Port merge-user-metadata to augur curate #1495
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Noticed while I was removing executable permission for new script that this file still had executable permissions.
Copy the `merge-user-metadata` script from nextstrain/ingest in preparation for porting the functionality into the new `augur curate apply-record-annotations` command. Copied from <https://github.com/nextstrain/ingest/blob/c94d78d1f38b99e893007a76526f3d3824ecded0/merge-user-metadata>
Includes changes to make the copied script work as a new Augur subcommand and fit in with the codebase: - remove unneeded executable permissions and shebang - add as a subcommand of augur curate - replace main entrypoint with register_parser() and run() - let augur curate handle records I/O - use AugurError and print_err()
The `annotating-new-fields` test reveals undesired behavior which will be addressed in the next commit.
I don't think we should support adding new fields with record annotations because it's hard to ensure that the new field gets added across all records that are streamed through the command. This is a deviation from the original nextstrain/ingest script, but I think a necessary one to avoid bugs in the final output metadata.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1495 +/- ##
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+ Coverage 69.15% 69.28% +0.13%
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Files 70 71 +1
Lines 7694 7727 +33
Branches 1887 1895 +8
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+ Hits 5321 5354 +33
Misses 2087 2087
Partials 286 286 ☔ View full report in Codecov by Sentry. |
genehack
approved these changes
Jun 28, 2024
genehack
approved these changes
Jun 28, 2024
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Description of proposed changes
Porting over
merge-user-metadatafrom nextstrain/ingest toaugur curate apply-record-annotations.Includes a functional change to skip annotations for fields that do not exist in the record because it's hard to ensure that the new field gets added across all records that are streamed through the command.
This is a deviation from the original nextstrain/ingest script, but I think a necessary one to avoid bugs in the final output metadata.
Related issue(s)
Resolves #1482
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