Merge pull request #214 from uc-cdis/feat/local-hatchery

Add support for workspaces in single-node clusters

.pre-commit-config.yaml

@@ -4,6 +4,8 @@ repos:
     hooks:
       - id: detect-secrets
         args: ["--baseline", ".secrets.baseline"]
+        additional_dependencies: ["gibberish-detector"]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.5.0
     hooks:
@@ -15,15 +17,16 @@ repos:
   #   hooks:
   #   - id: helmlint
 
-  - repo: local
+  - repo: https://github.com/norwoodj/helm-docs
+    rev: "v1.14.2"
     hooks:
-      - id: helm-docs
-        args: ["-c", "helm"]
-        description: Uses 'helm-docs' to create documentation from the Helm chart's 'values.yaml' file, and inserts the result into a corresponding 'README.md' file.
-        entry: git-hook/helm-docs.sh
-        language: script
-        name: Helm Docs
-        require_serial: true
+    #  Use a pinned version of helm-docs in a container to generate consistent documentation.
+      - name: helm-docs
+        id: helm-docs-container
+        entry: jnorwood/helm-docs:v1.14.2
+        args:
+        - "--chart-search-root=helm"
+        - "--skip-version-footer"
 
   - repo: local
     hooks:

.secrets.baseline

@@ -90,6 +90,10 @@
     {
       "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
     },
+    {
+      "path": "detect_secrets.filters.common.is_baseline_file",
+      "filename": ".secrets.baseline"
+    },
     {
       "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
       "min_level": 2
@@ -133,14 +137,16 @@
         "filename": "helm/portal/README.md",
         "hashed_secret": "eb9739c6625f06b4ab73035223366dda6262ae77",
         "is_verified": false,
-        "line_number": 34
+        "line_number": 34,
+        "is_secret": false
       },
       {
         "type": "Base64 High Entropy String",
         "filename": "helm/portal/README.md",
         "hashed_secret": "08eeb737b239bdb7362a875b90e22c10b8826b20",
         "is_verified": false,
-        "line_number": 39
+        "line_number": 39,
+        "is_secret": false
       }
     ],
     "helm/portal/values.yaml": [
@@ -149,14 +155,16 @@
         "filename": "helm/portal/values.yaml",
         "hashed_secret": "08eeb737b239bdb7362a875b90e22c10b8826b20",
         "is_verified": false,
-        "line_number": 473
+        "line_number": 473,
+        "is_secret": false
       },
       {
         "type": "Base64 High Entropy String",
         "filename": "helm/portal/values.yaml",
         "hashed_secret": "eb9739c6625f06b4ab73035223366dda6262ae77",
         "is_verified": false,
-        "line_number": 475
+        "line_number": 475,
+        "is_secret": false
       }
     ],
     "helm/revproxy/nginx/helpers.js": [
@@ -165,9 +173,10 @@
         "filename": "helm/revproxy/nginx/helpers.js",
         "hashed_secret": "1d278d3c888d1a2fa7eed622bfc02927ce4049af",
         "is_verified": false,
-        "line_number": 10
+        "line_number": 10,
+        "is_secret": false
       }
     ]
   },
-  "generated_at": "2024-11-11T22:26:01Z"
+  "generated_at": "2024-11-18T20:39:22Z"
 }

helm/alloy/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/alloy/README.md

@@ -1,6 +1,6 @@
 # alloy
 
-![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: master](https://img.shields.io/badge/AppVersion-master-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: master](https://img.shields.io/badge/AppVersion-master-informational?style=flat-square)
 
 A Helm chart for deploying Grafana Alloy
 
@@ -27,6 +27,3 @@ A Helm chart for deploying Grafana Alloy
 | alloy.controller.affinity.nodeAffinity.requiredDuringSchedulingIgnoredDuringExecution.nodeSelectorTerms[0].matchExpressions[0].operator | string | `"In"` |  |
 | alloy.controller.affinity.nodeAffinity.requiredDuringSchedulingIgnoredDuringExecution.nodeSelectorTerms[0].matchExpressions[0].values[0] | string | `"us-east-1a"` |  |
 | alloy.controller.type | string | `"deployment"` |  |
-
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/ambassador/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
@@ -25,5 +25,5 @@ appVersion: "1.4.2"
 
 dependencies:
   - name: common
-    version: 0.1.15
+    version: 0.1.16
     repository: file://../common

helm/ambassador/README.md

@@ -1,14 +1,14 @@
 # ambassador
 
-![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: 1.4.2](https://img.shields.io/badge/AppVersion-1.4.2-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: 1.4.2](https://img.shields.io/badge/AppVersion-1.4.2-informational?style=flat-square)
 
 A Helm chart for deploying ambassador for gen3
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.15 |
+| file://../common | common | 0.1.16 |
 
 ## Values
 
@@ -56,6 +56,3 @@ A Helm chart for deploying ambassador for gen3
 | serviceAccount.name | string | `""` | The name of the service account to use. If not set and create is true, a name is generated using the fullname template. |
 | tolerations | list | `[]` | Tolerations to use for the deployment. |
 | userNamespace | string | `"jupyter-pods"` | Namespace to use for user resources. |
-
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/arborist/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: 0.1.13
+version: 0.1.14
 
 # 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
@@ -25,7 +25,7 @@ appVersion: "master"
 
 dependencies:
   - name: common
-    version: 0.1.15
+    version: 0.1.16
     repository: file://../common
   - name: postgresql
     version: 11.9.13

helm/arborist/README.md

@@ -1,14 +1,14 @@
 # arborist
 
-![Version: 0.1.13](https://img.shields.io/badge/Version-0.1.13-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: 0.1.14](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)
 
 A Helm chart for gen3 arborist
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.15 |
+| file://../common | common | 0.1.16 |
 | https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
 
 ## Values
@@ -101,6 +101,3 @@ A Helm chart for gen3 arborist
 | tolerations | list | `[]` | Tolerations to apply to the pod |
 | volumeMounts | list | `[]` | Volume mounts to attach to the container |
 | volumes | list | `[]` | 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/argo-wrapper/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: 0.1.9
+version: 0.1.10
 
 # 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: 0.1.15
+    version: 0.1.16
     repository: file://../common

helm/argo-wrapper/README.md

@@ -1,14 +1,14 @@
 # argo-wrapper
 
-![Version: 0.1.9](https://img.shields.io/badge/Version-0.1.9-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: 0.1.10](https://img.shields.io/badge/Version-0.1.10-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 Argo Wrapper Service
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.15 |
+| file://../common | common | 0.1.16 |
 
 ## Values
 
@@ -66,6 +66,3 @@ A Helm chart for gen3 Argo Wrapper Service
 | strategy.rollingUpdate.maxUnavailable | int | `0` | Maximum amount of pods that can be unavailable during the update. |
 | volumeMounts | list | `[{"mountPath":"/argo.json","name":"argo-config","readOnly":true,"subPath":"argo.json"}]` | Volumes to mount to the pod. |
 | volumes | list | `[{"configMap":{"items":[{"key":"argo.json","path":"argo.json"}],"name":"manifest-argo"},"name":"argo-config"}]` | 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/argo-wrapper/templates/deployment.yaml

@@ -29,6 +29,7 @@ spec:
         netnolimit: 'yes'
         public: 'yes'
       annotations:
+        checksum/config: {{ include (print $.Template.BasePath "/argo-wrapper-config.yaml") . | sha256sum }}
         {{- if .Values.metricsEnabled }}
         {{- include "common.grafanaAnnotations" . | nindent 8 }}
         {{- end }}

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: 0.1.15
+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
@@ -24,7 +24,7 @@ appVersion: "master"
 
 dependencies:
   - name: common
-    version: 0.1.15
+    version: 0.1.16
     repository: file://../common
   - name: postgresql
     version: 11.9.13

helm/audit/README.md

@@ -1,14 +1,14 @@
 # audit
 
-![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 Kubernetes
 
 ## Requirements
 
 | Repository | Name | Version |
 |------------|------|---------|
-| file://../common | common | 0.1.15 |
+| file://../common | common | 0.1.16 |
 | https://charts.bitnami.com/bitnami | postgresql | 11.9.13 |
 
 ## Values
@@ -122,6 +122,3 @@ A Helm chart for Kubernetes
 | tolerations | list | `[]` | Tolerations for the pods |
 | volumeMounts | list | `[]` | Volumes to mount to the container. |
 | volumes | list | `[]` | 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/audit/templates/deployment.yaml

@@ -14,6 +14,7 @@ spec:
   template:
     metadata:
       annotations:
+        checksum/config: {{ include (print $.Template.BasePath "/secrets.yaml") . | sha256sum }}
       {{- with .Values.podAnnotations }}
         {{- toYaml . | nindent 8 }}
       {{- end }}

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: 0.1.12
+version: 0.1.13
 
 # 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: 0.1.15
+    version: 0.1.16
     repository: file://../common

helm/aws-es-proxy/README.md

@@ -1,14 +1,14 @@
 # aws-es-proxy
 
-![Version: 0.1.12](https://img.shields.io/badge/Version-0.1.12-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: 0.1.13](https://img.shields.io/badge/Version-0.1.13-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 | 0.1.15 |
+| file://../common | common | 0.1.16 |
 
 ## Values
 
@@ -67,6 +67,3 @@ A Helm chart for AWS ES Proxy Service for gen3
 | strategy.rollingUpdate.maxUnavailable | int | `0` | Maximum amount of pods that can be unavailable during the update. |
 | volumeMounts | list | `[{"mountPath":"/root/.aws","name":"credentials","readOnly":true}]` | Volumes to mount to the pod. |
 | volumes | list | `nil` | 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/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: 0.1.15
+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/common/README.md

@@ -1,6 +1,6 @@
 # common
 
-![Version: 0.1.15](https://img.shields.io/badge/Version-0.1.15-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: 0.1.16](https://img.shields.io/badge/Version-0.1.16-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
 
@@ -32,6 +32,3 @@ A Helm chart for provisioning databases in gen3
 | 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.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` |
-
-----------------------------------------------
-Autogenerated from chart metadata using [helm-docs v1.14.2](https://github.com/norwoodj/helm-docs/releases/v1.14.2)

helm/dicom-server/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: 0.1.10
+version: 0.1.11
 
 # 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: 0.1.15
+    version: 0.1.16
     repository: file://../common