Handle NCBI taxdump members with a leading './' (fixes #810)#813
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apoorvdarshan wants to merge 1 commit into
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Handle NCBI taxdump members with a leading './' (fixes #810)#813apoorvdarshan wants to merge 1 commit into
apoorvdarshan wants to merge 1 commit into
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Tarballs created with GNU tar (e.g. `tar -c -C dir .`) name their members like `./names.dmp`, `./nodes.dmp` and `./merged.dmp`. The extractfile() lookups used the bare name and raised `KeyError: "filename 'names.dmp' not found"`, so NCBITaxa(taxdump_file=...) failed to build the database. Add a small extractfile_dmp() helper that falls back to the './'-prefixed member name, and use it at the three .dmp call sites. Add a regression test covering both plain and './'-prefixed tarballs. Fixes etetoolkit#810.
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Summary
NCBITaxa(taxdump_file=...)fails when the taxdump tarball is created with GNU tar (e.g.tar -c -C dir .), because such archives name their members with a leading./(./names.dmp,./nodes.dmp,./merged.dmp). The code inete4/ncbi_taxonomy/ncbiquery.pylooked those members up by their bare name, sotarfileraised:This reproduces on the current
ete4branch (commit9562dfb, the same one referenced in #810).Fix
Add a small
extractfile_dmp(tar, name)helper that first tries the bare member name and, onKeyError, falls back to the'./'-prefixed name. It is used at the three.dmpextraction sites (names.dmp,nodes.dmp,merged.dmp). The change is localized and does not affect the existing (non-prefixed) tarballs.Tests
Added
test_extract_dmp_with_leading_dotslashintests/test_ncbiquery.py, parametrized over both plain and'./'-prefixed members. It builds a minimal in-memory taxdump, runsupdate_db, and checks the resulting database. The'./'case fails onmain/ete4before the fix (KeyError) and passes after. The fulltest_ncbiquery.pysuite (9 tests) passes.Fixes #810.
Disclosure: prepared with AI assistance; reviewed and verified locally.