Remove the requirement for a database field in augur curate parse-genbank-location [#1511]
#1513
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Per discussion on #1508 and #1511, the field standardization across records (cf #1510) makes the need to verify a `database` field less important — essentially, if there's a `geo_loc_name` field (or a field with the name given in the `--location-field` argument), parse it. Otherwise, warn that it's not found.
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The requirement of a |
joverlee521
approved these changes
Jul 2, 2024
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1513 +/- ##
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- Coverage 69.57% 69.54% -0.03%
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Files 73 73
Lines 7792 7786 -6
Branches 1906 1904 -2
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- Hits 5421 5415 -6
Misses 2086 2086
Partials 285 285 ☔ View full report in Codecov by Sentry. |
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Description of proposed changes
Per discussion on #1508 and #1511, the field standardization across records (cf #1510) makes the need to verify a
databasefield less important — essentially, if there's ageo_loc_namefield (or a field with the name given in the--location-fieldargument), parse it. Otherwise, warn that it's not found.Related issue(s)
databasecheck #1511translate-genbank-locationtoaugur curate parse-genbank-location[#1485] #1508Checklist
If making user-facing changes, add a message in CHANGES.md summarizing the changes in this PR