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chore: migrate etl_target → pts_target (rename pts_target → pts_pre_target)#178

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d0choa wants to merge 5 commits intodevfrom
migrate_target
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chore: migrate etl_target → pts_target (rename pts_target → pts_pre_target)#178
d0choa wants to merge 5 commits intodevfrom
migrate_target

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@d0choa d0choa commented Apr 14, 2026

Summary

  • Rename pts_target: step definition → pts_pre_target: in unified_pipeline.yaml (preprocessing step)
  • Remove etl_target: block from unified_pipeline.yaml
  • Add pts_target: block with correct dependencies (pts_pre_target, pts_reactome, pts_target_safety, pts_target_gene_essentiality, pts_disease)
  • Replace all 26 occurrences of - etl_target with - pts_target in unified_pipeline.yaml
  • Update gentropy_study and pts_drug_mechanism_of_action depends_on to reference pts_pre_target
  • Rename target:pre_target: in pts.yaml and add new target: pyspark step
  • Remove target { ... } block from etl.conf, leaving a stub with output path

Validation

grep "etl_target" src/orchestration/dags/config/unified_pipeline.yaml
# Expected: empty output ✓

Test plan

  • No etl_target references remain in unified_pipeline.yaml
  • DAG validation in staging environment

Tracking issue: opentargets/issues#4347

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