Merge pull request #5 from HUPO-PSI/develop

Develop > Master
HUPO-PSI · Oct 10, 2023 · fd155f8 · fd155f8
2 parents 05ead03 + e66860c
commit fd155f8
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Showing 8 changed files with 56 additions and 34 deletions.
diff --git a/cv-rule-reader/pom.xml b/cv-rule-reader/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.tools</groupId>
         <artifactId>master-pom</artifactId>
-        <version>2.0.14-SNAPSHOT</version>
+        <version>2.1.0</version>
     </parent>
 
     <artifactId>cv-rule-reader</artifactId>

diff --git a/object-rule-reader/pom.xml b/object-rule-reader/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.tools</groupId>
         <artifactId>master-pom</artifactId>
-        <version>2.0.14-SNAPSHOT</version>
+        <version>2.1.0</version>
     </parent>
 
     <artifactId>object-rule-reader</artifactId>

diff --git a/ontology-config-reader/pom.xml b/ontology-config-reader/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.tools</groupId>
         <artifactId>master-pom</artifactId>
-        <version>2.0.14-SNAPSHOT</version>
+        <version>2.1.0</version>
     </parent>
 
     <artifactId>ontology-config-reader</artifactId>

diff --git a/ontology-manager/pom.xml b/ontology-manager/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.tools</groupId>
         <artifactId>master-pom</artifactId>
-        <version>2.0.14-SNAPSHOT</version>
+        <version>2.1.0</version>
     </parent>
 
     <artifactId>ontology-manager</artifactId>
@@ -51,6 +51,18 @@
             <version>${project.version}</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-web</artifactId>
+            <version>${spring.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+            <version>2.13.3</version>
+        </dependency>
+
         <!-- OBO parser -->
         <dependency>
             <groupId>uk.ac.ebi.ols</groupId>
@@ -151,6 +163,25 @@
             <version>2.3</version>
         </dependency>
 
+        <!-- Logging -->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>${org.slf4j-version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>jcl-over-slf4j</artifactId>
+            <version>${org.slf4j-version}</version>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-log4j12</artifactId>
+            <version>${org.slf4j-version}</version>
+            <scope>runtime</scope>
+        </dependency>
+
         <!-- Tests -->
         <dependency>
             <groupId>junit</groupId>

diff --git a/pom.xml b/pom.xml
@@ -1,10 +1,11 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>psidev.psi.tools</groupId>
     <artifactId>master-pom</artifactId>
     <packaging>pom</packaging>
-    <version>2.0.14-SNAPSHOT</version>
+    <version>2.1.0</version>
 
     <name>PSI :: Tools :: Master pom</name>
 
@@ -52,6 +53,8 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <spring.version>4.3.30.RELEASE</spring.version>
+        <org.slf4j-version>1.6.6</org.slf4j-version>
     </properties>
 
     <modules>
@@ -76,18 +79,6 @@
         <url>http://www.ebi.ac.uk/</url>
     </organization>
 
-    <profiles>
-        <profile>
-            <id>disable-java8-doclint</id>
-            <activation>
-                <jdk>[1.8,)</jdk>
-            </activation>
-            <properties>
-                <additionalparam>-Xdoclint:none</additionalparam>
-            </properties>
-        </profile>
-    </profiles>
-
     <build>
         <defaultGoal>clean install</defaultGoal>
         <plugins>
@@ -96,14 +87,14 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.10.1</version>
                 <configuration>
-                    <source>1.8</source>
-                    <target>1.8</target>
+                    <source>11</source>
+                    <target>11</target>
                 </configuration>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-source-plugin</artifactId>
-                <version>3.0.1</version>
+                <version>3.2.1</version>
                 <executions>
                     <execution>
                         <id>attach-source</id>
@@ -146,9 +137,9 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-javadoc-plugin</artifactId>
-                    <version>2.10.3</version>
+                    <version>3.2.0</version>
                     <configuration>
-                        <source>1.8</source>
+                        <source>11</source>
                         <aggregate>true</aggregate>
                     </configuration>
                 </plugin>
@@ -177,7 +168,7 @@
                 <artifactId>maven-pmd-plugin</artifactId>
                 <version>3.19.0</version>
                 <configuration>
-                    <targetJdk>1.8</targetJdk>
+                    <targetJdk>11</targetJdk>
                     <sourceEncoding>utf-8</sourceEncoding>
                     <linkXref>true</linkXref>
                     <rulesets>
@@ -251,7 +242,7 @@
             <dependency>
                 <groupId>junit</groupId>
                 <artifactId>junit</artifactId>
-                <version>4.3.1</version>
+                <version>4.13.2</version>
                 <scope>test</scope>
             </dependency>
         </dependencies>
@@ -273,14 +264,14 @@
         <repository>
             <id>pst-release</id>
             <name>EBI Nexus Repository</name>
-            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
+            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release/</url>
         </repository>
         <!-- EBI SNAPSHOT repo -->
         <snapshotRepository>
             <uniqueVersion>false</uniqueVersion>
             <id>pst-snapshots</id>
             <name>EBI Nexus Snapshots Repository</name>
-            <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots</url>
+            <url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-snapshots/</url>
         </snapshotRepository>
     </distributionManagement>
 

diff --git a/validator-tutorial/spe-model/pom.xml b/validator-tutorial/spe-model/pom.xml
@@ -15,7 +15,7 @@
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.3.1</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -41,8 +41,8 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <source>1.5</source>
-                    <target>1.5</target>
+                    <source>11</source>
+                    <target>11</target>
                 </configuration>
             </plugin>
         </plugins>

diff --git a/validator-tutorial/spe-validator/pom.xml b/validator-tutorial/spe-validator/pom.xml
@@ -15,7 +15,7 @@
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.3.1</version>
+            <version>4.13.2</version>
             <scope>test</scope>
         </dependency>
 
@@ -42,8 +42,8 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <source>1.5</source>
-                    <target>1.5</target>
+                    <source>11</source>
+                    <target>11</target>
                 </configuration>
             </plugin>
         </plugins>

diff --git a/validator/pom.xml b/validator/pom.xml
@@ -4,7 +4,7 @@
     <parent>
         <groupId>psidev.psi.tools</groupId>
         <artifactId>master-pom</artifactId>
-        <version>2.0.14-SNAPSHOT</version>
+        <version>2.1.0</version>
     </parent>
 
     <artifactId>validator</artifactId>