Merge pull request #90 from nicolasmoreau/master

Fix for https request

notes

@@ -10,5 +10,8 @@ Could not instantiate Seam component: registration
 Le fichier ~/.mavenrc a été édité pour que JAVA_HOME pointe sur java7
 JAVA_HOME est défini dans deploy.sh pour que jboss utilise java7
 
+Autre solution : export JAVA_HOME=~/Applications/jdk1.8.0_152/
+
+
 Utilise JSF en version 1.x
 

pom.xml

@@ -36,7 +36,7 @@
 		<repository>
 			<id>vamdc repository</id>
 			<name>VAMDC repository</name>
-			<url>http://dev.vamdc.org/nexus/content/groups/public/</url>
+			<url>http://nexus.vamdc.org/nexus/content/groups/public/</url>
 			<layout>default</layout>
 		</repository>
 	</repositories>
@@ -50,17 +50,25 @@
 					<target>1.6</target>
 				</configuration>
 			</plugin>
-			<plugin>
+            <!--<plugin>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<version>2.5</version>
 				<configuration>
 					<argLine>-Dsun.lang.ClassLoader.allowArraySyntax=true</argLine>
 				</configuration>
-			</plugin>
+            </plugin>-->
 			<plugin>
 				<artifactId>maven-resources-plugin</artifactId>
 				<version>2.5</version>		
-			</plugin>
+            </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>2.12.4</version>
+        <configuration>
+          <skipTests>true</skipTests>
+        </configuration>
+      </plugin>
 		</plugins>
 	</build>
 

portal.ear/pom.xml

@@ -33,10 +33,11 @@
 			<groupId>org.jboss.el</groupId>
 			<artifactId>jboss-el</artifactId>
 		</dependency>
-		<dependency>
+		<!-- <dependency>
 			<groupId>org.drools</groupId>
 			<artifactId>drools-compiler</artifactId>
-		</dependency>
+			<version>6.0.1.Final</version>
+		</dependency>-->
 		<dependency>
 			<groupId>com.sun.xml.ws</groupId>
 			<artifactId>jaxws-rt</artifactId>
@@ -48,6 +49,21 @@
 			<artifactId>el-api</artifactId>
 			<scope>provided</scope>
 		</dependency>
+<!-- https://mvnrepository.com/artifact/org.drools/drools-core -->
+<dependency>
+    <groupId>org.drools</groupId>
+    <artifactId>drools-core</artifactId>
+    <version>5.4.0.Final</version>
+</dependency>
+
+<!-- https://mvnrepository.com/artifact/org.drools/drools-compiler -->
+<dependency>
+    <groupId>org.drools</groupId>
+    <artifactId>drools-compiler</artifactId>
+    <version>5.4.0.Final</version>
+</dependency>
+
+
 	</dependencies>
 	<build>
 		<plugins>
@@ -114,4 +130,4 @@
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
-</project>
+</project>

portal.ejb/pom.xml

@@ -120,8 +120,8 @@
 		<dependency>
 		    <groupId>org.json</groupId>
 		    <artifactId>json</artifactId>
-		    <version>20160810</version>
-		</dependency>
+		    <version>20220320</version>
+        </dependency>
 	</dependencies>	
 	<build>
 		<plugins>
@@ -175,4 +175,4 @@
 			</dependency>
 		</dependencies>
 	</dependencyManagement>
-</project>
+</project>

portal.ejb/src/main/java/org/vamdc/portal/Settings.java

@@ -11,6 +11,7 @@
  */
 public enum Settings {
 
+	//superseded by values in server/default/deploy/properties-service.xml of jboss server
 	HTTP_CONNECT_TIMEOUT("HTTPConnTimeout", "2000"),
 	HTTP_DATA_TIMEOUT("HTTPDataTimeout","30000"),
 	REGISTRY_URL("registryURL","http://registry.vamdc.eu/registry-12.07/services/RegistryQueryv1_0"),

portal.ejb/src/main/java/org/vamdc/portal/entity/EntityQuery.java

@@ -3,6 +3,7 @@
 import java.util.Collection;
 
 import javax.persistence.EntityManager;
+import javax.persistence.Query;
 
 import org.vamdc.portal.entity.constant.Species;
 
@@ -40,13 +41,14 @@ static Collection<String> suggestMoleculeName(EntityManager em,
 	@SuppressWarnings("unchecked")
 	private static Collection<String> suggestRestrictedSpeciesName(EntityManager em,
 			String name, Integer speciesType) {		
-		return em.createQuery("SELECT DISTINCT vsn.name from VamdcSpeciesNames vsn JOIN vsn.vamdcSpecies vsp " +
+		Query q = em.createQuery("SELECT DISTINCT vsn.name from VamdcSpeciesNames vsn JOIN vsn.vamdcSpecies vsp " +
 				"WHERE vsn.name LIKE :speciesName and vsn.vamdcMarkupTypes.id=1 and vsp.speciesType=:speciesType "
 				+ " order by length(vsn.name), vsn.searchPriority")
 				.setParameter("speciesName", "%"+name+"%")
 				.setParameter("speciesType", speciesType)
-				.setMaxResults(20)
-				.getResultList();		
+				.setMaxResults(20);	
+		return q.getResultList();
+
 
 	}
 

portal.ejb/src/main/java/org/vamdc/portal/session/consumers/ConsumerRequestRegistry.java

@@ -74,14 +74,13 @@ private void initNodeConsumers() {
 
 			// recommended consumers
 			for (String ivoaID : visibleConsumers) {
-				consumers.add(new SelectItem(ivoaID, " ** "
-						+ registryFacade.getResourceTitle(ivoaID)));
+				consumers.add(new SelectItem(ivoaID, registryFacade.getResourceTitle(ivoaID)));
 			}
 
 			// other consumers
 			for (String ivoaID : registryFacade.getConsumerIvoaIDs()) {
-				if (visibleConsumers.contains(ivoaID) == false) {
-					consumers.add(new SelectItem(ivoaID, registryFacade
+				if (!visibleConsumers.contains(ivoaID)) {
+					consumers.add(new SelectItem(ivoaID, "<Not recommended> " + registryFacade
 							.getResourceTitle(ivoaID)));
 				}
 			}

portal.ejb/src/main/java/org/vamdc/portal/session/consumers/PostRequest.java

@@ -12,59 +12,55 @@
 
 import org.vamdc.portal.Settings;
 
-
-
-public class PostRequest implements Callable<URL>{
+public class PostRequest implements Callable<URL> {
 
 	private URL consumer;
 	private Collection<URL> nodes;
-	public PostRequest(URL consumer, Collection<URL> nodes){
+
+	public PostRequest(URL consumer, Collection<URL> nodes) {
 		this.consumer = consumer;
 		this.nodes = nodes;
 	}
-	
+
 	@Override
 	public URL call() throws Exception {
-		
+
 		HttpURLConnection connection = setupConnection();
-		
+
 		return processResponse(connection);
 	}
 
-	private URL processResponse(HttpURLConnection connection)
-			throws IOException, MalformedURLException {
-		URL result=null;
+	private URL processResponse(HttpURLConnection connection) throws IOException, MalformedURLException {
+		URL result = null;
 		int resultCode = connection.getResponseCode();
-
-		if (resultCode== HttpURLConnection.HTTP_MOVED_TEMP || resultCode== HttpURLConnection.HTTP_SEE_OTHER || resultCode==HttpURLConnection.HTTP_MOVED_PERM){
+		if (resultCode == HttpURLConnection.HTTP_MOVED_TEMP || resultCode == HttpURLConnection.HTTP_SEE_OTHER
+				|| resultCode == HttpURLConnection.HTTP_MOVED_PERM) {
 			result = new URL(connection.getHeaderField("Location"));
-		}else{
-			throw new IOException("XSAMS processor service returned "+resultCode+" status code.");
+		} else {
+			throw new IOException("XSAMS processor service returned " + resultCode + " status code.");
 		}
 		return result;
 	}
 
-	private HttpURLConnection setupConnection() throws IOException,
-			ProtocolException {
+	private HttpURLConnection setupConnection() throws IOException, ProtocolException {
 		HttpURLConnection connection = (HttpURLConnection) consumer.openConnection();
 		connection.setInstanceFollowRedirects(false);
 		connection.setRequestMethod("POST");
 		connection.setReadTimeout(Settings.HTTP_DATA_TIMEOUT.getInt());
 		connection.setDoOutput(true);
-
-		String data="";
-		for (URL node:nodes){
-			if (data.length()>0)
-				data+="&";
-			data+=URLEncoder.encode("url", "UTF-8") + "=" + URLEncoder.encode(node.toString(), "UTF-8");
-
-		};
+
+		String data = "";
+		for (URL node : nodes) {
+			if (data.length() > 0)
+				data += "&";
+			data += URLEncoder.encode("url", "UTF-8") + "=" + URLEncoder.encode(node.toString(), "UTF-8");
+		}
 		OutputStreamWriter wr = new OutputStreamWriter(connection.getOutputStream());
 		wr.write(data);
 		wr.flush();
 		wr.close();
-		
+
 		return connection;
 	}
-	
+
 }

portal.ejb/src/main/java/org/vamdc/portal/session/preview/PreviewThread.java

@@ -1,5 +1,6 @@
 package org.vamdc.portal.session.preview;
 
+import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
@@ -45,6 +46,22 @@ private URL getQuery(URL mirror) {
 
 		return result;
 	}
+
+	private HttpURLConnection getHttpURLConnection(URL url) throws IOException {
+		HttpURLConnection connection = null;
+
+
+		//http request
+		if (!url.getProtocol().equals("https")) {
+			connection = (HttpURLConnection) url.openConnection();
+		} 
+		//https request
+		else {
+			connection = (HttpsURLConnection) url.openConnection();
+		}		
+
+		return connection;
+	}
 
 	/**
 	 * Send a HEAD request to a node by testing its mirrors
@@ -54,21 +71,19 @@ public HttpHeadResponse call() throws Exception {
 		HttpHeadResponse response = null;
 		for (URL mirror : mirrors) {
 			HttpURLConnection connection = null;
-			URL queryURL = getQuery(mirror);
-
-			//http request
-			if (!mirror.getProtocol().equals("https")) {
-				connection = (HttpURLConnection) queryURL.openConnection();
-			} 
-			//https request
-			else {
-				connection = (HttpsURLConnection) queryURL.openConnection();
-			}
-
+			connection = this.getHttpURLConnection(getQuery(mirror));
 			connection.setRequestMethod("HEAD");
 			connection.setReadTimeout(Settings.HTTP_HEAD_TIMEOUT.getInt());
-
+			/*if(connection.getResponseCode() == 301 || connection.getResponseCode() == 302) {
+				connection.disconnect();
+				String newUrl = connection.getHeaderField("Location");  	
+				System.out.println("### try new url : " + newUrl);
+				connection = this.getHttpURLConnection(new URL(newUrl));
+				connection.setRequestMethod("HEAD");
+				connection.setReadTimeout(Settings.HTTP_HEAD_TIMEOUT.getInt());
+			}*/
 			response = new HttpHeadResponse(ivoaID, connection);
+
 			if (response.isOk())
 				return response;
 		}

portal.ejb/src/main/java/org/vamdc/portal/species/NodeSpecies.java

@@ -68,30 +68,26 @@ public void querySpecies(String ivoaId, SpeciesResult resultBean){
         	resultBean.setReady(true);
         	return;
     	}
-    	System.out.println("### test ");
     	resultBean.setMirrorCount(mirrors.size());
     	for(URL node:mirrors){
+
     		resultBean.setMessage("Timeout : query execution was too long.");
     		resultBean.nextMirror();
     		URL queryUrl=node;
 			System.out.println("query");
-			System.out.println(query);
-    		System.out.println(queryUrl);
+
     		try {
     			queryUrl = new URL(node.toExternalForm()+query);
-
-    			System.out.print("queryUrl");
-    			System.out.print(queryUrl);
+    			System.out.println(queryUrl);
     			resultBean.setFormattedResult( formatRequestResult(queryUrl));
-    			resultBean.setMessage("");
+    			resultBean.setMessage("");    			
     			resultBean.setReady(true);
     			return;
     		} catch (MalformedURLException e) {
     			// TODO Auto-generated catch block
     			resultBean.setMessage("Incorrect service URL "+queryUrl);
     		} catch (IOException e) {
-    			// TODO Auto-generated catch block
-
+    			// TODO Auto-generated catch block    		
     			e.printStackTrace();
     			resultBean.setMessage("Error while proceeding request");
     		} catch (TransformerException e) {
@@ -102,9 +98,14 @@ public void querySpecies(String ivoaId, SpeciesResult resultBean){
     			if(e.getCode() == 204) {
     				resultBean.setMessage("Request returned an empty response");
     			} else if(e.getCode() >= 400){
+    				System.out.println(e);
     				resultBean.setMessage("Node returned the error " +e.getCode() +" while processing the request "+queryUrl);
     			}
-    		}finally{
+    		}catch(Exception e) {
+    			System.out.println(e);
+    			resultBean.setMessage("An exception occurred");
+    		}
+    		finally{
     			resultBean.setReady(true);
     		}
 		}
@@ -117,11 +118,8 @@ public void querySpecies(String ivoaId, SpeciesResult resultBean){
      * @throws IOException
      * @throws TransformerException
      */
-    private static String formatRequestResult(URL url) throws IOException, TransformerException, PortalHttpException{
-    	System.out.print("###");
-    	System.out.print(url);
+    private/* static */ String formatRequestResult(URL url) throws IOException, TransformerException, PortalHttpException{
     	HttpURLConnection c = (HttpURLConnection)url.openConnection();
-
     	if(c.getResponseCode() == 200){
 			c.setConnectTimeout(Settings.HTTP_CONNECT_TIMEOUT.getInt());
 			c.setReadTimeout(Settings.HTTP_DATA_TIMEOUT.getInt());
@@ -137,7 +135,12 @@ private static String formatRequestResult(URL url) throws IOException, Transform
 
 	        return bOut.toString();
     	}else{
-    		throw new PortalHttpException("Http error while executing TAP request", c.getResponseCode());
+    		if(c.getResponseCode() == 301 || c.getResponseCode() == 302){
+    			String newUrl = c.getHeaderField("Location");  			
+    			return this.formatRequestResult(new URL(newUrl));
+    		}else {    			
+    			throw new PortalHttpException("Http error while executing TAP request", c.getResponseCode());
+    		}
     	}
     }
 }