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feat: build DSSTox database from a local zip - #347
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seanthimons wants to merge 2 commits into
Draft
seanthimons wants to merge 2 commits into
seanthimons wants to merge 2 commits into
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DSSTOX_ZIP points data-raw/dsstox.R at a local DSSTox zip, skipping the
Clowder lookup and the staleness check. Raw headers are normalized
("preferred name" -> PREFERRED_NAME), columns missing from an export
become NULL, and DTXCID/INCHI are added as lookup identifiers.
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Blocked by #349 (synonym source policy). Do not merge or publish a rebuilt DB until it is resolved.
Summary
DSSTOX_ZIP=/path/to/DSSTox.zip Rscript data-raw/dsstox.Rbuilds from a local zip: no Clowder lookup, no 180-day staleness skip. Version sidecar becomes<zip mtime date>|local; the next Clowder release reads as new and rebuilds once.UPPER_SNAKEso newer exports (preferred name,IUPAC name,molecular formula) map onto the existing columns.IDENTIFIERsynonym column).DTXCID(sort_order 9),INCHI(10),QSAR_READY_SMILES(11),MS_READY_SMILES(12). MS-ready SMILES are shared across salts/parents, so a match there can return several DTXSIDs. Masses and last-updated are left out (not identifiers).inst/dsstox/dsstox_build.Rstays a byte-for-byte copy (it's whatdss_install(build = TRUE)sources).Known gap
The new export has no
IDENTIFIERcolumn (pipe-delimited synonyms in older dumps), so synonym lookups viadss_*will only hit preferred/IUPAC names.Test plan
parent_colset,_metadata+ sidecar2026-10-05|localDB_NAME=dsstox Rscript dev/db_smoke_check.R, thengh release upload db-latest dsstox.duckdb dsstox.version --clobber