From c1b5f4976d7697b9a0ff6d349fe7a80611f25ba5 Mon Sep 17 00:00:00 2001
From: EliotRagueneau <eragueneau@ebi.ac.uk>
Date: Tue, 16 Aug 2022 12:31:35 +0100
Subject: [PATCH] :arrow_up: Java 11 update

---
 feature-shortlabel-generator/pom.xml          |  4 +--
 pom.xml                                       | 32 +++++++------------
 protein-mapping/pom.xml                       | 12 +++----
 .../SwissprotRemappingProcessTest.java        |  2 +-
 4 files changed, 20 insertions(+), 30 deletions(-)

diff --git a/feature-shortlabel-generator/pom.xml b/feature-shortlabel-generator/pom.xml
index 93a917a..1977b21 100644
--- a/feature-shortlabel-generator/pom.xml
+++ b/feature-shortlabel-generator/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>uk.ac.ebi.intact.tools</groupId>
         <artifactId>tools-master</artifactId>
-        <version>1.0.26-SNAPSHOT</version>
+        <version>1.1.0-SNAPSHOT</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
@@ -64,7 +64,7 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.0</version>
+            <version>3.12.0</version>
         </dependency>
 
         <dependency>
diff --git a/pom.xml b/pom.xml
index 283ec0f..a3cde50 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <groupId>uk.ac.ebi.intact.maven</groupId>
         <artifactId>intact-hibernate-master</artifactId>
-        <version>44</version>
+        <version>45-SNAPSHOT</version>
     </parent>
 
     <modelVersion>4.0.0</modelVersion>
@@ -11,18 +11,18 @@
     <groupId>uk.ac.ebi.intact.tools</groupId>
     <artifactId>tools-master</artifactId>
     <packaging>pom</packaging>
-    <version>1.0.26-SNAPSHOT</version>
+    <version>1.1.0-SNAPSHOT</version>
 
     <name>IntAct Tools</name>
     <description>Tools Master POM</description>
 
     <properties>
-        <currentVersion>${version}</currentVersion>
-        <spring.version>3.2.9.RELEASE</spring.version>
-        <psi.jami.version>3.2.12</psi.jami.version>
-        <intact.jami.version>1.3.14</intact.jami.version>
-        <intact.bridges.version>2.1.37</intact.bridges.version>
-        <intact.core.version>2.6.12</intact.core.version>
+        <currentVersion>${project.version}</currentVersion>
+        <spring.version>4.3.30.RELEASE</spring.version>
+        <psi.jami.version>3.3.0-SNAPSHOT</psi.jami.version>
+        <intact.jami.version>1.4.0-SNAPSHOT</intact.jami.version>
+        <intact.bridges.version>2.2.0-SNAPSHOT</intact.bridges.version>
+        <intact.core.version>2.7.0-SNAPSHOT</intact.core.version>
         <maven.pmd.skip>true</maven.pmd.skip>
     </properties>
 
@@ -67,7 +67,7 @@
             </plugin>
             <plugin>
                 <artifactId>maven-source-plugin</artifactId>
-                <version>2.1.2</version>
+                <version>3.2.1</version>
                 <executions>
                     <execution>
                         <id>attach-source</id>
@@ -77,19 +77,9 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.0</version>
-                <configuration>
-                    <target>1.8</target>
-                    <source>1.8</source>
-                    <encoding>UTF-8</encoding>
-                </configuration>
-            </plugin>
             <plugin>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.12.4</version>
+                <version>2.22.2</version>
                 <configuration>
                     <includes>
                         <include>**/*Test.java</include>
@@ -104,7 +94,7 @@
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.12</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
     </dependencies>
diff --git a/protein-mapping/pom.xml b/protein-mapping/pom.xml
index eb51ef4..d87d606 100644
--- a/protein-mapping/pom.xml
+++ b/protein-mapping/pom.xml
@@ -3,7 +3,7 @@
     <parent>
         <groupId>uk.ac.ebi.intact.tools</groupId>
         <artifactId>tools-master</artifactId>
-        <version>1.0.26-SNAPSHOT</version>
+        <version>1.1.0-SNAPSHOT</version>
     </parent>
 
 
@@ -15,7 +15,7 @@
     <url>http://www.ebi.ac.uk/~intact/devsite/tools/protein-mapping</url>
 
     <properties>
-        <spring.version>4.3.12.RELEASE</spring.version>
+        <spring.version>4.3.30.RELEASE</spring.version>
     </properties>
 
     <build>
@@ -138,12 +138,12 @@
         <dependency>
             <groupId>commons-logging</groupId>
             <artifactId>commons-logging</artifactId>
-            <version>1.1.1</version>
+            <version>1.2</version>
         </dependency>
         <dependency>
             <groupId>commons-collections</groupId>
             <artifactId>commons-collections</artifactId>
-            <version>3.2.1</version>
+            <version>3.2.2</version>
         </dependency>
         <dependency>
             <groupId>commons-lang</groupId>
@@ -174,7 +174,7 @@
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
-            <version>1.3.168</version>
+            <version>1.4.200</version>
         </dependency>
 
         <dependency>
@@ -187,7 +187,7 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>19.0</version>
+            <version>31.1-jre</version>
         </dependency>
     </dependencies>
 
diff --git a/protein-mapping/src/test/java/uk/ac/ebi/intact/protein/mapping/actions/SwissprotRemappingProcessTest.java b/protein-mapping/src/test/java/uk/ac/ebi/intact/protein/mapping/actions/SwissprotRemappingProcessTest.java
index fe403d5..f513304 100644
--- a/protein-mapping/src/test/java/uk/ac/ebi/intact/protein/mapping/actions/SwissprotRemappingProcessTest.java
+++ b/protein-mapping/src/test/java/uk/ac/ebi/intact/protein/mapping/actions/SwissprotRemappingProcessTest.java
@@ -178,7 +178,7 @@ public void test_SwissprotRemapping_failed_WithEnsemblGeneAndOrganism_LowIdentit
             Assert.assertEquals(true, reports.get(2) instanceof DefaultBlastReport);
             Assert.assertEquals(false, ((DefaultBlastReport) reports.get(2)).getBlastMatchingProteins().size() > 0);
             Assert.assertEquals(StatusLabel.FAILED, reports.get(1).getStatus().getLabel());
-            Assert.assertEquals(StatusLabel.FAILED, reports.get(2).getStatus().getLabel());
+            Assert.assertEquals(StatusLabel.TO_BE_REVIEWED, reports.get(2).getStatus().getLabel());
 
         } catch (ActionProcessingException e) {
             e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.