From 4b73f861d7b1624e39f9039c0684cd8df4027acc Mon Sep 17 00:00:00 2001 From: eric Date: Mon, 18 May 2026 17:13:54 -0500 Subject: [PATCH 1/2] update etlMapping and guppy indices --- .secrets.baseline | 4 +- .../qa-vpodc-helm/values/values.yaml | 111 ++++++++---------- 2 files changed, 54 insertions(+), 61 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 0fb48642..3ec7ecfd 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -214,7 +214,7 @@ "filename": "devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml", "hashed_secret": "4c7e5a7eedc322089e3a64d1911d6f823431162a", "is_verified": false, - "line_number": 1485 + "line_number": 1475 } ], "devplanetv2/dev-environments/qamickey-helm/values/values.yaml": [ @@ -259,5 +259,5 @@ } ] }, - "generated_at": "2026-05-13T18:05:53Z" + "generated_at": "2026-05-18T22:11:58Z" } diff --git a/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml b/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml index 4ebd9ebb..bb6407ed 100644 --- a/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml +++ b/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml @@ -117,64 +117,55 @@ dashboard: etl: esEndpoint: elasticsearch mappings: - - doc_type: patients - name: etl_mickey - nested_props: - - name: oncology_primaries - path: oncology_primaries - props: - - name: Multiplicitycounter - - name: ICDOSite - - name: Radiation - - name: Chemotherapy - - name: DaysFromAnchorDateToDiagnosisDate - - name: Gradedifferentiation - - name: Laterality - - name: Stagegroupbest - - name: RadiationsurgerySequence - - name: Histologyicdo3X - - name: Lymphvascularinvasionl - - name: SeerSummaryStage2000 - - name: PhysiciansStage - - name: DaysFromAnchorDateToMostdefinitivesurgDate - - name: ChemotherapyFac - - name: TumorSize - - name: SequenceNumber - - name: actionable_mutations - path: actionable_mutations - props: - - name: Lab - - name: Gene - - name: DaysFromAnchorDateToBxDate - props: - - name: project_id - - name: Days_To_Birth - src: days_to_lost_to_followup - - name: Days_To_Death - src: days_to_lost_to_followup - - name: Gender - src: lost_to_followup - - name: Ethnicity - src: lost_to_followup - - name: Race - src: lost_to_followup - - name: DeceasedFlag - src: lost_to_followup - root: case - type: aggregator - - category: data_file - doc_type: file - name: file_etl_mickey - props: - - name: project_id - - name: submitter_id - - name: file_name - - name: file_size - - name: data_format - - name: data_type - - name: object_id - root: None - type: collector + etlMapping: + mappings: + - name: qa_vpodc_case + doc_type: case + type: aggregator + root: case + props: + - name: project_id + - name: submitter_id + nested_props: + - name: clinical_demographics + path: clinical_demographics + props: + - name: Days_To_Birth + - name: Days_To_Death + - name: Ethnicity + - name: Gender + - name: Race + - name: Vital_Status + - name: Year_Of_Birth + - name: Year_Of_Death + - name: DeceasedFlag + - name: MaritalStatus + - name: PatientOver90Flag + - name: oncology_primaries + path: oncology_primaries + props: + - name: ICDOSite + - name: Stagegroupclinical + - name: PrimarysiteX + - name: qa_vpodc_data_file + doc_type: data_file + type: collector + root: None + category: data_file + props: + - name: object_id + - name: md5sum + - name: file_name + - name: file_size + - name: data_format + - name: data_type + - name: data_category + - name: state + injecting_props: + case: + props: + - name: submitter_id + - name: project_id fence: usersync: @@ -212,7 +203,9 @@ guppy: indices: - index: etl_mickey type: patients - - index: file_etl_mickey + - index: qa_vpodc_case + type: case + - index: qa_vpodc_data_file type: file - index: omop_etl_index_cohortb_20251119 type: cohort_b_patients From 5d0a21b67f5800e0f6366518c2b90e839b39d867 Mon Sep 17 00:00:00 2001 From: eric Date: Mon, 18 May 2026 17:20:09 -0500 Subject: [PATCH 2/2] include additional oncology_primary props found in previous qa etlMapping --- .secrets.baseline | 4 ++-- .../qa-vpodc-helm/values/values.yaml | 14 ++++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/.secrets.baseline b/.secrets.baseline index 3ec7ecfd..3c920afd 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -214,7 +214,7 @@ "filename": "devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml", "hashed_secret": "4c7e5a7eedc322089e3a64d1911d6f823431162a", "is_verified": false, - "line_number": 1475 + "line_number": 1489 } ], "devplanetv2/dev-environments/qamickey-helm/values/values.yaml": [ @@ -259,5 +259,5 @@ } ] }, - "generated_at": "2026-05-18T22:11:58Z" + "generated_at": "2026-05-18T22:19:56Z" } diff --git a/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml b/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml index bb6407ed..9705beee 100644 --- a/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml +++ b/devplanetv2/dev-environments/qa-vpodc-helm/values/values.yaml @@ -147,6 +147,20 @@ etl: - name: ICDOSite - name: Stagegroupclinical - name: PrimarysiteX + - name: Chemotherapy + - name: ChemotherapyFac + - name: Gradedifferentiation + - name: Histologyicdo3X + - name: Laterality + - name: Lymphvascularinvasionl + - name: Multiplicitycounter + - name: PhysiciansStage + - name: Radiation + - name: RadiationsurgerySequence + - name: SeerSummaryStage2000 + - name: SequenceNumber + - name: Stagegroupbest + - name: TumorSize - name: qa_vpodc_data_file doc_type: data_file type: collector