Merge branch 'release-4.3.x'

Author: imedina

.github/workflows/build-java-app-workflow.yml

@@ -15,16 +15,12 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '10'
-      - name: Setup Maven Action
-        uses: s4u/[email protected]
-        with:
-          java-version: 8
-          maven-version: 3.6.3
-      - name: Set up JDK 1.8
+      - name: Set up JDK 8
         uses: actions/setup-java@v2
         with:
-          distribution: 'zulu'
+          distribution: 'temurin'
           java-version: '8'
+          cache: 'maven'
       - name: Cache Maven packages
         uses: actions/cache@v2
         with:

.github/workflows/deploy-maven-repository-workflow.yml

@@ -24,16 +24,12 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '10'
-      - name: Setup Maven Action
-        uses: s4u/[email protected]
-        with:
-          java-version: 8
-          maven-version: 3.6.3
-      - name: Set up JDK 1.8
+      - name: Set up JDK 8
         uses: actions/setup-java@v2
         with:
-          distribution: 'zulu'
+          distribution: 'temurin'
           java-version: '8'
+          cache: 'maven'
           server-id: ossrh                          # Value of the distributionManagement/repository/id field of the pom.xml
           server-username: MAVEN_NEXUS_USER         # env variable for username in deploy
           server-password: MAVEN_NEXUS_PASSWORD     # env variable for token in deploy

.github/workflows/develop.yml

@@ -29,11 +29,12 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '10'
-      - name: Set up JDK 1.8
+      - name: Set up JDK 8
         uses: actions/setup-java@v2
         with:
-          distribution: 'zulu'
+          distribution: 'temurin'
           java-version: '8'
+          cache: 'maven'
       - name: Cache Maven packages
         uses: actions/cache@v2
         with:

.github/workflows/release.yml

@@ -28,11 +28,12 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: '10'
-      - name: Set up JDK 1.8
+      - name: Set up JDK 8
         uses: actions/setup-java@v2
         with:
-          distribution: 'zulu'
+          distribution: 'temurin'
           java-version: '8'
+          cache: 'maven'
       - name: Cache Maven packages
         uses: actions/cache@v2
         with:

.github/workflows/sonar-analysis-workflow.yml

@@ -17,16 +17,12 @@ jobs:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
-      - name: Setup Maven Action
-        uses: s4u/[email protected]
-        with:
-          java-version: 8
-          maven-version: 3.6.3
-      - name: Set up JDK 11
+      - name: Set up JDK 8
         uses: actions/setup-java@v2
         with:
-          distribution: 'zulu'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
       - name: Cache SonarCloud packages
         uses: actions/cache@v1
         with:

.github/workflows/task.yml

@@ -0,0 +1,49 @@
+name: Push java-common-libs develop
+
+on:
+  push:
+    branches:
+      - TASK-*
+
+jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
+  sonar:
+    uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
+    needs: build
+    with:
+      sonarProjectKey: opencb_java-common-libs
+    secrets:
+      SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+
+  test:
+    name: Test java-common-libs
+    runs-on: ubuntu-20.04
+    needs: build
+    strategy:
+      matrix:
+        mongodb: ["4.2"]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '10'
+      - name: Set up JDK 8
+        uses: actions/setup-java@v2
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
+      - name: Cache Maven packages
+        uses: actions/cache@v2
+        with:
+          path: ~/.m2/repository
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: ${{ runner.os }}-maven
+      - name: Start MongoDB v${{ matrix.mongodb }}
+        uses: supercharge/[email protected]
+        with:
+          mongodb-version: ${{ matrix.mongodb }}
+          mongodb-replica-set: rs-test
+      - name: Run Maven Tests
+        run: mvn -T 2 clean install -DskipTests

commons-datastore/commons-datastore-core/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>4.2.1</version>
+        <version>4.3.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

commons-datastore/commons-datastore-mongodb/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>4.2.1</version>
+        <version>4.3.0</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -23,7 +23,7 @@
         <dependency>
             <groupId>org.mongodb</groupId>
             <artifactId>mongo-java-driver</artifactId>
-            <version>3.11.3</version>
+            <version>3.12.10</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBCollection.java

@@ -58,6 +58,8 @@ public class MongoDBCollection {
     public static final String SPARSE = "sparse";
     public static final String NAME = "index_name";
 
+    public static final String NO_CURSOR_TIMEOUT = "noCursorTimeout";
+
     private MongoDBNativeQuery mongoDBNativeQuery;
     private QueryResultWriter<Object> queryResultWriter;
 

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java

@@ -221,6 +221,10 @@ public FindIterable<Document> nativeFind(ClientSession clientSession, Bson query
             findIterable.maxTime(options.getLong(QueryOptions.TIMEOUT), TimeUnit.MILLISECONDS);
         }
 
+        if (options != null && options.getBoolean(MongoDBCollection.NO_CURSOR_TIMEOUT)) {
+            findIterable.noCursorTimeout(true);
+        }
+
         return findIterable;
     }