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ingest: Remove use of ncov-ingest geolocation rules #8

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merged 1 commit into from
Mar 5, 2025

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@j23414 j23414 commented Mar 5, 2025

Description of proposed changes

Remove the use of the ncov-ingest geolocation rules since Augur now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Related issue(s)

Part of nextstrain/public#17

Checklist

  • Checks pass

Remove the use of the ncov-ingest geolocation rules since Augur
now uses the built-in geolocation rules by default.

Depends on the release of
<nextstrain/augur#1745>

Part of larger migration
nextstrain/public#17
@j23414
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j23414 commented Mar 5, 2025

Manual check of metadata changes

# Pull changes
git clone https://github.com/nextstrain/norovirus.git remove-ncov-ingest-geolocation-rules
cd remove-ncov-ingest-geolocation-rules
git checkout remove-ncov-ingest-geolocation-rules
cd ..

# Pull original
git clone https://github.com/nextstrain/norovirus.git original

# Run ingest
nextstrain build remove-ncov-ingest-geolocation-rules/ingest
nextstrain build original/ingest

# Compare results
daff diff original/ingest/results/metadata.tsv remove-ncov-ingest-geolocation-rules/ingest/results/metadata.tsv > diff.tsv

# Only differences
grep "\->" diff.tsv > only_diffs.tsv

# Open only_diffs.tsv and create pivot table
Screenshot 2025-03-05 at 12 06 03 PM

Only minor changes to the metadata, and mainly changes that seem geographically reasonable (e.g. for a phylo-geographic analysis).

@j23414 j23414 merged commit 514d06d into main Mar 5, 2025
@j23414 j23414 deleted the remove-ncov-ingest-geolocation-rules branch March 5, 2025 22:39
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2 participants