From 31e3bd7c7eb894a8a765ecdf636c28475b40e254 Mon Sep 17 00:00:00 2001
From: eric <egiger@uchicago.edu>
Date: Mon, 6 Jul 2026 13:53:23 -0500
Subject: [PATCH 1/2] remove case from etlMapping

---
 .../vpodc.data-commons.org/values/values.yaml | 49 -------------------
 1 file changed, 49 deletions(-)

diff --git a/vadcprod/vpodc.data-commons.org/values/values.yaml b/vadcprod/vpodc.data-commons.org/values/values.yaml
index 9e1959b85..503f459dd 100644
--- a/vadcprod/vpodc.data-commons.org/values/values.yaml
+++ b/vadcprod/vpodc.data-commons.org/values/values.yaml
@@ -62,55 +62,6 @@ etl:
   esEndpoint: elasticsearch
   etlMapping:
     mappings:
-      - name: etl_mickey_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: Ethnicity
-              - name: Gender
-              - name: Race
-          - name: oncology_primaries
-            path: oncology_primaries
-            props:
-              - name: ICDOSite
-              - name: Stagegroupclinical
-              - name: Texthistologytitle
-              - name: Gradedifferentiation
-              - name: Stagegroupbest
-          - name: somatic_mutations
-            path: somatic_mutations
-            props:
-              - name: Gene
-              - name: Mutation
-        joining_props:
-          - index: file
-            join_on: _case_id
-            props:
-              - name: object_id
-                src: object_id
-                fn: set
-              - name: data_format
-                src: data_format
-                fn: set
-              - name: data_type
-                src: data_type
-                fn: set
-              - name: data_category
-                src: data_category
-                fn: set
-              - name: modality
-                src: modality
-                fn: set
-              - name: body_part_examined
-                src: body_part_examined
-                fn: set
       - name: etl_mickey_file
         doc_type: file
         type: collector

From 83f409fea54fa442efb9ef48d11385e7a71e5c63 Mon Sep 17 00:00:00 2001
From: eric <egiger@uchicago.edu>
Date: Mon, 6 Jul 2026 13:54:00 -0500
Subject: [PATCH 2/2] remove etl_mickey_case guppy index

---
 vadcprod/vpodc.data-commons.org/values/values.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/vadcprod/vpodc.data-commons.org/values/values.yaml b/vadcprod/vpodc.data-commons.org/values/values.yaml
index 503f459dd..e631de202 100644
--- a/vadcprod/vpodc.data-commons.org/values/values.yaml
+++ b/vadcprod/vpodc.data-commons.org/values/values.yaml
@@ -175,8 +175,6 @@ guppy:
   indices:
     - index: etl_mickey
       type: patients
-    - index: etl_mickey_case
-      type: case
     - index: etl_mickey_file
       type: file
     - index: omop_etl_index_cohortb_20251119