Merge branch 'develop' into 'master'

Develop

See merge request !2

nb-configuration.xml

@@ -18,6 +18,5 @@ Any value defined here will override the pom.xml file value but is only applicab
         <netbeans.hint.license>nibio_open_source_license.ftl</netbeans.hint.license>
         <org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_deploy_2e_server>WildFly</org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_deploy_2e_server>
         <org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_j2eeVersion>1.7-web</org-netbeans-modules-maven-j2ee.netbeans_2e_hint_2e_j2eeVersion>
-        <netbeans.hint.jdkPlatform>JDK_1.8_SUN</netbeans.hint.jdkPlatform>
     </properties>
 </project-shared-configuration>

pom.xml

@@ -9,7 +9,17 @@
 
   <name>VIPSCore</name>
   <url>http://maven.apache.org</url>
-
+<repositories>
+  <repository>
+    <id>bedatadriven</id>
+    <name>bedatadriven public repo</name>
+    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
+  </repository>
+    <repository>
+        <id>jitpack.io</id>
+        <url>https://jitpack.io</url>
+    </repository>
+</repositories>
   <dependencies>
     <dependency>
     <groupId>org.reflections</groupId>
@@ -21,18 +31,129 @@
       <artifactId>cors-filter</artifactId>
       <version>1.7.1</version>
     </dependency>
+   
+    <dependency>
+        <groupId>org.graalvm</groupId>
+        <artifactId>graal-sdk</artifactId>
+        <version>1.0.0-rc7</version>
+    </dependency>
     <dependency>
-      <groupId>no.bioforsk.vips.common</groupId>
+      <groupId>com.bedatadriven</groupId>
+      <artifactId>jackson-datatype-jts</artifactId>
+      <version>2.4</version>
+      <type>jar</type>
+    </dependency>
+    <dependency>
+      <groupId>no.nibio.vips.common</groupId>
       <artifactId>VIPSCommon</artifactId>
       <version>1.0-SNAPSHOT</version>
+    </dependency>
+    <dependency>
+      <groupId>javax</groupId>
+      <artifactId>javaee-web-api</artifactId>
+      <version>7.0</version>
       <type>jar</type>
+    </dependency>
+     <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>com.bedatadriven</groupId>
-      <artifactId>jackson-datatype-jts</artifactId>
-      <version>2.2</version>
+      <groupId>axis</groupId>
+      <artifactId>axis</artifactId>
+      <version>1.4</version>
+    </dependency>
+    <dependency>
+       <groupId>external.lib</groupId>
+       <artifactId>dnmi-ws</artifactId>
+       <version>1.0</version>
+      <scope>provided</scope>
+    </dependency>
+     <dependency>
+       <groupId>commons-logging</groupId>
+       <artifactId>commons-logging</artifactId>
+       <version>1.0.4</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+       <groupId>external.lib</groupId>
+       <artifactId>xerces</artifactId>
+       <version>1.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+       <groupId>external.lib</groupId>
+       <artifactId>xalan</artifactId>
+       <version>1.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>javax.servlet</groupId>
+      <artifactId>servlet-api</artifactId>
+      <version>2.5</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>javax.servlet.jsp</groupId>
+      <artifactId>jsp-api</artifactId>
+      <version>2.1</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+       <groupId>external.lib</groupId>
+       <artifactId>tidy</artifactId>
+       <version>1.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+       <groupId>external.lib</groupId>
+       <artifactId>relayclient</artifactId>
+       <version>1.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+       <groupId>external.lib</groupId>
+       <artifactId>UserAgentUtils</artifactId>
+       <version>1.6</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>commons-validator</groupId>
+      <artifactId>commons-validator</artifactId>
+      <version>1.2.0</version>
       <type>jar</type>
     </dependency>
+    <dependency>
+            <groupId>javax</groupId>
+            <artifactId>javaee-api</artifactId>
+            <version>6.0</version>
+            <scope>provided</scope>
+        </dependency>
+    <dependency>
+       <groupId>commons-math</groupId>
+       <artifactId>commons-math</artifactId>
+       <version>1.2</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+       <groupId>commons-net</groupId>
+       <artifactId>commons-net</artifactId>
+       <version>1.4.1</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+	<groupId>external.lib</groupId>
+	<artifactId>commons-codec</artifactId>
+	<version>1.6</version>
+        <scope>provided</scope>
+    </dependency>
+    <dependency>
+                <groupId>external.lib</groupId>
+                <artifactId>json-simple</artifactId>
+                <version>1.1</version>
+    </dependency>
   </dependencies>
 
   <build>
@@ -42,8 +163,8 @@
         <artifactId>maven-compiler-plugin</artifactId>
         <version>2.0.2</version>
         <configuration>
-          <source>1.8</source>
-          <target>1.8</target>
+          <source>10</source>
+          <target>10</target>
         </configuration>
       </plugin>
       <plugin>

src/main/java/no/nibio/vips/core/VIPSCoreApplication.java

@@ -56,6 +56,5 @@ public class VIPSCoreApplication extends Application
      */
     private void addRestResourceClasses(Set<Class<?>> resources) {
         resources.add(no.nibio.vips.core.config.JacksonConfig.class);
-        resources.add(no.nibio.vips.core.service.ModelResourceImpl.class);
     }
 }
\ No newline at end of file

src/main/java/no/nibio/vips/core/config/JacksonConfig.java

@@ -20,6 +20,7 @@
 package no.nibio.vips.core.config;
 
 import com.bedatadriven.jackson.datatype.jts.JtsModule;
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import javax.ws.rs.Produces;
 import javax.ws.rs.core.MediaType;
 import javax.ws.rs.ext.ContextResolver;
@@ -43,6 +44,8 @@ public class JacksonConfig  implements ContextResolver<ObjectMapper>{
         objectMapper = new ObjectMapper();
         objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
         objectMapper.registerModule(new JtsModule());
+        objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+        objectMapper.registerModule(new JtsModule());
     }
 
     @Override

src/main/java/no/nibio/vips/core/service/ModelResourceImpl.java

@@ -24,6 +24,7 @@ import java.net.URLClassLoader;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.servlet.http.HttpServletRequest;
@@ -252,6 +253,7 @@ public class ModelResourceImpl implements ModelResource{
     @Override
     public Response runModel(ModelConfiguration config)
     {
+        System.out.println("runModel 1");
         try
         {
             Model calledModel = ModelFactory.getInstance().getModelInstance(config.getModelId());

src/main/webapp/WEB-INF/jboss-deployment-structure.xml

@@ -21,9 +21,13 @@ along with VIPSCore.  If not, see <http://www.nibio.no/licenses/>.
   <deployment>  
     <dependencies>  
       <module name="no.nibio.vips.modelcontainer"/>  
+      <module name="org.graalvm"/>
       <module name="no.nibio.vips.VIPSCommon" export="true"/>  
       <module name="com.fasterxml.jackson.core.jackson-core" />
       <module name="com.fasterxml.jackson.core.jackson-databind" />
     </dependencies>  
+    <exclusions>
+          <module name="org.jboss.resteasy.resteasy-json-binding-provider"/>
+     </exclusions>
   </deployment>  
 </jboss-deployment-structure>