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This moves the script to the vendored directory, which is a git subtree of https://github.com/nextstrain/ingest (currently at branch apply-geolocation-rules). The file suffix is removed to match how it appears in the other repos which use it. As per [Overview of duplicated scripts](#1) this script also appears in: * [monkeypox](https://github.com/nextstrain/monkeypox/blob/a1f0d7b757d323d87edcbe61c6c5ccfbdf47722c/ingest/bin/apply-geolocation-rules) * [rsv](https://github.com/nextstrain/rsv/blob/ba171f4a43110382c38b6154be3febd50408d7bf/ingest/bin/apply-geolocation-rules) * [dengue, branch new_ingest](https://github.com/nextstrain/dengue/blob/247b2fd897361f2548627de1d97d45fae4115c5c/ingest/bin/apply-geolocation-rules) All three of those scripts are identical to each other. The script vendored here contains two code changes (whitespace removed from diffs): **Ignore comment lines in the location-rules TSV** ```diff < if line.lstrip()[0] == '#': --- > if line.strip()=="" or line.lstrip()[0] == '#': ``` **Allow fields to be missing from the input NDJSON** The script previously mandated that the input NDJSON had all four fields (region/country/division/location). This is relaxed here, with an empty string used if the field is not present. ```diff < annotated_values = transform_geolocations(geolocation_rules, [record[field] for field in location_fields]) --- > annotated_values = transform_geolocations(geolocation_rules, [record.get(field, '') for field in location_fields]) ```
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See the commit message for the other occurrences of this script, and the changes between the different versions.
This was tested in both the hepatitisB and monkeypox ingest pipelines, with no changes to the resulting outputs.
I've made an issue to discuss the specifics of using
git subtreeto create & test this commit.