[DS-707] Stack trace loss in exceptions

git-svn-id: http://scm.dspace.org/svn/repo/dspace/trunk@5552 9c30dcfa-912a-0410-8fc2-9e0234be79fd

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java

@@ -224,7 +224,7 @@ public class MetadataImport
                         }
                         catch (Exception ex)
                         {
-                            throw new MetadataImportException("'" + handle + "' is not a Collection! You must specify a valid collection for new items");
+                            throw new MetadataImportException("'" + handle + "' is not a Collection! You must specify a valid collection for new items", ex);
                         }
                     }
 

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImportException.java

@@ -53,4 +53,15 @@ public class MetadataImportException extends Exception
     {
        super(message);
     }
+
+    /**
+     * Instantiate a new MetadataImportException
+     *
+     * @param message the error message
+     * @param exception the root cause
+     */
+    public MetadataImportException(String message, Exception exception)
+    {
+       super(message, exception);
+    }
 }

dspace-api/src/main/java/org/dspace/app/mets/METSExport.java

@@ -561,7 +561,7 @@ public class METSExport
             // We don't pass up a MetsException, so callers don't need to
             // know the details of the METS toolkit
             e.printStackTrace();
-            throw new IOException(e.getMessage());
+            throw new IOException(e.getMessage(), e);
         }
     }
 

dspace-api/src/main/java/org/dspace/app/sfx/SFXFileReader.java

@@ -40,7 +40,6 @@ package org.dspace.app.sfx;
 
 import java.io.File;
 import java.io.IOException;
-import java.lang.String;
 import java.net.URLEncoder;
 
 import org.apache.log4j.Logger;

dspace-api/src/main/java/org/dspace/app/statistics/LogAnalyser.java

@@ -38,8 +38,6 @@
 
 package org.dspace.app.statistics;
 
-import org.dspace.app.statistics.LogLine;
-
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
@@ -48,9 +46,6 @@ import org.dspace.storage.rdbms.TableRow;
 
 import java.sql.SQLException;
 
-import java.lang.Long;
-import java.lang.StringBuffer;
-
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 

dspace-api/src/main/java/org/dspace/app/util/OpenSearch.java

@@ -187,7 +187,7 @@ public class OpenSearch
         catch (FeedException e)
             {
             log.error(e.toString(), e);
-            	throw new IOException("Unable to generate feed");
+            	throw new IOException("Unable to generate feed", e);
             }
         }
     
@@ -214,7 +214,7 @@ public class OpenSearch
         catch (FeedException e)
         	{
             log.error(e.toString(), e);
-            throw new IOException("Unable to generate feed");
+            throw new IOException("Unable to generate feed", e);
         	}
     
         }
@@ -350,7 +350,7 @@ public class OpenSearch
         }
         catch(JDOMException jde)
         {
-        	throw new IOException("JDOM output exception");
+        	throw new IOException("JDOM output exception", jde);
         }
     }
 }

dspace-api/src/main/java/org/dspace/content/Collection.java

@@ -1131,7 +1131,7 @@ public class Collection extends DSpaceObject
         catch (BrowseException e)
         {
         	log.error("caught exception: ", e);
-        	throw new IOException(e.getMessage());
+        	throw new IOException(e.getMessage(), e);
         }
         finally
         {

dspace-api/src/main/java/org/dspace/content/Item.java

@@ -1934,7 +1934,7 @@ public class Item extends DSpaceObject
         catch (BrowseException e)
         {
             log.error("caught exception: ", e);
-            throw new SQLException(e.getMessage());
+            throw new SQLException(e.getMessage(), e);
         }
 
         // Delete the Dublin Core

dspace-api/src/main/java/org/dspace/content/crosswalk/MODSDisseminationCrosswalk.java

@@ -272,7 +272,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
             {
                 log.error("Error opening or reading MODS properties file: "+propsFile.toString()+": "+e.toString());
                 throw new CrosswalkInternalException("MODS crosswalk cannot "+
-                    "open config file: "+e.toString());
+                    "open config file: "+e.toString(), e);
             }
             finally
             {

dspace-api/src/main/java/org/dspace/content/crosswalk/OREIngestionCrosswalk.java

@@ -146,7 +146,7 @@ public class OREIngestionCrosswalk
 	        xpathLinks.addNamespace(ATOM_NS);
 	        entryId = ((Attribute)xpathLinks.selectSingleNode(doc)).getValue();
 		} catch (JDOMException e) {
-			throw new CrosswalkException("JDOM exception occured while ingesting the ORE");
+			throw new CrosswalkException("JDOM exception occured while ingesting the ORE", e);
 		}
 
 		// Next for each resource, create a bitstream

dspace-api/src/main/java/org/dspace/content/crosswalk/QDCCrosswalk.java

@@ -320,7 +320,7 @@ public class QDCCrosswalk extends SelfNamedPlugin
             }
             catch (org.jdom.JDOMException je)
             {
-                throw new CrosswalkInternalException("Failed parsing XML fragment in properties file: \""+prolog+val+postlog+"\": "+je.toString());
+                throw new CrosswalkInternalException("Failed parsing XML fragment in properties file: \""+prolog+val+postlog+"\": "+je.toString(), je);
             }
         }
     }

dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTDisseminationCrosswalk.java

@@ -231,7 +231,7 @@ public class XSLTDisseminationCrosswalk
         catch (XSLTransformException e)
         {
             log.error("Got error: "+e.toString());
-            throw new CrosswalkInternalException("XSL translation failed: "+e.toString());
+            throw new CrosswalkInternalException("XSL translation failed: "+e.toString(), e);
         }
     }
 
@@ -263,7 +263,7 @@ public class XSLTDisseminationCrosswalk
         catch (XSLTransformException e)
         {
             log.error("Got error: "+e.toString());
-            throw new CrosswalkInternalException("XSL translation failed: "+e.toString());
+            throw new CrosswalkInternalException("XSL translation failed: "+e.toString(), e);
         }
     }
 

dspace-api/src/main/java/org/dspace/content/crosswalk/XSLTIngestionCrosswalk.java

@@ -162,7 +162,7 @@ public class XSLTIngestionCrosswalk
         catch (XSLTransformException e)
         {
             log.error("Got error: "+e.toString());
-            throw new CrosswalkInternalException("XSL Transformation failed: "+e.toString());
+            throw new CrosswalkInternalException("XSL Transformation failed: "+e.toString(), e);
         }
     }
 
@@ -185,7 +185,7 @@ public class XSLTIngestionCrosswalk
         catch (XSLTransformException e)
         {
             log.error("Got error: "+e.toString());
-            throw new CrosswalkInternalException("XSL Transformation failed: "+e.toString());
+            throw new CrosswalkInternalException("XSL Transformation failed: "+e.toString(), e);
         }
 
     }

dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSDisseminator.java

@@ -660,11 +660,11 @@ public abstract class AbstractMETSDisseminator
         }
         catch (InstantiationException e)
         {
-            throw new PackageValidationException("Error instantiating Mdsec object: "+ e.toString());
+            throw new PackageValidationException("Error instantiating Mdsec object: "+ e.toString(), e);
         }
         catch (IllegalAccessException e)
         {
-            throw new PackageValidationException("Error instantiating Mdsec object: "+ e.toString());
+            throw new PackageValidationException("Error instantiating Mdsec object: "+ e.toString(), e);
         }
     }
 

dspace-api/src/main/java/org/dspace/content/packager/PackageValidationException.java

@@ -71,4 +71,9 @@ public class PackageValidationException extends PackageException
     {
         super(exception);
     }
+
+    public PackageValidationException(String message, Exception exception)
+    {
+        super(message, exception);
+    }
 }

dspace-api/src/main/java/org/dspace/core/ConfigurationManager.java

@@ -279,7 +279,7 @@ public class ConfigurationManager
 
             // FIXME: Maybe something more graceful here, but with the
             // configuration we can't do anything
-            throw new RuntimeException("Failed to read default license.");
+            throw new RuntimeException("Failed to read default license.", e);
         }
         finally
         {

dspace-api/src/main/java/org/dspace/handle/HandlePlugin.java

@@ -302,6 +302,7 @@ public class HandlePlugin implements HandleStorage
                 log.debug("Exception in getRawHandleValues", e);
             }
 
+            // Stack loss as exception does not support cause
             throw new HandleException(HandleException.INTERNAL_ERROR);
         }
         finally
@@ -419,6 +420,7 @@ public class HandlePlugin implements HandleStorage
                 log.debug("Exception in getHandlesForNA", sqle);
             }
 
+            // Stack loss as exception does not support cause
             throw new HandleException(HandleException.INTERNAL_ERROR);
         }
         finally

dspace-api/src/main/java/org/dspace/harvest/OAIHarvester.java

@@ -287,11 +287,11 @@ public class OAIHarvester {
 	    	}
 	    	catch (FileNotFoundException fe) {
 	    		log.error("The OAI server did not respond.");
-	    		throw new HarvestingException("The OAI server did not respond.");
+	    		throw new HarvestingException("The OAI server did not respond.", fe);
 	    	}
 	    	catch (ConnectException fe) {
 	    		log.error("The OAI server did not respond.");
-	    		throw new HarvestingException("The OAI server did not respond.");
+	    		throw new HarvestingException("The OAI server did not respond.", fe);
 	    	}	    	
 			if (descMDPrefix == null) {
 				log.error("The OAI server does not support this metadata format");

dspace-api/src/main/java/org/dspace/plugin/PluginException.java

@@ -37,8 +37,6 @@
  */
 package org.dspace.plugin;
 
-import java.lang.Exception;
-
 /**
  * General exception class for all code that runs as a plugin in DSpace
  * 

dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageManager.java

@@ -448,7 +448,7 @@ public class BitstreamStorageManager
 			catch (NoSuchAlgorithmException e) 
 			{
 				log.warn("Caught NoSuchAlgorithmException", e);
-				throw new IOException("Invalid checksum algorithm");
+				throw new IOException("Invalid checksum algorithm", e);
 			}
 			catch (IOException e) 
 			{
@@ -491,7 +491,7 @@ public class BitstreamStorageManager
 			catch (NoSuchAlgorithmException e) 
 			{
 				log.error("Caught NoSuchAlgorithmException", e);
-				throw new IOException("Invalid checksum algorithm");
+				throw new IOException("Invalid checksum algorithm", e);
 			}
 			bitstream.setColumn("checksum", 
 					Utils.toHex(md.digest(sFilename.getBytes())));

dspace-api/src/main/java/org/dspace/storage/rdbms/DataSourceInit.java

@@ -178,7 +178,7 @@ public class DataSourceInit {
             // Need to be able to catch other exceptions. Pretend they are
             // SQLExceptions, but do log
             log.warn("Exception initializing DB pool", e);
-            throw new SQLException(e.toString());
+            throw new SQLException(e.toString(), e);
         }
     }
 }

dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseManager.java

@@ -1676,7 +1676,7 @@ public class DatabaseManager
             // Need to be able to catch other exceptions. Pretend they are
             // SQLExceptions, but do log
             log.warn("Exception initializing DB pool", e);
-            throw new SQLException(e.toString());
+            throw new SQLException(e.toString(), e);
         }
     }
 

dspace-api/src/test/java/org/dspace/AbstractUnitTest.java

@@ -57,7 +57,6 @@ import org.dspace.administer.RegistryLoader;
 import org.dspace.browse.IndexBrowse;
 import org.dspace.browse.MockBrowseCreateDAOOracle;
 import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/jsptag/BrowseListTag.java

@@ -824,11 +824,11 @@ public class BrowseListTag extends TagSupport
         }
         catch (SQLException sqle)
         {
-            throw new JspException(sqle.getMessage());
+            throw new JspException(sqle.getMessage(), sqle);
         }
         catch (IOException ioe)
         {
-            throw new JspException(ioe.getMessage());
+            throw new JspException(ioe.getMessage(), ioe);
         }
 
         // now get the image dimensions
@@ -906,7 +906,7 @@ public class BrowseListTag extends TagSupport
         }
         catch (SQLException sqle)
         {
-        	throw new JspException(sqle.getMessage());
+        	throw new JspException(sqle.getMessage(), sqle);
         }
         catch (UnsupportedEncodingException e)
         {

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/jsptag/ItemListTag.java

@@ -789,11 +789,11 @@ public class ItemListTag extends TagSupport
         }
         catch (SQLException sqle)
         {
-            throw new JspException(sqle.getMessage());
+            throw new JspException(sqle.getMessage(), sqle);
         }
         catch (IOException ioe)
         {
-            throw new JspException(ioe.getMessage());
+            throw new JspException(ioe.getMessage(), ioe);
         }
 
         // now get the image dimensions
@@ -871,7 +871,7 @@ public class ItemListTag extends TagSupport
         }
         catch (SQLException sqle)
         {
-            throw new JspException(sqle.getMessage());
+            throw new JspException(sqle.getMessage(), sqle);
         }
         catch (UnsupportedEncodingException e)
         {

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/jsptag/ItemTag.java

@@ -962,7 +962,7 @@ public class ItemTag extends TagSupport
         }
         catch(SQLException sqle)
         {
-        	throw new IOException(sqle.getMessage());
+        	throw new IOException(sqle.getMessage(), sqle);
         }
 
         out.println("</td></tr></table>");
@@ -990,7 +990,7 @@ public class ItemTag extends TagSupport
         }
         catch(SQLException sqle)
         {
-        	throw new IOException(sqle.getMessage());
+        	throw new IOException(sqle.getMessage(), sqle);
         }
 
         out.println("<table align=\"center\" class=\"attentionTable\"><tr>");

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/servlet/AuthorityChooseServlet.java

@@ -89,7 +89,7 @@ public class AuthorityChooseServlet extends DSpaceServlet {
         }
         catch(SAXException e)
         {
-            throw new IOException(e.toString());
+            throw new IOException(e.toString(), e);
         }
         finally
         {

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/servlet/FeedServlet.java

@@ -283,7 +283,7 @@ public class FeedServlet extends DSpaceServlet
         }
         catch( FeedException fex )
         {
-        	throw new IOException(fex.getMessage());
+        	throw new IOException(fex.getMessage(), fex);
         }
     }
        
@@ -374,12 +374,12 @@ public class FeedServlet extends DSpaceServlet
         catch (SortException se)
         {
             log.error("caught exception: ", se);
-            throw new IOException(se.getMessage());
+            throw new IOException(se.getMessage(), se);
         }
     	catch (BrowseException e)
     	{
     		log.error("caught exception: ", e);
-    		throw new IOException(e.getMessage());
+    		throw new IOException(e.getMessage(), e);
     	}
     }
     

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/servlet/OpenSearchServlet.java

@@ -238,7 +238,7 @@ public class OpenSearchServlet extends DSpaceServlet
         catch (TransformerException e)
         {
             log.error(e);
-            throw new ServletException(e.toString());
+            throw new ServletException(e.toString(), e);
         }
     }
     

dspace-jspui/dspace-jspui-api/src/main/java/org/dspace/app/webui/util/FileUploadRequest.java

@@ -128,9 +128,7 @@ public class FileUploadRequest extends HttpServletRequestWrapper
         }
         catch (Exception e)
         {
-            IOException t = new IOException(e.getMessage());
+            throw new IOException(e.getMessage(), e);
-            t.initCause(e);
-            throw t;
         }
     }
 

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVBitstream.java

@@ -246,7 +246,7 @@ class DAVBitstream extends DAVDSpaceObject
         catch (NumberFormatException nfe)
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Invalid Bitstream Sequence ID in URI: " + pathElt);
+                    "Invalid Bitstream Sequence ID in URI: " + pathElt, nfe);
         }
     }
 

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVCollection.java

@@ -587,7 +587,7 @@ class DAVCollection extends DAVDSpaceObject
         {
             pe.log(log);
             throw new DAVStatusException(
-                    HttpServletResponse.SC_INTERNAL_SERVER_ERROR, pe.toString());
+                    HttpServletResponse.SC_INTERNAL_SERVER_ERROR, pe.toString(), pe);
         }
         catch (CrosswalkException ie)
         {
@@ -599,7 +599,7 @@ class DAVCollection extends DAVDSpaceObject
             log.error(ie.toString() + reason);
             throw new DAVStatusException(
                     HttpServletResponse.SC_INTERNAL_SERVER_ERROR, ie.toString()
-                            + reason);
+                            + reason, ie);
         }
     }
 

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVEPersonEPerson.java

@@ -249,7 +249,7 @@ class DAVEPersonEPerson extends DAVResource
         catch (NumberFormatException ne)
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Error parsing number in request URI.");
+                    "Error parsing number in request URI.", ne);
         }
     }
 

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVItem.java

@@ -227,7 +227,7 @@ class DAVItem extends DAVDSpaceObject
         catch (NumberFormatException ne)
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Error parsing number in request URI.");
+                    "Error parsing number in request URI.", ne);
         }
     }
 
@@ -518,14 +518,14 @@ class DAVItem extends DAVDSpaceObject
             {
                 throw new DAVStatusException(
                         HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
-                        "Failed in crosswalk of metadata: " + pe.toString());
+                        "Failed in crosswalk of metadata: " + pe.toString(), pe);
             }
             catch (PackageException pe)
             {
                 pe.log(log);
                 throw new DAVStatusException(
                         HttpServletResponse.SC_INTERNAL_SERVER_ERROR, pe
-                                .toString());
+                                .toString(), pe);
             }
         }
     }

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVResource.java

@@ -567,7 +567,7 @@ abstract class DAVResource
             {
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
-                        "Bad Depth header: " + sdepth);
+                        "Bad Depth header: " + sdepth, nfe);
             }
         }
 
@@ -671,14 +671,14 @@ abstract class DAVResource
                         .toString()));
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
-                        "Could not parse request document: " + je.toString());
+                        "Could not parse request document: " + je.toString(), je);
             }
         }
         catch (JDOMException je)
         {
             log.error(LogManager.getHeader(this.context, "propfind", je.toString()));
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Could not parse request document: " + je.toString());
+                    "Could not parse request document: " + je.toString(), je);
         }
 
         // At this point, pfProps, pfType and URI define the whole request.
@@ -883,7 +883,7 @@ abstract class DAVResource
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
                         "Could not parse PROPERTYUPDATE request document: "
-                                + je.toString());
+                                + je.toString(), je);
             }
         }
         catch (JDOMException je)
@@ -893,7 +893,7 @@ abstract class DAVResource
                             .toString()));
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
                     "Could not parse PROPERTYUPDATE request document: "
-                            + je.toString());
+                            + je.toString(), je);
         }
         if (reqdoc == null)
         {
@@ -1178,7 +1178,7 @@ abstract class DAVResource
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
                     "Illegal URI syntax in value of \"Destination\" header: "
-                            + destination);
+                            + destination, e);
         }
 
         // Depth arg from header
@@ -1202,7 +1202,7 @@ abstract class DAVResource
             {
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
-                        "Illegal value in Depth request header: " + sdepth);
+                        "Illegal value in Depth request header: " + sdepth, nfe);
             }
         }
 
@@ -1229,14 +1229,14 @@ abstract class DAVResource
             {
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
-                        "Error parsing XML document in COPY request.");
+                        "Error parsing XML document in COPY request.", je);
             }
         }
         catch (JDOMException je)
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
                     "Error parsing XML document in COPY request: "
-                            + je.toString());
+                            + je.toString(), je);
         }
         if (reqdoc != null)
         {
@@ -1700,14 +1700,14 @@ abstract class DAVResource
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
                         "Could not parse DELETE request document: "
-                                + je.toString());
+                                + je.toString(), je);
             }
         }
         catch (JDOMException je)
         {
             log.error(LogManager.getHeader(this.context, "delete", je.toString()));
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Could not parse DELETE request document: " + je.toString());
+                    "Could not parse DELETE request document: " + je.toString(), je);
         }
         if (reqdoc == null)
         {
@@ -1793,14 +1793,14 @@ abstract class DAVResource
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
                         "Could not parse MKCOL request document: "
-                                + je.toString());
+                                + je.toString(), je);
             }
         }
         catch (JDOMException je)
         {
             log.error(LogManager.getHeader(this.context, "mkcol", je.toString()));
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Could not parse MKCOL request document: " + je.toString());
+                    "Could not parse MKCOL request document: " + je.toString(), je);
         }
         if (reqdoc == null)
         {

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVWorkflowItem.java

@@ -211,7 +211,7 @@ class DAVWorkflowItem extends DAVInProgressSubmission
         catch (NumberFormatException ne)
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Error parsing number in request URI.");
+                    "Error parsing number in request URI.", ne);
         }
     }
 

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/DAVWorkspaceItem.java

@@ -197,7 +197,7 @@ class DAVWorkspaceItem extends DAVInProgressSubmission
         catch (NumberFormatException ne)
         {
             throw new DAVStatusException(HttpServletResponse.SC_BAD_REQUEST,
-                    "Error parsing number in request URI.");
+                    "Error parsing number in request URI.", ne);
         }
     }
 
@@ -285,7 +285,7 @@ class DAVWorkspaceItem extends DAVInProgressSubmission
             {
                 throw new DAVStatusException(
                         HttpServletResponse.SC_BAD_REQUEST,
-                        "Error parsing number in property value.");
+                        "Error parsing number in property value.", ne);
             }
         }
         else

dspace-lni/dspace-lni-core/src/main/java/org/dspace/app/dav/LNISoapServlet.java

@@ -310,7 +310,7 @@ public class LNISoapServlet extends AxisServlet
         catch (DAVStatusException e)
         {
             throw new LNIRemoteException("PROPFIND request failed: "
-                    + e.getStatusLine());
+                    + e.getStatusLine(), e);
         }
         catch (AuthorizeException e)
         {
@@ -386,7 +386,7 @@ public class LNISoapServlet extends AxisServlet
         catch (DAVStatusException e)
         {
             throw new LNIRemoteException("PROPPATCH request failed: "
-                    + e.getStatusLine());
+                    + e.getStatusLine(), e);
         }
         catch (AuthorizeException e)
         {
@@ -516,7 +516,7 @@ public class LNISoapServlet extends AxisServlet
         catch (DAVStatusException e)
         {
             throw new LNIRemoteException("COPY request failed: "
-                    + e.getStatusLine());
+                    + e.getStatusLine(), e);
         }
         catch (AuthorizeException e)
         {

dspace-oai/dspace-oai-api/src/main/java/org/dspace/app/oai/DSpaceOAICatalog.java

@@ -149,6 +149,7 @@ public class DSpaceOAICatalog extends AbstractCatalog
             // Log the error
             log.warn(LogManager.getHeader(context, "database_error", ""), se);
 
+            // Stack trace loss as OAI Exception does not support cause
             throw new OAIInternalServerError(se.toString());
         }
         finally
@@ -276,10 +277,12 @@ public class DSpaceOAICatalog extends AbstractCatalog
             // Log the error
             log.warn(LogManager.getHeader(context, "database_error", ""), se);
 
+            // Stack trace loss as OAI Exception does not support cause
             throw new OAIInternalServerError(se.toString());
         }
         catch (ParseException pe)
         {
+            // Stack trace loss as OAI Exception does not support cause
             throw new OAIInternalServerError(pe.toString());
         }
         finally
@@ -412,6 +415,7 @@ public class DSpaceOAICatalog extends AbstractCatalog
             // Log the error
             log.warn(LogManager.getHeader(context, "database_error", ""), se);
 
+            // Stack trace loss as OAI Exception does not support cause
             throw new OAIInternalServerError(se.toString());
         }
         finally
@@ -656,10 +660,12 @@ public class DSpaceOAICatalog extends AbstractCatalog
             // Log the error
             log.warn(LogManager.getHeader(context, "database_error", ""), se);
 
+            // Stack trace loss as OAI Exception does not support cause
             throw new OAIInternalServerError(se.toString());
         }
         catch (ParseException pe)
         {
+            // Stack trace loss as OAI Exception does not support cause
         	throw new OAIInternalServerError(pe.toString());
         }
         finally
@@ -678,7 +684,7 @@ public class DSpaceOAICatalog extends AbstractCatalog
      * 
      * @return a Map object containing "sets" Iterator object (contains
      *         <setSpec/>XML Strings) as well as an optional resumptionMap Map.
-     * @exception OAIBadRequestException
+     * @exception NoSetHierarchyException
      *                signals an http status code 400 problem
      * @exception OAIInternalServerError
      *                signals an http status code 500 problem
@@ -751,6 +757,7 @@ public class DSpaceOAICatalog extends AbstractCatalog
             // Log the error
             log.warn(LogManager.getHeader(context, "database_error", ""), se);
 
+            // Stack trace loss as OAI Exception does not support cause
             throw new OAIInternalServerError(se.toString());
         }
         finally
@@ -950,10 +957,12 @@ public class DSpaceOAICatalog extends AbstractCatalog
         }
         catch (NumberFormatException nfe)
         {
+            // Stack trace loss as OAI Exception does not support cause
             throw new BadResumptionTokenException();
         }
         catch (NoSuchElementException nsee)
         {
+            // Stack trace loss as OAI Exception does not support cause
             throw new BadResumptionTokenException();
         }
 

dspace-oai/dspace-oai-api/src/main/java/org/dspace/app/oai/OAIDCCrosswalk.java

@@ -281,6 +281,7 @@ public class OAIDCCrosswalk extends Crosswalk
             }
                     catch (SQLException e)
                     {
+                        // Stack loss as exception does not support cause
                         throw new CannotDisseminateFormatException(e.toString());
         }
                 }

dspace-oai/dspace-oai-api/src/main/java/org/dspace/app/oai/PluginCrosswalk.java

@@ -190,6 +190,7 @@ public class PluginCrosswalk extends Crosswalk
                 log.error("*** Stack trace follows:");
                 log.error(sw.toString());
 
+            // Stack loss as exception does not support cause
             throw new CannotDisseminateFormatException(schemaLabel);
         }
     }

dspace-sword/dspace-sword-api/src/main/java/org/purl/sword/server/DepositServlet.java

@@ -115,7 +115,7 @@ public class DepositServlet extends HttpServlet {
 								+ className);
 				throw new ServletException(
 						"Unable to instantiate class from 'sword-server-class': "
-								+ className);
+								+ className, e);
 			}
 		}
 

dspace-sword/dspace-sword-api/src/main/java/org/purl/sword/server/DummyServer.java

@@ -261,7 +261,7 @@ public class DummyServer implements SWORDServer {
                 filenames.append(" ").append(ze.toString());
 			}
 		} catch (IOException ioe) {
-			throw new SWORDException("Failed to open deposited zip file", null, ErrorCodes.ERROR_CONTENT);
+			throw new SWORDException("Failed to open deposited zip file", ioe, ErrorCodes.ERROR_CONTENT);
 		}
 		
 		// Handle the deposit

dspace-sword/dspace-sword-api/src/main/java/org/purl/sword/server/ServiceDocumentServlet.java

@@ -94,7 +94,7 @@ public class ServiceDocumentServlet extends HttpServlet {
 						+ className);
 				throw new ServletException(
 						"Unable to instantiate class from 'server-class': "
-								+ className);
+								+ className, e);
 			}
 		}
 

dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/aspect/submission/FlowUtils.java

@@ -195,7 +195,7 @@ public class FlowUtils {
             }
             catch(Exception e)
             {
-                throw new SQLException("Error loading Submission Info: " + e.getMessage());
+                throw new SQLException("Error loading Submission Info: " + e.getMessage(), e);
             }
         }    
         else if(subInfo==null && submission==null)

dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/cocoon/DSpaceFeedGenerator.java

@@ -269,7 +269,7 @@ public class DSpaceFeedGenerator extends AbstractGenerator
         }
         catch (IllegalArgumentException iae)
         {
-                throw new ResourceNotFoundException("Syndication feed format, '"+this.format+"', is not supported.");
+                throw new ResourceNotFoundException("Syndication feed format, '"+this.format+"', is not supported.", iae);
         }
         catch (FeedException fe)
         {

dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/objectmanager/ContainerAdapter.java

@@ -306,9 +306,7 @@ public class ContainerAdapter extends AbstractAdapter
 	                }
 	                catch(ItemCountException e)
 	                {
-	                    IOException ioe = new IOException("Could not obtain Collection item-count");
+	                    throw new IOException("Could not obtain Collection item-count", e);
-	                    ioe.initCause(e);
-	                	throw ioe;
 	                }
         		}
             } 
@@ -342,9 +340,7 @@ public class ContainerAdapter extends AbstractAdapter
 	                }
 	                catch(ItemCountException e)
 	                {
-	                	IOException ioe = new IOException("Could not obtain Collection item-count");
+	                	throw new IOException("Could not obtain Collection item-count", e);
-		                ioe.initCause(e);
-		                throw ioe;
 	                }
         		}
             }