Chore/make data library item schemas configurable

.secrets.baseline

@@ -423,29 +423,6 @@
         "line_number": 13
       }
     ],
-    "helm/gen3-user-data-library/README.md": [
-      {
-        "type": "Secret Keyword",
-        "filename": "helm/gen3-user-data-library/README.md",
-        "hashed_secret": "4f2a84424eb908cfbe25c1e486024ae59b5a6085",
-        "is_verified": false,
-        "line_number": 28
-      },
-      {
-        "type": "Secret Keyword",
-        "filename": "helm/gen3-user-data-library/README.md",
-        "hashed_secret": "d84ce25b0f9bc2cc263006ae39453efb22cc2900",
-        "is_verified": false,
-        "line_number": 45
-      },
-      {
-        "type": "Secret Keyword",
-        "filename": "helm/gen3-user-data-library/README.md",
-        "hashed_secret": "f09dd6e359833a12f48c4c4255d6e87a6e55cfe9",
-        "is_verified": false,
-        "line_number": 66
-      }
-    ],
     "helm/guppy/README.md": [
       {
         "type": "Secret Keyword",
@@ -718,5 +695,5 @@
       }
     ]
   },
-  "generated_at": "2025-06-30T19:20:23Z"
+  "generated_at": "2025-07-03T17:59:41Z"
 }

helm/gen3-user-data-library/Chart.yaml

@@ -15,7 +15,7 @@ type: application
 # This is the chart version. This version number should be incremented each time you make changes
 # to the chart and its templates, including the app version.
 # Versions are expected to follow Semantic Versioning (https://semver.org/)
-version: 0.1.2
+version: 0.1.3
 
 # This is the version number of the application being deployed. This version number should be
 # incremented each time you make changes to the application. Versions are not expected to

helm/gen3-user-data-library/README.md

@@ -1,6 +1,6 @@
 # gen3-user-data-library
 
-![Version: 0.1.2](https://img.shields.io/badge/Version-0.1.2-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: main](https://img.shields.io/badge/AppVersion-main-informational?style=flat-square)
+![Version: 0.1.3](https://img.shields.io/badge/Version-0.1.3-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: main](https://img.shields.io/badge/AppVersion-main-informational?style=flat-square)
 
 A Helm chart for Kubernetes
 
@@ -48,6 +48,7 @@ A Helm chart for Kubernetes
 | global.postgres.master.port | string | `"5432"` | Port for Postgres. |
 | global.postgres.master.username | string | `"postgres"` | username of superuser in postgres. This is used to create or restore databases |
 | gunicornWorkers | int | `1` |  |
+| hostAliases | list | `[]` |  |
 | image.pullPolicy | string | `"Always"` |  |
 | image.repository | string | `"quay.io/cdis/gen3-user-data-library"` |  |
 | image.tag | string | `"main"` |  |
@@ -58,6 +59,7 @@ A Helm chart for Kubernetes
 | ingress.hosts[0].paths[0].path | string | `"/"` |  |
 | ingress.hosts[0].paths[0].pathType | string | `"ImplementationSpecific"` |  |
 | ingress.tls | list | `[]` |  |
+| itemSchemas | string | `nil` |  |
 | livenessProbe.httpGet.path | string | `"/"` |  |
 | livenessProbe.httpGet.port | string | `"http"` |  |
 | metricsEnabled | bool | `false` | Whether Metrics are enabled. |

helm/gen3-user-data-library/templates/configmap.yaml

@@ -0,0 +1,9 @@
+{{- if .Values.itemSchemas}}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ include "gen3-user-data-library.fullname" . }}-config
+data:
+  item_schemas.json: |-
+    {{ .Values.itemSchemas| toJson | indent 4}}
+{{- end}}

helm/gen3-user-data-library/templates/deployment.yaml

@@ -30,18 +30,31 @@ spec:
         {{- include "common.grafanaAnnotations" . | nindent 8 }}
         {{- end }}
     spec:
+      {{- with .Values.hostAliases}}
+      hostAliases:
+        {{- toYaml . | nindent 4}}
+      {{- end}}
       {{- with .Values.affinity }}
       affinity:
         {{- toYaml . | nindent 8 }}
       {{- end }}
       automountServiceAccountToken: {{ .Values.automountServiceAccountToken }}
+
       volumes:
         - name: gen3-user-data-library-g3auto-volume
           secret:
             secretName: gen3userdatalibrary-g3auto
+        {{- if .Values.itemSchemas }}
+        - name: gen3-user-data-library-config-volume
+          configMap:
+            name: {{ include "gen3-user-data-library.fullname" . }}-config
+        {{- end }}
+
       containers:
         - name: {{ .Chart.Name }}
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+
           env:
             {{- toYaml .Values.env | nindent 12 }}
             - name: URL_PREFIX
@@ -76,33 +89,46 @@ spec:
                   name: gen3-user-data-library-dbcreds
                   key: dbcreated
                   optional: false
-          imagePullPolicy: {{ .Values.image.pullPolicy }}
+
           ports:
             - containerPort: 80
               name: http
+
           livenessProbe:
             httpGet:
               path: /_status
               port: 80
             initialDelaySeconds: 30
             periodSeconds: 60
             timeoutSeconds: 30
+
           readinessProbe:
             httpGet:
               path: /_status
               port: 80
-          {{- with .Values.volumeMounts }}
+          {{- if or .Values.itemSchemas .Values.volumeMounts }}
           volumeMounts:
-            {{- toYaml . | nindent 10 }}
-          {{- end }}
+            {{- with .Values.volumeMounts }}
+            {{ toYaml . | nindent 12 }}
+            {{- end }}
+            {{- if .Values.itemSchemas }}
+            - name: gen3-user-data-library-config-volume
+              mountPath: /gen3userdatalibrary/config/item_schemas.json
+              readOnly: true
+              subPath: item_schemas.json
+            {{- end }}
+          {{- end}}
+
           {{- with .Values.resources }}
           resources:
             {{- toYaml . | nindent 12 }}
           {{- end }}
+
       initContainers:
         - name: gen3-user-data-library-init
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
+
           env:
             - name: GEN3_DEBUG
               value: "False"
@@ -137,14 +163,23 @@ spec:
                   key: dbcreated
                   optional: false
 
-          {{- with .Values.volumeMounts }}
+          {{- if or .Values.itemSchemas .Values.volumeMounts }}
           volumeMounts:
-            {{- toYaml . | nindent 12 }}
-          {{- end }}
+            {{- with .Values.volumeMounts }}
+            {{ toYaml . | nindent 12 }}
+            {{- end }}
+            {{- if .Values.itemSchemas }}
+            - name: gen3-user-data-library-config-volume
+              mountPath: /gen3userdatalibrary/config/item_schemas.json
+              readOnly: true
+              subPath: item_schemas.json
+            {{- end }}
+          {{- end}}
           {{- with .Values.resources }}
           resources:
             {{- toYaml . | nindent 12 }}
           {{- end }}
+
           command: [ "/bin/sh" ]
           args:
             - "-c"

helm/gen3-user-data-library/values.yaml

@@ -128,6 +128,7 @@ volumeMounts:
     readOnly: true
     subPath: gen3-user-data-library.env
 
+
 affinity: {}
 automountServiceAccountToken: false
 
@@ -188,3 +189,10 @@ secrets:
   # -- (str) AWS secret access key ID. Overrides global key.
   awsSecretAccessKey:
 gunicornWorkers: 1
+
+
+# Item Schema
+itemSchemas: Null
+
+# Host Aliases
+hostAliases: []