Adding nginx sidecar image to our services.

helm/audit/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: 0.1.30
+version: 0.1.31
 
 # 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
@@ -24,7 +24,7 @@ appVersion: "master"
 
 dependencies:
   - name: common
-    version: 0.1.23
+    version: 0.1.25
     repository: file://../common
   - name: postgresql
     version: 11.9.13

helm/audit/README.md

@@ -1,14 +1,14 @@
 # audit
 
-![Version: 0.1.30](https://img.shields.io/badge/Version-0.1.30-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: 0.1.31](https://img.shields.io/badge/Version-0.1.31-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 Kubernetes
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.23 |
+| file://../common | common | 0.1.25 |
 | https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
 
 ## Values

helm/aws-es-proxy/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: 0.1.30
+version: 0.1.31
 
 # 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
@@ -25,5 +25,5 @@ appVersion: "master"
 
 dependencies:
   - name: common
-    version: 0.1.23
+    version: 0.1.25
     repository: file://../common

helm/aws-es-proxy/README.md

@@ -1,14 +1,14 @@
 # aws-es-proxy
 
-![Version: 0.1.30](https://img.shields.io/badge/Version-0.1.30-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: 0.1.31](https://img.shields.io/badge/Version-0.1.31-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 AWS ES Proxy Service for gen3
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.23 |
+| file://../common | common | 0.1.25 |
 
 ## Values
 

helm/common/Chart.yaml

@@ -15,7 +15,7 @@ type: library
 # 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: 0.1.23
+version: 0.1.25
 
 # 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/common/README.md

@@ -1,6 +1,6 @@
 # common
 
-![Version: 0.1.23](https://img.shields.io/badge/Version-0.1.23-informational?style=flat-square) ![Type: library](https://img.shields.io/badge/Type-library-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
+![Version: 0.1.25](https://img.shields.io/badge/Version-0.1.25-informational?style=flat-square) ![Type: library](https://img.shields.io/badge/Type-library-informational?style=flat-square) ![AppVersion: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
 
 A Helm chart for provisioning databases in gen3
 

helm/common/templates/_nginx_sidecar.tpl

@@ -0,0 +1,21 @@
+{{- define "common.sidecar.container" -}}
+        - name: sidecar-nginx
+          image: "quay.io/cdis/nginx:master"
+          imagePullPolicy: Always
+          ports:
+            - name: http
+              containerPort: 8080
+              protocol: TCP
+          volumeMounts:
+            - name: "nginx-config"
+              mountPath: "/etc/nginx/conf.d/default.conf"
+              subPath: default.conf
+          readinessProbe:
+            httpGet:
+              path: /_status
+              port: http
+          livenessProbe:
+            httpGet:
+              path: /_status
+              port: http
+{{- end }}

helm/datareplicate/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: 0.0.29
+version: 0.0.30
 
 # 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
@@ -25,5 +25,5 @@ appVersion: "master"
 
 dependencies:
   - name: common
-    version: 0.1.23
+    version: 0.1.25
     repository: file://../common

helm/datareplicate/README.md

@@ -1,14 +1,14 @@
 # datareplicate
 
-![Version: 0.0.29](https://img.shields.io/badge/Version-0.0.29-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: 0.0.30](https://img.shields.io/badge/Version-0.0.30-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 datareplicate
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.23 |
+| file://../common | common | 0.1.25 |
 
 ## Values
 

helm/fence/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: 0.1.59
+version: 0.1.60
 
 # 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
@@ -24,7 +24,7 @@ appVersion: "master"
 
 dependencies:
   - name: common
-    version: 0.1.23
+    version: 0.1.25
     repository: file://../common
   - name: postgresql
     version: 11.9.13

helm/fence/README.md

@@ -1,14 +1,14 @@
 # fence
 
-![Version: 0.1.59](https://img.shields.io/badge/Version-0.1.59-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: 0.1.60](https://img.shields.io/badge/Version-0.1.60-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 Fence
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.23 |
+| file://../common | common | 0.1.25 |
 | https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
 
 ## Values
@@ -151,12 +151,13 @@ A Helm chart for gen3 Fence
 | global.postgres.master.username | string | `"postgres"` | username of superuser in postgres. This is used to create or restore databases |
 | global.publicDataSets | bool | `true` | Whether public datasets are enabled. |
 | global.revproxyArn | string | `"arn:aws:acm:us-east-1:123456:certificate"` | ARN of the reverse proxy certificate. |
+| global.sidecar.enabled | bool | `true` |  |
 | global.tierAccessLevel | string | `"libre"` | Access level for tiers. acceptable values for `tier_access_level` are: `libre`, `regular` and `private`. If omitted, by default common will be treated as `private` |
 | global.tierAccessLimit | int | `"1000"` | Only relevant if tireAccessLevel is set to "regular". Summary charts below this limit will not appear for aggregated data. |
 | googleCronJobs | map | `{"enabled":false}` | Configuration for the Google Cloud Storage cron jobs. |
 | image.pullPolicy | string | `"Always"` | When to pull the image. This value should be "Always" to ensure the latest image is used. |
 | image.repository | string | `"quay.io/cdis/fence"` | The Docker image repository for the fence service |
-| image.tag | string | `"master"` | Overrides the image tag whose default is the chart appVersion. |
+| image.tag | string | `"feat_nginx-sidecar"` | Overrides the image tag whose default is the chart appVersion. |
 | imagePullSecrets | list | `[]` | Docker image pull secrets. |
 | initEnv | list | `[{"name":"PGHOST","valueFrom":{"secretKeyRef":{"key":"host","name":"fence-dbcreds","optional":false}}},{"name":"PGUSER","valueFrom":{"secretKeyRef":{"key":"username","name":"fence-dbcreds","optional":false}}},{"name":"PGPASSWORD","valueFrom":{"secretKeyRef":{"key":"password","name":"fence-dbcreds","optional":false}}},{"name":"PGDB","valueFrom":{"secretKeyRef":{"key":"database","name":"fence-dbcreds","optional":false}}},{"name":"DBREADY","valueFrom":{"secretKeyRef":{"key":"dbcreated","name":"fence-dbcreds","optional":false}}},{"name":"DB","value":"postgresql://$(PGUSER):$(PGPASSWORD)@$(PGHOST):5432/$(PGDB)"},{"name":"FENCE_DB","value":"postgresql://$(PGUSER):$(PGPASSWORD)@$(PGHOST):5432/$(PGDB)"},{"name":"PYTHONPATH","value":"/var/www/fence"}]` | Volumes to attach to the init container. |
 | initVolumeMounts | list | `[{"mountPath":"/var/www/fence/fence-config-secret.yaml","name":"config-volume","readOnly":true,"subPath":"fence-config.yaml"},{"mountPath":"/var/www/fence/fence-config-public.yaml","name":"config-volume-public","readOnly":true,"subPath":"fence-config-public.yaml"},{"mountPath":"/var/www/fence/yaml_merge.py","name":"yaml-merge","readOnly":true,"subPath":"yaml_merge.py"},{"mountPath":"/var/www/fence/fence_google_app_creds_secret.json","name":"fence-google-app-creds-secret-volume","readOnly":true,"subPath":"fence_google_app_creds_secret.json"},{"mountPath":"/var/www/fence/fence_google_storage_creds_secret.json","name":"fence-google-storage-creds-secret-volume","readOnly":true,"subPath":"fence_google_storage_creds_secret.json"}]` | Volumes to mount to the init container. |
@@ -204,6 +205,7 @@ A Helm chart for gen3 Fence
 | serviceAccount.annotations."eks.amazonaws.com/role-arn" | string | `nil` | The Amazon Resource Name (ARN) of the role to associate with the service account |
 | serviceAccount.create | bool | `true` | Specifies whether a service account should be created. |
 | serviceAccount.name | string | `"fence-sa"` | The name of the service account |
+| sidecar.enabled | bool | `false` |  |
 | tolerations | list | `[]` | Tolerations for the pods |
 | usersync | map | `{"addDbgap":false,"custom_image":null,"env":null,"onlyDbgap":false,"schedule":"*/30 * * * *","slack_send_dbgap":false,"slack_webhook":"None","sshKnownHosts":"# example: <host> <keytype> <base64-key>\nsftp-dev.planx-pla.net ssh-rsa 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\nsftp-dev.planx-pla.net ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAII12G7WwOj4xWHLwj2ZnpA8e/FwOwy97SlYslOpzKctT\ns-5745d53f10e1421eb.server.transfer.us-east-1.amazonaws.com ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCNIOMhn0C6cf6pG0XnrXUP/TbzFgYN+tVoWzGuo4h8P5Foqev6Rs6gOXomu/vxONpNJ7/fl9oOAT3kD1Pdg0XkmEI2gksonwO5FRXEaMuz9be5d+uekrSuGSBV5ttoaiWvUootqbT8ZfG9aOHla/JbnvG9o8uijXdZsMZKgMRM/7tz+wF4Jp2+MqxMnpOS4NIknih16ZK2GTG4K2WmG4wsHmsLC+KMITc0UzDpD5aYWa+bicK4dsAk02Vu3R4FHsFdyMOZvdRbBRINlcmTYS7Ajd6Dow/iTDQGD5u2bOfPF0DGTg4jbwx7nnauEoMM20Ewr0QYdge6iac8VAzFfMOJ\n","syncFromDbgap":false,"userYamlS3Path":"s3://cdis-gen3-users/helm-test/user.yaml","usersync":false}` | Configuration options for usersync cronjob. |
 | usersync.addDbgap | bool | `false` | Force attempting a dbgap sync if "true", falls back on user.yaml |

helm/fence/templates/fence-deployment.yaml

@@ -41,31 +41,37 @@ spec:
       serviceAccountName: {{ include "fence.serviceAccountName" . }}
       volumes:
         {{- toYaml .Values.volumes | nindent 8 }}
+        - name: nginx-config
+          configMap:
+            name: nginx-configmap
       containers:
         - name: fence
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           ports:
-            - name: http
-              containerPort: 80
+            {{- if .Values.sidecar.enabled  | default .Values.global.sidecar.enabled }}
+            - name: app
+              containerPort: 8000
               protocol: TCP
-            - name: https
-              containerPort: 443
+            {{- else }}
+            - name: app
+              containerPort: 80
               protocol: TCP
+            {{- end }}
             - name: container
               containerPort: 6567
               protocol: TCP
           livenessProbe:
             httpGet:
               path: /_status
-              port: http
+              port: app
             initialDelaySeconds: 60
             periodSeconds: 60
             timeoutSeconds: 30
           readinessProbe:
             httpGet:
               path: /_status
-              port: http
+              port: app
           resources:
             {{- toYaml .Values.resources | nindent 12 }}
           command: ["/bin/bash"]
@@ -81,17 +87,17 @@ spec:
             {{- toYaml .Values.env | nindent 12 }}
           volumeMounts:
             {{- toYaml .Values.volumeMounts | nindent 12 }}
+        {{- if .Values.sidecar.enabled | default .Values.global.sidecar.enabled }}
+        {{ include "common.sidecar.container" . }}
+        {{- end }}
       initContainers:
         - name: fence-init
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           ports:
-            - name: http
+            - name: app
               containerPort: 80
               protocol: TCP
-            - name: https
-              containerPort: 443
-              protocol: TCP
             - name: container
               containerPort: 6567
               protocol: TCP

helm/fence/values.yaml

@@ -105,6 +105,8 @@ global:
     maxReplicas: 100
     targetCPUUtilizationPercentage: 80
     targetMemoryUtilizationPercentage: 80
+  sidecar:
+    enabled: true
 
 #  -- (map) This section is for setting up autoscaling more information can be found here: https://kubernetes.io/docs/concepts/workloads/autoscaling/
 autoscaling: {}
@@ -231,7 +233,10 @@ image:
   # -- (string) When to pull the image. This value should be "Always" to ensure the latest image is used.
   pullPolicy: Always
   # -- (string) Overrides the image tag whose default is the chart appVersion.
-  tag: "master"
+  tag: "feat_nginx-sidecar"
+
+sidecar:
+  enabled: false
 
 # -- (list) Docker image pull secrets.
 imagePullSecrets: []

helm/gen3/Chart.yaml

@@ -21,11 +21,11 @@ dependencies:
     repository: "file://../argo-wrapper"
     condition: argo-wrapper.enabled
   - name: audit
-    version: 0.1.30
+    version: 0.1.31
     repository: "file://../audit"
     condition: audit.enabled
   - name: aws-es-proxy
-    version: 0.1.30
+    version: 0.1.31
     repository: "file://../aws-es-proxy"
     condition: aws-es-proxy.enabled
   - name: cedar
@@ -37,14 +37,14 @@ dependencies:
     repository: "file://../cohort-middleware"
     condition: cohort-middleware.enabled
   - name: common
-    version: 0.1.23
+    version: 0.1.25
     repository: file://../common
   - name: dashboard
     version: 0.1.8
     repository: file://../dashboard
     condition: dashboard.enabled
   - name: datareplicate
-    version: 0.0.29
+    version: 0.0.30
     repository: "file://../datareplicate"
     condition: datareplicate.enabled
   - name: etl
@@ -56,7 +56,7 @@ dependencies:
     repository: "file://../frontend-framework"
     condition: frontend-framework.enabled
   - name: fence
-    version: 0.1.59
+    version: 0.1.60
     repository: "file://../fence"
     condition: fence.enabled
   - name: gen3-user-data-library
@@ -68,51 +68,51 @@ dependencies:
     repository: "file://../guppy"
     condition: guppy.enabled
   - name: hatchery
-    version: 0.1.28
+    version: 0.1.29
     repository: "file://../hatchery"
     condition: hatchery.enabled
   - name: indexd
-    version: 0.1.33
+    version: 0.1.34
     repository: "file://../indexd"
     condition: indexd.enabled
   - name: manifestservice
-    version: 0.1.32
+    version: 0.1.33
     repository: "file://../manifestservice"
     condition: manifestservice.enabled
   - name: metadata
-    version: 0.1.30
+    version: 0.1.31
     repository: "file://../metadata"
     condition: metadata.enabled
   - name: peregrine
     version: 0.1.31
     repository: "file://../peregrine"
     condition: peregrine.enabled
   - name: portal
-    version: 0.1.45
+    version: 0.1.46
     repository: "file://../portal"
     condition: portal.enabled
   - name: requestor
     version: 0.1.24
     repository: "file://../requestor"
     condition: requestor.enabled
   - name: revproxy
-    version: 0.1.42
+    version: 0.1.43
     repository: "file://../revproxy"
     condition: revproxy.enabled
   - name: sheepdog
     version: 0.1.29
     repository: "file://../sheepdog"
     condition: sheepdog.enabled
   - name: ssjdispatcher
-    version: 0.1.31
+    version: 0.1.32
     repository: "file://../ssjdispatcher"
     condition: ssjdispatcher.enabled
   - name: sower
-    version: 0.1.34
+    version: 0.1.35
     condition: sower.enabled
     repository: "file://../sower"
   - name: wts
-    version: 0.1.29
+    version: 0.1.30
     repository: "file://../wts"
     condition: wts.enabled
   - name: gen3-network-policies
@@ -168,7 +168,7 @@ 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: 0.2.50
+version: 0.2.51
 
 # 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