Merge develop to master (#77)

* Helm Chart for Auspice * Update README.md (#49) * Update README.md * Delete auspice.yaml * adding a job to create indices so guppy pod can run on startup * Fixed values.yaml formatting (#52) * Fixed values.yaml formatting * adding common library chart to gen3 umbrella chart * forgot to update chart.lock file * adding small changes to the weight and hooks for the startup jobs to play nice with umbrella chart * feat(autodoc): add helm docs * add helm docs * Orchestration updates * Add useryaml, delete hooks, delete elb * Fix wts, hatchery on laptop * Add useryaml, delete hooks, delete elb * Fix wts, hatchery on laptop * Removed a space between .service and "-dbcreds" * Update _postgres_secrets.tpl * Attempted to wrap cat in a nospace to look up secrets * Trying another method of concatenation * Trying to fix the same concatenation * Add postgres as subchart, and update portal image * Update default values for gen3 umbrella * Fix dbsecret random generation * Read DB strings from env vars * Add env vars to useryaml job * Move sheepdog init job to init container * Initial indexd env var db string work Co-authored-by: Jawad Qureshi <[email protected]> Co-authored-by: J. Q <[email protected]> * - adding a job to gen3 helm chart that will upload a pgdump or elasticsearch dump to es or dbs (metadata, sheepdog, indexd) - corrected small issue with metadata values * Add WTS OIDC job, Read DB connection from env vars (#66) * Add wts OIDC job, all db connection is read from env * Add alb capabilites to ingress * Fix fence-config * adding a configuration file for argocd to our helm charts * fixing argocd security * updating typo * adding the dependency for the gen3-db-restore job to the gen3 umbrella chart * forgot to update the chart.lock * turning the default to false for the restore db job for now so we can test argo * (fix): Clusterrole naming, hatchery manifest templating (#68) * CI and Documentation updates (#72) * (docs/ci): Add documentation, and CI * Add automated documentation using helm-docs in pre-commit hooks (#71) * (docs): Add helm-docs in pre-commit hooks * (ci): Bump up all chart versions (#73) * (ci): Bump up all chart dependencies * (ci): Bump up all chart dependencies * (ci): Add linting of all charts (#75) * (ci): Add linting of charts Co-authored-by: Ajo Augustine <[email protected]> Co-authored-by: EliseCastle23 <[email protected]> Co-authored-by: Aidan Hilt <[email protected]> Co-authored-by: EliseCastle23 <[email protected]> Co-authored-by: René Pollard <[email protected]>
uc-cdis · Dec 8, 2022 · 9ccd25c · 9ccd25c
1 parent 56ef406
commit 9ccd25c
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diff --git a/.github/ct.yaml b/.github/ct.yaml
@@ -0,0 +1,10 @@
+remote: origin
+target-branch: master
+chart-dirs:
+  - helm
+chart-repos:
+  - bitnami=https://charts.bitnami.com/bitnami
+helm-extra-args: --timeout 600s
+check-version-increment: true
+debug: false
+validate-maintainers: false
diff --git a/.github/workflows/lint_test.yaml b/.github/workflows/lint_test.yaml
@@ -0,0 +1,50 @@
+name: Lint and Test Charts
+
+on: pull_request
+
+jobs:
+  lint-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Helm
+        uses: azure/setup-helm@v3
+        with:
+          version: v3.10.0
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          check-latest: true
+
+      - name: Set up chart-testing
+        uses: helm/[email protected]
+
+      - name: Run chart-testing (list-changed)
+        id: list-changed
+        run: |
+          changed=$(ct list-changed --config .github/ct.yaml)
+          if [[ -n "$changed" ]]; then
+            echo "::set-output name=changed::true"
+          fi
+
+      - name: Run chart-testing (lint)
+        run: ct lint --config .github/ct.yaml
+
+  # deploy-charts-to-kind:
+  #   name: ${{ matrix.environments }} - gen3 data portal build
+  #   timeout-minutes: 20
+  #   runs-on: ubuntu-latest
+  #   needs: [get-changes-for-envs]
+  #   if: ${{ needs.get-changes-for-envs.outputs.matrix != '[]' && needs.get-changes-for-envs.outputs.matrix != '' }}
+  #   steps:
+  #     - name: Create kind cluster
+  #       uses: helm/[email protected]
+  #       if: steps.list-changed.outputs.changed == 'true'
+
+  #     - name: Run chart-testing (install)
+  #       run: ct install
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -4,6 +4,8 @@ on:
   push:
     branches:
       - master
+env:
+  HELM_DOCS_VERSION: "1.7.0"
 
 jobs:
   release:
@@ -20,13 +22,21 @@ jobs:
         run: |
           git config user.name "$GITHUB_ACTOR"
           git config user.email "[email protected]"
+      
       - name: Install Helm
-        uses: azure/setup-helm@v1
+        uses: azure/setup-helm@v3
         with:
-          version: v3.8.1
+          version: v3.10.0
+
+      - name: Install Helm-docs
+        run: |
+          cd /tmp
+          wget https://github.com/norwoodj/helm-docs/releases/download/v${{env.HELM_DOCS_VERSION}}/helm-docs_${{env.HELM_DOCS_VERSION}}_Linux_x86_64.tar.gz
+          tar -xvf helm-docs_${{env.HELM_DOCS_VERSION}}_Linux_x86_64.tar.gz
+          sudo mv helm-docs /usr/local/sbin
 
       - name: Run chart-releaser
-        uses: helm/[email protected].0
+        uses: helm/[email protected].1
         with:
           charts_dir: helm
         env:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,3 +9,18 @@ repos:
     hooks:
       - id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
+
+  # - repo: https://github.com/gruntwork-io/pre-commit
+  #   rev: v0.1.17 # Get the latest from: https://github.com/gruntwork-io/pre-commit/releases
+  #   hooks:
+  #   - id: helmlint
+
+  - repo: local 
+    hooks: 
+    - id: helm-docs
+      args: []
+      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
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -3,7 +3,7 @@
     "files": "^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2022-10-25T14:38:38Z",
+  "generated_at": "2022-12-08T17:27:52Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -58,81 +58,44 @@
     }
   ],
   "results": {
-    "helm/audit/templates/secrets.yaml": [
+    "README.md": [
       {
-        "hashed_secret": "57d8659e51a2da40fda65f6a4cc294cc3f59cf6d",
+        "hashed_secret": "ac0fedaac180de6bd70a97b711692a92dade479e",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 25,
+        "line_number": 80,
         "type": "Secret Keyword"
-      }
-    ],
-    "helm/common/templates/_db_setup_job.tpl": [
+      },
       {
-        "hashed_secret": "d2e2ab0f407e4ee3cf2ab87d61c31b25a74085e5",
+        "hashed_secret": "64ab0c1d3edc1c8c166351207b840ac7b2a90523",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 85,
+        "line_number": 109,
         "type": "Secret Keyword"
       }
     ],
-    "helm/common/templates/_postgres_secrets.tpl": [
+    "docs/databases.md": [
       {
-        "hashed_secret": "07b87392697bbdd9d97f6cd887f901820a0150df",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 27,
-        "type": "Secret Keyword"
-      },
-      {
-        "hashed_secret": "e343239977fa87adac52528619fc6bf2e1a82ee7",
+        "hashed_secret": "ac0fedaac180de6bd70a97b711692a92dade479e",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 55,
-        "type": "Secret Keyword"
-      },
-      {
-        "hashed_secret": "d2e2ab0f407e4ee3cf2ab87d61c31b25a74085e5",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 92,
+        "line_number": 22,
         "type": "Secret Keyword"
       }
     ],
-    "helm/common/templates/_secrets.tpl": [
-      {
-        "hashed_secret": "e540cdd1328b2b21e29a95405c301b9313b7c346",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 96,
-        "type": "Secret Keyword"
-      },
-      {
-        "hashed_secret": "67caac52553e052426982b6f096e73318b151765",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 115,
-        "type": "Secret Keyword"
-      },
-      {
-        "hashed_secret": "17849dced8de4397e88a8b1c746477aead486a2b",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 116,
-        "type": "Secret Keyword"
-      },
+    "helm/common/templates/_postgres_secrets.tpl": [
       {
-        "hashed_secret": "df39b4caf493869772ff3a0f95cca6a9ae7934dc",
+        "hashed_secret": "07b87392697bbdd9d97f6cd887f901820a0150df",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 117,
+        "line_number": 34,
         "type": "Secret Keyword"
       },
       {
-        "hashed_secret": "07b87392697bbdd9d97f6cd887f901820a0150df",
+        "hashed_secret": "e343239977fa87adac52528619fc6bf2e1a82ee7",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 119,
+        "line_number": 62,
         "type": "Secret Keyword"
       }
     ],
@@ -141,7 +104,7 @@
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 69,
+        "line_number": 65,
         "type": "Secret Keyword"
       }
     ],
@@ -205,34 +168,34 @@
         "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 870,
+        "line_number": 1796,
         "type": "Secret Keyword"
       }
     ],
-    "helm/hatchery/templates/hatchery-manifest.yaml": [
+    "helm/hatchery/README.md": [
       {
-        "hashed_secret": "0da0e0005ca04acb407af2681d0bede6d9406039",
+        "hashed_secret": "1740c48fa3141d4851b14f97e3bc0f46f7670672",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 147,
+        "line_number": 45,
         "type": "Secret Keyword"
       }
     ],
-    "helm/indexd/indexd-secret/config_helper.py": [
+    "helm/hatchery/values.yaml": [
       {
-        "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f",
+        "hashed_secret": "9b5925ea817163740dfb287a9894e8ab3aba2c18",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 66,
-        "type": "Basic Auth Credentials"
+        "line_number": 128,
+        "type": "Secret Keyword"
       }
     ],
-    "helm/indexd/indexd-secret/local_settings.py": [
+    "helm/indexd/indexd-settings/local_settings.py": [
       {
         "hashed_secret": "0a0d18c85e096611b5685b62bc60ec534d19bacc",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 59,
+        "line_number": 60,
         "type": "Basic Auth Credentials"
       }
     ],
@@ -241,7 +204,7 @@
         "hashed_secret": "c2dae5a3c7ce218639b38d8a0256f02fe81d439e",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 25,
+        "line_number": 19,
         "type": "Secret Keyword"
       }
     ],
@@ -304,7 +267,7 @@
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 150,
+        "line_number": 168,
         "type": "Secret Keyword"
       }
     ],
@@ -322,16 +285,7 @@
         "hashed_secret": "13d9ed7e3d69f1b6330dff80bc4658931708eddc",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 153,
-        "type": "Secret Keyword"
-      }
-    ],
-    "helm/wts/templates/secret.yaml": [
-      {
-        "hashed_secret": "d2e2ab0f407e4ee3cf2ab87d61c31b25a74085e5",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 29,
+        "line_number": 108,
         "type": "Secret Keyword"
       }
     ]