Merge pull request #213 from uc-cdis/feat/helm-albased-updates

Making various updates to ensure helm works with the new AL based images

helm/gen3/Chart.yaml

@@ -48,7 +48,7 @@ dependencies:
     repository: "file://../hatchery"
     condition: hatchery.enabled
   - name: indexd
-    version: 0.1.16
+    version: 0.1.17
     repository: "file://../indexd"
     condition: indexd.enabled
   - name: manifestservice
@@ -60,7 +60,7 @@ dependencies:
     repository: "file://../metadata"
     condition: metadata.enabled
   - name: peregrine
-    version: 0.1.15
+    version: 0.1.16
     repository: "file://../peregrine"
     condition: peregrine.enabled
   - name: pidgin
@@ -72,15 +72,15 @@ dependencies:
     repository: "file://../portal"
     condition: portal.enabled
   - name: requestor
-    version: 0.1.14
+    version: 0.1.15
     repository: "file://../requestor"
     condition: requestor.enabled
   - name: revproxy
     version: 0.1.18
     repository: "file://../revproxy"
     condition: revproxy.enabled
   - name: sheepdog
-    version: 0.1.17
+    version: 0.1.18
     repository: "file://../sheepdog"
     condition: sheepdog.enabled
   - name: ssjdispatcher
@@ -92,7 +92,7 @@ dependencies:
     condition: sower.enabled
     repository: "file://../sower"
   - name: wts
-    version: 0.1.16
+    version: 0.1.17
     repository: "file://../wts"
     condition: wts.enabled
   - name: gen3-network-policies
@@ -132,7 +132,7 @@ 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: 0.1.47
+version: 0.1.48
 
 # 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/README.md

@@ -1,6 +1,6 @@
 # gen3
 
-![Version: 0.1.47](https://img.shields.io/badge/Version-0.1.47-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: 0.1.48](https://img.shields.io/badge/Version-0.1.48-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
 
@@ -30,19 +30,19 @@ Helm chart to deploy Gen3 Data Commons
 | file://../frontend-framework | frontend-framework | 0.1.4 |
 | file://../guppy | guppy | 0.1.15 |
 | file://../hatchery | hatchery | 0.1.11 |
-| file://../indexd | indexd | 0.1.16 |
+| file://../indexd | indexd | 0.1.17 |
 | file://../manifestservice | manifestservice | 0.1.16 |
 | file://../metadata | metadata | 0.1.15 |
 | file://../neuvector | neuvector | 0.1.1 |
-| file://../peregrine | peregrine | 0.1.15 |
+| file://../peregrine | peregrine | 0.1.16 |
 | file://../pidgin | pidgin | 0.1.12 |
 | file://../portal | portal | 0.1.20 |
-| file://../requestor | requestor | 0.1.14 |
+| file://../requestor | requestor | 0.1.15 |
 | file://../revproxy | revproxy | 0.1.18 |
-| file://../sheepdog | sheepdog | 0.1.17 |
+| file://../sheepdog | sheepdog | 0.1.18 |
 | file://../sower | sower | 0.1.14 |
 | file://../ssjdispatcher | ssjdispatcher | 0.1.12 |
-| file://../wts | wts | 0.1.16 |
+| file://../wts | wts | 0.1.17 |
 | https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
 | https://helm.elastic.co | elasticsearch | 7.10.2 |
 
@@ -167,7 +167,7 @@ Helm chart to deploy Gen3 Data Commons
 | neuvector.policies.include | bool | `false` |  |
 | neuvector.policies.policyMode | string | `"Monitor"` |  |
 | peregrine.enabled | bool | `true` | Whether to deploy the peregrine subchart. |
-| pidgin.enabled | bool | `true` | Whether to deploy the pidgin subchart. |
+| pidgin.enabled | bool | `false` | Whether to deploy the pidgin subchart. |
 | portal.enabled | bool | `true` | Whether to deploy the portal subchart. |
 | postgresql | map | `{"primary":{"persistence":{"enabled":false}}}` | To configure postgresql subchart Disable persistence by default so we can spin up and down ephemeral environments |
 | postgresql.primary.persistence.enabled | bool | `false` | Option to persist the dbs data. |
@@ -181,5 +181,3 @@ Helm chart to deploy Gen3 Data Commons
 | ssjdispatcher.enabled | bool | `false` | Whether to deploy the ssjdispatcher subchart. |
 | wts.enabled | bool | `true` | Whether to deploy the wts subchart. |
 
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/gen3/values.yaml

@@ -238,7 +238,7 @@ peregrine:
 
 pidgin:
   # -- (bool) Whether to deploy the pidgin subchart.
-  enabled: true
+  enabled: false
 
 portal:
   # -- (bool) Whether to deploy the portal subchart.

helm/indexd/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: 0.1.16
+version: 0.1.17
 
 # 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/indexd/README.md

@@ -1,6 +1,6 @@
 # indexd
 
-![Version: 0.1.16](https://img.shields.io/badge/Version-0.1.16-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: 0.1.17](https://img.shields.io/badge/Version-0.1.17-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 indexd
 
@@ -107,5 +107,3 @@ A Helm chart for gen3 indexd
 | volumeMounts | list | `[{"mountPath":"/var/www/indexd/local_settings.py","name":"config-volume","readOnly":true,"subPath":"local_settings.py"}]` | Volumes to mount to the container. |
 | volumes | list | `[{"configMap":{"name":"indexd-uwsgi"},"name":"uwsgi-config"},{"name":"config-volume","secret":{"secretName":"indexd-settings"}}]` | Volumes to attach to the pod |
 
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/indexd/templates/pre-install.yaml

@@ -82,8 +82,15 @@ spec:
             # Script always succeeds if it runs (echo exits with 0)
             # indexd image does not include jq, so use python 
             - |
-              echo 'python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}'
-              python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}"
-              echo 'python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}'
-              python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}"
+              if command -v python &> /dev/null; then
+                echo 'python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}'
+                python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}"
+                echo 'python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}'
+                python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}"
+              else
+                echo 'poetry run python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}'
+                poetry run python /indexd/bin/index_admin.py create --username "fence" --password "${FENCE_PASS}"
+                echo 'poetry run python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}'
+                poetry run python /indexd/bin/index_admin.py create --username "sheepdog" --password "${SHEEPDOG_PASS}"
+              fi
       restartPolicy: Never

helm/observability/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: 0.1.1
+version: 0.1.2
 
 # 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/observability/README.md

@@ -1,6 +1,6 @@
 # lgtma-chart
 
-![Version: 0.1.1](https://img.shields.io/badge/Version-0.1.1-informational?style=flat-square) ![Type: application](https://img.shields.io/badge/Type-application-informational?style=flat-square) ![AppVersion: 1.0.0](https://img.shields.io/badge/AppVersion-1.0.0-informational?style=flat-square)
+![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: 1.0.0](https://img.shields.io/badge/AppVersion-1.0.0-informational?style=flat-square)
 
 A Helm chart for deploying the LGTM stack with additional resources
 
@@ -307,5 +307,3 @@ A Helm chart for deploying the LGTM stack with additional resources
 | lgtm.role.arn | string | `nil` | The arn of the aws role to associate with the service account that will be used for Loki and Mimir. Documentation on IRSA setup https://docs.aws.amazon.com/eks/latest/userguide/iam-roles-for-service-accounts.html |
 | lgtm.tempo.enabled | bool | `false` | Enable or disable tempo. |
 
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/observability/SETUP.md

@@ -117,7 +117,7 @@ This Helm chart comes equipped with built-in Gen3 alerts, defined in the 'alerti
 
 ### Built-in Gen3 Dashboards
 
-We'll soon be releasing Gen3 dashboards, providing users with Gen3-specific visualizations. Please check back here to see if they have been released.
+You can utilize Gen3-specific visualizations by visiting our [grafana-dashboards repo](https://github.com/uc-cdis/grafana-dashboards).
 
 ## Configuring Mimir
 

helm/peregrine/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: 0.1.15
+version: 0.1.16
 
 # 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/peregrine/README.md

@@ -1,6 +1,6 @@
 # peregrine
 
-![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)
+![Version: 0.1.16](https://img.shields.io/badge/Version-0.1.16-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 Peregrine service
 
@@ -99,8 +99,6 @@ A Helm chart for gen3 Peregrine service
 | serviceAccount.create | bool | `true` | Specifies whether a service account should be created. |
 | serviceAccount.name | string | `""` | The name of the service account |
 | tolerations | list | `[]` | Tolerations for the pods |
-| volumeMounts | list | `[{"mountPath":"/var/www/peregrine/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
+| volumeMounts | list | `[{"mountPath":"/var/www/peregrine/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"},{"mountPath":"peregrine/bin/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
 | volumes | list | `[{"emptyDir":{},"name":"shared-data"},{"name":"config-volume","secret":{"secretName":"peregrine-secret"}}]` | Volumes to attach to the container. |
 
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/peregrine/values.yaml

@@ -222,6 +222,10 @@ volumeMounts:
     readOnly: true
     mountPath: "/var/www/peregrine/settings.py"
     subPath: "settings.py"
+  - name: "config-volume"
+    readOnly: true
+    mountPath: "peregrine/bin/settings.py"
+    subPath: "settings.py"
 
 # Values to determine the labels that are used for the deployment, pod, etc.
 # -- (string) Valid options are "production" or "dev". If invalid option is set- the value will default to "dev".

helm/requestor/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

helm/requestor/README.md

@@ -1,6 +1,6 @@
 # requestor
 
-![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 Requestor Service
 
@@ -114,5 +114,3 @@ A Helm chart for gen3 Requestor Service
 | strategy.rollingUpdate.maxUnavailable | int | `0` | Maximum amount of pods that can be unavailable during the update. |
 | volumeMounts | list | `nil` | Volumes to mount to the container. |
 
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/requestor/templates/deployment.yaml

@@ -152,4 +152,4 @@ spec:
           args:
             - "-c"
             - |
-              /env/bin/alembic upgrade head
+              poetry run alembic upgrade head || /env/bin/alembic upgrade head

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: 0.1.17
+version: 0.1.18
 
 # 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/sheepdog/README.md

@@ -1,6 +1,6 @@
 # sheepdog
 
-![Version: 0.1.17](https://img.shields.io/badge/Version-0.1.17-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: 0.1.18](https://img.shields.io/badge/Version-0.1.18-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
 
@@ -105,7 +105,5 @@ A Helm chart for gen3 Sheepdog Service
 | strategy.rollingUpdate.maxSurge | int | `1` | Number of additional replicas to add during rollout. |
 | strategy.rollingUpdate.maxUnavailable | int | `0` | Maximum amount of pods that can be unavailable during the update. |
 | terminationGracePeriodSeconds | int | `50` | sheepdog transactions take forever - try to let the complete before termination |
-| volumeMounts | list | `[{"mountPath":"/var/www/sheepdog/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
+| volumeMounts | list | `[{"mountPath":"/var/www/sheepdog/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"},{"mountPath":"sheepdog/bin/settings.py","name":"config-volume","readOnly":true,"subPath":"settings.py"}]` | Volumes to mount to the container. |
 
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/sheepdog/templates/deployment.yaml

@@ -49,6 +49,7 @@ spec:
       initContainers:
         - name: sheepdog-init
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
           env:
           - name: DICTIONARY_URL
             value: {{ .Values.dictionaryUrl }}
@@ -93,11 +94,17 @@ spec:
               # sheepdog sets up core data model now,
               # but suffers from a race condition doing it ...
               #
-              echo datamodel_postgres_admin create-all -U "${PGUSER}" -P XXXXXXX -H "${PGHOST}" -D "${PGDB}"
-              datamodel_postgres_admin create-all -U "${PGUSER}" -P "${PGPASSWORD}" -H "${PGHOST}" -D "${PGDB}"
-              
-              echo python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}"  --password XXXXX --host "${PGHOST}" --database "${PGDB}"
-              python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}"  --password "${PGPASSWORD}" --host "${PGHOST}" --database "${PGDB}"
+              if command -v python &> /dev/null; then
+                echo datamodel_postgres_admin create-all -U "${PGUSER}" -P XXXXXXX -H "${PGHOST}" -D "${PGDB}"
+                datamodel_postgres_admin create-all -U "${PGUSER}" -P "${PGPASSWORD}" -H "${PGHOST}" -D "${PGDB}"
+                echo python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}"  --password XXXXX --host "${PGHOST}" --database "${PGDB}"
+                python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}"  --password "${PGPASSWORD}" --host "${PGHOST}" --database "${PGDB}"
+              else
+                echo poetry run datamodel_postgres_admin create-all -U "${PGUSER}" -P XXXXXXX -H "${PGHOST}" -D "${PGDB}"
+                poetry run datamodel_postgres_admin create-all -U "${PGUSER}" -P "${PGPASSWORD}" -H "${PGHOST}" -D "${PGDB}"
+                echo poetry run python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}"  --password XXXXX --host "${PGHOST}" --database "${PGDB}"
+                poetry run python /sheepdog/bin/setup_transactionlogs.py --user "${PGUSER}"  --password "${PGPASSWORD}" --host "${PGHOST}" --database "${PGDB}"
+              fi
       containers:
         - name: sheepdog
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"

helm/sheepdog/values.yaml

@@ -188,6 +188,10 @@ volumeMounts:
     readOnly: true
     mountPath: "/var/www/sheepdog/settings.py"
     subPath: "settings.py"
+  - name: "config-volume"
+    readOnly: true
+    mountPath: "sheepdog/bin/settings.py"
+    subPath: "settings.py"
 
 # -- (map) Resource requests and limits for the containers in the pod
 resources: