Merge pull request #1613 from alliance-genome/release/v0.34.0

Release v0.34.0
alliance-genome · Jul 15, 2024 · 6894975 · 6894975
2 parents df44887 + 05f70cc
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diff --git a/.github/workflows/checkstyle.yml b/.github/workflows/checkstyle.yml
@@ -0,0 +1,19 @@
+name: Checkstyle Action
+on: pull_request
+
+jobs:
+  checkstyle_job:
+    runs-on: ubuntu-latest
+    name: Checkstyle Job
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Run check style
+      uses: dbelyaev/action-checkstyle@master
+      with:
+        level: 'error'
+        fail_on_error: 'true'
+        github_token: ${{ secrets.GH_DEVOPS_PAT }}
+        reporter: github-pr-review
+        checkstyle_config: checkstyle.xml
+        checkstyle_version: "10.17.0"
diff --git a/.github/workflows/github-actions-PR-validation.yml b/.github/workflows/github-actions-PR-validation.yml
@@ -8,6 +8,7 @@ on:
       - production
 jobs:
   check-branching-rules:
+    name: Check Branching Rules
     runs-on: ubuntu-20.04
     steps:
       - name: Check out repository code
@@ -17,7 +18,40 @@ jobs:
       - name: Check branching rules
         run: |
           bash ci-scripts/check-branching.sh ${{ github.base_ref }} ${{ github.head_ref }}
-  verify-test-api:
+
+  checkstyle-api:
+    name: Checkstyle API
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Report workflow details
+        run: |
+          echo "Repository ${{ github.repository }}."
+          echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
+      - name: Report files updated in PR
+        run: |
+          git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
+          git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+      - name: Report runtime details
+        run: |
+          echo "Github runner OS: ${{ runner.os }}"
+      - name: Report Maven version
+        run: |
+          mvn --version
+      - name: Run Check Styles
+        run: |
+          mvn -ntp checkstyle:check
+
+
+  verify-api:
+    name: Verify API
     runs-on: ubuntu-20.04
     steps:
       - name: Report workflow details
@@ -36,11 +70,42 @@ jobs:
         with:
           java-version: '17'
           distribution: 'temurin'
+      - name: Report runtime details
+        run: |
+          echo "Github runner OS: ${{ runner.os }}"
       - id: install-secret-key
         name: Install gpg secret key
         run: |
           cat <(echo -e "${{ secrets.OSSRH_GPG_SECRET_KEY }}") | gpg --batch --import
           gpg --list-secret-keys --keyid-format LONG
+      - name: Report Maven version
+        run: |
+          mvn --version
+      - name: Run Maven verify
+        run: |
+          mvn -ntp --batch-mode --update-snapshots verify
+
+
+  test-api:
+    name: Test API
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Report workflow details
+        run: |
+          echo "Repository ${{ github.repository }}."
+          echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
+      - name: Report files updated in PR
+        run: |
+          git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
+          git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'temurin'
       - name: Report runtime details
         run: |
           echo "Github runner OS: ${{ runner.os }}"
@@ -49,13 +114,65 @@ jobs:
           mvn --version
       - name: Run Maven test
         run: |
-          mvn --no-transfer-progress test
-      - name: Run Maven verify
+          mvn -ntp test
+
+  package-api:
+    name: Package API
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Report workflow details
+        run: |
+          echo "Repository ${{ github.repository }}."
+          echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
+      - name: Report files updated in PR
         run: |
-          mvn --no-transfer-progress --batch-mode --update-snapshots verify
+          git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
+          git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+      - name: Report runtime details
+        run: |
+          echo "Github runner OS: ${{ runner.os }}"
+      - name: Report Maven version
+        run: |
+          mvn --version
       - name: Package API
         run: |
-          mvn clean package -Dquarkus.package.type=uber-jar -ntp
+          mvn -ntp clean package -Dquarkus.package.type=uber-jar -ntp
+
+
+  integration-test-api:
+    name: Integration Test API
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Report workflow details
+        run: |
+          echo "Repository ${{ github.repository }}."
+          echo "Trigger ref ${{ github.ref }}, base-ref ${{ github.base_ref }}, head_ref ${{ github.head_ref }}."
+      - name: Check out repository code
+        uses: actions/checkout@v3
+      - run: cp src/main/resources/application.properties.defaults src/main/resources/application.properties
+      - name: Report files updated in PR
+        run: |
+          git fetch -q origin ${{ github.base_ref }} ${{ github.head_ref }}
+          git diff --name-only origin/${{ github.base_ref }} origin/${{ github.head_ref }}
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+      - name: Report runtime details
+        run: |
+          echo "Github runner OS: ${{ runner.os }}"
+      - name: Report Maven version
+        run: |
+          mvn --version
       - name: Create test containers properties file
         run: |
           touch ~/.testcontainers.properties
@@ -64,6 +181,7 @@ jobs:
           make integration-test
 
   verify-test-ui:
+    name: Verify Test UI
     runs-on: ubuntu-20.04
     steps:
       - name: Report workflow details
@@ -87,9 +205,11 @@ jobs:
         working-directory: src/main/cliapp
         run: |
           npm ci
+          npx prettier --check .
           npm test -- --watchAll=false
           npm run build
   test-build-docker-image:
+      name: Test Build Docker Image
       runs-on: ubuntu-20.04
       steps:
         - name: Check out repository code

diff --git a/Makefile b/Makefile
@@ -58,13 +58,22 @@ docker-run:
 debug:
 	java -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=5045 -jar target/agr_curation_api-bootable.jar
 
+checkstyle:
+	mvn checkstyle:check
+
+prettier-check:
+	npx prettier 'src/main/cliapp/**/*.js' --check
+
+prettier-write:
+	npx prettier 'src/main/cliapp/**/*.js' --write
+
 test:
 	mvn test
 
 integration-test:
-	mvn clean package
+	mvn -ntp clean package
 	mvn -ntp failsafe:integration-test -Dokta.authentication=false
-	mvn failsafe:verify
+	mvn -ntp failsafe:verify
 
 verify:
 	mvn verify

diff --git a/README.md b/README.md
@@ -15,6 +15,9 @@ These instructions will get you a copy of the project and the API up and running
    *  [Postgres](#postgres)
    *  [OpenSearch](#opensearch-elastic-search-alternative)
    *  [Cerebro](#cerebro)
+-  [Code Style](#codestyle)
+   *  [Running Checkstyle](#running-checkstyle)
+   *  [Checkstyle Links](#checkstyle-links)
 -  [Building](#building)
    *  [Building Docker Image](#building-docker-image)
 -  [Running](#running)
@@ -239,6 +242,100 @@ CONTAINER ID   IMAGE                                   COMMAND
 7de3cf028e9c   postgres:13                             "docker-entrypoint.s…"   3 days ago       Up 3 days       0.0.0.0:5432->5432/tcp, :::5432->5432/tcp                                                                         postgres
 ```
 
+## Code Style
+
+This repository uses checkstyle to validate formatting of code to a coding standard. [Checkstyle](https://checkstyle.sourceforge.io/) is a development tool to help programmers write Java code that adheres to a coding standard. It automates the process of checking Java code to spare humans of this boring (but important) task. This makes it ideal for projects that want to enforce a coding standard.
+
+This repository also uses [Prettier](https://prettier.io/) to validate and update the formatting of code in the frontend codebase.
+
+### Running Checkstyle
+
+To run checkstyle locally in order to check your code before committing run the following:
+
+```bash
+> mvn checkstyle:check
+```
+
+Or the make target:
+
+```bash
+> make checkstyle
+```
+
+This will check all the style of the code and report any issues that it finds with the code. Here is an example output:
+
+```bash
+> make checkstyle
+[INFO] Scanning for projects...
+[INFO] Inspecting build with total of 1 modules...
+[INFO] Installing Nexus Staging features:
+[INFO]   ... total of 1 executions of maven-deploy-plugin replaced with nexus-staging-maven-plugin
+[INFO] 
+[INFO] ----------------< org.alliancegenome:agr_curation_api >-----------------
+[INFO] Building AGR Curation :: API 0.0.0
+[INFO]   from pom.xml
+[INFO] --------------------------------[ jar ]---------------------------------
+[INFO] 
+[INFO] --- checkstyle:3.3.1:check (default-cli) @ agr_curation_api ---
+[INFO] There is 1 error reported by Checkstyle 10.17.0 with checkstyle.xml ruleset.
+[ERROR] src/main/java/org/alliancegenome/curation_api/main/Main.java:[9] (regexp) RegexpSinglelineJava: Indent must use tab characters
+[INFO] ------------------------------------------------------------------------
+[INFO] BUILD FAILURE
+[INFO] ------------------------------------------------------------------------
+[INFO] Total time:  6.107 s
+[INFO] Finished at: 2024-05-29T05:23:33-04:00
+[INFO] ------------------------------------------------------------------------
+[ERROR] Failed to execute goal org.apache.maven.plugins:maven-checkstyle-plugin:3.3.1:check (default-cli) on project agr_curation_api: You have 1 Checkstyle violation. -> [Help 1]
+[ERROR] 
+[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
+[ERROR] Re-run Maven using the -X switch to enable full debug logging.
+[ERROR] 
+[ERROR] For more information about the errors and possible solutions, please read the following articles:
+[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
+make: *** [checkstyle] Error 1
+```
+
+Checkstyle can be configured via the checkstyle.xml file in the root of the project, this file can also be used by IDE's to keep code in line with the ruleset.
+
+### Running Prettier
+
+To validate formatting on JavaScript files locally with Prettier: 
+
+```bash
+> npx prettier --check **/*.js
+```
+
+Or the make target:
+
+```bash
+> make prettier-check
+```
+
+To update formatting on JavaScript files locally with Prettier: 
+
+```bash
+> npx prettier --write **/*.js
+```
+
+Or the make target:
+
+```bash
+> make prettier-write
+```
+
+Prettier can be configured via the .prettierrc.yaml file in the src/main/cliapp director of this project, this file can also be used by IDE's to keep code in line with the ruleset.
+
+### Checkstyle Links
+
+* Checkstyle for vscode: [https://marketplace.visualstudio.com/items?itemName=shengchen.vscode-checkstyle](https://marketplace.visualstudio.com/items?itemName=shengchen.vscode-checkstyle)
+* Checkstyle for Intellij: [https://stackoverflow.com/questions/26955766/intellij-idea-checkstyle](https://stackoverflow.com/questions/26955766/intellij-idea-checkstyle)
+* Checkstyle for Eclipse: [https://www.youtube.com/watch?v=H90QoBp2NSQ](https://www.youtube.com/watch?v=H90QoBp2NSQ) or [https://checkstyle.org/eclipse-cs/#!/](https://checkstyle.org/eclipse-cs/#!/)
+
+### Prettier Links
+
+* Prettier for vscode: [https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode)
+* Prettier for Intellij: [https://www.jetbrains.com/help/idea/prettier.html](https://www.jetbrains.com/help/idea/prettier.html)
+
 ## Building
 
 Before building locally, make sure and create a copy of the application.properties file

diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -2,6 +2,26 @@
 
 https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview
 
+## v0.34.0
+* New features
+  * Paralogy annotations loaded into persistent store (SCRUM-4086, SCRUM-4088, SCRUM-4089, SCRUM-4090)
+  * Expression annotations loaded into persistent store (SCRUM-3708)
+  * HTPTags loaded into persistent store (SCRUM-4221)
+  * Data load file history sorted by Load Started timestamp (SCRUM-4204)
+  * Data loads stopped if error rate exceeds cutoff threshold (SCRUM-3871)
+  * SGD strain background added to defining fields of disease/phenotype annotations (SCRUM-4137)
+  * Turned off cleanup of associated annotations/associations (SCRUM-4107)
+* Fixes and maintenance
+  * Fixed reporting of out-of-date errors in data loads tooltip (SCRUM-4210)
+  * Fixed loading of genes with duplicate cross-references (SCRUM-4160)
+  * Fixed lading of interactions via NCBI_Gene cross-references (SCRUM-4159)
+  * Fixed orthology load cleanup (SCRUM-4146)
+  * Fixed duplicate references on interactions (SCRUM-4114)
+  * Fixed subject filter on disease annotations table (SCRUM-4113)
+  * Fixed association of secondary phenotype annotations with primary annotations that have condition relations (SCRUM-4062)
+  * Fixed downloads of large exception lists (SCRUM-3871)
+  * Fixed missing exception messages in downloads (SCRUM-4162)
+
 ## v0.33.0
 * New features 
   * Importing gene interactions into the persistent store (phase 2) (SCRUM-3809)