Merge pull request #47 from uc-cdis/fix/orchestration

Orchestration updates
uc-cdis · Oct 24, 2022 · 32a219a · 32a219a
2 parents 88ddcfc + 1e4cb9e
commit 32a219a
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Showing 126 changed files with 1,505 additions and 1,875 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,3 @@
 postgres.txt
+**/charts/
+values.yaml
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -3,7 +3,7 @@
     "files": "^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2022-09-19T14:03:53Z",
+  "generated_at": "2022-10-24T21:24:09Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -74,58 +74,90 @@
         "type": "Secret Keyword"
       }
     ],
-    "helm/arborist/values.yaml": [
+    "helm/audit/templates/secrets.yaml": [
       {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
+        "hashed_secret": "57d8659e51a2da40fda65f6a4cc294cc3f59cf6d",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 116,
+        "line_number": 25,
         "type": "Secret Keyword"
       }
     ],
-    "helm/audit/values.yaml": [
+    "helm/common/templates/_db_setup_job.tpl": [
       {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
+        "hashed_secret": "d2e2ab0f407e4ee3cf2ab87d61c31b25a74085e5",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 167,
+        "line_number": 85,
         "type": "Secret Keyword"
       }
     ],
-    "helm/db-setup/templates/_db_setup.tpl": [
+    "helm/common/templates/_postgres_secrets.tpl": [
+      {
+        "hashed_secret": "07b87392697bbdd9d97f6cd887f901820a0150df",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 27,
+        "type": "Secret Keyword"
+      },
+      {
+        "hashed_secret": "e343239977fa87adac52528619fc6bf2e1a82ee7",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 55,
+        "type": "Secret Keyword"
+      },
       {
         "hashed_secret": "d2e2ab0f407e4ee3cf2ab87d61c31b25a74085e5",
+        "is_secret": false,
         "is_verified": false,
-        "line_number": 24,
+        "line_number": 92,
         "type": "Secret Keyword"
       }
     ],
-    "helm/db-setup/values.yaml": [
+    "helm/common/templates/_secrets.tpl": [
       {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
+        "hashed_secret": "e540cdd1328b2b21e29a95405c301b9313b7c346",
+        "is_secret": false,
         "is_verified": false,
-        "line_number": 6,
+        "line_number": 96,
         "type": "Secret Keyword"
       },
       {
-        "hashed_secret": "a70646783e43f444ba3430a4110bb7bdd65bdb3a",
+        "hashed_secret": "67caac52553e052426982b6f096e73318b151765",
+        "is_secret": false,
         "is_verified": false,
-        "line_number": 12,
+        "line_number": 115,
         "type": "Secret Keyword"
       },
       {
-        "hashed_secret": "874947acc1ffd819b836f6e049b2f1ab8303cb6c",
+        "hashed_secret": "17849dced8de4397e88a8b1c746477aead486a2b",
+        "is_secret": false,
         "is_verified": false,
-        "line_number": 15,
+        "line_number": 116,
+        "type": "Secret Keyword"
+      },
+      {
+        "hashed_secret": "df39b4caf493869772ff3a0f95cca6a9ae7934dc",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 117,
+        "type": "Secret Keyword"
+      },
+      {
+        "hashed_secret": "07b87392697bbdd9d97f6cd887f901820a0150df",
+        "is_secret": false,
+        "is_verified": false,
+        "line_number": 119,
         "type": "Secret Keyword"
       }
     ],
-    "helm/fence/fence-config/fence-config.yaml": [
+    "helm/dicom-server/values.yaml": [
       {
-        "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db",
+        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 587,
+        "line_number": 69,
         "type": "Secret Keyword"
       }
     ],
@@ -163,7 +195,7 @@
     ],
     "helm/fence/templates/fence-creds.yaml": [
       {
-        "hashed_secret": "d2e2ab0f407e4ee3cf2ab87d61c31b25a74085e5",
+        "hashed_secret": "c2dae5a3c7ce218639b38d8a0256f02fe81d439e",
         "is_secret": false,
         "is_verified": false,
         "line_number": 11,
@@ -185,18 +217,11 @@
       }
     ],
     "helm/fence/values.yaml": [
-      {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 29,
-        "type": "Secret Keyword"
-      },
       {
         "hashed_secret": "5d07e1b80e448a213b392049888111e1779a52db",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 864,
+        "line_number": 870,
         "type": "Secret Keyword"
       }
     ],
@@ -227,12 +252,12 @@
         "type": "Basic Auth Credentials"
       }
     ],
-    "helm/indexd/values.yaml": [
+    "helm/indexd/templates/indexd-secret.yaml": [
       {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
+        "hashed_secret": "c2dae5a3c7ce218639b38d8a0256f02fe81d439e",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 108,
+        "line_number": 25,
         "type": "Secret Keyword"
       }
     ],
@@ -245,15 +270,6 @@
         "type": "Secret Keyword"
       }
     ],
-    "helm/metadata/values.yaml": [
-      {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 146,
-        "type": "Secret Keyword"
-      }
-    ],
     "helm/peregrine/peregrine-secret/config_helper.py": [
       {
         "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f",
@@ -268,36 +284,29 @@
         "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 46,
+        "line_number": 45,
         "type": "Basic Auth Credentials"
       }
     ],
-    "helm/peregrine/values.yaml": [
-      {
-        "hashed_secret": "c286f6974f94aab4cfaf2ef49ee0465a8495f563",
-        "is_secret": false,
-        "is_verified": false,
-        "line_number": 4,
-        "type": "Secret Keyword"
-      },
+    "helm/sheepdog/sheepdog-secret/config_helper.py": [
       {
-        "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
+        "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 195,
-        "type": "Secret Keyword"
+        "line_number": 66,
+        "type": "Basic Auth Credentials"
       }
     ],
-    "helm/sheepdog/sheepdog-secret/config_helper.py": [
+    "helm/sheepdog/sheepdog-secret/wsgi.py": [
       {
-        "hashed_secret": "bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f",
+        "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 66,
+        "line_number": 45,
         "type": "Basic Auth Credentials"
       }
     ],
-    "helm/sheepdog/sheepdog-secret/wsgi.py": [
+    "helm/sheepdog/sheepdog-secret/wsgi_copy.py": [
       {
         "hashed_secret": "347cd9c53ff77d41a7b22aa56c7b4efaf54658e3",
         "is_secret": false,
@@ -311,7 +320,7 @@
         "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 132,
+        "line_number": 150,
         "type": "Secret Keyword"
       }
     ],
@@ -341,20 +350,6 @@
         "line_number": 29,
         "type": "Secret Keyword"
       }
-    ],
-    "helm/wts/values.yaml": [
-      {
-        "hashed_secret": "7f8d4ff76d11ef5e9aa633658ed42694b91d3da9",
-        "is_verified": false,
-        "line_number": 116,
-        "type": "Secret Keyword"
-      },
-      {
-        "hashed_secret": "a70646783e43f444ba3430a4110bb7bdd65bdb3a",
-        "is_verified": false,
-        "line_number": 122,
-        "type": "Secret Keyword"
-      }
     ]
   },
   "version": "0.13.1",

diff --git a/helm/ambassador/Chart.yaml b/helm/ambassador/Chart.yaml
@@ -1,6 +1,6 @@
 apiVersion: v2
 name: ambassador
-description: A Helm chart for Kubernetes
+description: A Helm chart for deploying ambassador for gen3
 
 # A chart can be either an 'application' or a 'library' chart.
 #
@@ -15,10 +15,10 @@ 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: 0.1.0
+version: 0.0.1
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "1.16.0"
+appVersion: "1.4.2"
diff --git a/helm/arborist/Chart.lock b/helm/arborist/Chart.lock
@@ -0,0 +1,6 @@
+dependencies:
+- name: common
+  repository: file://../common
+  version: 0.0.1
+digest: sha256:a25c79b74ec6d89ca5c732e4222f8726ed02aa6a4a21f376afc499e53696c9b5
+generated: "2022-10-20T21:34:32.587406-05:00"
diff --git a/helm/arborist/Chart.yaml b/helm/arborist/Chart.yaml
@@ -1,6 +1,6 @@
 apiVersion: v2
 name: arborist
-description: A Helm chart for Kubernetes
+description: A Helm chart for gen3 arborist
 
 # A chart can be either an 'application' or a 'library' chart.
 #
@@ -15,10 +15,15 @@ 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: 0.1.0
+version: 0.0.1
 
 # 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
 # follow Semantic Versioning. They should reflect the version the application is using.
 # It is recommended to use it with quotes.
-appVersion: "2022.05"
+appVersion: "2022.10"
+
+dependencies:
+- name: common
+  version: 0.0.1
+  repository: file://../common
diff --git a/helm/arborist/templates/_helpers.tpl b/helm/arborist/templates/_helpers.tpl
@@ -69,6 +69,6 @@ Create the name of the service account to use
 {{- if $localpass }}
 {{- default (index $localpass.data "postgres-password" | b64dec) }}
 {{- else }}
-{{- default .Values.database.password }}
+{{- default .Values.postgres.password }}
 {{- end }}
 {{- end }}
diff --git a/helm/arborist/templates/arborist-creds.yaml b/helm/arborist/templates/arborist-creds.yaml
diff --git a/helm/arborist/templates/db-init.yaml b/helm/arborist/templates/db-init.yaml
@@ -0,0 +1,3 @@
+{{- include "common.db-setup-job" . }}
+---
+{{- include "common.db-secret" . }}
diff --git a/helm/arborist/templates/deployment.yaml b/helm/arborist/templates/deployment.yaml
@@ -59,14 +59,8 @@ spec:
             - "-c"
             - |
               # set env vars
-              export PGDATABASE=$(cat /var/www/arborist/dbcreds.json | jq -r '.db_database')
-              export PGUSER=$(cat /var/www/arborist/dbcreds.json | jq -r '.db_username')
-              export PGPASSWORD=$(cat /var/www/arborist/dbcreds.json | jq -r '.db_password')
-              export PGHOST=$(cat /var/www/arborist/dbcreds.json | jq -r '.db_host')
-              export PGPORT="5432"
               export PGSSLMODE="disable"
               
-
               # bring the database schema up to the latest version
               /go/src/github.com/uc-cdis/arborist/migrations/latest