[DCJ-400-gradle]: Bump io.zonky.test.postgres:embedded-postgres-binaries-bom from 12.8.0 to 16.4.0 (#1775)

* [DCJ-400-gradle]: Bump io.zonky.test.postgres:embedded-postgres-binaries-bom

Bumps [io.zonky.test.postgres:embedded-postgres-binaries-bom](https://github.com/zonkyio/embedded-postgres-binaries) from 12.8.0 to 16.4.0.
- [Release notes](https://github.com/zonkyio/embedded-postgres-binaries/releases)
- [Commits](zonkyio/embedded-postgres-binaries@v12.8.0...v16.4.0)

---
updated-dependencies:
- dependency-name: io.zonky.test.postgres:embedded-postgres-binaries-bom
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Upgrade Postgres image used in PR tests: 11 -> 16.4

* Postgres 15 revokes the CREATE permission from all non-owners

* update compose.yaml

* update documentation, rm pgcrypto extension

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Olivia Kotsopoulos <[email protected]>
Co-authored-by: rjohanek <[email protected]>

Author: 3 people

.github/workflows/int-and-connected-test-run.yml

@@ -78,7 +78,7 @@ jobs:
     timeout-minutes: 300
     services:
       postgres:
-        image: postgres:11
+        image: postgres:16.4
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

build.gradle

@@ -269,7 +269,7 @@ dependencies {
     testImplementation 'org.springframework.boot:spring-boot-starter-test'
     testImplementation 'io.zonky.test:embedded-database-spring-test:2.6.0'
     testImplementation 'io.zonky.test:embedded-postgres:2.1.0'
-    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:12.8.0')
+    implementation enforcedPlatform('io.zonky.test.postgres:embedded-postgres-binaries-bom:16.4.0')
 
     generatedCompile 'org.springframework.boot:spring-boot-starter-web'
     // boot-starter-validation required for jakarta.validation.Valid references, @Valid tags

docs/jade-getting-started.md

@@ -254,7 +254,7 @@ export HOST=localhost
 * Ensure docker is running
 * Auth as your broadinstitute.org to pull from Google Secrets Manager `gcloud auth login <you>@broadinstitute.org`
 * Run `./scripts/run-db start` to start the DB in a docker container
-* Run `./scripts/run local` to run TDR locally or `./scripts/run docker` to run TDR in a docker container
+* Run `./scripts/run start_local` to run TDR locally or `./scripts/run start_docker` to run TDR in a docker container
 * To Build the code and run the unit tests:
 
 ```

scripts/compose.yaml

@@ -27,7 +27,7 @@ services:
       - /tmp/jade-dev-account.json:/tmp/jade-dev-account.json
 
   database:
-    image: postgres:14
+    image: postgres:16.4
     environment:
       - POSTGRES_PASSWORD=drpasswd
     ports:

scripts/init-db/postgres-init.sql

@@ -2,7 +2,7 @@
 CREATE USER drmanager WITH PASSWORD 'drpasswd';
 CREATE DATABASE datarepo;
 GRANT ALL PRIVILEGES ON DATABASE datarepo to drmanager;
+ALTER DATABASE datarepo OWNER to drmanager;
 CREATE DATABASE stairway;
 GRANT ALL PRIVILEGES ON DATABASE stairway to drmanager;
-\c datarepo
-CREATE EXTENSION IF NOT EXISTS pgcrypto;
+ALTER DATABASE stairway OWNER to drmanager;