bcgov · NickPhura · Sep 27, 2024 · Oct 22, 2024 · Oct 22, 2024 · Oct 22, 2024
diff --git a/database/.docker/db/Dockerfile b/database/.docker/db/Dockerfile
@@ -2,7 +2,7 @@
 # This DockerFile is used for local development (via compose.yml) only.
 # ########################################################################################################
 
-ARG POSTGRES_VERSION=14.2
+ARG POSTGRES_VERSION=15-bullseye
 
 FROM postgres:$POSTGRES_VERSION
 

diff --git a/database/.pipeline/lib/db.deploy.js b/database/.pipeline/lib/db.deploy.js
@@ -31,7 +31,7 @@ const dbDeploy = async (settings) => {
         DATABASE_SERVICE_NAME: `${name}-postgresql${phases[phase].suffix}`,
         IMAGE_STREAM_NAME: name,
         IMAGE_STREAM_VERSION: phases.build.tag,
-        POSTGRESQL_DATABASE: 'biohubbc',
+        POSTGRES_DB: 'biohubbc',
         TZ: phases[phase].tz,
         IMAGE_STREAM_NAMESPACE: phases.build.namespace,
         VOLUME_CAPACITY: phases[phase].volumeCapacity,
@@ -46,7 +46,7 @@ const dbDeploy = async (settings) => {
 
   oc.applyRecommendedLabels(objects, name, phase, changeId, instance);
   oc.importImageStreams(objects, phases[phase].tag, phases.build.namespace, phases.build.tag);
-  
+
   await oc.applyAndDeploy(objects, instance);
 };
 

diff --git a/database/.pipeline/templates/db.bc.yaml b/database/.pipeline/templates/db.bc.yaml
@@ -1,7 +1,7 @@
 kind: Template
 apiVersion: template.openshift.io/v1
 metadata:
-  name: postgresql null
+  name: postgresql
 parameters:
   - name: NAME
     displayName: Name
@@ -29,7 +29,7 @@ objects:
           annotations:
           from:
             kind: ImageStreamTag
-            name: postgis-postgres:12-31
+            name: postgres-postgis:15-bullseye
             namespace: af2668-tools
           generation: 1
           importPolicy: {}

diff --git a/database/.pipeline/templates/db.dc.yaml b/database/.pipeline/templates/db.dc.yaml
@@ -12,46 +12,43 @@ parameters:
     name: NAME
     required: true
     value: 'postgresql'
-  - description: The OpenShift ImageStream name.
-    displayName: IMAGE_STREAM_NAME
-    name: IMAGE_STREAM_NAME
-    value: 'postgis-postgres'
-  - description: The OpenShift Namespace where the ImageStream resides.
-    displayName: Namespace
-    name: IMAGE_STREAM_NAMESPACE
+  - name: IMAGE_STREAM_NAMESPACE
+    description: The OpenShift Namespace where the ImageStream resides.
+    required: true
     value: 'af2668-tools'
+  - name: IMAGE_STREAM_NAME
+    description: The OpenShift ImageStream name.
+    required: true
+    value: 'postgres-postgis'
+  - name: IMAGE_STREAM_VERSION
+    description: Version of PostgreSQL image to be used (9.2, 9.4, 9.5 or latest).
+    required: true
+    value: '15-bullseye'
   - description: The name of the OpenShift Service exposed for the database.
     displayName: Database Service Name
     name: DATABASE_SERVICE_NAME
     required: true
     value: 'postgresql'
   - description: Username for PostgreSQL user that will be used for accessing the database.
     displayName: PostgreSQL Connection Username
-    name: POSTGRESQL_USER
-    required: true
-    value: 'postgres'
-  - description: Admin Username for PostgreSQL user that will be used for accessing the database.
-    displayName: PostgreSQL Admin Connection Username
-    name: POSTGRESQL_ADMIN_USER
+    name: POSTGRES_USER
     required: true
     value: 'postgres'
   - description: Password for the PostgreSQL connection user.
     displayName: PostgreSQL Connection Password
     from: '[a-zA-Z0-9]{16}'
     generate: expression
-    name: POSTGRESQL_PASSWORD
-    required: true
-  - description: Password for the PostgreSQL admin user.
-    displayName: PostgreSQL Admin Connection Password
-    from: '[a-zA-Z0-9]{16}'
-    generate: expression
-    name: POSTGRESQL_ADMIN_PASSWORD
+    name: POSTGRES_PASSWORD
     required: true
   - description: Name of the PostgreSQL database accessed.
     displayName: PostgreSQL Database Name
-    name: POSTGRESQL_DATABASE
+    name: POSTGRES_DB
     required: true
     value: 'biohubbc'
+  - name: PGDATA
+    description: Path to PostgreSQL data directory
+    value: '/var/lib/pgsql/data/userdata'
+    required: false
   - name: TZ
     description: Database timezone
     required: false
@@ -61,19 +58,6 @@ parameters:
     name: VOLUME_CAPACITY
     required: true
     value: '500Mi'
-  - description: Version of PostgreSQL image to be used (9.2, 9.4, 9.5 or latest).
-    displayName: Version of PostgreSQL Image
-    name: IMAGE_STREAM_VERSION
-    required: true
-    value: '12-31'
-  - description: Indicator to enable pgcrypto extension (provided out-of-the-box with PostgreSQL).
-    displayName: Flag to enable pgcrypto PostgreSQL extension.
-    name: PGCRYPTO_EXTENSION
-    value: 'Y'
-  - description: Indicator to enable postgis extension (from official PostgeSQL YUM repo).
-    displayName: Flag to enable postgis PostgreSQL extension.
-    name: POSTGIS_EXTENSION
-    value: 'Y'
   - name: CPU_REQUEST
     value: '50m'
   - name: CPU_LIMIT
@@ -90,16 +74,14 @@ objects:
     metadata:
       annotations:
         template.openshift.io/expose-database_name: "{.data['database-name']}"
-        template.openshift.io/expose-password: "{.data['database-user-password']}"
-        template.openshift.io/expose-admin-password: "{.data['database-admin-password']}"
-        template.openshift.io/expose-admin-username: "{.data['database-user']}"
+        template.openshift.io/expose-database-user: "{.data['database-admin']}"
+        template.openshift.io/expose-database-user-password: "{.data['database-admin-password']}"
         as-copy-of: biohubbc-creds
       name: '${DATABASE_SERVICE_NAME}'
     stringData:
-      database-name: '${POSTGRESQL_DATABASE}'
-      database-user-password: '${POSTGRESQL_PASSWORD}'
-      database-admin-password: '${POSTGRESQL_ADMIN_PASSWORD}'
-      database-user: '${POSTGRESQL_USER}'
+      database-name: '${POSTGRES_DB}'
+      database-user: '${POSTGRES_USER}'
+      database-user-password: '${POSTGRES_PASSWORD}'
 
   - kind: Service
     apiVersion: v1
@@ -165,30 +147,23 @@ objects:
           containers:
             - name: postgresql
               env:
-                - name: POSTGRESQL_USER
+                - name: POSTGRES_DB
                   valueFrom:
                     secretKeyRef:
-                      key: database-user
+                      key: database-name
                       name: '${DATABASE_SERVICE_NAME}'
-                - name: POSTGRESQL_PASSWORD
+                - name: POSTGRES_USER
                   valueFrom:
                     secretKeyRef:
-                      key: database-user-password
+                      key: database-admin
                       name: '${DATABASE_SERVICE_NAME}'
-                - name: POSTGRESQL_ADMIN_PASSWORD
+                - name: POSTGRES_PASSWORD
                   valueFrom:
                     secretKeyRef:
                       key: database-admin-password
                       name: '${DATABASE_SERVICE_NAME}'
-                - name: POSTGRESQL_DATABASE
-                  valueFrom:
-                    secretKeyRef:
-                      key: database-name
-                      name: '${DATABASE_SERVICE_NAME}'
-                - name: PGCRYPTO_EXTENSION
-                  value: 'N'
-                - name: POSTGIS_EXTENSION
-                  value: 'N'
+                - name: PGDATA
+                  value: '${PGDATA}'
                 - name: PGOPTIONS
                   value: '-c maintenance_work_mem=128MB'
                 - name: PGTZ
@@ -209,7 +184,7 @@ objects:
                     - '/bin/sh'
                     - '-i'
                     - '-c'
-                    - psql -h 127.0.0.1 -U $POSTGRESQL_USER -q -d $POSTGRESQL_DATABASE -c 'SELECT 1'
+                    - psql -h 127.0.0.1 -U $POSTGRES_USER -q -d $POSTGRES_DB -c 'SELECT 1'
                 initialDelaySeconds: 5
                 timeoutSeconds: 1
               resources:
@@ -219,23 +194,21 @@ objects:
                 limits:
                   cpu: ${CPU_LIMIT}
                   memory: ${MEMORY_LIMIT}
-              securityContext:
-                capabilities: {}
-                privileged: false
+              securityContext: {}
               terminationMessagePath: '/dev/termination-log'
               volumeMounts:
-                - mountPath: '/var/lib/pgsql/data'
-                  name: '${DATABASE_SERVICE_NAME}-data'
-                - mountPath: '/var/run/postgresql'
-                  name: '${DATABASE_SERVICE_NAME}-run'
+                - name: '${DATABASE_SERVICE_NAME}-data'
+                  mountPath: '/var/lib/pgsql/data'
+                # - name: '${DATABASE_SERVICE_NAME}-run'
+                #   mountPath: '/var/run/postgresql'
           dnsPolicy: ClusterFirst
           restartPolicy: Always
           volumes:
             - name: '${DATABASE_SERVICE_NAME}-data'
               persistentVolumeClaim:
                 claimName: '${DATABASE_SERVICE_NAME}'
-            - name: '${DATABASE_SERVICE_NAME}-run'
-              emptyDir: {}
+            # - name: '${DATABASE_SERVICE_NAME}-run'
+            #   emptyDir: {}
       triggers:
         - imageChangeParams:
             automatic: true
@@ -245,6 +218,5 @@ objects:
               kind: ImageStreamTag
               name: '${IMAGE_STREAM_NAME}:${IMAGE_STREAM_VERSION}'
               namespace: '${IMAGE_STREAM_NAMESPACE}'
-            lastTriggeredImage: ''
           type: ImageChange
         - type: ConfigChange
diff --git a/database/.pipeline/templates/prereqs/postgres-postgis.is.yaml b/database/.pipeline/templates/prereqs/postgres-postgis.is.yaml
@@ -0,0 +1,80 @@
+# ########################################################################################################
+# Creates a build config that builds the database dockerfile
+# Creates an imagestream that references the built database image
+# ########################################################################################################
+
+kind: Template
+apiVersion: template.openshift.io/v1
+metadata:
+  name: postgresql
+parameters:
+  # Imagestream
+  - name: IMAGE_STREAM_NAMESPACE
+    value: af2668-tools
+  - name: IMAGE_STREAM_NAME
+    value: postgres-postgis
+  - name: IMAGE_STREAM_VERSION
+    value: 15-bullseye
+  # Dockerfile
+  - name: SOURCE_CONTEXT_DIR
+    value: 'database'
+  - name: SOURCE_REPOSITORY_REF
+    value: dev
+  - name: SOURCE_REPOSITORY_URL
+    value: https://github.com/bcgov/biohubbc.git
+  - name: DOCKER_FILE_PATH
+    value: Dockerfile
+  # Resources
+  - name: CPU_REQUEST
+    value: '50m'
+  - name: CPU_LIMIT
+    value: '200m'
+  - name: MEMORY_REQUEST
+    value: '100Mi'
+  - name: MEMORY_LIMIT
+    value: '2Gi'
+objects:
+  - kind: ImageStream
+    apiVersion: image.openshift.io/v1
+    metadata:
+      name: '${IMAGE_STREAM_NAME}'
+      labels:
+        shared: 'true'
+    spec:
+      lookupPolicy:
+        local: false
+
+  - kind: BuildConfig
+    apiVersion: v1
+    metadata:
+      name: '${IMAGE_STREAM_NAME}'
+    spec:
+      failedBuildsHistoryLimit: 5
+      nodeSelector:
+      output:
+        to:
+          kind: ImageStreamTag
+          name: '${IMAGE_STREAM_NAME}:${IMAGE_STREAM_VERSION}'
+      postCommit: {}
+      resources:
+        requests:
+          cpu: ${CPU_REQUEST}
+          memory: ${MEMORY_REQUEST}
+        limits:
+          cpu: ${CPU_LIMIT}
+          memory: ${MEMORY_LIMIT}
+      runPolicy: SerialLatestOnly
+      source:
+        type: Git
+        git:
+          uri: '${SOURCE_REPOSITORY_URL}'
+          ref: '${SOURCE_REPOSITORY_REF}'
+        contextDir: '${SOURCE_CONTEXT_DIR}'
+      strategy:
+        type: Docker
+        dockerStrategy:
+          dockerfilePath: ${DOCKER_FILE_PATH}
+      successfulBuildsHistoryLimit: 5
+      triggers:
+        - type: ConfigChange
+        - type: ImageChange
diff --git a/database/Dockerfile b/database/Dockerfile
@@ -0,0 +1,37 @@
+# ########################################################################################################
+# This DockerFile is used for Openshift deployments only.
+# ########################################################################################################
+
+ARG POSTGRES_VERSION=15-bullseye
+
+FROM postgres:$POSTGRES_VERSION
+
+# read env variables
+ARG TZ=America/Vancouver
+ARG POSTGIS_VERSION=3
+
+ENV PORT=5432
+
+# install postgis packages
+RUN mkdir -p /opt/apps
+RUN apt-get -qq update
+RUN apt-get -qq install -y --no-install-recommends postgresql-$PG_MAJOR-postgis-$POSTGIS_VERSION
+RUN apt-get -qq install -y --no-install-recommends postgresql-$PG_MAJOR-postgis-$POSTGIS_VERSION-scripts
+RUN apt-get -qq install -y --no-install-recommends postgresql-$PG_MAJOR-pgrouting
+RUN apt-get -qq install -y --no-install-recommends postgresql-$PG_MAJOR-pgrouting-scripts
+RUN apt-get -qq install -y --no-install-recommends postgresql-server-dev-$PG_MAJOR
+RUN apt-get -qq install -y --no-install-recommends pgbadger pg-activity wget unzip nano
+RUN apt-get -qq purge -y --auto-remove postgresql-server-dev-$PG_MAJOR
+RUN apt-get -qq autoremove -y
+RUN apt-get -qq clean
+
+# set time zone
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+# copy postgis init script to docker init directory
+RUN mkdir -p /docker-entrypoint-initdb.d
+COPY ./.docker/db/create_postgis.sql /docker-entrypoint-initdb.d/postgis.sql
+
+EXPOSE $PORT
+
+CMD ["postgres"]
diff --git a/database/README.md b/database/README.md
@@ -6,7 +6,7 @@
 | ---------- | ------- | ------------------------------------ | -------------------- |
 | node       | 18.x.x  | https://nodejs.org/en/               | JavaScript Runtime   |
 | npm        | 10.x.x  | https://www.npmjs.com/               | Node Package Manager |
-| PostgreSQL | 12.5    | https://www.postgresql.org/download/ | PSQL database        |
+| PostgreSQL | 14.2    | https://www.postgresql.org/download/ | PSQL database        |
 | PostGIS    | 3       | https://postgis.net/                 | GIS (spatial) tools  |
 
 <br />

diff --git a/env_config/env.docker b/env_config/env.docker
@@ -126,7 +126,7 @@ CB_API_HOST=https://moe-critterbase-api-dev.apps.silver.devops.gov.bc.ca/api
 #
 # See `biohubbc-creds` secret in openshift
 # ------------------------------------------------------------------------------
-POSTGRES_VERSION=14.2
+POSTGRES_VERSION=15-bullseye
 POSTGIS_VERSION=3
 DB_HOST=db
 DB_ADMIN=postgres