
| symlink = os.path.join(str(busco_db), "busco_downloads", "lineages", | |||
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I'm wondering whether we should make this a bit more universal and try to detect any symlink and remove it, just in case this happens again in the future. Do you know whether this is the only link that exists there or are there more and this one is simply broken?
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This is the only symlink in the database. Because it's the only one and because its broken I think it's a mistake that it's there in the first place.
But i can implement something that searches for any symlinks and removes them.
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Hmmm, I'd say let's implement something like that then - hopefully there won't be more mistakes like this in the future but if there are then we won't need more PRs...
| no_hits = model.File( | ||
| r'busco_downloads\/lineages\/pectobacteriaceae_odb12\/no_hits$', | ||
| format=BuscoGenericTextFileFmt, | ||
| optional=True | ||
| ) |
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I think this should also be generalized, in case it happens in the future, by replacing the pectobacteriaceae lineage with a wildcard.
closes #215