Merge branch '1.4' into 1.4

.github/workflows/ALL-testMigrate.yml

@@ -0,0 +1,38 @@
+name: Testing Flyway Migrations
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [opened, synchronize]
+
+jobs:
+  run-tests:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        pgsql-version:
+          - "12"
+          - "13"
+          - "14"
+          - "15"
+          - "16"
+    steps:
+      # Check out the repo
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      # Here we fully build a docker using the current checked out code
+      # to ensure we test the current migrations.
+      - name: Build Docker Image
+        run: |
+          docker build --tag gmod/chado:local \
+          --file docker/Dockerfile \
+          --build-arg PGSQL_VERSION="${{ matrix.pgsql-version }}" \
+          --build-arg APPLY_MIGRATIONS=0 ./
+      # Just spin up docker the good ol' fashion way
+      # then run flyway baseline and migrate.
+      - name: Run Flyway Migrate
+        run: |
+          docker run --name=chadodocker -tid gmod/chado:local
+          sleep 30
+          docker exec chadodocker flyway migrate

.github/workflows/MAIN-buildDocker.yml

@@ -0,0 +1,62 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish Docker image
+on:
+  push:
+    branches:
+      - '1.4'
+      - '142-github-workflows-to-help-with-review'
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      id-token: write
+      attestations: write
+
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+      - name: Make Image Name all lowercase
+        run: |
+          echo "IMAGE_NAME=${IMAGE_NAME,,}" >>${GITHUB_ENV}
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          build-args: |
+            PGSQL_VERSION=16
+            APPLY_MIGRATIONS=1
+          file: 'docker/Dockerfile'
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:1.4
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/PRs-buildDocker.yml

@@ -0,0 +1,61 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+# GitHub recommends pinning actions to a commit SHA.
+# To get a newer version, you will need to update the SHA.
+# You can also reference a tag or branch, but the action may change without warning.
+
+name: Publish Docker image
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [opened, synchronize]
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      id-token: write
+      attestations: write
+
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+      - name: Make Image Name all lowercase
+        run: |
+          echo "IMAGE_NAME=${IMAGE_NAME,,}" >>${GITHUB_ENV}
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          build-args: |
+            PGSQL_VERSION=16
+          file: 'docker/Dockerfile'
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+

README.md

@@ -83,14 +83,75 @@ are currently using PostgreSQL.
 Please read the included [chado/INSTALL.Chado.md](./chado/INSTALL.Chado.md) document for instructions on how to
 install the Chado schema.
 
-### Running the Docker Image
+## Docker
+
+Chado has been dockerized with Flyway so that you can look around, and test migrations easily.
+The following instructions are going to show you how to pull the already build images. If you would like to build your own image locally, there are instructins for that at the very bottom.
+
+### Using the Chado Docker Image
+
+You can start and work within the Chado container by using the following commands. You will want to replace the `<version>` with a current version available on Github. You can see the available options [on the github package repository](https://github.com/GMOD/Chado/pkgs/container/chado).
 
 ```bash
+docker run -it ghcr.io/gmod/chado:<version>
+```
+If you don't have the image locally, this will pull it down from the Github package repository first and then start a container for you. PostgreSQL and flyway will be running within the container and Chado will be cloned in the current working directory.
 
-docker build -t chado .
-docker run -it -d chado
+The container will be shut down once you exit the opened bash terminal. If you want the container to remain running then you would use `-dit` instead of `-it` to run docker in detached mode.
+
+As a test, you can run the `flyway info` command after starting the container:
+
+```bash
+flyway info
 ```
 
+You can explore the Chado tables using the `psql` command in the following way:
+
+```bash
+psql -U postgres -h localhost -d chado
+```
+You will be prompted for a password. The default password is `chadotest`
+
+### Testing a Pull Request
+
+In order to allow you to modify the migrations while running the container, you will mount your current directory inside the container using the following approach. This way you can edit the files locally and they will be automatically updated within the container and available to flyway.
+
+```bash
+git clone https://github.com/GMOD/Chado chado-pr<number>
+cd chado-pr<number>
+git checkout <prBranch>
+docker run -it -rm --volume=$(pwd):/Chado ghcr.io/gmod/chado:pr-<number>
+```
+
+You can test FlyWay migrations by running these flyway commands:
+
+  - See what migrations need to be applied:
+
+  ```bash
+  flyway info
+  ```
+
+  - Run the migrations available:
+
+  ```bash
+  flyway migrate
+  ```
+
+The migrations have been applied correctly if you do not see any red errors. However, it is good practice to run `flyway info` again to confirm.
+
+### Locally Build the Docker Image
+
+*The following commands should be carried out in a cloned version of this repository, in the root directory.*
+
+To build the docker image using the default values, run the following command:
+```bash
+docker build --tag gmod/chado:local --file docker/Dockerfile ./
+```
+
+If you would like to build a docker that uses a specific version of PostgreSQL then you can run the following command instead. In this case you will replace `<version>` with the version of PostgreSQL. We currently support 12, 13, 14, 15, and 16.
+```bash
+docker build --tag gmod/chado:local --file docker/Dockerfile --build-arg PGSQL_VERSION=<version> ./
+```
 
 ## Chado Support
 

chado/migrations/V1.3.3.011__fix_db_relationship_type_id.sql

@@ -0,0 +1,4 @@
+/* Delete the improperly added foreign key from v1.3.3.002 */
+ALTER TABLE db_relationship DROP CONSTRAINT db_relationship_type_id_fkey;
+/* Add it back in with type_id => cvterm.cvterm_id as it should have */
+ALTER TABLE db_relationship ADD CONSTRAINT db_relationship_type_id_fkey FOREIGN KEY  (type_id) REFERENCES cvterm(cvterm_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED;

docker/Dockerfile

@@ -0,0 +1,53 @@
+FROM ubuntu:24.04
+
+ARG CHADO_VERSION='1.31'
+ARG PGSQL_VERSION='16'
+ARG APPLY_MIGRATIONS='0'
+
+RUN apt-get update
+
+#for some reason, this has to be installed by itself
+RUN apt-get install -y tzdata
+RUN apt-get install -y apt-utils
+RUN apt-get install -y wget \
+                       unzip \
+                       git \
+                       make \
+                       gcc \
+                       vim \
+                       uuid-dev
+
+RUN  apt-get install -y postgresql-common \
+   && /usr/share/postgresql-common/pgdg/apt.postgresql.org.sh -y \
+   && apt-get install -y postgresql-${PGSQL_VERSION}
+
+RUN cd /usr/local \
+   && wget -qO- https://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/10.12.0/flyway-commandline-10.12.0-linux-x64.tar.gz | tar xvz \
+   && ln -s `pwd`/flyway-10.12.0/flyway /usr/local/bin
+
+COPY . /Chado
+
+RUN /etc/init.d/postgresql start \
+   && su -c "createdb chado" - postgres \
+   && su -c "psql chado < /Chado/schemas/${CHADO_VERSION}/default_schema.sql" - postgres \
+   && su -c "psql -c \"ALTER USER postgres PASSWORD 'chadotest';\"" - postgres \
+   && /etc/init.d/postgresql stop;
+
+WORKDIR /Chado/docker
+RUN cp flyway.toml /root/flyway.toml \
+   && cp entrypoint.sh /usr/bin/entrypoint.sh \
+   && chmod +x /usr/bin/entrypoint.sh \
+   && cp motd /etc/motd
+
+RUN /etc/init.d/postgresql start \
+   && sleep 30 \
+   && flyway baseline \
+   && if [ "$APPLY_MIGRATIONS" = "1" ] ; then \
+     flyway migrate; \
+   fi
+
+WORKDIR /Chado
+
+RUN echo '[ ! -z "$TERM" -a -r /etc/motd ] && cat /etc/issue && cat /etc/motd' >> /etc/bash.bashrc
+
+ENTRYPOINT ["entrypoint.sh"]

docker/entrypoint.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+/etc/init.d/postgresql start
+flyway baseline
+/bin/bash

docker/flyway.toml

@@ -0,0 +1,12 @@
+# More information on the parameters can be found here:
+# https://documentation.red-gate.com/flyway/flyway-cli-and-api/configuration/parameters
+
+[environments.core]
+url = "jdbc:postgresql://localhost:5432/chado"
+user = "postgres"
+password = "chadotest"
+schemas = ["public"]
+
+[flyway]
+environment = "core"
+locations = ["filesystem:/Chado"]

docker/motd

@@ -0,0 +1,10 @@
+   ________  _____    ____  ____
+  / ____/ / / /   |  / __ \/ __ \
+ / /   / /_/ / /| | / / / / / / /
+/ /___/ __  / ___ |/ /_/ / /_/ /
+\____/_/ /_/_/  |_/_____/\____/
+
+This Chado docker image uses default security settings for
+PostgreSQL and has a hard-coded password for the postgres
+user.  Do not use this image for a production service without
+first correcting