Fix download.yaml: metatraits GDrive entries + comment out inactive sources#528
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realmarcin merged 4 commits intomasterfrom Mar 20, 2026
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Fix download.yaml: metatraits GDrive entries + comment out inactive sources#528realmarcin merged 4 commits intomasterfrom
realmarcin merged 4 commits intomasterfrom
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…e sources - Replace duplicate metatraits placeholder blocks with the three actual GDrive entries for ncbi_species_summary.jsonl.gz, ncbi_genus_summary.jsonl.gz, and ncbi_family_summary.jsonl.gz (recovered from commit e7e2508) - Comment out download entries for inactive transforms: uniprot_proteomes, uniprot_human, CTD, fermentation_explorer, disbiome, wallen_etal - upa.owl (used by OntologiesTransform) remains active Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Pull request overview
Updates the project’s download.yaml configuration to align downloads with the currently active transforms and to restore the correct MetaTraits Google Drive file references.
Changes:
- Replaced placeholder/duplicate MetaTraits Google Drive entries with three concrete GDrive IDs for species/genus/family JSONL summaries.
- Commented out download entries for sources whose transforms are currently not enabled in
DATA_SOURCES.
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The download.yaml entries use local_name: metatraits/ncbi_*_summary.jsonl.gz, placing files in data/raw/metatraits/. Update the transform's input_base to append the metatraits/ subdir, and update the test and runbook accordingly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
crocodile27
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Mar 19, 2026
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Fixed in new commit " Fix metatraits transform to l
ook in data/raw/metatraits/ subdirectory"
realmarcin
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Mar 20, 2026
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a few more things are commented out in download.yaml now -- some are for the biomedical version of the transform. but its OK to have this smaller download set as the default, can revisit on next release when multiple KGs are built.
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Summary
gdrive:<metatraits_folder_id>/metatraits.tsv) and a manual-placement comment with the three actual GDrive entries recovered from commite7e2508onmetatraits-isolated:metatraits/ncbi_species_summary.jsonl.gz(GDrive ID:1vL9wujvty4Xh2ZG2HHquX0RE7968Dkbm)metatraits/ncbi_genus_summary.jsonl.gz(GDrive ID:1WL6VhD2I6MGuI3iHKbCQYTncG1UB-u6e)metatraits/ncbi_family_summary.jsonl.gz(GDrive ID:1pgOugA5jQG96GbCktkTJN9FGn6rypTOI)DATA_SOURCES:uniprot_proteomes.tar.gz,uniprot_human.tar.gz,CTD_chemicals_diseases.tsv.gz,fermentation_explorer.csv,disbiome.json,wallen_etal.xlsxupa.owlremains active (used by OntologiesTransform)Test results
poetry run pytest tests/ -q)poetry run kg downloadruns without errorsdata/raw/metatraits/is populated with the three JSONL files after download (requires GDrive access via antheaguo@berkeley.edu)🤖 Generated with Claude Code