uc-cdis · jawadqur · Dec 5, 2024 · Dec 5, 2024 · Dec 5, 2024 · Dec 5, 2024
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -155,15 +155,15 @@
         "filename": "helm/portal/values.yaml",
         "hashed_secret": "08eeb737b239bdb7362a875b90e22c10b8826b20",
         "is_verified": false,
-        "line_number": 473,
+        "line_number": 475,
         "is_secret": false
       },
       {
         "type": "Base64 High Entropy String",
         "filename": "helm/portal/values.yaml",
         "hashed_secret": "eb9739c6625f06b4ab73035223366dda6262ae77",
         "is_verified": false,
-        "line_number": 475,
+        "line_number": 477,
         "is_secret": false
       }
     ],
@@ -178,5 +178,5 @@
       }
     ]
   },
-  "generated_at": "2024-11-18T20:39:22Z"
+  "generated_at": "2024-12-05T20:32:52Z"
 }
diff --git a/helm/frontend-framework/Chart.yaml b/helm/frontend-framework/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: 0.1.5
+version: 0.1.6
 
 # 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

diff --git a/helm/frontend-framework/README.md b/helm/frontend-framework/README.md
@@ -1,6 +1,6 @@
 # frontend-framework
 
-![Version: 0.1.5](https://img.shields.io/badge/Version-0.1.5-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: develop](https://img.shields.io/badge/AppVersion-develop-informational?style=flat-square)
+![Version: 0.1.6](https://img.shields.io/badge/Version-0.1.6-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: develop](https://img.shields.io/badge/AppVersion-develop-informational?style=flat-square)
 
 A Helm chart for the gen3 frontend framework
 
@@ -68,6 +68,7 @@ A Helm chart for the gen3 frontend framework
 | partOf | string | `"Front-End"` | Label to help organize pods and their use. Any value is valid, but use "_" or "-" to divide words. |
 | podAnnotations | map | `{}` | Annotations to add to the pod |
 | podSecurityContext | map | `{}` | Security context to apply to the pod |
+| port | int | `3000` |  |
 | release | string | `"dev"` | Valid options are "production" or "dev". If invalid option is set- the value will default to "dev". |
 | replicaCount | int | `1` | Number of replicas for the deployment. |
 | resources | map | `{"limits":{"cpu":0.6,"memory":"4096Mi"},"requests":{"cpu":0.6,"memory":"512Mi"}}` | Resource requests and limits for the containers in the pod |

diff --git a/helm/frontend-framework/templates/deployment.yaml b/helm/frontend-framework/templates/deployment.yaml
@@ -35,36 +35,41 @@ spec:
         - name: frontend-framework
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
-          # livenessProbe:
-          #   httpGet:
-          #     path: /ff
-          #     port: 80
-          #   initialDelaySeconds: 60
-          #   periodSeconds: 30
-          #   timeoutSeconds: 30
-          #   failureThreshold: 30
+          livenessProbe:
+            httpGet:
+              {{- if eq "portal" .Values.global.frontendRoot }}
+              path: /ff
+              {{- else }}
+              path: /
+              {{- end }}
+              port: {{ .Values.port }}
+            initialDelaySeconds: 3
+            periodSeconds: 10
+            timeoutSeconds: 30
           readinessProbe:
             httpGet:
               {{- if eq "portal" .Values.global.frontendRoot }}
               path: /ff
               {{- else }}
               path: /
               {{- end }}
-              port: 3000
+              port: {{ .Values.port }}
             initialDelaySeconds: 3
             periodSeconds: 10
             timeoutSeconds: 30
           resources:
             {{- toYaml .Values.resources | nindent 12 }}
           ports:
-            - containerPort: 3000
+            - containerPort: {{ .Values.port }}
               name: http
               protocol: TCP
           envFrom:
             - configMapRef:
                 name: {{ include "frontend-framework.fullname" . }}-configmap
                 optional: true
           env:
+            - name: PORT
+              value: {{ .Values.port | quote }}
             - name: HOSTNAME
               value: revproxy-service
             {{- if eq "portal" .Values.global.frontendRoot }}
@@ -74,27 +79,4 @@ spec:
             - name: NEXT_PUBLIC_PORTAL_BASENAME
               value: /portal
             {{- end }}
-            # disable npm 7's brand new update notifier to prevent Portal from stuck at starting up
-            # see https://github.com/npm/cli/issues/3163
-            - name: NPM_CONFIG_UPDATE_NOTIFIER
-              value: "false"
-#needed to be adjusted to use the gen3 umbrella chart or local var ^ 
-#adding a var in helpers.tpl for later- Elise
-             {{- with .Values.datadogApplicationId  }}      
-            - name: DATADOG_APPLICATION_ID
-              # Optional client token for Datadog
-              value: {{ . }}
-            {{- end }}
-            {{- with .Values.datadogClientToken  }}      
-            - name: DATADOG_CLIENT_TOKEN
-              # Optional client token for Datadog
-              value: {{ . }}
-            {{- end }}
-            {{- with .Values.dataUploadBucket  }}
-            - name: DATA_UPLOAD_BUCKET
-              value: {{ . }}
-            {{- end }}
-              # S3 bucket name for data upload, for setting up CSP
-              #GEN3_DATA_UPLOAD_BUCKET|-value: ""-|
-            # - name: BASENAME
 
diff --git a/helm/frontend-framework/templates/service.yaml b/helm/frontend-framework/templates/service.yaml
@@ -8,11 +8,11 @@ spec:
   ports:
     - protocol: TCP
       port: 80
-      targetPort: 3000
+      targetPort: {{ .Values.port }}
       name: http
     - protocol: TCP
       port: 443
-      targetPort: 3000
+      targetPort: {{ .Values.port }}
       name: https
   type: ClusterIP
   selector:

diff --git a/helm/frontend-framework/values.yaml b/helm/frontend-framework/values.yaml
@@ -126,6 +126,8 @@ autoscaling:
   targetCPUUtilizationPercentage: 80
   # targetMemoryUtilizationPercentage: 80
 
+port: 3000
+
 # -- (list) List of environment variables to add to the deployment.
 env: []
 

diff --git a/helm/gen3/Chart.yaml b/helm/gen3/Chart.yaml
@@ -32,7 +32,7 @@ dependencies:
     repository: file://../etl
     condition: etl.enabled
   - name: frontend-framework
-    version: 0.1.5
+    version: 0.1.6
     repository: "file://../frontend-framework"
     condition: frontend-framework.enabled
   - name: fence
@@ -64,7 +64,7 @@ dependencies:
     repository: "file://../peregrine"
     condition: peregrine.enabled
   - name: portal
-    version: 0.1.21
+    version: 0.1.22
     repository: "file://../portal"
     condition: portal.enabled
   - name: requestor
@@ -76,11 +76,11 @@ dependencies:
     repository: "file://../revproxy"
     condition: revproxy.enabled
   - name: sheepdog
-    version: 0.1.19
+    version: 0.1.20
     repository: "file://../sheepdog"
     condition: sheepdog.enabled
   - name: ssjdispatcher
-    version: 0.1.14
+    version: 0.1.15
     repository: "file://../ssjdispatcher"
     condition: ssjdispatcher.enabled
   - name: sower
@@ -128,7 +128,7 @@ 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: 0.1.50
+version: 0.1.51
 
 # 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

diff --git a/helm/gen3/README.md b/helm/gen3/README.md
@@ -1,6 +1,6 @@
 # gen3
 
-![Version: 0.1.50](https://img.shields.io/badge/Version-0.1.50-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
+![Version: 0.1.51](https://img.shields.io/badge/Version-0.1.51-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
 
 Helm chart to deploy Gen3 Data Commons
 
@@ -26,7 +26,7 @@ Helm chart to deploy Gen3 Data Commons
 | file://../common | common | 0.1.16 |
 | file://../etl | etl | 0.1.6 |
 | file://../fence | fence | 0.1.26 |
-| file://../frontend-framework | frontend-framework | 0.1.5 |
+| file://../frontend-framework | frontend-framework | 0.1.6 |
 | file://../gen3-network-policies | gen3-network-policies | 0.1.2 |
 | file://../guppy | guppy | 0.1.16 |
 | file://../hatchery | hatchery | 0.1.12 |
@@ -35,12 +35,12 @@ Helm chart to deploy Gen3 Data Commons
 | file://../metadata | metadata | 0.1.16 |
 | file://../neuvector | neuvector | 0.1.2 |
 | file://../peregrine | peregrine | 0.1.17 |
-| file://../portal | portal | 0.1.21 |
+| file://../portal | portal | 0.1.22 |
 | file://../requestor | requestor | 0.1.16 |
 | file://../revproxy | revproxy | 0.1.19 |
-| file://../sheepdog | sheepdog | 0.1.19 |
+| file://../sheepdog | sheepdog | 0.1.20 |
 | file://../sower | sower | 0.1.15 |
-| file://../ssjdispatcher | ssjdispatcher | 0.1.14 |
+| file://../ssjdispatcher | ssjdispatcher | 0.1.15 |
 | file://../wts | wts | 0.1.18 |
 | https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
 | https://helm.elastic.co | elasticsearch | 7.10.2 |

diff --git a/helm/portal/Chart.yaml b/helm/portal/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: 0.1.21
+version: 0.1.22
 
 # 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

diff --git a/helm/portal/README.md b/helm/portal/README.md
diff --git a/helm/portal/templates/deployment.yaml b/helm/portal/templates/deployment.yaml
@@ -117,8 +117,7 @@ spec:
             - name: APP
               value: {{ .Values.global.portalApp | quote }}
             - name: GEN3_BUNDLE
-              # optional: true
-              value: ""
+              value: {{ .Values.gitops.gen3Bundle | quote }}
             - name: LOGOUT_INACTIVE_USERS
               valueFrom:
                 configMapKeyRef:

diff --git a/helm/portal/values.yaml b/helm/portal/values.yaml
@@ -205,6 +205,8 @@ extraImages:
 
 # -- (map) GitOps configuration for portal
 gitops:
+  # -- (string)
+  gen3Bundle: ""
   # -- (string) multiline string - gitops.json
   json: |
     {

diff --git a/helm/sheepdog/Chart.yaml b/helm/sheepdog/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: 0.1.19
+version: 0.1.20
 
 # 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

diff --git a/helm/sheepdog/README.md b/helm/sheepdog/README.md
@@ -1,6 +1,6 @@
 # sheepdog
 
-![Version: 0.1.19](https://img.shields.io/badge/Version-0.1.19-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
+![Version: 0.1.20](https://img.shields.io/badge/Version-0.1.20-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
 
 A Helm chart for gen3 Sheepdog Service
 
@@ -23,7 +23,7 @@ A Helm chart for gen3 Sheepdog Service
 | affinity.podAntiAffinity.preferredDuringSchedulingIgnoredDuringExecution[0].podAffinityTerm.labelSelector.matchExpressions[0].values | list | `["sheepdog"]` | Value for the match expression key. |
 | affinity.podAntiAffinity.preferredDuringSchedulingIgnoredDuringExecution[0].podAffinityTerm.topologyKey | string | `"kubernetes.io/hostname"` | Value for topology key label. |
 | arboristUrl | string | `"http://arborist-service"` | URL for the arborist service |
-| authNamespace | string | `"default"` |  |
+| authNamespace | string | `""` |  |
 | automountServiceAccountToken | bool | `false` | Automount the default service account token |
 | autoscaling | map | `{"enabled":false,"maxReplicas":100,"minReplicas":1,"targetCPUUtilizationPercentage":80}` | Configuration for autoscaling the number of replicas |
 | autoscaling.enabled | bool | `false` | Whether autoscaling is enabled |

diff --git a/helm/sheepdog/values.yaml b/helm/sheepdog/values.yaml
@@ -180,7 +180,7 @@ indexdUrl: http://indexd-service
 fenceUrl: http://fence-service
 # -- (string) URL for the arborist service
 arboristUrl: http://arborist-service
-authNamespace: default
+authNamespace: ""
 
 # -- (list) Volumes to mount to the container.
 volumeMounts:

diff --git a/helm/ssjdispatcher/Chart.yaml b/helm/ssjdispatcher/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: 0.1.14
+version: 0.1.15
 
 # 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

diff --git a/helm/ssjdispatcher/README.md b/helm/ssjdispatcher/README.md
@@ -1,6 +1,6 @@
 # ssjdispatcher
 
-![Version: 0.1.14](https://img.shields.io/badge/Version-0.1.14-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
+![Version: 0.1.15](https://img.shields.io/badge/Version-0.1.15-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
 
 A Helm chart for gen3 ssjdispatcher
 
@@ -44,6 +44,9 @@ A Helm chart for gen3 ssjdispatcher
 | global.dictionaryUrl | string | `"https://s3.amazonaws.com/dictionary-artifacts/datadictionary/develop/schema.json"` | URL of the data dictionary. |
 | global.dispatcherJobNum | int | `"10"` | Number of dispatcher jobs. |
 | global.environment | string | `"default"` | Environment name. This should be the same as vpcname if you're doing an AWS deployment. Currently this is being used to share ALB's if you have multiple namespaces. Might be used other places too. |
+| global.externalSecrets | map | `{"deploy":false,"separateSecretStore":false}` | External Secrets settings. |
+| global.externalSecrets.deploy | bool | `false` | Will use ExternalSecret resources to pull secrets from Secrets Manager instead of creating them locally. Be cautious as this will override any indexd secrets you have deployed. |
+| global.externalSecrets.separateSecretStore | string | `false` | Will deploy a separate External Secret Store for this service. |
 | global.hostname | string | `"localhost"` | Hostname for the deployment. |
 | global.kubeBucket | string | `"kube-gen3"` | S3 bucket name for Kubernetes manifest files. |
 | global.logsBucket | string | `"logs-gen3"` | S3 bucket name for log files. |