Rebuild ranksParents from a pinned ncbi-taxon-db release
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 48/100
Research direction
Start with inst/scripts/sysdata.R and inspect how ranksParents is built from sheet taxids; compare its coverage with the taxids in the sheets and sources/manifest.tsv. The issue describes missing Rank and parent values in physiologies() for newly added RefSeq species. Choose whether to pin a dated ncbi-taxon-db release with taxoniq or compute ranks at read time, then record the release tag in the script and NEWS if using the pinned database.
Written by the indexing model from the issue text.
Description
ranksParents in R/sysdata.rda supplies Rank and Parent_NCBI_ID to every row that comes without them, which now means every programmatic source under sources/. It holds 16,927 taxids, built by inst/scripts/sysdata.R with taxizedb from the sheet ids of the day, so the 77,673 RefSeq species added in waldronlab/bugphyzzExports#81 get NA Rank and no parent in physiologies(). The export does not depend on it (taxPPro re-ranks with taxizedb), so this is about physiologies() output and strain-to-species propagation for sources.
Proposal: rebuild ranksParents with taxoniq and a dated ncbi-taxon-db release, covering every taxid in the sheets and in sources/manifest.tsv, and record the release tag in the script and NEWS. Alternatively drop the static table and compute Rank and parent at read time, which removes the need to rebuild it whenever a source grows.
Related: https://github.com/waldronlab/taxPPro/issues/15 (the export-side lookup).
Drafted with Claude Code.
- Dominant language
- R
- Stars
- 6
- Forks
- 6
- Avg merge
- 1h
- Merged PRs (30d)
- 10
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