Merge branch 'develop' into TASK-1294

opencb · Jan 23, 2024 · 7db00c0 · 7db00c0
2 parents f77353b + cbf92a9
commit 7db00c0
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Showing 6 changed files with 27 additions and 20 deletions.
diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml
@@ -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-server/pom.xml b/opencga-server/pom.xml
@@ -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>

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/pom.xml b/pom.xml
@@ -52,13 +52,13 @@
 
         <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>
@@ -146,6 +146,13 @@
         <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>
 
         <!--TO REMOVE:
@@ -256,6 +263,11 @@
                 <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>
@@ -938,11 +950,6 @@
                 <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>