Merge pull request #2 from ypriverol/master

major changes in psi-tools
HUPO-PSI · Nov 3, 2022 · 05ead03 · 05ead03
2 parents 55560c9 + caf1aad
commit 05ead03
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Showing 38 changed files with 281 additions and 268 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>2.0.13</version>
+        <version>2.0.14-SNAPSHOT</version>
     </parent>
 
     <artifactId>cv-rule-reader</artifactId>
@@ -22,7 +22,7 @@
             <plugin>
                 <groupId>org.jvnet.jaxb2.maven2</groupId>
                 <artifactId>maven-jaxb2-plugin</artifactId>
-                <version>0.7.4</version>
+                <version>0.15.1</version>
                 <configuration>
                     <schemaDirectory>${project.basedir}/src/main/resources/</schemaDirectory>
                     <bindingDirectory>${project.basedir}/src/main/resources/</bindingDirectory>
@@ -47,17 +47,24 @@
         </dependency>
 
         <!-- JAXB related deps -->
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>com.sun.xml.bind</groupId>
             <artifactId>jaxb-impl</artifactId>
         </dependency>
+
         <dependency>
-            <groupId>stax</groupId>
-            <artifactId>stax</artifactId>
+            <groupId>com.sun.xml.bind</groupId>
+            <artifactId>jaxb-core</artifactId>
         </dependency>
+
         <dependency>
-            <groupId>javax.xml.bind</groupId>
-            <artifactId>jaxb-api</artifactId>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-xjc</artifactId>
         </dependency>
 
         <!-- Tests -->

diff --git a/cv-rule-reader/src/test/java/psidev/psi/tools/cvrReader/MockMemoryStreamHandler.java b/cv-rule-reader/src/test/java/psidev/psi/tools/cvrReader/MockMemoryStreamHandler.java
@@ -36,7 +36,7 @@ public class MockMemoryStreamHandler extends URLStreamHandler {
 
     public static final String MEMORY_PROTOCOL = "memory";
 
-    private static Map<String, String> url2content = new HashMap<String, String>();
+    private static Map<String, String> url2content = new HashMap<>();
 
     public static void addContent( URL url, String content ) {
         url2content.put( url.toString(), content );
@@ -64,15 +64,12 @@ public InputStream getInputStream() throws IOException {
      */
     public static void initHandler() {
         try {
-            URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory() {
-
-                public URLStreamHandler createURLStreamHandler( String protocol ) {
-                    if ( "memory".equals( protocol ) ) {
-                        return new MockMemoryStreamHandler();
-                    }
-                    return null;
+            URL.setURLStreamHandlerFactory(protocol -> {
+                if ( "memory".equals( protocol ) ) {
+                    return new MockMemoryStreamHandler();
                 }
-            } );
+                return null;
+            });
         } catch ( Throwable ex ) {
             // we just ignore this exception, because m2 does not fork properly
             // and URL does not like double handler definitions.

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>2.0.13</version>
+        <version>2.0.14-SNAPSHOT</version>
     </parent>
 
     <artifactId>object-rule-reader</artifactId>
@@ -20,9 +20,9 @@
         <plugins>
             <!-- Conversion of XML Schema into Java source code using JAXB-XJC -->
             <plugin>
-                <groupId>com.sun.tools.xjc.maven2</groupId>
-                <artifactId>maven-jaxb-plugin</artifactId>
-                <version>1.0</version>
+                <groupId>org.jvnet.jaxb2.maven2</groupId>
+                <artifactId>maven-jaxb2-plugin</artifactId>
+                <version>0.15.1</version>
                 <configuration>
                     <generatePackage>psidev.psi.tools.objectRuleReader.mapping.jaxb</generatePackage>
                     <includeSchemas>
@@ -50,17 +50,24 @@
         </dependency>
 
         <!-- JAXB related deps -->
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>com.sun.xml.bind</groupId>
             <artifactId>jaxb-impl</artifactId>
         </dependency>
+
         <dependency>
-            <groupId>stax</groupId>
-            <artifactId>stax</artifactId>
+            <groupId>com.sun.xml.bind</groupId>
+            <artifactId>jaxb-core</artifactId>
         </dependency>
+
         <dependency>
-            <groupId>javax.xml.bind</groupId>
-            <artifactId>jaxb-api</artifactId>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-xjc</artifactId>
         </dependency>
 
         <!-- Tests -->

diff --git a/object-rule-reader/src/main/java/psidev/psi/tools/objectRuleReader/ObjectRuleReader.java b/object-rule-reader/src/main/java/psidev/psi/tools/objectRuleReader/ObjectRuleReader.java
@@ -129,9 +129,7 @@ public ObjectRuleList read( String s ) throws ObjectRuleReaderException {
     public ObjectRuleList read( File file ) throws ObjectRuleReaderException {
         try {
             return unmarshall( file );
-        } catch ( JAXBException e ) {
-            throw new ObjectRuleReaderException( e );
-        } catch ( FileNotFoundException e ) {
+        } catch (JAXBException | FileNotFoundException e ) {
             throw new ObjectRuleReaderException( e );
         }
     }
@@ -147,9 +145,7 @@ public ObjectRuleList read( InputStream is ) throws ObjectRuleReaderException {
     public ObjectRuleList read( URL url ) throws ObjectRuleReaderException {
         try {
             return unmarshall( url );
-        } catch ( JAXBException e ) {
-            throw new ObjectRuleReaderException( e );
-        } catch ( FileNotFoundException e ) {
+        } catch (JAXBException | FileNotFoundException e ) {
             throw new ObjectRuleReaderException( e );
         }
     }

diff --git a/...-rule-reader/src/test/java/psidev/psi/tools/objectRuleReader/MockMemoryStreamHandler.java b/...-rule-reader/src/test/java/psidev/psi/tools/objectRuleReader/MockMemoryStreamHandler.java
@@ -36,7 +36,7 @@ public class MockMemoryStreamHandler extends URLStreamHandler {
 
     public static final String MEMORY_PROTOCOL = "memory";
 
-    private static Map<String, String> url2content = new HashMap<String, String>();
+    private static Map<String, String> url2content = new HashMap<>();
 
     public static void addContent( URL url, String content ) {
         url2content.put( url.toString(), content );
@@ -64,15 +64,12 @@ public InputStream getInputStream() throws IOException {
      */
     public static void initHandler() {
         try {
-            URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory() {
-
-                public URLStreamHandler createURLStreamHandler( String protocol ) {
-                    if ( "memory".equals( protocol ) ) {
-                        return new MockMemoryStreamHandler();
-                    }
-                    return null;
+            URL.setURLStreamHandlerFactory(protocol -> {
+                if ( "memory".equals( protocol ) ) {
+                    return new MockMemoryStreamHandler();
                 }
-            } );
+                return null;
+            });
         } catch ( Throwable ex ) {
             // we just ignore this exception, because m2 does not fork properly
             // and URL does not like double handler definitions.

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>2.0.13</version>
+        <version>2.0.14-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontology-config-reader</artifactId>
@@ -20,9 +20,9 @@
         <plugins>
             <!-- Conversion of XML Schema into Java source code using JAXB-XJC -->
             <plugin>
-                <groupId>com.sun.tools.xjc.maven2</groupId>
-                <artifactId>maven-jaxb-plugin</artifactId>
-                <version>1.0</version>
+                <groupId>org.jvnet.jaxb2.maven2</groupId>
+                <artifactId>maven-jaxb2-plugin</artifactId>
+                <version>0.15.1</version>
                 <configuration>
                     <generatePackage>psidev.psi.tools.ontologyCfgReader.mapping.jaxb</generatePackage>
                     <includeSchemas>
@@ -50,17 +50,24 @@
         </dependency>
 
         <!-- JAXB related deps -->
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>com.sun.xml.bind</groupId>
             <artifactId>jaxb-impl</artifactId>
         </dependency>
+
         <dependency>
-            <groupId>stax</groupId>
-            <artifactId>stax</artifactId>
+            <groupId>com.sun.xml.bind</groupId>
+            <artifactId>jaxb-core</artifactId>
         </dependency>
+
         <dependency>
-            <groupId>javax.xml.bind</groupId>
-            <artifactId>jaxb-api</artifactId>
+            <groupId>org.glassfish.jaxb</groupId>
+            <artifactId>jaxb-xjc</artifactId>
         </dependency>
 
         <!-- Tests -->

diff --git a/...nfig-reader/src/main/java/psidev/psi/tools/ontologyConfigReader/OntologyConfigReader.java b/...nfig-reader/src/main/java/psidev/psi/tools/ontologyConfigReader/OntologyConfigReader.java
@@ -129,9 +129,7 @@ public CvSourceList read( String s ) throws OntologyConfigReaderException {
     public CvSourceList read( File file ) throws OntologyConfigReaderException {
         try {
             return unmarshall( file );
-        } catch ( JAXBException e ) {
-            throw new OntologyConfigReaderException( e );
-        } catch ( FileNotFoundException e ) {
+        } catch (JAXBException | FileNotFoundException e ) {
             throw new OntologyConfigReaderException( e );
         }
     }
@@ -147,9 +145,7 @@ public CvSourceList read( InputStream is ) throws OntologyConfigReaderException
     public CvSourceList read( URL url ) throws OntologyConfigReaderException {
         try {
             return unmarshall( url );
-        } catch ( JAXBException e ) {
-            throw new OntologyConfigReaderException( e );
-        } catch ( FileNotFoundException e ) {
+        } catch (JAXBException | FileNotFoundException e ) {
             throw new OntologyConfigReaderException( e );
         }
     }

diff --git a/...g-reader/src/test/java/psidev/psi/tools/ontologyConfigReader/MockMemoryStreamHandler.java b/...g-reader/src/test/java/psidev/psi/tools/ontologyConfigReader/MockMemoryStreamHandler.java
@@ -36,7 +36,7 @@ public class MockMemoryStreamHandler extends URLStreamHandler {
 
     public static final String MEMORY_PROTOCOL = "memory";
 
-    private static Map<String, String> url2content = new HashMap<String, String>();
+    private static Map<String, String> url2content = new HashMap<>();
 
     public static void addContent( URL url, String content ) {
         url2content.put( url.toString(), content );
@@ -64,15 +64,12 @@ public InputStream getInputStream() throws IOException {
      */
     public static void initHandler() {
         try {
-            URL.setURLStreamHandlerFactory( new URLStreamHandlerFactory() {
-
-                public URLStreamHandler createURLStreamHandler( String protocol ) {
-                    if ( "memory".equals( protocol ) ) {
-                        return new MockMemoryStreamHandler();
-                    }
-                    return null;
+            URL.setURLStreamHandlerFactory(protocol -> {
+                if ( "memory".equals( protocol ) ) {
+                    return new MockMemoryStreamHandler();
                 }
-            } );
+                return null;
+            });
         } catch ( Throwable ex ) {
             // we just ignore this exception, because m2 does not fork properly
             // and URL does not like double handler definitions.