Merge branch 'develop' into TASK-4158

opencb · Feb 1, 2024 · 3c256ba · 3c256ba
2 parents b24f92d + 930d67f
commit 3c256ba
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diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh
@@ -7,10 +7,6 @@ if [[ -z $BRANCH_NAME  ]]; then
   exit 1
 fi
 
-if [[ $BRANCH_NAME != "TASK-"*   ]]; then
-  echo "No need to check dependencies."
-  exit 0
-fi
 
 function install(){
   local REPO=$1

diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml
@@ -27,7 +27,7 @@ jobs:
         uses: actions/setup-java@v3
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '17'
           cache: 'maven'
       - name: Install dependencies branches
         run: |

diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -56,6 +56,10 @@
             <groupId>org.opencb.opencga</groupId>
             <artifactId>opencga-master</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.opencb.opencga</groupId>
+            <artifactId>opencga-test</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.opencb.opencga</groupId>
             <artifactId>opencga-client</artifactId>
@@ -495,11 +499,11 @@
                                     <arg value="${project.basedir}/../opencga-test/target/appassembler/bin/opencga-test.sh"/>
                                     <arg value="${build.dir}/bin"/>
                                 </exec>
-                                <exec executable="cp">
-                                    <arg value="-r"/>
-                                    <arg value="${project.basedir}/../opencga-test/target/appassembler/libs"/>
-                                    <arg value="${build.dir}"/>
-                                </exec>
+                                <!--  <exec executable="cp">
+                                  <arg value="-r"/>
+                                  <arg value="${project.basedir}/../opencga-test/target/appassembler/libs"/>
+                                  <arg value="${build.dir}"/>
+                              </exec>-->
                                 <exec executable="sed">
                                     <arg value="-i"/>
                                     <arg value="s/REPLACEME_OPENCGA_VERSION/${project.parent.version}/"/>

diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml
@@ -23,7 +23,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <artifactId>opencga</artifactId>
         <groupId>org.opencb.opencga</groupId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -106,10 +106,6 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.codehaus.jackson</groupId>
-            <artifactId>jackson-mapper-asl</artifactId>
-        </dependency>
         <dependency>
             <groupId>com.google.protobuf</groupId>
             <artifactId>protobuf-java</artifactId>
@@ -252,7 +248,6 @@
         <plugins>
             <plugin>
                 <artifactId>maven-war-plugin</artifactId>
-                <version>2.6</version>
                 <configuration>
                     <warName>${opencga.war.name}</warName>
                     <!--

diff --git a/opencga-server/src/test/java/org/opencb/opencga/server/rest/ProjectWSServerTest.java b/opencga-server/src/test/java/org/opencb/opencga/server/rest/ProjectWSServerTest.java
@@ -146,7 +146,7 @@ public void modifyProject(long projectId, String sessionId) {
         System.out.println("\nJSON RESPONSE");
         System.out.println(s);
         try {
-            org.codehaus.jackson.map.ObjectMapper objectMapper = new org.codehaus.jackson.map.ObjectMapper();
+            ObjectMapper objectMapper = new ObjectMapper();
             QueryResponse queryResponse = objectMapper.readValue(s, QueryResponse.class);
             //Map<String,Object> userData = objectMapper.readValue(s, Map.class);
             assertEquals("Expected [], actual [" + queryResponse.getError() + "]", "", queryResponse.getError());

diff --git a/opencga-server/src/test/java/org/opencb/opencga/server/rest/UserWSServerTest.java b/opencga-server/src/test/java/org/opencb/opencga/server/rest/UserWSServerTest.java
@@ -16,7 +16,7 @@
 
 package org.opencb.opencga.server.rest;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.experimental.categories.Category;
 import org.opencb.commons.datastore.core.ObjectMap;
 import org.opencb.commons.datastore.core.QueryResponse;

diff --git a/opencga-server/src/test/java/org/opencb/opencga/server/rest/VariableSetWSServerTest.java b/opencga-server/src/test/java/org/opencb/opencga/server/rest/VariableSetWSServerTest.java
@@ -16,7 +16,7 @@
 
 package org.opencb.opencga.server.rest;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.junit.*;
 import org.junit.experimental.categories.Category;
 import org.junit.rules.ExpectedException;

diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <artifactId>opencga-storage</artifactId>
         <groupId>org.opencb.opencga</groupId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml
@@ -23,7 +23,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop-deps</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop-deps</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/...cga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop-deps</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml
@@ -50,7 +50,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage-hadoop</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml
@@ -28,7 +28,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga-storage</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml
@@ -24,7 +24,7 @@
     <parent>
         <groupId>org.opencb.opencga</groupId>
         <artifactId>opencga</artifactId>
-        <version>2.13.0-SNAPSHOT</version>
+        <version>3.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/pom.xml b/pom.xml
@@ -22,7 +22,7 @@
 
     <groupId>org.opencb.opencga</groupId>
     <artifactId>opencga</artifactId>
-    <version>2.13.0-SNAPSHOT</version>
+    <version>3.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>OpenCGA</name>
@@ -43,22 +43,22 @@
     </modules>
 
     <properties>
-        <pyopencga.version>2.13.0_dev</pyopencga.version>
-        <opencgar.version>2.13.0_dev</opencgar.version>
-        <cellbase.version>5.9.0-SNAPSHOT</cellbase.version>
-        <biodata.version>2.13.0-SNAPSHOT</biodata.version>
-        <java-common-libs.version>4.13.0-SNAPSHOT</java-common-libs.version>
-        <iva.version>2.13.0-SNAPSHOT</iva.version>
+        <pyopencga.version>3.0.0_dev</pyopencga.version>
+        <opencgar.version>3.0.0_dev</opencgar.version>
+        <cellbase.version>6.0.0-SNAPSHOT</cellbase.version>
+        <biodata.version>3.0.0-SNAPSHOT</biodata.version>
+        <java-common-libs.version>5.0.0-SNAPSHOT</java-common-libs.version>
+        <iva.version>3.0.0-SNAPSHOT</iva.version>
 
         <oskar.version>0.2.0</oskar.version>
 
-        <jackson.version>2.11.4</jackson.version>
+        <jackson.version>2.14.3</jackson.version>
         <jersey.version>2.30.1</jersey.version>
         <collections.version>4.4</collections.version>
         <avro.version>1.7.7</avro.version>
         <protobuf.version>3.11.4</protobuf.version>
         <grpc.version>1.28.1</grpc.version>
-        <slf4j.version>1.7.32</slf4j.version>
+        <slf4j.version>1.7.36</slf4j.version>
         <log4j2.version>2.17.2</log4j2.version>
         <solr.version>8.8.2</solr.version>
         <jjwt.version>0.11.2</jjwt.version>
@@ -67,7 +67,7 @@
         <htsjdk.version>2.23.0</htsjdk.version>
         <snpeff.version>4.3.1</snpeff.version>
         <mongodb-driver.version>4.8.2</mongodb-driver.version>
-        <commons-lang3.version>3.12.0</commons-lang3.version>
+        <commons-lang3.version>3.14.0</commons-lang3.version>
         <commons-io.version>2.5</commons-io.version>
         <commons-codec.version>1.7</commons-codec.version>
         <reflections.version>0.9.10</reflections.version>
@@ -146,7 +146,16 @@
         <jcl-over-slf4j.version>1.7.24</jcl-over-slf4j.version>
         <servlet-api.version>2.5-20081211</servlet-api.version>
 
+
+        <!--TO REMOVE:
+            The version of Java (11.0.21) used to run this analysis is deprecated, and SonarCloud no longer supports it. Please upgrade to Java 17 or later.
+            As a temporary measure, you can set the property 'sonar.scanner.force-deprecated-java-version' to 'true' to continue using Java 11.0.21
+            This workaround will only be effective until January 28, 2024. After this date, all scans using the deprecated Java 11 will fail.
+         -->
+        <sonar.scanner.force-deprecated-java-version>true</sonar.scanner.force-deprecated-java-version>
         <kryo.version>2.23.0</kryo.version>
+        <lombok.version>1.18.30</lombok.version>
+        <maven-war-plugin.version>3.4.0</maven-war-plugin.version>
     </properties>
 
     <scm>
@@ -249,6 +258,11 @@
                 <artifactId>opencga-storage-app</artifactId>
                 <version>${project.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.opencb.opencga</groupId>
+                <artifactId>opencga-test</artifactId>
+                <version>${project.version}</version>
+            </dependency>
             <dependency>
                 <groupId>org.opencb.opencga</groupId>
                 <artifactId>opencga-storage-core</artifactId>
@@ -931,11 +945,6 @@
                 <artifactId>log4j</artifactId>
                 <version>${log4j.version}</version>
             </dependency>
-            <dependency>
-                <groupId>org.codehaus.jackson</groupId>
-                <artifactId>jackson-mapper-asl</artifactId>
-                <version>${jackson-codehaus.version}</version>
-            </dependency>
             <dependency>
                 <groupId>org.codehaus.jackson</groupId>
                 <artifactId>jackson-core-asl</artifactId>
@@ -964,6 +973,12 @@
                 <artifactId>grep4j</artifactId>
                 <version>${grep4j.version}</version>
             </dependency>
+            <dependency>
+                <groupId>org.projectlombok</groupId>
+                <artifactId>lombok</artifactId>
+                <version>${lombok.version}</version>
+                <scope>provided</scope>
+            </dependency>
             <dependency>
                 <groupId>org.redisson</groupId>
                 <artifactId>redisson</artifactId>
@@ -1052,6 +1067,7 @@
                 <artifactId>kryo</artifactId>
                 <version>${kryo.version}</version>
             </dependency>
+
         </dependencies>
     </dependencyManagement>
 
@@ -1076,6 +1092,11 @@
                     <artifactId>maven-surefire-report-plugin</artifactId>
                     <version>${maven-surefire-plugin.version}</version>
                 </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-war-plugin</artifactId>
+                    <version>${maven-war-plugin.version}</version>
+                </plugin>
             </plugins>
         </pluginManagement>