fix: remove deprecated Project Score cross-references#203
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Mirror the pis and pts cleanup: drop the Sanger Project Score fetch tasks from pis.yaml and the matching pre-processing + source entries from pts.yaml. The deprecated resource (cog.sanger.ac.uk/cmp/download/ gene_identifiers_latest.csv.gz + essentiality_matrices.zip) is no longer consumed by the pts target step. The Sanger Cell Model Passport download (model_list_latest.csv.gz, used by the Project Score v2 CRISPR evidence parser) is untouched. Companion PRs: - pts: opentargets/pts#138 - pis: opentargets/pis#201 Refs opentargets/issues#4367
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DSuveges
approved these changes
Jun 5, 2026
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Summary
Mirror the pis and pts cleanup of the deprecated Project Score resource. No new code — this just keeps the orchestration configs aligned with the upstream changes.
dags/config/pis.yaml— drop the twocog.sanger.ac.uk/cmp/download/fetches underinput/target/project-scores/dags/config/pts.yaml— drop the 3 pre-processing tasks (unzip essentiality matrix,csv_to_parquet essentiality matrix,csv_to_parquet gene identifier) and the 2project_scores_*source entries on thetargetpyspark stepOut of scope (intentionally unaffected):
dags/config/clusters.yaml— Project Score v2 CRISPR evidence parser (different dataset, still maintained)target_gene_essentialitystepCompanion PRs:
_build_project_scoresand matching source entries)Refs opentargets/issues#4367
Test plan
input/target/project-scores/anddbXrefsno longer containssource: ProjectScoreentries