feat(pts): wire aact_extraction_batch_results into chembl_molecule (via pis_drug)#207
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Mirror the PTS config change (opentargets/pts#142): the chembl_molecule step now reads input/clinical_report/aact_extraction_batch_results to mine clinical-trial (AACT) synonyms. That input is staged by pis_clinical_report, so pts_chembl_molecule now also depends on it in the unified pipeline (otherwise the DAG could run chembl_molecule before the AACT batch is present).
This was referenced Jun 11, 2026
…_molecule dep Mirror opentargets/pis#202: download aact_extraction_batch_results in the PIS drug step (clinical_report glob split into top-level / aact / chembl subtrees to exclude it). Since pts_chembl_molecule already depends on pis_drug, revert the earlier pts_chembl_molecule -> pis_clinical_report edge — the DAG dependencies stay as they were.
d0choa
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DSuveges
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Jun 11, 2026
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Summary
Propagates the PTS
chembl_moleculeconfig change (opentargets/pts#142, tracking issue opentargets/issues#4414) into orchestration, with the AACT batch downloaded inpis_drugso the DAG dependencies stay unchanged.pts.yaml—chembl_moleculestep gains the sourceaact_extraction_batch_results: input/clinical_report/aact_extraction_batch_results(mirrors the PTSconfig.yamlchange).pis.yaml— mirrors feat(drug): download aact_extraction_batch_results in the drug step pis#202: the drug step usescopy_manyto copy the AACT batch from its standalone sourcegs://ot-team/irene/clinical_mining/aact_extraction_batch_result/output/*→input/clinical_report/aact_extraction_batch_results/. The clinical_report step is unchanged.unified_pipeline.yaml— no change. The AACT input is staged bypis_drug, whichpts_chembl_moleculealready depends on.Test plan
pytest tests/test_dag_validation.py— 6 passedpts.yaml+pis.yamlonlyRelated