Resolve conflicts after merging develop, #TASK-4225

opencb · Jun 27, 2023 · 1ae5500 · 1ae5500
2 parents 4cf8320 + 5431981
commit 1ae5500
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Showing 57 changed files with 881 additions and 539 deletions.
diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -10,6 +10,8 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase
 
   test:
     uses: ./.github/workflows/test-analysis.yml
@@ -20,14 +22,14 @@ jobs:
       report_dir: ${{ github.ref_name }}/cellbase/${{ github.sha }}
 
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.6.x
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.6.x
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -9,6 +9,8 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase
 
   test:
     uses: ./.github/workflows/test-analysis.yml
@@ -19,27 +21,27 @@ jobs:
       report_dir: cellbase
 
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.6.x
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.6.x
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base
     secrets: inherit
 
   deploy-python:
-    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.6.x
     needs: test
     with:
       cli: bash ./clients/python/python-build.sh push
       artifact: build-folder
     secrets: inherit
 
   release:
-    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.6.x
     needs: [deploy-maven, deploy-docker, deploy-python]
diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+BRANCH_NAME=$1
+
+if [[ -z $BRANCH_NAME  ]]; then
+  echo "The first parameter is mandatory and must be a valid branch name."
+  exit 1
+fi
+
+if [[ $BRANCH_NAME != "TASK-"*   ]]; then
+  echo "No need to check dependencies."
+  exit 0
+fi
+
+function install(){
+  local REPO=$1
+  cd /home/runner/work/ || exit 2
+  git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME"
+  if [ -d "./$REPO" ]; then
+    cd "$REPO" || exit 2
+    echo "Branch name $BRANCH_NAME already exists."
+    mvn clean install -DskipTests
+  else
+    echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME "
+  fi
+}
+
+install "java-common-libs"
+install "biodata"
diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml
@@ -5,10 +5,12 @@ on:
     branches:
       - TASK-*
   workflow_dispatch:
-
+    
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase
 
   test:
     uses: ./.github/workflows/test-analysis.yml
@@ -19,36 +21,10 @@ jobs:
       report_dir: ${{ github.ref_name }}/cellbase/${{ github.sha }}
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.6.x
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base --tag ${{ github.ref_name }}
     secrets: inherit
 
-  deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
-    needs: [ build, test ]
-    with:
-      maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
-    if: contains( needs.build.outputs.version ,'TASK')
-    secrets: inherit
-
-  #The following jobs are to see that the previous if does not fail and that the maven deploy is executed because it is true
-  snapshot-version:
-    name: Check SNAPSHOT version
-    needs: [ build, test ]
-    if: contains(needs.build.outputs.version ,'SNAPSHOT')
-    runs-on: ubuntu-22.04
-    steps:
-      - name: test-version-from-check
-        run: echo "Project version is " ${{ needs.build.outputs.version }}
-
-  task-version:
-    name: Check TASK version
-    needs: [ build, test ]
-    if: contains(needs.build.outputs.version ,'TASK')
-    runs-on: ubuntu-22.04
-    steps:
-      - name: test-version-from-check
-        run: echo "Project version is " ${{ needs.build.outputs.version }}
 
diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -20,7 +20,7 @@ on:
         type: string
         required: true
 env:
-  xb_version: "1.6.1"
+  xb_version: "1.7.0"
 jobs:
   test:
     name: Test and push Sonar analysis
@@ -40,6 +40,14 @@ jobs:
         with:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
+      - name: Install dependencies branches
+        run: |
+          if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
+            chmod +x ./.github/workflows/scripts/get_same_branch.sh
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+          else
+             echo "./.github/workflows/scripts/get_same_branch.sh does not exist."
+          fi
       - name: Test and Analyze
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any

diff --git a/cellbase-app/app/cloud/docker/cellbase-base/Dockerfile b/cellbase-app/app/cloud/docker/cellbase-base/Dockerfile
@@ -1,5 +1,6 @@
-## Based on Debian 11 (bullseye)
-FROM openjdk:11-jre
+## Based on Ubuntu 22.04 (jammy)
+## We are now using OpenJDK 8u372 to support "cgroup v2", see https://developers.redhat.com/articles/2023/04/19/openjdk-8u372-feature-cgroup-v2-support#
+FROM eclipse-temurin:8u372-b07-jre-jammy
 
 LABEL org.label-schema.vendor="OpenCB" \
       org.label-schema.name="cellbase-base" \

diff --git a/cellbase-app/app/cloud/docker/cellbase-base/Dockerfile.alpine b/cellbase-app/app/cloud/docker/cellbase-base/Dockerfile.alpine
diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.5.0-SNAPSHOT</version>
+        <version>5.6.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CommandExecutor.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CommandExecutor.java
@@ -18,13 +18,13 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.core.config.Configurator;
 import org.opencb.cellbase.client.config.ClientConfiguration;
 import org.opencb.cellbase.core.config.CellBaseConfiguration;
 import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.commons.utils.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.apache.logging.log4j.core.config.Configurator;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -204,5 +204,4 @@ protected void makeDir(Path folderPath) throws IOException {
             Files.createDirectories(folderPath);
         }
     }
-
 }
diff --git a/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java b/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java
@@ -145,8 +145,11 @@ public class DataReleaseCommandOptions {
         @Parameter(names = {"--list"}, description = "List the data releases present in the database", arity = 0)
         public boolean list;
 
-        @Parameter(names = {"--set-active"}, description = "Set the data release active", arity = 1)
-        public int active;
+        @Parameter(names = {"--update"}, description = "Data release to be updated by adding CellBase vesions", arity = 1)
+        public int update;
+
+        @Parameter(names = {"--add-versions"}, description = "CellBase versions separated by commas, e.g.: v5.2,v5.3. This parameter has to be used together to the parameter --update", arity = 1)
+        public String versions;
     }
 
     @Parameters(commandNames = {"data-token"}, commandDescription = "Manage data access tokens in order to access to restricted/licensed data sources")

diff --git a/...p/src/main/java/org/opencb/cellbase/app/cli/admin/executors/CustomiseCommandExecutor.java b/...p/src/main/java/org/opencb/cellbase/app/cli/admin/executors/CustomiseCommandExecutor.java
@@ -19,7 +19,9 @@
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.cellbase.app.cli.CommandExecutor;
 import org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser;
+import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.cellbase.lib.loader.LoadRunner;
+import org.opencb.cellbase.lib.loader.LoaderException;
 import org.opencb.commons.utils.FileUtils;
 
 import java.io.File;
@@ -112,9 +114,9 @@ public void execute() {
         }
     }
 
-    private void loadIfExists(Path path, String collection) throws NoSuchMethodException, InterruptedException,
-            ExecutionException, InstantiationException, IOException, IllegalAccessException, InvocationTargetException,
-            ClassNotFoundException {
+    private void loadIfExists(Path path, String collection) throws NoSuchMethodException, InterruptedException, ExecutionException,
+            InstantiationException, IOException, IllegalAccessException, InvocationTargetException, ClassNotFoundException,
+            LoaderException, CellBaseException {
         File file = new File(path.toString());
         if (file.exists()) {
             if (file.isFile()) {

diff --git a/...src/main/java/org/opencb/cellbase/app/cli/admin/executors/DataReleaseCommandExecutor.java b/...src/main/java/org/opencb/cellbase/app/cli/admin/executors/DataReleaseCommandExecutor.java
@@ -17,12 +17,14 @@
 package org.opencb.cellbase.app.cli.admin.executors;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.commons.lang3.StringUtils;
 import org.opencb.cellbase.app.cli.CommandExecutor;
 import org.opencb.cellbase.app.cli.admin.AdminCliOptionsParser;
 import org.opencb.cellbase.core.models.DataRelease;
 import org.opencb.cellbase.core.result.CellBaseDataResult;
 import org.opencb.cellbase.lib.managers.DataReleaseManager;
 
+import java.util.Arrays;
 import java.util.List;
 
 public class DataReleaseCommandExecutor extends CommandExecutor {
@@ -51,29 +53,28 @@ public void execute() {
 
             DataReleaseManager dataReleaseManager = new DataReleaseManager(database, configuration);
 
+            DataRelease dataRelease;
             if (dataReleaseCommandOptions.create) {
                 // Create release
-                DataRelease dataRelease = dataReleaseManager.createRelease();
+                dataRelease = dataReleaseManager.createRelease();
                 System.out.println("\nData release " + dataRelease.getRelease() + " was created.");
                 System.out.println("Data release description (in JSON format):");
                 System.out.println(new ObjectMapper().writerFor(DataRelease.class).writeValueAsString(dataRelease));
-            } else if (dataReleaseCommandOptions.active > 0) {
-                // Set-active release
-                CellBaseDataResult<DataRelease> results = dataReleaseManager.getReleases();
-                for (DataRelease dr : results.getResults()) {
-                    if (dr.isActive() && dr.getRelease() == dataReleaseCommandOptions.active) {
-                        logger.info("Data release " + dataReleaseCommandOptions.active + " is already active");
-                        return;
-                    }
-                }
-                DataRelease dataRelease = dataReleaseManager.active(dataReleaseCommandOptions.active);
-                if (dataRelease != null) {
-                    System.out.println("\nThe data release " + dataRelease.getRelease() + " is the active one.");
-                    System.out.println("Data release description (in JSON format):");
-                    System.out.println(new ObjectMapper().writerFor(DataRelease.class).writeValueAsString(dataRelease));
-                } else {
-                    logger.error("It could not set to active the data release " + dataReleaseCommandOptions.active);
+            } else if (dataReleaseCommandOptions.update > 0) {
+                if (StringUtils.isEmpty(dataReleaseCommandOptions.versions)) {
+                    throw new IllegalArgumentException("Missing CellBase versions to be added when updating data release");
                 }
+
+                // Versions to be added
+                List<String> versions = Arrays.asList(dataReleaseCommandOptions.versions.split(","));
+
+                // Update data release
+                dataReleaseManager.update(dataReleaseCommandOptions.update, versions);
+
+                dataRelease = dataReleaseManager.get(dataReleaseCommandOptions.update);
+                System.out.println("\nData release " + dataRelease.getRelease() + " was updated.");
+                System.out.println("Data release description (in JSON format):");
+                System.out.println(new ObjectMapper().writerFor(DataRelease.class).writeValueAsString(dataRelease));
             } else if (dataReleaseCommandOptions.list) {
                 // List releases
                 CellBaseDataResult<DataRelease> dataReleases = dataReleaseManager.getReleases();
@@ -94,11 +95,11 @@ private void checkParameters() {
         if (dataReleaseCommandOptions.list) {
             opts++;
         }
-        if (dataReleaseCommandOptions.active > 0) {
+        if (dataReleaseCommandOptions.update > 0) {
             opts++;
         }
-        if (opts > 1) {
-            throw new IllegalArgumentException("Please, select only one of these input parameters: create, list or set-active");
+        if (opts != 1) {
+            throw new IllegalArgumentException("Please, select only one of these input parameters: create, update or list");
         }
     }
 }