2606 public release#201
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This was referenced Jun 11, 2026
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- The file has the same schema and identical format - The new release has 33k fewer lines, which might indicate we are not getting all ratings. It might not impact the number of evidence and associations at the end.
The ETL stage in the unified pipeline DAG has had zero step consumers since PR #195. Remove the now-orphan configuration, loaders, DAG stage function, and supporting operator/enum entries: - clusters.yaml: drop the `etl` and `etl_literature` clusters plus the `step_job_properties.etl` block. - unified_pipeline.yaml: drop `etl_version` and the `etl_literature` step entry. - etl.conf: deleted (no longer loaded). - config/unified_pipeline.py: drop the `etl` AppConfig loader (and its PPP overlay), `etl_version`/`etl_jar_origin_uri`, the now-unused `jar_uri()` helper, and the `exts` map in `config_uri()`. - dags/unified_pipeline.py: drop the `etl_stage()` function, its call, and the imports that only it used (`ETLJobBuilder`, `CopyBlobOperator`, `to_hocon`). - operators/dataproc.py: delete `ETLJobBuilder`. - models/step.py: drop `UnifiedPipelineStage.ETL`. - operators/diff.py: refresh docstring examples that referenced the removed `etl_stage` task IDs.
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).
…_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.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Removed 'UNVALIDATED_INDICATION' from invalid clinical report QC settings.
@DSuveges This change was uncommitted in Airflow. Can you confirm this is correct?
project-defiant
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Jun 17, 2026
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Summary
Upon prepping for the 2026.06 release, the following changes were made in the configuration and orchestration framework.
Config changes
Unified pipeline config
Clusters
PIS
PTS
ETL
Gentropy
Code changes
For certain changes it was not enough to update configuration but the logic how the configuration is interpreted.