SIMSBIOHUB-449: Upgrade to Postgres 17 (#1428)

- Upgrade Postgres from 12.5 to 17-bullseye - Wrap most instances of "system_user" in double quotes, as it is not a reserved word in postgres. - Add migration to drop biohub_dapi_v1 schema - Disable static deploy db setup step - Delete deprecated custom postgres image - Remove user name search path
bcgov · Jan 15, 2025 · 6ae74e0 · 6ae74e0
1 parent 4e00fba
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diff --git a/.github/workflows/deployStatic.yml b/.github/workflows/deployStatic.yml
@@ -431,62 +431,62 @@ jobs:
           DEBUG=* npm run db:deploy -- --pr=$PR_NUMBER --env=$BRANCH --branch=$BRANCH --type=static
 
   # Deploy Database setup image
-  deployDatabaseSetup:
-    name: Deploy Database Setup Image
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    if: ${{ github.event.pull_request.merged == true }}
-    env:
-      PR_NUMBER: ${{ github.event.number }}
-      BRANCH: ${{ github.base_ref }}
-    needs:
-      - scaleDownPods
-      - buildDatabaseSetup
-      - deployDatabase
-    steps:
-      # Install Node - for `node` and `npm` commands
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: 20
-
-      # Load repo from cache
-      - name: Cache repo
-        uses: actions/cache@v4
-        id: cache-repo
-        env:
-          cache-name: cache-repo
-        with:
-          path: ${{ github.workspace }}/*
-          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ github.sha }}
-
-      # Checkout the branch if not restored via cache
-      - name: Checkout Target Branch
-        if: steps.cache-repo.outputs.cache-hit != 'true'
-        uses: actions/checkout@v4
-
-      # Install oc, which was removed from the ubuntu-latest image in v24.04
-      - name: Install OpenShift CLI tools
-        uses: redhat-actions/openshift-tools-installer@v1
-        with:
-          oc: "4.14"
-
-      # Log in to OpenShift.
-      # Note: The secrets needed to log in are NOT available if the PR comes from a FORK.
-      # PR's must originate from a branch off the original repo or else all openshift `oc` commands will fail.
-      - name: Log in to OpenShift
-        run: oc login --token=${{ secrets.TOOLS_SA_TOKEN }} --server=https://api.silver.devops.gov.bc.ca:6443
-
-      # Install database pipeline node modules
-      - name: Install database pipeline node modules
-        working-directory: "database/.pipeline/"
-        run: npm ci
-
-      # Deploy the database setup image
-      - name: Deploy Database Setup Image
-        working-directory: "database/.pipeline/"
-        run: |
-          DEBUG=* npm run db-setup:deploy -- --pr=$PR_NUMBER --env=$BRANCH --branch=$BRANCH --type=static
+  #   deployDatabaseSetup:
+  #     name: Deploy Database Setup Image
+  #     runs-on: ubuntu-latest
+  #     timeout-minutes: 30
+  #     if: ${{ github.event.pull_request.merged == true }}
+  #     env:
+  #       PR_NUMBER: ${{ github.event.number }}
+  #       BRANCH: ${{ github.base_ref }}
+  #     needs:
+  #       - scaleDownPods
+  #       - buildDatabaseSetup
+  #       - deployDatabase
+  #     steps:
+  #       # Install Node - for `node` and `npm` commands
+  #       - name: Setup Node.js
+  #         uses: actions/setup-node@v4
+  #         with:
+  #           node-version: 20
+
+  #       # Load repo from cache
+  #       - name: Cache repo
+  #         uses: actions/cache@v4
+  #         id: cache-repo
+  #         env:
+  #           cache-name: cache-repo
+  #         with:
+  #           path: ${{ github.workspace }}/*
+  #           key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ github.sha }}
+
+  #       # Checkout the branch if not restored via cache
+  #       - name: Checkout Target Branch
+  #         if: steps.cache-repo.outputs.cache-hit != 'true'
+  #         uses: actions/checkout@v4
+
+  #       # Install oc, which was removed from the ubuntu-latest image in v24.04
+  #       - name: Install OpenShift CLI tools
+  #         uses: redhat-actions/openshift-tools-installer@v1
+  #         with:
+  #           oc: "4.14"
+
+  #       # Log in to OpenShift.
+  #       # Note: The secrets needed to log in are NOT available if the PR comes from a FORK.
+  #       # PR's must originate from a branch off the original repo or else all openshift `oc` commands will fail.
+  #       - name: Log in to OpenShift
+  #         run: oc login --token=${{ secrets.TOOLS_SA_TOKEN }} --server=https://api.silver.devops.gov.bc.ca:6443
+
+  #       # Install database pipeline node modules
+  #       - name: Install database pipeline node modules
+  #         working-directory: "database/.pipeline/"
+  #         run: npm ci
+
+  #       # Deploy the database setup image
+  #       - name: Deploy Database Setup Image
+  #         working-directory: "database/.pipeline/"
+  #         run: |
+  #           DEBUG=* npm run db-setup:deploy -- --pr=$PR_NUMBER --env=$BRANCH --branch=$BRANCH --type=static
 
   # Deploy API image
   deployAPI:
@@ -554,7 +554,7 @@ jobs:
     if: ${{ github.event.pull_request.merged == true }}
     needs:
       - deployDatabase
-      - deployDatabaseSetup
+      #   - deployDatabaseSetup
       - deployAPI
       - deployAPP
     env:

diff --git a/api/src/repositories/administrative-activity-repository.ts b/api/src/repositories/administrative-activity-repository.ts
@@ -82,7 +82,7 @@ export class AdministrativeActivityRepository extends BaseRepository {
       ON
         aa.administrative_activity_type_id = aat.administrative_activity_type_id
       LEFT OUTER JOIN
-        system_user su 
+        "system_user" su 
       ON 
         su.system_user_id = aa.update_user
       WHERE
@@ -223,7 +223,7 @@ export class AdministrativeActivityRepository extends BaseRepository {
         FROM
           project_participation pp
         LEFT JOIN
-          system_user su 
+          "system_user" su 
         ON
           pp.system_user_id = su.system_user_id 
         WHERE

diff --git a/api/src/repositories/project-participation-repository.ts b/api/src/repositories/project-participation-repository.ts
@@ -151,7 +151,7 @@ export class ProjectParticipationRepository extends BaseRepository {
         ON pp.project_role_id = prp.project_role_id
       LEFT JOIN project_permission pp2
         ON pp2.project_permission_id = prp.project_permission_id
-      LEFT JOIN system_user su
+      LEFT JOIN "system_user" su
         ON pp.system_user_id = su.system_user_id
       LEFT JOIN
         system_user_role sur
@@ -365,7 +365,7 @@ export class ProjectParticipationRepository extends BaseRepository {
         ON pp.project_role_id = prp.project_role_id
       LEFT JOIN project_permission pp2
         ON pp2.project_permission_id = prp.project_permission_id
-      LEFT JOIN system_user su
+      LEFT JOIN "system_user" su
         ON pp.system_user_id = su.system_user_id
       LEFT JOIN
         system_user_role sur
@@ -503,7 +503,7 @@ export class ProjectParticipationRepository extends BaseRepository {
         ON pp.project_role_id = prp.project_role_id
       LEFT JOIN project_permission pp2
         ON pp2.project_permission_id = prp.project_permission_id
-      LEFT JOIN system_user su
+      LEFT JOIN "system_user" su
         ON pp.system_user_id = su.system_user_id
       LEFT JOIN
         system_user_role sur

diff --git a/api/src/repositories/survey-participation-repository.ts b/api/src/repositories/survey-participation-repository.ts
@@ -121,7 +121,7 @@ export class SurveyParticipationRepository extends BaseRepository {
         LEFT JOIN
         survey_job sj
         ON sj.survey_job_id = sp.survey_job_id
-      LEFT JOIN system_user su
+      LEFT JOIN "system_user" su
         ON sp.system_user_id = su.system_user_id
       LEFT JOIN
         system_user_role sur
@@ -192,7 +192,7 @@ export class SurveyParticipationRepository extends BaseRepository {
       LEFT JOIN
         survey_job sj
         ON sj.survey_job_id = sp.survey_job_id
-      LEFT JOIN system_user su
+      LEFT JOIN "system_user" su
         ON sp.system_user_id = su.system_user_id
       LEFT JOIN
         system_user_role sur

diff --git a/api/src/repositories/user-repository.ts b/api/src/repositories/user-repository.ts
@@ -83,7 +83,7 @@ export class UserRepository extends BaseRepository {
       su.family_name,
       su.agency
     FROM
-      system_user su
+      "system_user" su
     LEFT JOIN
       system_user_role sur
     ON
@@ -147,7 +147,7 @@ export class UserRepository extends BaseRepository {
       su.family_name,
       su.agency
     FROM
-      system_user su
+      "system_user" su
     LEFT JOIN
       system_user_role sur
     ON
@@ -205,7 +205,7 @@ export class UserRepository extends BaseRepository {
         su.family_name,
         su.agency
       FROM
-        system_user su
+        "system_user" su
       LEFT JOIN
         system_user_role sur
       ON
@@ -264,7 +264,7 @@ export class UserRepository extends BaseRepository {
   ): Promise<{ system_user_id: number }> {
     const sqlStatement = SQL`
     INSERT INTO
-      system_user
+      "system_user"
     (
       user_guid,
       user_identity_source_id,
@@ -328,7 +328,7 @@ export class UserRepository extends BaseRepository {
       su.family_name,
       su.agency
     FROM
-      system_user su
+      "system_user" su
     LEFT JOIN
       system_user_role sur
     ON
@@ -369,7 +369,7 @@ export class UserRepository extends BaseRepository {
   async activateSystemUser(systemUserId: number) {
     const sqlStatement = SQL`
       UPDATE
-        system_user
+        "system_user"
       SET
         record_end_date = NULL
       WHERE
@@ -401,7 +401,7 @@ export class UserRepository extends BaseRepository {
   async deactivateSystemUser(systemUserId: number) {
     const sqlStatement = SQL`
       UPDATE
-        system_user
+        "system_user"
       SET
         record_end_date = now()
       WHERE

diff --git a/compose.yml b/compose.yml
@@ -23,10 +23,11 @@ services:
       - POSTGRES_PASSWORD=${DB_ADMIN_PASS}
       - POSTGRES_DB=${DB_DATABASE}
       - PORT=5432
+      - PGDATA=${PGDATA}/${POSTGRES_VERSION}
     networks:
       - sims-network
     volumes:
-      - postgres:/var/lib/postgresql/data
+      - postgres:${PGDATA}
 
   ## Build the api docker image
   api:

diff --git a/containers/postgres12-postgis31/.gitattributes b/containers/postgres12-postgis31/.gitattributes
diff --git a/containers/postgres12-postgis31/.gitignore b/containers/postgres12-postgis31/.gitignore