this should work

broadinstitute · Nov 27, 2024 · f9ee249 · f9ee249
1 parent 92d8a4e
commit f9ee249
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Showing 8 changed files with 36 additions and 14 deletions.
diff --git a/charts/hail-search/values.yaml b/charts/hail-search/values.yaml
@@ -54,8 +54,3 @@ tolerations: []
 
 global:
   seqrPlatformDeploy: false
-
-exports:
-  environment:
-    global:
-      SEQR_APP_HAIL_SEARCH_DATA_DIR: '/var/seqr/seqr-hail-search-data'
diff --git a/charts/pipeline-runner/Chart.yaml b/charts/pipeline-runner/Chart.yaml
@@ -8,7 +8,7 @@ maintainers:
   - name: seqr
     email: [email protected]
 type: application
-version: 0.2.3
+version: 0.2.4
 appVersion: "ab13f4cf8ab6a0d48ec0b5e4beb101a532566a3b"
 dependencies:
   - name: lib

diff --git a/charts/pipeline-runner/templates/deployment.yaml b/charts/pipeline-runner/templates/deployment.yaml
@@ -22,7 +22,7 @@ spec:
   template:
     metadata:
       labels:
-        name: {{ $.Chart.Name }}-{{ $p.name }} 
+        name: {{ $.Chart.Name }}-{{ $p.name }}
         {{- include "pipeline-runner.labels" $ | nindent 8 }}
       annotations:
         checksum/config: {{ include (print $.Template.BasePath "/environment.yaml") $ | sha256sum }}
@@ -81,6 +81,9 @@ spec:
           envFrom:
             - configMapRef:
                 name: {{ $.Chart.Name }}
+            - configMapRef:
+                name: seqr-platform
+                optional: true
           resources:
             {{- toYaml .resources | nindent 12 }}
           {{- with $.Values.volumeMounts }}

diff --git a/charts/pipeline-runner/templates/environment.yaml b/charts/pipeline-runner/templates/environment.yaml
@@ -8,6 +8,3 @@ data:
   {{- with .Values.environment }}
     {{- toYaml . | nindent 2 }}
   {{- end }}
-  {{- if ne .Values.environment.HAIL_SEARCH_DATA_DIR .Values.global.SEQR_APP_HAIL_SEARCH_DATA_DIR }}
-  SEQR_APP_HAIL_SEARCH_DATA_DIR: {{ .Values.global.SEQR_APP_HAIL_SEARCH_DATA_DIR | quote }}
-  {{- end }}
diff --git a/charts/seqr-platform/Chart.lock b/charts/seqr-platform/Chart.lock
@@ -15,4 +15,4 @@ dependencies:
   repository: https://broadinstitute.github.io/seqr-helm
   version: 0.1.4
 digest: sha256:75d23e5b0c4955c1dac7929fbc4ce27bad0e822f62e833b0b330dc424d3e835b
-generated: "2024-11-26T17:12:31.096616-05:00"
+generated: "2024-11-27T15:57:08.295828-05:00"
diff --git a/charts/seqr-platform/Chart.yaml b/charts/seqr-platform/Chart.yaml
@@ -9,7 +9,7 @@ maintainers:
   - name: seqr
     email: [email protected]
 type: application
-version: 0.3.20
+version: 0.3.21
 dependencies:
   - name: seqr
     version: 1.4.9
@@ -21,8 +21,6 @@ dependencies:
   - name: hail-search
     version: 0.5.1
     repository: "https://broadinstitute.github.io/seqr-helm"
-    import-values:
-      - environment
   - name: vlm
     version: 0.0.9
     repository: "https://broadinstitute.github.io/seqr-helm"

diff --git a/charts/seqr-platform/templates/_helpers.tpl b/charts/seqr-platform/templates/_helpers.tpl
@@ -0,0 +1,19 @@
+{{/*
+Common labels
+*/}}
+{{- define "seqr-platform.labels" -}}
+helm.sh/chart: {{printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{ include "seqr-platform.selectorLabels" . }}
+app.kubernetes.io/version: {{ .Chart.Version | quote }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+app.kubernetes.io/part-of: seqr-platform
+{{- end }}
+
+
+{{/*
+Selector labelsh
+*/}}
+{{- define "seqr-platform.selectorLabels" -}}
+app.kubernetes.io/name: {{ .Chart.Name }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
diff --git a/charts/seqr-platform/templates/environment.yaml b/charts/seqr-platform/templates/environment.yaml
@@ -0,0 +1,10 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Chart.Name }}
+  labels:
+    {{- include "seqr-platform.labels" . | nindent 4 }}
+data:
+  {{- if ne (index .Values "hail-search" "environment" "HAIL_SEARCH_DATA_DIR") (index .Values "pipeline-runner" "environment" "HAIL_SEARCH_DATA_DIR") }}
+  SEQR_APP_HAIL_SEARCH_DATA_DIR: "{{ index .Values "hail-search" "environment" "HAIL_SEARCH_DATA_DIR" }}"
+  {{- end }}