From a68ed9e98b06a53b49cc4a2c1405d93d1caa717e Mon Sep 17 00:00:00 2001
From: "nikolas.laskaris" <nikolas.laskaris@mycompany.com>
Date: Thu, 5 Jun 2014 10:03:56 +0000
Subject: [PATCH] Removed dependency on xerces

git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/application-support-layer/applicationSupportLayerCore@96733 82a268e6-3cf1-43bd-a215-b396298e98cf
---
 pom.xml                                       |   8 +-
 .../framework/core/util/GenericResource.java  |  20 +-
 .../framework/core/util/TransformXSLT.java    | 255 +++++++++---------
 3 files changed, 150 insertions(+), 133 deletions(-)

diff --git a/pom.xml b/pom.xml
index ad8f0ef..b5be0ae 100644
--- a/pom.xml
+++ b/pom.xml
@@ -71,13 +71,14 @@
 			<version>1.6.4</version>
 			<scope>test</scope>
 		</dependency>
-		
+<!-- 
+should be removed after release 3.2.0
 		<dependency>
 		  <groupId>xerces</groupId>
 		  <artifactId>xerces</artifactId>
-		  <version>[2.0.0, 3.0.0]</version>
+		  <version>[2.0.0, 3.0.0)</version>
 		</dependency>
-
+ -->
 		<dependency>
 		  <groupId>org.gcube.resources</groupId>
 		  <artifactId>registry-publisher</artifactId>
@@ -97,6 +98,7 @@
 		  <version>2.3.0</version>
 		</dependency>
 <!-- 
+should be removed after release 3.2.0
 		<dependency>
 		  <groupId>net.sourceforge.addressing</groupId>
 		  <artifactId>addressing</artifactId>
diff --git a/src/main/java/org/gcube/application/framework/core/util/GenericResource.java b/src/main/java/org/gcube/application/framework/core/util/GenericResource.java
index e3d9376..a134044 100644
--- a/src/main/java/org/gcube/application/framework/core/util/GenericResource.java
+++ b/src/main/java/org/gcube/application/framework/core/util/GenericResource.java
@@ -33,6 +33,7 @@ import org.gcube.informationsystem.publisher.stubs.registry.faults.PublisherExce
 import org.gcube.resources.discovery.client.api.DiscoveryClient;
 import org.gcube.resources.discovery.client.queries.api.SimpleQuery;
 import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 import org.slf4j.Logger;
@@ -89,7 +90,6 @@ public class GenericResource implements GenericResourceInfoI {
 			try {
 				client = clientFor(org.gcube.common.resources.gcore.GenericResource.class); //GHNContext.getImplementation(ISClient.class);
 			} catch (Exception e) {
-				// TODO Auto-generated catch block
 				logger.error("Exception:", e);
 				client = null;
 			}
@@ -158,19 +158,27 @@ public class GenericResource implements GenericResourceInfoI {
 		SimpleQuery query = null;
 		try {
 			query = queryFor(org.gcube.common.resources.gcore.GenericResource.class);
-			query.addCondition("$resource/Profile/SecondaryType eq 'DataSource'");
+			query.addCondition("$resource/Profile/SecondaryType eq 'DataSource'"); //this brings all collections, need to filter out the opensearch ones.
 			if(onlyUserCollections)
 				query.addCondition("$resource/Profile/Body/SourceProperties/user eq 'true'");
 			List<org.gcube.common.resources.gcore.GenericResource> results = client.submit(query);
 			if (results == null || results.size() == 0)
 				logger.debug("Couldn't find any tree collections within that scope! Will return empty list.");
-			else
-				logger.debug("# of Tree Collections found: "+ results.size());
 			for (org.gcube.common.resources.gcore.GenericResource gr : results)
 				pairs.put(gr.id(), gr);
 		} catch (Exception e) {
 			logger.debug("Remote Exception:" + e.toString());
 		}
+		//remove from all collections set, the opensearch ones !
+		for(String key : pairs.keySet()){
+			org.gcube.common.resources.gcore.GenericResource collection = pairs.get(key);
+			Element body = collection.profile().body();
+			if(body.getElementsByTagName("type").getLength()==0)
+				pairs.remove(key);
+			else
+				logger.debug("Found tree collection: "+key);
+		}
+		logger.debug("# of Tree Collections found: "+ pairs.size());
 		return pairs;	
 	}
 
@@ -185,7 +193,9 @@ public class GenericResource implements GenericResourceInfoI {
 		SimpleQuery query = null;
 		try {
 			query = queryFor(org.gcube.common.resources.gcore.GenericResource.class);
-			query.addCondition("$resource/Profile/SecondaryType eq 'GCUBECollection'");
+//			query.addCondition("$resource/Profile/SecondaryType eq 'GCUBECollection'");
+			query.addCondition("$resource/Profile/SecondaryType eq 'DataSource'");  //changed from GCUBECollection to DataSource (2 be same as the tree collections)
+			query.addCondition("$resource/Profile/Body/SourceProperties/type eq 'opensearch'");
 			if(onlyUserCollections)
 				query.addCondition("$resource/Profile/Body/CollectionInfo/user eq 'true'");
 			List<org.gcube.common.resources.gcore.GenericResource> results = client.submit(query);
diff --git a/src/main/java/org/gcube/application/framework/core/util/TransformXSLT.java b/src/main/java/org/gcube/application/framework/core/util/TransformXSLT.java
index 5e8cb77..748a748 100644
--- a/src/main/java/org/gcube/application/framework/core/util/TransformXSLT.java
+++ b/src/main/java/org/gcube/application/framework/core/util/TransformXSLT.java
@@ -1,127 +1,132 @@
-package org.gcube.application.framework.core.util;
+///////
+//      should be removed after release 3.2.0
+//////
 
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringWriter;
 
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-
-import org.apache.xml.serialize.OutputFormat;
-import org.apache.xml.serialize.XMLSerializer;
-import org.w3c.dom.Document;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * @author Valia Tsagkalidou (NKUA)
- * @author Nikolas Laskaris (NKUA)
- *
- */
-public class TransformXSLT {
-	
-	/** The logger. */
-	private static final Logger logger = LoggerFactory.getLogger(TransformXSLT.class);
-	
-	/**
-	 * Transforms an xml document based on the given xslt
-	 * @param xslt the xslt for transforming the xml
-	 * @param xml the xml to be transformed
-	 * @return a string containing the transformed xml (output of the transformation)
-	 */
-	public static String transform(String xslt, String xml)
-	{
-		Transformer transformer;
-		try
-		{//Retrieve the XSLT from the DIS (generic resource), and create the transformer
-			ByteArrayInputStream xsltStream = new ByteArrayInputStream(xslt.getBytes());
-			TransformerFactory tFactory = TransformerFactory.newInstance();
-			transformer = tFactory.newTransformer(new StreamSource(xsltStream));
-		
-			DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
-			Document doc = null;
-			
-			doc = dfactory.newDocumentBuilder().parse(xml);
-			// Apply the transformation
-			ByteArrayOutputStream ba_stream = new ByteArrayOutputStream();
-			OutputFormat format = new OutputFormat(doc);
-			format.setIndenting(false);
-			format.setOmitDocumentType(true);
-			format.setOmitXMLDeclaration(true);
-			StringWriter writer = new StringWriter();
-			XMLSerializer serial = new XMLSerializer(writer,format);
-			serial.serialize(doc);
-			transformer.transform(new StreamSource(new ByteArrayInputStream(writer.toString().getBytes())), new StreamResult(ba_stream));
-			//Prepares the object to be returned
-			    StringBuffer buffer = new StringBuffer();
-			    try {
-				InputStreamReader isr = new InputStreamReader( new ByteArrayInputStream(ba_stream.toByteArray()),
-									      "UTF8");
-				Reader in2 = new BufferedReader(isr);
-				int ch;
-				while ((ch = in2.read()) > -1) {
-					buffer.append((char)ch);
-				}
-				in2.close();
-				return buffer.toString();
-			    } catch (Exception e) {
-				logger.error("Exception:", e);
-			}
-		}
-		catch (Exception e) {
-			logger.error("Exception:", e);
-		}
-		return null;
-	}
-	
-	/**
-	 * Transforms an xml document based on the given transformer
-	 * @param transformer the transformer based on which the transformation will be applied
-	 * @param xml the xml document to be transformed
-	 * @return a string containing the transformed xml (output of the transformation)
-	 */
-	public static String transform(Transformer transformer, String xml)
-	{
-		DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
-		Document doc = null;
-		
-		try
-		{
-			doc = dfactory.newDocumentBuilder().parse(xml);
-			ByteArrayOutputStream ba_stream = new ByteArrayOutputStream();
-			OutputFormat format = new OutputFormat(doc);
-			format.setIndenting(false);
-			format.setOmitDocumentType(true);
-			format.setOmitXMLDeclaration(true);
-			StringWriter writer = new StringWriter();
-			XMLSerializer serial = new XMLSerializer(writer,format);
-			serial.serialize(doc);
-			transformer.transform(new StreamSource(new ByteArrayInputStream(writer.toString().getBytes())), new StreamResult(ba_stream));
-			//Prepares the object to be returned
-			    StringBuffer buffer = new StringBuffer();
-			    try {
-				InputStreamReader isr = new InputStreamReader( new ByteArrayInputStream(ba_stream.toByteArray()),
-									      "UTF8");
-				Reader in2 = new BufferedReader(isr);
-				int ch;
-				while ((ch = in2.read()) > -1) {
-					buffer.append((char)ch);
-				}
-				in2.close();
-				return buffer.toString();
-			    } catch (Exception e) {
-				logger.error("Exception:", e);
-			}
-		}
-		catch (Exception e) {
-			logger.error("Exception:", e);
-		}
-		return null;    
-	}
-}
+//package org.gcube.application.framework.core.util;
+//
+//import java.io.BufferedReader;
+//import java.io.ByteArrayInputStream;
+//import java.io.ByteArrayOutputStream;
+//import java.io.InputStreamReader;
+//import java.io.Reader;
+//import java.io.StringWriter;
+//
+//import javax.xml.parsers.DocumentBuilderFactory;
+//import javax.xml.transform.Transformer;
+//import javax.xml.transform.TransformerFactory;
+//import javax.xml.transform.stream.StreamResult;
+//import javax.xml.transform.stream.StreamSource;
+//
+//import org.apache.xml.serialize.OutputFormat;
+//import org.apache.xml.serialize.XMLSerializer;
+//import org.w3c.dom.Document;
+//import org.slf4j.Logger;
+//import org.slf4j.LoggerFactory;
+//
+///**
+// * @author Valia Tsagkalidou (NKUA)
+// * @author Nikolas Laskaris (NKUA)
+// *
+// */
+//public class TransformXSLT {
+//	
+//	/** The logger. */
+//	private static final Logger logger = LoggerFactory.getLogger(TransformXSLT.class);
+//	
+//	/**
+//	 * Transforms an xml document based on the given xslt
+//	 * @param xslt the xslt for transforming the xml
+//	 * @param xml the xml to be transformed
+//	 * @return a string containing the transformed xml (output of the transformation)
+//	 */
+//	public static String transform(String xslt, String xml)
+//	{
+//		Transformer transformer;
+//		try
+//		{//Retrieve the XSLT from the DIS (generic resource), and create the transformer
+//			ByteArrayInputStream xsltStream = new ByteArrayInputStream(xslt.getBytes());
+//			TransformerFactory tFactory = TransformerFactory.newInstance();
+//			transformer = tFactory.newTransformer(new StreamSource(xsltStream));
+//		
+//			DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
+//			Document doc = null;
+//			
+//			doc = dfactory.newDocumentBuilder().parse(xml);
+//			// Apply the transformation
+//			ByteArrayOutputStream ba_stream = new ByteArrayOutputStream();
+//			OutputFormat format = new OutputFormat(doc);
+//			format.setIndenting(false);
+//			format.setOmitDocumentType(true);
+//			format.setOmitXMLDeclaration(true);
+//			StringWriter writer = new StringWriter();
+//			XMLSerializer serial = new XMLSerializer(writer,format);
+//			serial.serialize(doc);
+//			transformer.transform(new StreamSource(new ByteArrayInputStream(writer.toString().getBytes())), new StreamResult(ba_stream));
+//			//Prepares the object to be returned
+//			    StringBuffer buffer = new StringBuffer();
+//			    try {
+//				InputStreamReader isr = new InputStreamReader( new ByteArrayInputStream(ba_stream.toByteArray()),
+//									      "UTF8");
+//				Reader in2 = new BufferedReader(isr);
+//				int ch;
+//				while ((ch = in2.read()) > -1) {
+//					buffer.append((char)ch);
+//				}
+//				in2.close();
+//				return buffer.toString();
+//			    } catch (Exception e) {
+//				logger.error("Exception:", e);
+//			}
+//		}
+//		catch (Exception e) {
+//			logger.error("Exception:", e);
+//		}
+//		return null;
+//	}
+//	
+//	/**
+//	 * Transforms an xml document based on the given transformer
+//	 * @param transformer the transformer based on which the transformation will be applied
+//	 * @param xml the xml document to be transformed
+//	 * @return a string containing the transformed xml (output of the transformation)
+//	 */
+//	public static String transform(Transformer transformer, String xml)
+//	{
+//		DocumentBuilderFactory dfactory = DocumentBuilderFactory.newInstance();
+//		Document doc = null;
+//		
+//		try
+//		{
+//			doc = dfactory.newDocumentBuilder().parse(xml);
+//			ByteArrayOutputStream ba_stream = new ByteArrayOutputStream();
+//			OutputFormat format = new OutputFormat(doc);
+//			format.setIndenting(false);
+//			format.setOmitDocumentType(true);
+//			format.setOmitXMLDeclaration(true);
+//			StringWriter writer = new StringWriter();
+//			XMLSerializer serial = new XMLSerializer(writer,format);
+//			serial.serialize(doc);
+//			transformer.transform(new StreamSource(new ByteArrayInputStream(writer.toString().getBytes())), new StreamResult(ba_stream));
+//			//Prepares the object to be returned
+//			    StringBuffer buffer = new StringBuffer();
+//			    try {
+//				InputStreamReader isr = new InputStreamReader( new ByteArrayInputStream(ba_stream.toByteArray()),
+//									      "UTF8");
+//				Reader in2 = new BufferedReader(isr);
+//				int ch;
+//				while ((ch = in2.read()) > -1) {
+//					buffer.append((char)ch);
+//				}
+//				in2.close();
+//				return buffer.toString();
+//			    } catch (Exception e) {
+//				logger.error("Exception:", e);
+//			}
+//		}
+//		catch (Exception e) {
+//			logger.error("Exception:", e);
+//		}
+//		return null;    
+//	}
+//}