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Add biobank merge code#1304

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callachennault wants to merge 2 commits into
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callachennault:biobank-merge
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Add biobank merge code#1304
callachennault wants to merge 2 commits into
knowledgesystems:masterfrom
callachennault:biobank-merge

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@callachennault callachennault commented Feb 24, 2026

For msk_solid_heme and msk_archer, the following steps have been added:

  1. pull data_clinical_patient_biobank and data_timeline_biobank_specimen from mskimpact-databricks S3 bucket
  2. merge data_clinical_patient_biobank into data_clinical_patient, remove data_clinical_patient_biobank
  3. data_timeline_biobank_specimen and ALIQUOT_STATUS now included in study import

questions:

  • maybe for curation - should data_clinical_patient_biobank be a standalone file or should it be merged into data_clinical_patient?
  • to discuss - if merged - what should happen if merging data_clinical_patient_biobank and data_clinical_patient fails?

TODO

  • test this code with an import into triage

@callachennault callachennault marked this pull request as ready for review February 26, 2026 20:54
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