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[Treebase-guts] [ treebase-Bugs-2945410 ] Proxy Error for taxon->tree search

From: SourceForge.net <no...@so...> - 2010-02-11 16:19:49

Bugs item #2945410, was opened at 2010-02-03 13:36
Message generated for change (Settings changed) made by youjun
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945410&group_id=248804

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including the initial issue submission, for this request,
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Category: performance
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: youjun guo (youjun)
Summary: Proxy Error for taxon->tree search

Initial Comment:
If I do a taxon search (e.g. search for "Homo sapiens" as taxon variant name under the Taxa tab), and then click on the Trees tab (i.e. to get a selection of trees based on the selection of two Homo sapiens records) I get the proxy error below after exactly 2 minutes. That suggests to me that there is a time-out in operation, but it also says that the query is taking too long. By comparison, the exact same query on the SDSC/DB2 version (http://8ball.sdsc.edu:6666/treebase-web/) resulted in 630 trees returned in 31 seconds. I have created an artifact with priority 8 (https://sourceforge.net/tracker/?func=detail&aid=2945391&group_id=248804&atid=1126676) requesting that new indexes be added to speed up this query. But in addition, we should probably increase the 2 minute limit before getting a proxy error, seeing as some queries will take longer than two minutes no matter what we do -- and since a taxon search is such a basic type of query, I'm giving this proxy time-out error a priority of 9.  

Bill

===========
Proxy Error

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /treebase-web/search/treeSearch.html.

Reason: Error reading from remote server

Apache/2.2.3 (CentOS) Server at treebasedb-dev.nescent.org Port 80


----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2948080 ] Make lat/lon available in nexml

From: SourceForge.net <no...@so...> - 2010-02-11 14:48:19

Bugs item #2948080, was opened at 2010-02-08 21:18
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
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Category: internals
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Ryan Scherle (rscherle)
>Assigned to: Rutger Vos (rvos)
Summary: Make lat/lon available in nexml

Initial Comment:
Check whether lat/lon information is available in nexml records exported from TreeBASE. If not, add it.

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2010-02-11 14:48

Message:
The lat/long information is currently not available in the NeXML
serialization. How would we best add this? Would you say that in this
instance it's metadata (i.e. presumably requiring a semantic annotation,
perhaps using DarwinCore predicates) or data (requiring a lat/long datatype
in core NeXML, perhaps). I think it's the former, what do you think?

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2010-02-11 14:48

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

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[Treebase-guts] SF.net SVN: treebase:[490] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceRDFa.java

From: <rv...@us...> - 2010-02-11 06:52:03

Revision: 490
          http://treebase.svn.sourceforge.net/treebase/?rev=490&view=rev
Author:   rvos
Date:     2010-02-11 06:51:56 +0000 (Thu, 11 Feb 2010)

Log Message:
-----------
Fixed org.dom4j.IllegalAddException

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-02-11 06:37:11 UTC (rev 489)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-02-11 06:51:56 UTC (rev 490)
@@ -109,9 +109,11 @@
 		QName qName = QName.get("base", "xml", "http://www.w3.org/XML/1998/namespace");
 		String sourceBase = nexmlDocument.getRootElement().attributeValue(qName);
 		cdaoDoc.getRootElement().setAttributeValue(qName, sourceBase);
-		Iterator<org.dom4j.Element> elementIterator = rdfaDoc.getRootElement().elementIterator(); 
+		Iterator<org.dom4j.Element> elementIterator = rdfaDoc.getRootElement().elementIterator();
 		while ( elementIterator.hasNext() ) {
-			cdaoDoc.getRootElement().add(elementIterator.next());
+			org.dom4j.Element elt = elementIterator.next();
+			elt.detach();
+			cdaoDoc.getRootElement().add(elt);
 		}
 		return cdaoDoc.asXML();		
 	}


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[Treebase-guts] SF.net SVN: treebase:[489] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceRDFa.java

From: <rv...@us...> - 2010-02-11 06:37:25

Revision: 489
          http://treebase.svn.sourceforge.net/treebase/?rev=489&view=rev
Author:   rvos
Date:     2010-02-11 06:37:11 +0000 (Thu, 11 Feb 2010)

Log Message:
-----------
Completed nexml2cdao conversion.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-02-10 02:04:54 UTC (rev 488)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-02-11 06:37:11 UTC (rev 489)
@@ -1,6 +1,12 @@
 package org.cipres.treebase.service.nexus;
 
 import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Iterator;
 import java.util.Properties;
 
 import javax.xml.parsers.ParserConfigurationException;
@@ -72,32 +78,41 @@
 	private String transform(String input) {
 		SAXReader reader = new SAXReader();
 		ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
-		org.dom4j.Document jDomDocument = null;
+		org.dom4j.Document nexmlDocument = null;
 		try {
-			jDomDocument = reader.read( bs );
+			nexmlDocument = reader.read( bs );
 		} catch (DocumentException e) {
-			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}
+				
 		TransformerFactory factory = TransformerFactory.newInstance();
-		Transformer transformer = null;
+		Transformer rdfaTransformer = null;
+		Transformer cdaoTransformer = null;
 		try {
-			transformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/RDFa2RDFXML.xsl" ) );
+			rdfaTransformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/RDFa2RDFXML.xsl" ) );
+			cdaoTransformer = factory.newTransformer( new StreamSource( "http://www.nexml.org/nexml/xslt/nexml2cdao.xsl"  ) );
 		} catch (TransformerConfigurationException e1) {
 			e1.printStackTrace();
 		}		
-		DocumentSource source = new DocumentSource( jDomDocument );
-		DocumentResult result = new DocumentResult();
+		DocumentSource nexmlSource = new DocumentSource( nexmlDocument );
+		DocumentResult rdfaResult = new DocumentResult();
+		DocumentResult cdaoResult = new DocumentResult();
 		try {
-			transformer.transform( source, result );
-		} catch (TransformerException e) {
-			// TODO Auto-generated catch block
+			rdfaTransformer.transform( nexmlSource, rdfaResult );
+			cdaoTransformer.transform( nexmlSource, cdaoResult );
+		} catch (TransformerException e) {		
 			e.printStackTrace();
 		}
-		org.dom4j.Document transformedDoc = result.getDocument();
+				
+		org.dom4j.Document rdfaDoc = rdfaResult.getDocument();
+		org.dom4j.Document cdaoDoc = cdaoResult.getDocument();
 		QName qName = QName.get("base", "xml", "http://www.w3.org/XML/1998/namespace");
-		String sourceBase = jDomDocument.getRootElement().attributeValue(qName);
-		transformedDoc.getRootElement().setAttributeValue(qName, sourceBase);
-		return transformedDoc.asXML();		
+		String sourceBase = nexmlDocument.getRootElement().attributeValue(qName);
+		cdaoDoc.getRootElement().setAttributeValue(qName, sourceBase);
+		Iterator<org.dom4j.Element> elementIterator = rdfaDoc.getRootElement().elementIterator(); 
+		while ( elementIterator.hasNext() ) {
+			cdaoDoc.getRootElement().add(elementIterator.next());
+		}
+		return cdaoDoc.asXML();		
 	}
 }


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[Treebase-guts] SF.net SVN: treebase:[488] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlDocumentConverter.java

From: <rv...@us...> - 2010-02-10 02:05:01

Revision: 488
          http://treebase.svn.sourceforge.net/treebase/?rev=488&view=rev
Author:   rvos
Date:     2010-02-10 02:04:54 +0000 (Wed, 10 Feb 2010)

Log Message:
-----------
Fixed typo in prism property

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2010-02-09 20:51:58 UTC (rev 487)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java	2010-02-10 02:04:54 UTC (rev 488)
@@ -95,7 +95,7 @@
 	 * @param document
 	 */
 	private void copyCitationMetadata(Citation citation,Document document) {
-		attachAnnotation("dcterms.bibliographicCitation",citation.getAuthorsCitationStyleWithoutHtml(),mDCURI,document);
+		attachAnnotation("dcterms:bibliographicCitation",citation.getAuthorsCitationStyleWithoutHtml(),mDCURI,document);
 		if ( null != citation.getTitle() ) {
 			attachAnnotation("tb:title.study",citation.getTitle(),mTBTermsURI,document);
 		}


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[Treebase-guts] SF.net SVN: treebase:[487] trunk/treebase-core/src/main

From: <vga...@us...> - 2010-02-09 20:52:16

Revision: 487
          http://treebase.svn.sourceforge.net/treebase/?rev=487&view=rev
Author:   vgapeyev
Date:     2010-02-09 20:51:58 +0000 (Tue, 09 Feb 2010)

Log Message:
-----------
Split nexusService bean into 2: one for the webapp (init via JNDI) and another for the standalone tools (init from jdbc.properties)

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
    trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
    trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
    trunk/treebase-core/src/main/resources/applicationContext-service.xml

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2010-02-09 20:51:58 UTC (rev 487)
@@ -40,6 +40,9 @@
 	private MatrixDataTypeHome mMatrixDataTypeHome;
 	private ItemDefinitionHome mItemDefinitionHome;
 
+	private String mExplicitMesquiteFolder = null;
+	private String mJndiMesquiteFolder = null; 
+
 	/**
 	 * Constructor.
 	 */
@@ -104,24 +107,47 @@
 		return null; // do not need persistence service.
 	}
 	
-	/** Looks up where Mesquite is installed on the host system and informs MesquiteModule of the location.  
+
+	/**  Explicitly set Mesquite folder location that will be passed to mesquite.lib.MesquiteModule. 
+	 *   Only for use in tests and stand-alone tools (the webapp looks up the location in afterPropertiesSet()). 
+	 * 
+	 * @param pMesquiteFolderDir
+	 */
+	public void setMesquiteFolderDir(String pMesquiteFolderDir) {
+		mExplicitMesquiteFolder = pMesquiteFolderDir; 
+		LOGGER.info("Mesquite folder location set explicitly to " + mExplicitMesquiteFolder); 
+		//--
+		//System.setProperty(MESQUITE_FOLDER_DIR_KEY, pMesquiteFolderDir);
+		//MesquiteModule.mesquiteDirectory = new File(pMesquiteFolderDir);
+		//MesquiteModule.mesquiteDirectoryPath = pMesquiteFolderDir;
+	}
+	
+	
+	/** Looks up where Mesquite is installed on the host system and passes the location to mesquite.lib.MesquiteModule.  
         (This is an implementation of a standard Spring bean initialization method, 
          which is invoked after all properties are set.)
    */
 	public void afterPropertiesSet() throws Exception {
-		String mesquiteFolderDir = null; 
-		InitialContext ic;
 		try {
-			ic = new InitialContext();
-			mesquiteFolderDir  = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
+			InitialContext ic = new InitialContext();
+			mJndiMesquiteFolder  = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
 		} catch (NamingException e) {
-			LOGGER.fatal("Error looking up tb/MesquiteFolder via JNDI"); 
+			LOGGER.info("Failure looking up tb/MesquiteFolder via JNDI"); 
 		}
-		mesquiteFolderDir = mesquiteFolderDir + "/foo";   //since the last path element is somehow dropped subsequently... VG 2010-02-07
 
-		System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolderDir);
-		MesquiteModule.mesquiteDirectory = new File(mesquiteFolderDir);
-		MesquiteModule.mesquiteDirectoryPath = mesquiteFolderDir;				
+		String mesquiteFolder; 
+		if (mExplicitMesquiteFolder == null) 
+			if (mJndiMesquiteFolder == null) { mesquiteFolder = null; LOGGER.fatal("Failed to determine Mesquite folder location"); }
+			else { mesquiteFolder = mJndiMesquiteFolder; LOGGER.info("Setting mesquite folder location from JNDI: " + mJndiMesquiteFolder); }
+		else 
+			if (mJndiMesquiteFolder == null) { mesquiteFolder = mExplicitMesquiteFolder; LOGGER.info("Using explicitly set Mesquite folder: " + mExplicitMesquiteFolder);}
+			else { mesquiteFolder = mJndiMesquiteFolder; LOGGER.warn("Explicitly set Mesquite folder (" + mExplicitMesquiteFolder + 
+																	 ") is overwritten by the one from JNDI: " + mJndiMesquiteFolder); }
+		
+		mesquiteFolder = mesquiteFolder + "/foo";   //since the last path element is somehow dropped subsequently... VG 2010-02-07
+		System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolder);
+		MesquiteModule.mesquiteDirectory = new File(mesquiteFolder);
+		MesquiteModule.mesquiteDirectoryPath = mesquiteFolder;				
 	}
 	
 

Modified: trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml	2010-02-09 20:51:58 UTC (rev 487)
@@ -28,6 +28,12 @@
 		<property name="numHelperThreads" value="5" />
 	</bean>
 
+	<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+                <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+                <property name="taxonLabelHome" ref="taxonLabelHome"/>
+                <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+                <property name="mesquiteFolderDir" value="${mesquite.folder_dir}"/>
+    </bean>
 
 
 </beans>

Modified: trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml	2010-02-09 20:51:58 UTC (rev 487)
@@ -13,4 +13,10 @@
 		<property name="jndiName" value="java:comp/env/jdbc/TreebaseDB"/>
 	</bean>
 
+	<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
+                <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
+                <property name="taxonLabelHome" ref="taxonLabelHome"/>
+                <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
+   </bean>
+
 </beans>
\ No newline at end of file

Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml	2010-02-08 17:07:55 UTC (rev 486)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml	2010-02-09 20:51:58 UTC (rev 487)
@@ -137,13 +137,14 @@
                 <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>
    </bean-->
-	
+
+<!-- VG 2010-02-09 nexusService bean is now set in applicationContext-db-webappp.xml and in applicationContext-db-standalone.xml 	
 	<bean id="nexusService" class = "org.cipres.treebase.service.nexus.NexusServiceMesquite">
                 <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>
                 <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
    </bean>
-  
+-->  
   	<bean id="nexmlService" class = "org.cipres.treebase.service.nexus.NexusServiceNexml">
                 <!-- property name="domainHome" ref="domainHome"/ -->
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>


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[Treebase-guts] [ treebase-Bugs-2948080 ] Make lat/lon available in nexml

From: SourceForge.net <no...@so...> - 2010-02-08 21:18:53

Bugs item #2948080, was opened at 2010-02-08 16:18
Message generated for change (Tracker Item Submitted) made by rscherle
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2948080&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: internals
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Ryan Scherle (rscherle)
Assigned to: Nobody/Anonymous (nobody)
Summary: Make lat/lon available in nexml

Initial Comment:
Check whether lat/lon information is available in nexml records exported from TreeBASE. If not, add it.

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2945440 ] User cannot download his trees within his own submission

From: SourceForge.net <no...@so...> - 2010-02-08 18:37:07

Bugs item #2945440, was opened at 2010-02-03 14:24
Message generated for change (Settings changed) made by youjun
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945440&group_id=248804

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Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: youjun guo (youjun)
Summary: User cannot download his trees within his own submission

Initial Comment:
A basic user (in this case, username "tb3" with password "tb3", and submission 9923) who uploads a tree to his submission, is blocked from downloading the "reconstructed" tree from within the submission interface. To replicate the problem, login to submission 9923, go to the tree blocks:

http://treebasedb-dev.nescent.org:6666/treebase-web/user/treeBlockList.html

Then click on the "download reconstructed tree" links, e.g.:

http://treebasedb-dev.nescent.org:6666/treebase-web/user/downloadATreeBlock.html?treeblockid=9662

The result is "Access denied. Sorry! your action is not authorized." If you look inside the tree block and then try to download a reconstructed tree, you get a "Uncaught Exception Encountered" (see text below). 

These errors may be related to a recent fix that Rutger made to prevent "in progress" data from being accessed anonymously. The rules should be the following:

1. Anonymous users can only access data associated with studies that are considered "published" unless they use a /phylows/ url with a valid x-access-code parameter. Access as study with a valid x-access-code provides access to download links within that study throughout that session.

2. Users who create a submission can alway access the data in that submission regardless of status, but they can only edit data if the submission is "in progress"

3. Admin and Associate Editors can both access and edit all data regardless of status. 


bp


Uncaught Exception Encountered
java.lang.NullPointerException at org.cipres.treebase.web.controllers.AbstractDownloadController.generateAFileDynamically(AbstractDownloadController.java:125) at org.cipres.treebase.web.controllers.DownloadATreeController.handleRequest(DownloadATreeController.java:76) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/treeBlockList.html] itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/submissionList.html] JSESSIONID=[A56E40E535C9BD4451883A467D1473F0] __utma=[53240375.1924499357.1236724314.1264137469.1264687265.41] __utmz=[53240375.1263756485.39.6.utmccn]

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[Treebase-guts] [ treebase-Bugs-2947955 ] Submission Summary Info

From: SourceForge.net <no...@so...> - 2010-02-08 17:16:57

Bugs item #2947955, was opened at 2010-02-08 12:16
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2947955&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Submission Summary Info

Initial Comment:
When the user enter a submission, s/he sees a submission summary info page, like so:

http://treebasedb-dev.nescent.org/treebase-web/user/summary.html?id=1

The information presented is incomplete. In addition to a reviewer-access URL, we want the user to see the Study Accession URL; and we want the user to have a "Contact TreeBASE Help" link. This email link needs to include the submission ID in the email subject header.

Ideally, the Study Accession URL only shows up when the submission is "ready" or "published". Ideally, the Reviewer-access URL does not show up when the submission is "published". But these status-sensitive features are not strictly critical, and it's fine if everything is always displayed. Another non-critical feature is that in addition to a "submission initiated" date, it would be nice if there also was a "last modified" date.

Attached, please find an image showing what this might look like.

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[Treebase-guts] SF.net SVN: treebase:[486] trunk/treebase-core/db

From: <vga...@us...> - 2010-02-08 17:08:24

Revision: 486
          http://treebase.svn.sourceforge.net/treebase/?rev=486&view=rev
Author:   vgapeyev
Date:     2010-02-08 17:07:55 +0000 (Mon, 08 Feb 2010)

Log Message:
-----------
Added a few details. 

Modified Paths:
--------------
    trunk/treebase-core/db/README.txt
    trunk/treebase-core/db/TODO.txt

Modified: trunk/treebase-core/db/README.txt
===================================================================
--- trunk/treebase-core/db/README.txt	2010-02-08 00:23:34 UTC (rev 485)
+++ trunk/treebase-core/db/README.txt	2010-02-08 17:07:55 UTC (rev 486)
@@ -9,18 +9,14 @@
 in Ruby or Python (but with scripts written in SQL and no automation).
 
 The idea is that we store in SVN the initial snapshot of the DB schema  
-and sequential parches that we have been developing w.r.t  
+and sequential patches that we have been developing w.r.t  
 treebasedev.  These patches will be used to bring up-to-date  
 treebasestage, and then treebaseprod.   After that we can erase the  
 patches, refresh the snapshot, and continue for another cycle.   
 Official TB2 code releases are to be declared at the start of a cycle,  
 when there are no patches yet.  The snapshot is what should be used to  
-create a fresh TB2 instance.
+create a fresh TB2 instance by someone who wants to run their own. 
 
-I suggest to create the directory treebase-code/db to store patches  
-and snapshots.  (Another option would be a separate project, treebase- 
-db, a a sibling of treebase-core and treebase-web.)
-
 Patches are to be sequentially numbered (by hand).  To keep track  
 which DB instance has already been brought up to which patch version,  
 I suggest creating a special table with a number column.  Each patch  
@@ -28,3 +24,20 @@
 number.
 
 If this sounds ok, I hope to set this up by end of tomorrow.
+
+
+Some more details: 
+
+* Patch naming: 0001_short_name.sql
+* Each patch is wrapped into a transaction and starts by incrementing the number in the version table. 
+* Patches and snapshots must not include any ownership or permissions commands.
+* Version table schema: 
+CREATE TABLE versionhistory
+(
+  id serial NOT NULL,
+  patchnumber integer,
+  patchlabel character varying(50) NOT NULL,
+  patchdescription character varying(1000),
+  applied timestamp with time zone,
+  CONSTRAINT versionhistory_pkey PRIMARY KEY (id)
+)
\ No newline at end of file

Modified: trunk/treebase-core/db/TODO.txt
===================================================================
--- trunk/treebase-core/db/TODO.txt	2010-02-08 00:23:34 UTC (rev 485)
+++ trunk/treebase-core/db/TODO.txt	2010-02-08 17:07:55 UTC (rev 486)
@@ -3,5 +3,44 @@
 [To be put in as patches after the storage structure for them is in place in this directory -- VG 2010-02-04]:
 
 * Drop geospot_id_sequence -- there is no corresponding sequence
+
+* Drop hibernate_sequence
+
 * Correct PK name in stepmatrixelement and create stepmatrixelement_id_sequence
+
 * Create indexes, as suggested by Bill 2010-02-03 (and maybe later)
+     Bill's message of 2010-02-03: "Of the top of my head, I would assume that the following fields need to be indexed:
+        Table			Field
+        --------			-------
+        taxon			name
+        taxonvariant		fullname
+        taxonlabel		taxonlabel
+        citation			title
+        citation			abstract
+        person			lastname"
+     More details in bug https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945391&group_id=248804, 
+        esp phylotree, phylonode indexes. 
+     Also, compare to the end-of-Jan schema snapshot of treebasedev   
+
+
+Pending data cleanups (mostly, on staging):
+
+* Remove junk, particularly that created by tests
+
+* Known junk: Submission 22 and its related records
+    Youjun's email of 2010-01-28: 
+     "In table phylotree, many trees do not have a study_id value, but their phylotreenode related to study 22 via table taxonlabel.  
+      Their phylotree_id are: 
+       1129,1130,1131,1132,     2333,2334,2335,2336,2337,2338,  2339,2340,2341,2343,2556,2557,2686,2726,2727,2787,2788,2789,2790,     
+       3446,3671,3766,3767,3901,3902,3903,3904,3905,3906,3907,3908,3909,3910,3911,3912, 4062,4063, 5705,5706,5707,5708,5720,5721,5921,5941,5981,160000022341
+       I will delete those trees because their foreign key constrain  prevent me from cleaning up about 10,000 dummy taxonlabel records related to submission 22 
+       (study 22 and submission 22 happen to be the same)." 
+     VG: these IDs are from end-of-Jan treebasedev; the current treebasestage may have fewer.   
+
+* Replace "owner" nulls by the special "migration" owner (see Bill's message of around 2010-02-02)
+    "Also because we have reverted to an older instance of the data, the migrated records contain have NULL in the user_id of the submission table. This causes null pointer errors for the unit tests. To fix the problem, I did the following:
+     1. I created a user with username "migration" and email address "mig...@tr...". This is the dummy "user" who will now "own" all migrated submissions that lack an owner.
+     2. I got the user_id for the "migration" user, and it happened to be 9955
+     3. I ran this statement: "UPDATE submission SET user_id = 9955 WHERE user_id IS NULL"
+     Now all migrated data belong to the user "migration". "
+    
\ No newline at end of file


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[Treebase-guts] [ treebase-Bugs-2947925 ] Admin needs to search by study, submission, and legacy ids

From: SourceForge.net <no...@so...> - 2010-02-08 16:44:46

Bugs item #2947925, was opened at 2010-02-08 11:44
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2947925&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Admin needs to search by study, submission, and legacy ids

Initial Comment:
http://treebasedb-dev.nescent.org/treebase-web/admin/searchBySubmissionID.html

In the Search Submission page, which is used by editors and admin users, currently the "TreeBASE2 Id" actually searches the submission_id.  We need to make it so that the Admin person can search on (1) TreeBASE2 Submission ID, (2) TreeBASE2 Study ID, and (3) TreeBASE 1 Legacy ID. 


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[Treebase-guts] [ treebase-Bugs-2945391 ] New Indices Needed

From: SourceForge.net <no...@so...> - 2010-02-08 15:55:29

Bugs item #2945391, was opened at 2010-02-03 13:04
Message generated for change (Settings changed) made by sfrgpiel
You can respond by visiting: 
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including the initial issue submission, for this request,
not just the latest update.
Category: data
Group: None
Status: Open
>Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Hilmar Lapp (hlapp)
Summary: New Indices Needed

Initial Comment:
Because we have reverted to an older instance of the data (and schema), there are some changes that we may need to make. One is to create indexes on fields that are likely to be queried a lot using something like "CREATE INDEX taxonlabel_i ON taxonlabel USING btree (taxonlabel);". 

At the bottom is a list of all our existing indices -- although all the PKs are covered other fields would seem to benefit from an index. I would assume that the following fields need to be indexed:

Table			Field
--------			-------
taxon			name
taxonvariant		fullname
taxonlabel		taxonlabel
citation			title
citation			abstract
person			lastname

In addition, I would think that FKs need to be indexed as well, although I don't know which are the critical ones. What is clear is that some queries are very very slow. For example, do a taxon variant name search on "Homo sapiens" (this results in a selection of two taxon records) and then click the "Trees" tab -- after 2 minutes it returned a "Proxy Error: The proxy server received an invalid response from an upstream server. Reason: Error reading from remote host" which I'm guessing is a time-out of some sort. At any rate, the FK called taxonlabel_id and the FK called phylotree_id in the phylotreenode table probably should be indexed to speed up querying for trees based on a selection of taxa. 

Undoubtedly there are other FKs that need indexing, but this requires knowledge on how common queries are made via hibernate.

These changes to the schema should be applied to both the dev and stage databases, as well as noted in the instantiation scripts.

bp



SELECT n.nspname AS "Schema", t.relname AS "Table", c.relname AS "Index"
FROM pg_catalog.pg_class c
     JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace
     JOIN pg_catalog.pg_index i ON i.indexrelid = c.oid
     JOIN pg_catalog.pg_class t ON i.indrelid = t.oid
WHERE c.relkind = 'i'
    AND n.nspname NOT IN ('pg_catalog', 'pg_toast')
    AND pg_catalog.pg_table_is_visible(c.oid)
ORDER BY n.nspname, t.relname, c.relname;

 Schema |            Table            |                   Index                    
--------+-----------------------------+--------------------------------------------
 public | algorithm                   | algorithm_pkey
 public | analysis                    | analysis_pkey
 public | analysis                    | analysis_study_id_idx
 public | analysisstep                | analysisstep_pkey
 public | analyzeddata                | analyzeddata_pkey
 public | ancestralstate              | ancestralstate_pkey
 public | ancstateset                 | ancstateset_pkey
 public | chargroup                   | chargroup_pkey
 public | chargroup_colrange          | chargroup_colrange_columnrange_id_key
 public | charpartition               | charpartition_pkey
 public | charset                     | charset_pkey
 public | charset_colrange            | charset_colrange_columnrange_id_key
 public | charweight                  | charweight_pkey
 public | charweight_colrange         | charweight_colrange_columnrange_id_key
 public | charweightset               | charweightset_pkey
 public | citation                    | citation_pkey
 public | citation_author             | citation_author_pkey
 public | citation_editor             | citation_editor_pkey
 public | citationstatus              | citationstatus_pkey
 public | coderecord_colrange         | coderecord_colrange_columnrange_id_key
 public | codonchar1_colrange         | codonchar1_colrange_columnrange_id_key
 public | codonchar2_colrange         | codonchar2_colrange_columnrange_id_key
 public | codonchar3_colrange         | codonchar3_colrange_columnrange_id_key
 public | codonnoncoding_colrange     | codonnoncoding_colrange_columnrange_id_key
 public | codonpositionset            | codonpositionset_pkey
 public | columnrange                 | columnrange_pkey
 public | compound_element            | compound_element_element_id_key
 public | compound_element            | compound_element_pkey
 public | cstreenode                  | cstreenode_pkey
 public | discretecharstate           | discretecharstate_phylochar_id_idx
 public | discretecharstate           | discretecharstate_pkey
 public | distancematrixelement       | distancematrixelement_pkey
 public | gapmode                     | gapmode_pkey
 public | geneticcode                 | geneticcode_pkey
 public | geneticcoderecord           | geneticcoderecord_pkey
 public | geneticcodeset              | geneticcodeset_pkey
 public | help                        | help_pkey
 public | itemdefinition              | itemdefinition_pkey
 public | itemvalue                   | itemvalue_pkey
 public | matrix                      | matrix_pkey
 public | matrix_itemdefinition       | matrix_itemdefinition_pkey
 public | matrixcolumn                | matrixcolumn_phylochar_id_idx
 public | matrixcolumn                | matrixcolumn_pkey
 public | matrixcolumn_itemdefinition | matrixcolumn_itemdefinition_pkey
 public | matrixdatatype              | matrixdatatype_phylochar_id_idx
 public | matrixdatatype              | matrixdatatype_pkey
 public | matrixelement               | matrixelement_discretecharstate_id_idx
 public | matrixelement               | matrixelement_itemdefinition_id_idx
 public | matrixelement               | matrixelement_pkey
 public | matrixkind                  | matrixkind_pkey
 public | matrixrow                   | matrixrow_matrix_id_idx
 public | matrixrow                   | matrixrow_pkey
 public | matrixrow                   | matrixrow_taxonlabel_id_idx
 public | nodeattribute               | nodeattribute_pkey
 public | person                      | person_pkey
 public | phylochar                   | phylochar_pkey
 public | phylotree                   | phylotree_pkey
 public | phylotreenode               | phylotreenode_pkey
 public | polytcount                  | polytcount_pkey
 public | rowsegment                  | rowsegment_matrixrow_id_idx
 public | rowsegment                  | rowsegment_pkey
 public | software                    | software_pkey
 public | statechangeset              | statechangeset_pkey
 public | stateformat                 | stateformat_pkey
 public | statemodifier               | statemodifier_pkey
 public | stateset                    | stateset_pkey
 public | stepmatrixelement           | stepmatrixelement_pkey
 public | study                       | study_citation_id_idx
 public | study                       | study_pkey
 public | study_nexusfile             | study_nexusfile_pkey
 public | studystatus                 | studystatus_pkey
 public | sub_matrix                  | sub_matrix_matrix_id_key
 public | sub_matrix                  | sub_matrix_pkey
 public | sub_taxonlabel              | sub_taxonlabel_pkey
 public | sub_taxonlabel              | sub_taxonlabel_taxonlabel_id_key
 public | sub_treeblock               | sub_treeblock_pkey
 public | sub_treeblock               | sub_treeblock_treeblock_id_key
 public | submission                  | submission_pkey
 public | submission                  | submission_study_id_idx
 public | submission                  | submission_study_id_key
 public | taxon                       | taxon_pkey
 public | taxonauthority              | taxonauthority_pkey
 public | taxonlabel                  | taxonlabel_pkey
 public | taxonlabelgroup             | taxonlabelgroup_pkey
 public | taxonlabelpartition         | taxonlabelpartition_pkey
 public | taxonlabelset               | taxonlabelset_pkey
 public | taxonlabelset_taxonlabel    | taxonlabelset_taxonlabel_pkey
 public | taxonlink                   | taxonlink_pkey
 public | taxonset                    | taxonset_pkey
 public | taxonset_taxon              | taxonset_taxon_pkey
 public | taxonvariant                | taxonvariant_pkey
 public | treeattribute               | treeattribute_pkey
 public | treeblock                   | treeblock_pkey
 public | treegroup                   | treegroup_pkey
 public | treegroup_phylotree         | treegroup_phylotree_pkey
 public | treekind                    | treekind_pkey
 public | treenodeedge                | treenodeedge_pkey
 public | treepartition               | treepartition_pkey
 public | treequality                 | treequality_pkey
 public | treeset                     | treeset_pkey
 public | treeset_phylotree           | treeset_phylotree_pkey
 public | treetype                    | treetype_pkey
 public | typeset                     | typeset_pkey
 public | user                        | user_pkey
 public | user                        | user_username_key
 public | userrole                    | userrole_pkey
 public | usertype                    | usertype_pkey
 public | usertyperecord              | usertyperecord_pkey
 public | usertyperrd_colrange        | usertyperrd_colrange_columnrange_id_key
(109 rows)


----------------------------------------------------------------------

>Comment By: William Piel (sfrgpiel)
Date: 2010-02-08 10:55

Message:
This is assigned to Hilmar.

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[Treebase-guts] SF.net SVN: treebase:[485] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/mesquite/MesquiteConverter.java

From: <yo...@us...> - 2010-02-08 01:10:20

Revision: 485
          http://treebase.svn.sourceforge.net/treebase/?rev=485&view=rev
Author:   youjun
Date:     2010-02-08 00:23:34 +0000 (Mon, 08 Feb 2010)

Log Message:
-----------
add study_id to output phylotree

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteConverter.java	2010-02-07 21:38:04 UTC (rev 484)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/mesquite/MesquiteConverter.java	2010-02-08 00:23:34 UTC (rev 485)
@@ -340,6 +340,7 @@
 				phyloTree.setPublished(false);
 				phyloTree.setRootedTree(mesqTree.getRooted());
 				phyloTree.setNewickString(newick);
+				phyloTree.setStudy(pStudy);
 				// phyloTree.setBigTree(false); //TODO
 				// phyloTree.setTreeType(treeType);
 				// phyloTree.setTreeAttribute(pNewTreeAttribute);


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[Treebase-guts] SF.net SVN: treebase:[484] trunk

From: <vga...@us...> - 2010-02-07 21:38:11

Revision: 484
          http://treebase.svn.sourceforge.net/treebase/?rev=484&view=rev
Author:   vgapeyev
Date:     2010-02-07 21:38:04 +0000 (Sun, 07 Feb 2010)

Log Message:
-----------
Installation location for Mesquite is now looked up via JNDI. 

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
    trunk/treebase-core/src/main/resources/applicationContext-service.xml
    trunk/treebase-core/src/main/resources/jdbc.properties.example
    trunk/treebase-web/src/main/webapp/META-INF/context.xml.example
    trunk/treebase-web/src/main/webapp/WEB-INF/web.xml

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2010-02-04 17:46:20 UTC (rev 483)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceMesquite.java	2010-02-07 21:38:04 UTC (rev 484)
@@ -5,6 +5,9 @@
 import java.util.Collection;
 import java.util.Properties;
 
+import javax.naming.InitialContext;
+import javax.naming.NamingException;
+
 import mesquite.lib.MesquiteModule;
 
 import org.apache.log4j.Logger;
@@ -19,6 +22,7 @@
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
 import org.cipres.treebase.event.ProgressionListener;
 import org.cipres.treebase.service.AbstractServiceImpl;
+import org.springframework.beans.factory.InitializingBean;
 
 /**
  * NexusServiceMesquite.java
@@ -28,7 +32,7 @@
  * @author Jin Ruan
  * 
  */
-public class NexusServiceMesquite extends AbstractServiceImpl implements NexusService {
+public class NexusServiceMesquite extends AbstractServiceImpl implements NexusService, InitializingBean {
 	private static final Logger LOGGER = Logger.getLogger(NexusServiceMesquite.class);
 	private static final String MESQUITE_FOLDER_DIR_KEY = "mesquite.folder_dir";
 
@@ -99,7 +103,28 @@
 	protected DomainHome getDomainHome() {
 		return null; // do not need persistence service.
 	}
+	
+	/** Looks up where Mesquite is installed on the host system and informs MesquiteModule of the location.  
+        (This is an implementation of a standard Spring bean initialization method, 
+         which is invoked after all properties are set.)
+   */
+	public void afterPropertiesSet() throws Exception {
+		String mesquiteFolderDir = null; 
+		InitialContext ic;
+		try {
+			ic = new InitialContext();
+			mesquiteFolderDir  = (String) ic.lookup("java:comp/env/tb2/MesquiteFolder");
+		} catch (NamingException e) {
+			LOGGER.fatal("Error looking up tb/MesquiteFolder via JNDI"); 
+		}
+		mesquiteFolderDir = mesquiteFolderDir + "/foo";   //since the last path element is somehow dropped subsequently... VG 2010-02-07
 
+		System.setProperty(MESQUITE_FOLDER_DIR_KEY, mesquiteFolderDir);
+		MesquiteModule.mesquiteDirectory = new File(mesquiteFolderDir);
+		MesquiteModule.mesquiteDirectoryPath = mesquiteFolderDir;				
+	}
+	
+
 	/** 
 	 * 
 	 * @see org.cipres.treebase.domain.nexus.NexusService#parseNexus(org.cipres.treebase.domain.study.Study, java.io.File)
@@ -185,18 +210,7 @@
 
 		return data;
 	}
-
-	/**
-	 * Set the mesquite folder dirtory to be used inside mesquite file "MesquiteModule.java".
-	 * 
-	 * @param pMesquiteFolderDir
-	 */
-	public void setMesquiteFolderDir(String pMesquiteFolderDir) {
-		System.setProperty(MESQUITE_FOLDER_DIR_KEY, pMesquiteFolderDir);
-		MesquiteModule.mesquiteDirectory = new File(pMesquiteFolderDir);
-		MesquiteModule.mesquiteDirectoryPath = pMesquiteFolderDir;
-	}
-
+	
 	@Override
 	public Class defaultResultClass() {
 		return null;

Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml	2010-02-04 17:46:20 UTC (rev 483)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml	2010-02-07 21:38:04 UTC (rev 484)
@@ -142,8 +142,7 @@
                 <property name="matrixDataTypeHome" ref="matrixDataTypeHome"/>
                 <property name="taxonLabelHome" ref="taxonLabelHome"/>
                 <property name="itemDefinitionHome" ref="itemDefinitionHome"/>
-                <property name="mesquiteFolderDir" value="${mesquite.folder_dir}"/>
-  </bean>
+   </bean>
   
   	<bean id="nexmlService" class = "org.cipres.treebase.service.nexus.NexusServiceNexml">
                 <!-- property name="domainHome" ref="domainHome"/ -->

Modified: trunk/treebase-core/src/main/resources/jdbc.properties.example
===================================================================
--- trunk/treebase-core/src/main/resources/jdbc.properties.example	2010-02-04 17:46:20 UTC (rev 483)
+++ trunk/treebase-core/src/main/resources/jdbc.properties.example	2010-02-07 21:38:04 UTC (rev 484)
@@ -1,16 +1,3 @@
-#### VG 2010-01-12 DB credentials that are used by the web application are now in JNDI -- see /treebase-web/src/main/webapp/META-INF/context.xml
-#### The credentials below are only used by tests and, possibly, by data importing classes in cipres.teebase.util
-#### (see treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java)
-
-jdbc.driverClassName=org.postgresql.Driver
-
-# Login credentials, obtain the actual values from
-# other developers (or create your own on a fresh install).
-jdbc.url=jdbc:postgresql://YOUR.SERVER.ORG/YOUR-DB
-jdbc.username=YOUR_USERNAME
-jdbc.password=YOUT_PASSWORD
-
-
 # This tells our object-relational mapping libraries
 # to use postgres-specific SQL dialect
 hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
@@ -23,5 +10,19 @@
 # options are: validate | update | create | create-drop
 hibernate.hbm2ddl.auto=
 
+
+#### VG 2010-02-07 Properties below are not read by the webapp anymore. 
+#### Instead, equivalent resources are looked up through JNDI -- see /treebase-web/src/main/webapp/META-INF/context.xml
+#### These properties are only read by tests and, possibly, by data importing classes in cipres.teebase.util
+#### (see treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java)
+
+jdbc.driverClassName=org.postgresql.Driver
+
+# Login credentials, obtain the actual values from
+# other developers (or create your own on a fresh install).
+jdbc.url=jdbc:postgresql://YOUR.SERVER.ORG/YOUR-DB
+jdbc.username=YOUR_USERNAME
+jdbc.password=YOUT_PASSWORD
+
 # Mesquite installation directory
-mesquite.folder_dir=/home/rvosa/applications/mesquiteHeadless/Mesquite_Folder/
+mesquite.folder_dir=/PATH/TO/YOUR/mesquite-2.01.tb

Modified: trunk/treebase-web/src/main/webapp/META-INF/context.xml.example
===================================================================
--- trunk/treebase-web/src/main/webapp/META-INF/context.xml.example	2010-02-04 17:46:20 UTC (rev 483)
+++ trunk/treebase-web/src/main/webapp/META-INF/context.xml.example	2010-02-07 21:38:04 UTC (rev 484)
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<!-- An example of META-INF/context.xml - a Tomcat-specific shorthand to specify JNDI resources during development. 
+<!-- This is an example of META-INF/context.xml - a Tomcat-specific shorthand to specify JNDI resources during development. 
      See http://tomcat.apache.org/tomcat-5.5-doc/jndi-datasource-examples-howto.html
  -->
 
-<!-- Copy this file (context.xml.example) to context.xml and replace YOUR-XXX strings with suitable credentials. 
-     (Note that context.xml is set to be ignored by SVN, so storing passwords there is safe.)  
+<!-- Copy this file (context.xml.example) to context.xml and replace YOUR-XXX strings with suitable values. 
+     (Note that context.xml is set to be ignored by SVN, so placing passwords there is safe.)  
      Make sure that $CATALINA_HOME/common/lib contains a postgres JDBC driver jar. 
      Now, dropping treebase-web.war to $CATALINA_HOME/webapps of a vanilla Tomcat should automatically create 
      config file $CATALINA_HOME/conf/Catalina/localhost/treebase-web.xml, 
@@ -16,13 +16,19 @@
 
 <Context reloadable="true">
 
-  <Resource name="jdbc/TreebaseDB" auth="Container"
-            type="javax.sql.DataSource" driverClassName="org.postgresql.Driver" 
+	 <Resource name="jdbc/TreebaseDB" auth="Container"
+            type="javax.sql.DataSource" 
+            description="The JNDI DataSource for the Treebase postgres instance."
+            driverClassName="org.postgresql.Driver" 
             url="jdbc:postgresql://YOUR-URL"
             username="YOUR-NAME" password="YOUR-PASS"
 			maxActive="20" maxIdle="10" maxWait="-1"
             />
-
+            
+	  <Environment name="tb2/MesquiteFolder" value="/PATH/TO/YOUR/mesquite-2.01.tb"
+         type="java.lang.String" override="false"
+	     description="Absolute path to the directory where headless Mesquite is unpacked on the host system."/>	
+	
 </Context>
 
 

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml	2010-02-04 17:46:20 UTC (rev 483)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml	2010-02-07 21:38:04 UTC (rev 484)
@@ -48,6 +48,12 @@
        <res-type>javax.sql.DataSource</res-type>
        <res-auth>Container</res-auth>
 	</resource-ref>
+
+    <env-entry>
+      <description>Absolute path to the directory where headless Mesquite is unpacked on the host system.</description>
+      <env-entry-name>tb2/MesquiteFolder</env-entry-name>
+      <env-entry-type>java.lang.String</env-entry-type>
+    </env-entry>	
  	
 
 	<!-- ========================================================== -->


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[Treebase-guts] SF.net SVN: treebase:[483] trunk/treebase-core

From: <vga...@us...> - 2010-02-04 17:46:26

Revision: 483
          http://treebase.svn.sourceforge.net/treebase/?rev=483&view=rev
Author:   vgapeyev
Date:     2010-02-04 17:46:20 +0000 (Thu, 04 Feb 2010)

Log Message:
-----------
Adding the dir that will be set up to keep track of DB schema snapshots and patches. 

Added Paths:
-----------
    trunk/treebase-core/db/
    trunk/treebase-core/db/README.txt
    trunk/treebase-core/db/TODO.txt

Added: trunk/treebase-core/db/README.txt
===================================================================
--- trunk/treebase-core/db/README.txt	                        (rev 0)
+++ trunk/treebase-core/db/README.txt	2010-02-04 17:46:20 UTC (rev 483)
@@ -0,0 +1,30 @@
+[This will contain instructions on how to do and commit patches. 
+For now, it's just a message from my email 2010-02-03  --VG]
+
+"A setup/discipline for schema changes"
+
+This brings up something that was on my back burner for a while:  
+setting up a workflow and a file/directory structure to maintain  
+schema patches. That would be something similar to migration scripts  
+in Ruby or Python (but with scripts written in SQL and no automation).
+
+The idea is that we store in SVN the initial snapshot of the DB schema  
+and sequential parches that we have been developing w.r.t  
+treebasedev.  These patches will be used to bring up-to-date  
+treebasestage, and then treebaseprod.   After that we can erase the  
+patches, refresh the snapshot, and continue for another cycle.   
+Official TB2 code releases are to be declared at the start of a cycle,  
+when there are no patches yet.  The snapshot is what should be used to  
+create a fresh TB2 instance.
+
+I suggest to create the directory treebase-code/db to store patches  
+and snapshots.  (Another option would be a separate project, treebase- 
+db, a a sibling of treebase-core and treebase-web.)
+
+Patches are to be sequentially numbered (by hand).  To keep track  
+which DB instance has already been brought up to which patch version,  
+I suggest creating a special table with a number column.  Each patch  
+will have an UPDATE setting the number in the table to the patch's  
+number.
+
+If this sounds ok, I hope to set this up by end of tomorrow.

Added: trunk/treebase-core/db/TODO.txt
===================================================================
--- trunk/treebase-core/db/TODO.txt	                        (rev 0)
+++ trunk/treebase-core/db/TODO.txt	2010-02-04 17:46:20 UTC (rev 483)
@@ -0,0 +1,7 @@
+Pending schema patches: 
+
+[To be put in as patches after the storage structure for them is in place in this directory -- VG 2010-02-04]:
+
+* Drop geospot_id_sequence -- there is no corresponding sequence
+* Correct PK name in stepmatrixelement and create stepmatrixelement_id_sequence
+* Create indexes, as suggested by Bill 2010-02-03 (and maybe later)


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[Treebase-guts] [ treebase-Bugs-2945440 ] User cannot download his trees within his own submission

From: SourceForge.net <no...@so...> - 2010-02-03 19:24:39

Bugs item #2945440, was opened at 2010-02-03 14:24
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945440&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: User cannot download his trees within his own submission

Initial Comment:
A basic user (in this case, username "tb3" with password "tb3", and submission 9923) who uploads a tree to his submission, is blocked from downloading the "reconstructed" tree from within the submission interface. To replicate the problem, login to submission 9923, go to the tree blocks:

http://treebasedb-dev.nescent.org:6666/treebase-web/user/treeBlockList.html

Then click on the "download reconstructed tree" links, e.g.:

http://treebasedb-dev.nescent.org:6666/treebase-web/user/downloadATreeBlock.html?treeblockid=9662

The result is "Access denied. Sorry! your action is not authorized." If you look inside the tree block and then try to download a reconstructed tree, you get a "Uncaught Exception Encountered" (see text below). 

These errors may be related to a recent fix that Rutger made to prevent "in progress" data from being accessed anonymously. The rules should be the following:

1. Anonymous users can only access data associated with studies that are considered "published" unless they use a /phylows/ url with a valid x-access-code parameter. Access as study with a valid x-access-code provides access to download links within that study throughout that session.

2. Users who create a submission can alway access the data in that submission regardless of status, but they can only edit data if the submission is "in progress"

3. Admin and Associate Editors can both access and edit all data regardless of status. 


bp


Uncaught Exception Encountered
java.lang.NullPointerException at org.cipres.treebase.web.controllers.AbstractDownloadController.generateAFileDynamically(AbstractDownloadController.java:125) at org.cipres.treebase.web.controllers.DownloadATreeController.handleRequest(DownloadATreeController.java:76) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/treeBlockList.html] itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/submissionList.html] JSESSIONID=[A56E40E535C9BD4451883A467D1473F0] __utma=[53240375.1924499357.1236724314.1264137469.1264687265.41] __utmz=[53240375.1263756485.39.6.utmccn]

----------------------------------------------------------------------

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[Treebase-guts] [ treebase-Bugs-2944669 ] Uploading Matrix Causes SQL Type Casting Error

From: SourceForge.net <no...@so...> - 2010-02-03 19:02:37

Bugs item #2944669, was opened at 2010-02-02 10:19
Message generated for change (Comment added) made by youjun
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2944669&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
>Status: Closed
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: youjun guo (youjun)
Summary: Uploading Matrix Causes SQL Type Casting Error

Initial Comment:
When I upload a matrix, there is an SQL error. It seems that DB2 and Pg handle booleans differently. Hilmar says "I think the 0 or 1 just needs to either be cast to boolean (0::bool or 1::bool), or hibernate has to be taught that the type in the database is Boolean, or the type of the object's corresponding attribute has to be made boolean." I'll attach a nexus file in case people need it for testing.


Data Access Failure

Failed to batch discrete matrix elements.; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.; nested exception is java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.

org.springframework.jdbc.UncategorizedSQLException: Failed to batch discrete matrix elements.; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.; nested exception is java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause. Caused by: java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537) at org.postgresql.core.v3.QueryExecutorImpl$1.handleError(QueryExecutorImpl.java:403) at org.postgresql.core.v3.QueryExecutorImpl$ErrorTrackingResultHandler.handleError(QueryExecutorImpl.java:283) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:332) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674) at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297) at org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC.batchDiscreteElements(DiscreteMatrixElementJDBC.java:114) at org.cipres.treebase.domain.nexus.mesquite.MesquiteStandardMatrixConverter.processMatrixElements(MesquiteStandardMatrixConverter.java:510) at org.cipres.treebase.dao.jdbc.MatrixJDBC.processMatrixElements(MatrixJDBC.java:428) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:592) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.addNexusFilesJDBC(Unknown Source) at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:196) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) « Back

----------------------------------------------------------------------

>Comment By: youjun guo (youjun)
Date: 2010-02-03 14:02

Message:
new  build pass the test on port 6666 installation, 

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[Treebase-guts] [ treebase-Bugs-2945410 ] Proxy Error for taxon->tree search

From: SourceForge.net <no...@so...> - 2010-02-03 18:36:22

Bugs item #2945410, was opened at 2010-02-03 13:36
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2945410&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: performance
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Proxy Error for taxon->tree search

Initial Comment:
If I do a taxon search (e.g. search for "Homo sapiens" as taxon variant name under the Taxa tab), and then click on the Trees tab (i.e. to get a selection of trees based on the selection of two Homo sapiens records) I get the proxy error below after exactly 2 minutes. That suggests to me that there is a time-out in operation, but it also says that the query is taking too long. By comparison, the exact same query on the SDSC/DB2 version (http://8ball.sdsc.edu:6666/treebase-web/) resulted in 630 trees returned in 31 seconds. I have created an artifact with priority 8 (https://sourceforge.net/tracker/?func=detail&aid=2945391&group_id=248804&atid=1126676) requesting that new indexes be added to speed up this query. But in addition, we should probably increase the 2 minute limit before getting a proxy error, seeing as some queries will take longer than two minutes no matter what we do -- and since a taxon search is such a basic type of query, I'm giving this proxy time-out error a priority of 9.  

Bill

===========
Proxy Error

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /treebase-web/search/treeSearch.html.

Reason: Error reading from remote server

Apache/2.2.3 (CentOS) Server at treebasedb-dev.nescent.org Port 80


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[Treebase-guts] [ treebase-Bugs-2945391 ] New Indices Needed

From: SourceForge.net <no...@so...> - 2010-02-03 18:04:30

Bugs item #2945391, was opened at 2010-02-03 13:04
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting: 
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Category: data
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Mark Dominus (mjdominus)
Summary: New Indices Needed

Initial Comment:
Because we have reverted to an older instance of the data (and schema), there are some changes that we may need to make. One is to create indexes on fields that are likely to be queried a lot using something like "CREATE INDEX taxonlabel_i ON taxonlabel USING btree (taxonlabel);". 

At the bottom is a list of all our existing indices -- although all the PKs are covered other fields would seem to benefit from an index. I would assume that the following fields need to be indexed:

Table			Field
--------			-------
taxon			name
taxonvariant		fullname
taxonlabel		taxonlabel
citation			title
citation			abstract
person			lastname

In addition, I would think that FKs need to be indexed as well, although I don't know which are the critical ones. What is clear is that some queries are very very slow. For example, do a taxon variant name search on "Homo sapiens" (this results in a selection of two taxon records) and then click the "Trees" tab -- after 2 minutes it returned a "Proxy Error: The proxy server received an invalid response from an upstream server. Reason: Error reading from remote host" which I'm guessing is a time-out of some sort. At any rate, the FK called taxonlabel_id and the FK called phylotree_id in the phylotreenode table probably should be indexed to speed up querying for trees based on a selection of taxa. 

Undoubtedly there are other FKs that need indexing, but this requires knowledge on how common queries are made via hibernate.

These changes to the schema should be applied to both the dev and stage databases, as well as noted in the instantiation scripts.

bp



SELECT n.nspname AS "Schema", t.relname AS "Table", c.relname AS "Index"
FROM pg_catalog.pg_class c
     JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace
     JOIN pg_catalog.pg_index i ON i.indexrelid = c.oid
     JOIN pg_catalog.pg_class t ON i.indrelid = t.oid
WHERE c.relkind = 'i'
    AND n.nspname NOT IN ('pg_catalog', 'pg_toast')
    AND pg_catalog.pg_table_is_visible(c.oid)
ORDER BY n.nspname, t.relname, c.relname;

 Schema |            Table            |                   Index                    
--------+-----------------------------+--------------------------------------------
 public | algorithm                   | algorithm_pkey
 public | analysis                    | analysis_pkey
 public | analysis                    | analysis_study_id_idx
 public | analysisstep                | analysisstep_pkey
 public | analyzeddata                | analyzeddata_pkey
 public | ancestralstate              | ancestralstate_pkey
 public | ancstateset                 | ancstateset_pkey
 public | chargroup                   | chargroup_pkey
 public | chargroup_colrange          | chargroup_colrange_columnrange_id_key
 public | charpartition               | charpartition_pkey
 public | charset                     | charset_pkey
 public | charset_colrange            | charset_colrange_columnrange_id_key
 public | charweight                  | charweight_pkey
 public | charweight_colrange         | charweight_colrange_columnrange_id_key
 public | charweightset               | charweightset_pkey
 public | citation                    | citation_pkey
 public | citation_author             | citation_author_pkey
 public | citation_editor             | citation_editor_pkey
 public | citationstatus              | citationstatus_pkey
 public | coderecord_colrange         | coderecord_colrange_columnrange_id_key
 public | codonchar1_colrange         | codonchar1_colrange_columnrange_id_key
 public | codonchar2_colrange         | codonchar2_colrange_columnrange_id_key
 public | codonchar3_colrange         | codonchar3_colrange_columnrange_id_key
 public | codonnoncoding_colrange     | codonnoncoding_colrange_columnrange_id_key
 public | codonpositionset            | codonpositionset_pkey
 public | columnrange                 | columnrange_pkey
 public | compound_element            | compound_element_element_id_key
 public | compound_element            | compound_element_pkey
 public | cstreenode                  | cstreenode_pkey
 public | discretecharstate           | discretecharstate_phylochar_id_idx
 public | discretecharstate           | discretecharstate_pkey
 public | distancematrixelement       | distancematrixelement_pkey
 public | gapmode                     | gapmode_pkey
 public | geneticcode                 | geneticcode_pkey
 public | geneticcoderecord           | geneticcoderecord_pkey
 public | geneticcodeset              | geneticcodeset_pkey
 public | help                        | help_pkey
 public | itemdefinition              | itemdefinition_pkey
 public | itemvalue                   | itemvalue_pkey
 public | matrix                      | matrix_pkey
 public | matrix_itemdefinition       | matrix_itemdefinition_pkey
 public | matrixcolumn                | matrixcolumn_phylochar_id_idx
 public | matrixcolumn                | matrixcolumn_pkey
 public | matrixcolumn_itemdefinition | matrixcolumn_itemdefinition_pkey
 public | matrixdatatype              | matrixdatatype_phylochar_id_idx
 public | matrixdatatype              | matrixdatatype_pkey
 public | matrixelement               | matrixelement_discretecharstate_id_idx
 public | matrixelement               | matrixelement_itemdefinition_id_idx
 public | matrixelement               | matrixelement_pkey
 public | matrixkind                  | matrixkind_pkey
 public | matrixrow                   | matrixrow_matrix_id_idx
 public | matrixrow                   | matrixrow_pkey
 public | matrixrow                   | matrixrow_taxonlabel_id_idx
 public | nodeattribute               | nodeattribute_pkey
 public | person                      | person_pkey
 public | phylochar                   | phylochar_pkey
 public | phylotree                   | phylotree_pkey
 public | phylotreenode               | phylotreenode_pkey
 public | polytcount                  | polytcount_pkey
 public | rowsegment                  | rowsegment_matrixrow_id_idx
 public | rowsegment                  | rowsegment_pkey
 public | software                    | software_pkey
 public | statechangeset              | statechangeset_pkey
 public | stateformat                 | stateformat_pkey
 public | statemodifier               | statemodifier_pkey
 public | stateset                    | stateset_pkey
 public | stepmatrixelement           | stepmatrixelement_pkey
 public | study                       | study_citation_id_idx
 public | study                       | study_pkey
 public | study_nexusfile             | study_nexusfile_pkey
 public | studystatus                 | studystatus_pkey
 public | sub_matrix                  | sub_matrix_matrix_id_key
 public | sub_matrix                  | sub_matrix_pkey
 public | sub_taxonlabel              | sub_taxonlabel_pkey
 public | sub_taxonlabel              | sub_taxonlabel_taxonlabel_id_key
 public | sub_treeblock               | sub_treeblock_pkey
 public | sub_treeblock               | sub_treeblock_treeblock_id_key
 public | submission                  | submission_pkey
 public | submission                  | submission_study_id_idx
 public | submission                  | submission_study_id_key
 public | taxon                       | taxon_pkey
 public | taxonauthority              | taxonauthority_pkey
 public | taxonlabel                  | taxonlabel_pkey
 public | taxonlabelgroup             | taxonlabelgroup_pkey
 public | taxonlabelpartition         | taxonlabelpartition_pkey
 public | taxonlabelset               | taxonlabelset_pkey
 public | taxonlabelset_taxonlabel    | taxonlabelset_taxonlabel_pkey
 public | taxonlink                   | taxonlink_pkey
 public | taxonset                    | taxonset_pkey
 public | taxonset_taxon              | taxonset_taxon_pkey
 public | taxonvariant                | taxonvariant_pkey
 public | treeattribute               | treeattribute_pkey
 public | treeblock                   | treeblock_pkey
 public | treegroup                   | treegroup_pkey
 public | treegroup_phylotree         | treegroup_phylotree_pkey
 public | treekind                    | treekind_pkey
 public | treenodeedge                | treenodeedge_pkey
 public | treepartition               | treepartition_pkey
 public | treequality                 | treequality_pkey
 public | treeset                     | treeset_pkey
 public | treeset_phylotree           | treeset_phylotree_pkey
 public | treetype                    | treetype_pkey
 public | typeset                     | typeset_pkey
 public | user                        | user_pkey
 public | user                        | user_username_key
 public | userrole                    | userrole_pkey
 public | usertype                    | usertype_pkey
 public | usertyperecord              | usertyperecord_pkey
 public | usertyperrd_colrange        | usertyperrd_colrange_columnrange_id_key
(109 rows)


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[Treebase-guts] SF.net SVN: treebase:[482] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain

From: <vga...@us...> - 2010-02-03 14:53:03

Revision: 482
          http://treebase.svn.sourceforge.net/treebase/?rev=482&view=rev
Author:   vgapeyev
Date:     2010-02-03 14:52:56 +0000 (Wed, 03 Feb 2010)

Log Message:
-----------
Changed to a custom ID generator, which relies on the naming convention to translate a table name XXX to the sequence name XXX_id_sequence. 

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java

Added Paths:
-----------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TB2SequenceGenerator.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java	2010-02-02 20:54:48 UTC (rev 481)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java	2010-02-03 14:52:56 UTC (rev 482)
@@ -15,6 +15,7 @@
 import org.cipres.treebase.NamespacedGUID;
 import org.cipres.treebase.PhyloWSPath;
 import org.cipres.treebase.TreebaseIDString;
+import org.hibernate.annotations.GenericGenerator;
 
 /**
  * The abstract super class for all persisted domain objects.
@@ -53,8 +54,9 @@
 	 * @see org.cipres.treebase.domain.TBPersistable#getId()
 	 */
 	@Id
-	@GeneratedValue(strategy = GenerationType.SEQUENCE)
-	public Long getId() {
+	@GenericGenerator(name="TB2SEQGEN", strategy = "org.cipres.treebase.domain.TB2SequenceGenerator")	  
+	@GeneratedValue(generator="TB2SEQGEN")
+		public Long getId() {
 		return mId;
 	}
 

Added: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TB2SequenceGenerator.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TB2SequenceGenerator.java	                        (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/TB2SequenceGenerator.java	2010-02-03 14:52:56 UTC (rev 482)
@@ -0,0 +1,34 @@
+package org.cipres.treebase.domain;
+
+import java.util.Properties;
+
+import org.hibernate.MappingException;
+import org.hibernate.type.Type;
+import org.hibernate.dialect.Dialect;
+import org.hibernate.id.PersistentIdentifierGenerator;
+import org.hibernate.id.SequenceGenerator;
+
+
+
+/**  Custom id generator that translates table name to the name of an appropriate sequence.
+ *   Code taken from https://www.hibernate.org/296.html 2010-02-01, where it was attributed to  Mr. Rob Hasselbaum. 
+ *   Usage is in AbstractPersistedObject.java.
+ *   --VG
+ * */ 
+public class TB2SequenceGenerator extends SequenceGenerator {
+
+    /**
+     * If the parameters do not contain a {@link SequenceGenerator#SEQUENCE} name, we
+     * assign one based on the table name.
+     */
+    public void configure(Type type, Properties params, Dialect dialect) throws MappingException {
+        if(params.getProperty(SEQUENCE) == null || params.getProperty(SEQUENCE).length() == 0) {
+            String tableName = params.getProperty(PersistentIdentifierGenerator.TABLE);
+            if(tableName != null) {
+                String seqName = tableName + "_id_sequence";
+                params.setProperty(SEQUENCE, seqName);               
+            }
+        }
+        super.configure(type, params, dialect);
+    }
+}


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[Treebase-guts] SF.net SVN: treebase:[481] trunk/treebase-core/src/main/java/org/cipres/ treebase/dao/jdbc

From: <yo...@us...> - 2010-02-02 20:54:54

Revision: 481
          http://treebase.svn.sourceforge.net/treebase/?rev=481&view=rev
Author:   youjun
Date:     2010-02-02 20:54:48 +0000 (Tue, 02 Feb 2010)

Log Message:
-----------
fix sql, postgresql will not accept 1,0 for boolean type

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java	2010-01-25 20:27:40 UTC (rev 480)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/ContinuousMatrixElementJDBC.java	2010-02-02 20:54:48 UTC (rev 481)
@@ -83,7 +83,7 @@
 				// DISCRETECHARSTATE_ID
 
 				ps.setDouble(1, e.getValue()); // Value
-				ps.setShort(2, e.getGap()); // Gap
+				ps.setBoolean(2, e.getGap()); // Gap
 				ps.setLong(3, e.getMatrixColID()); // MATRIXCOLUMN_ID
 				// ps.setLong(4, 0); // ITEMDEFINITION_ID //Only by compound elements. 
 				ps.setLong(4, e.getMatrixRowID()); // MATRIXROW_ID
@@ -125,8 +125,8 @@
 	 * 
 	 * @return short mGap
 	 */
-	public short getGap() {
-		return mGap;
+	public boolean getGap() {
+		return (mGap!=0);
 	}
 
 	/**

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java	2010-01-25 20:27:40 UTC (rev 480)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/jdbc/DiscreteMatrixElementJDBC.java	2010-02-02 20:54:48 UTC (rev 481)
@@ -93,7 +93,7 @@
 				// Value: (continuous)
 				// ITEMDEFINITION_ID: (continuous)
 
-				ps.setShort(1, e.getGap()); // Gap
+				ps.setBoolean(1, e.getGap()); // Gap
 				ps.setLong(2, e.getMatrixColID()); // MATRIXCOLUMN_ID
 				ps.setLong(3, e.getMatrixRowID()); // MATRIXROW_ID
 
@@ -138,8 +138,8 @@
 	 * 
 	 * @return short mGap
 	 */
-	public short getGap() {
-		return mGap;
+	public boolean getGap() {
+		return (mGap!=0);
 	}
 
 	/**


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[Treebase-guts] [ treebase-Bugs-2944669 ] Uploading Matrix Causes SQL Type Casting Error

From: SourceForge.net <no...@so...> - 2010-02-02 16:02:52

Bugs item #2944669, was opened at 2010-02-02 10:19
Message generated for change (Settings changed) made by youjun
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2944669&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: youjun guo (youjun)
Summary: Uploading Matrix Causes SQL Type Casting Error

Initial Comment:
When I upload a matrix, there is an SQL error. It seems that DB2 and Pg handle booleans differently. Hilmar says "I think the 0 or 1 just needs to either be cast to boolean (0::bool or 1::bool), or hibernate has to be taught that the type in the database is Boolean, or the type of the object's corresponding attribute has to be made boolean." I'll attach a nexus file in case people need it for testing.


Data Access Failure

Failed to batch discrete matrix elements.; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.; nested exception is java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.

org.springframework.jdbc.UncategorizedSQLException: Failed to batch discrete matrix elements.; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.; nested exception is java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause. Caused by: java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537) at org.postgresql.core.v3.QueryExecutorImpl$1.handleError(QueryExecutorImpl.java:403) at org.postgresql.core.v3.QueryExecutorImpl$ErrorTrackingResultHandler.handleError(QueryExecutorImpl.java:283) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:332) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674) at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297) at org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC.batchDiscreteElements(DiscreteMatrixElementJDBC.java:114) at org.cipres.treebase.domain.nexus.mesquite.MesquiteStandardMatrixConverter.processMatrixElements(MesquiteStandardMatrixConverter.java:510) at org.cipres.treebase.dao.jdbc.MatrixJDBC.processMatrixElements(MatrixJDBC.java:428) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:592) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.addNexusFilesJDBC(Unknown Source) at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:196) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) « Back

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[Treebase-guts] [ treebase-Bugs-2944669 ] Uploading Matrix Causes SQL Type Casting Error

From: SourceForge.net <no...@so...> - 2010-02-02 15:19:27

Bugs item #2944669, was opened at 2010-02-02 10:19
Message generated for change (Tracker Item Submitted) made by sfrgpiel
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Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Uploading Matrix Causes SQL Type Casting Error

Initial Comment:
When I upload a matrix, there is an SQL error. It seems that DB2 and Pg handle booleans differently. Hilmar says "I think the 0 or 1 just needs to either be cast to boolean (0::bool or 1::bool), or hibernate has to be taught that the type in the database is Boolean, or the type of the object's corresponding attribute has to be made boolean." I'll attach a nexus file in case people need it for testing.


Data Access Failure

Failed to batch discrete matrix elements.; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.; nested exception is java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.

org.springframework.jdbc.UncategorizedSQLException: Failed to batch discrete matrix elements.; uncategorized SQLException for SQL []; SQL state [null]; error code [0]; Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause.; nested exception is java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause. Caused by: java.sql.BatchUpdateException: Batch entry 0 INSERT INTO MATRIXELEMENT(TYPE, MATRIXELEMENT_ID, VERSION, GAP, MATRIXCOLUMN_ID, MATRIXROW_ID, DISCRETECHARSTATE_ID, ELEMENT_ORDER) VALUES('D', default, 1, 0, 16000002789, 160000027790, 4, 0) was aborted. Call getNextException to see the cause. at org.postgresql.jdbc2.AbstractJdbc2Statement$BatchResultHandler.handleError(AbstractJdbc2Statement.java:2537) at org.postgresql.core.v3.QueryExecutorImpl$1.handleError(QueryExecutorImpl.java:403) at org.postgresql.core.v3.QueryExecutorImpl$ErrorTrackingResultHandler.handleError(QueryExecutorImpl.java:283) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1328) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:332) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeBatch(AbstractJdbc2Statement.java:2674) at org.apache.tomcat.dbcp.dbcp.DelegatingStatement.executeBatch(DelegatingStatement.java:297) at org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC.batchDiscreteElements(DiscreteMatrixElementJDBC.java:114) at org.cipres.treebase.domain.nexus.mesquite.MesquiteStandardMatrixConverter.processMatrixElements(MesquiteStandardMatrixConverter.java:510) at org.cipres.treebase.dao.jdbc.MatrixJDBC.processMatrixElements(MatrixJDBC.java:428) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:592) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.addNexusFilesJDBC(Unknown Source) at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:196) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) « Back

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[Treebase-guts] [ treebase-Bugs-2941145 ] Exception when editing a taxon label

From: SourceForge.net <no...@so...> - 2010-02-01 22:11:16

Bugs item #2941145, was opened at 2010-01-27 17:21
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
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Category: ui
Group: None
>Status: Closed
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: Exception when editing a taxon label

Initial Comment:
After uploading a tree, I tried to edit a taxon label (http://treebasedb-dev.nescent.org:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=160000022315) and got a big exception -- something about a missing class. 

Uncaught Exception Encountered
java.lang.NoClassDefFoundError: Could not initialize class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$3a7ae697 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at net.sf.cglib.proxy.Enhancer.setCallbacksHelper(Enhancer.java:616) at net.sf.cglib.proxy.Enhancer.setThreadCallbacks(Enhancer.java:609) at net.sf.cglib.proxy.Enhancer.registerCallbacks(Enhancer.java:578) at org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.getProxyInstance(CGLIBLazyInitializer.java:110) at org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.getProxy(CGLIBLazyInitializer.java:93) at org.hibernate.proxy.pojo.cglib.CGLIBProxyFactory.getProxy(CGLIBProxyFactory.java:49) at org.hibernate.tuple.entity.AbstractEntityTuplizer.createProxy(AbstractEntityTuplizer.java:379) at org.hibernate.persister.entity.AbstractEntityPersister.createProxy(AbstractEntityPersister.java:3460) at org.hibernate.event.def.DefaultLoadEventListener.createProxyIfNecessary(DefaultLoadEventListener.java:257) at org.hibernate.event.def.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:191) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:103) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.internalLoad(SessionImpl.java:846) at org.hibernate.type.EntityType.resolveIdentifier(EntityType.java:557) at org.hibernate.type.EntityType.resolve(EntityType.java:379) at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:120) at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854) at org.hibernate.loader.Loader.doQuery(Loader.java:729) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.doList(Loader.java:2213) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104) at org.hibernate.loader.Loader.list(Loader.java:2099) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569) at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283) at org.hibernate.impl.CriteriaImpl.uniqueResult(CriteriaImpl.java:305) at org.cipres.treebase.dao.AbstractDAO.findPersistedObjectByID(AbstractDAO.java:118) at sun.reflect.GeneratedMethodAccessor139.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy64.findPersistedObjectByID(Unknown Source) at org.cipres.treebase.service.taxon.TaxonLabelServiceImpl.findByID(TaxonLabelServiceImpl.java:106) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy81.findByID(Unknown Source) at org.cipres.treebase.web.controllers.EditTaxonLabelController.formBackingObject(EditTaxonLabelController.java:283) at org.springframework.web.servlet.mvc.AbstractFormController.getErrorsForNewForm(AbstractFormController.java:358) at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm(AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:278) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/taxaList.html] JSESSIONID=[D8DBFE309A8CE8933D7C825D25810660] __utma=[53240375.1924499357.1236724314.1263756485.1264137469.40] __utmz=[53240375.1263756485.39.6.utmccn]

----------------------------------------------------------------------

>Comment By: Rutger Vos (rvos)
Date: 2010-02-01 22:11

Message:
Rebuilding and re-deploying has fixed this missing class problem on
treebase-dev.nescent.org:6666

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Comment By: Rutger Vos (rvos)
Date: 2010-02-01 22:11

Message:
Your bug has been resolved.  Thanks for the report.


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[Treebase-guts] [ treebase-Bugs-2941145 ] Exception when editing a taxon label

From: SourceForge.net <no...@so...> - 2010-01-29 19:46:25

Bugs item #2941145, was opened at 2010-01-27 12:21
Message generated for change (Settings changed) made by youjun
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Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: youjun guo (youjun)
Summary: Exception when editing a taxon label

Initial Comment:
After uploading a tree, I tried to edit a taxon label (http://treebasedb-dev.nescent.org:6666/treebase-web/user/editTaxonLabel.html?taxonlabelid=160000022315) and got a big exception -- something about a missing class. 

Uncaught Exception Encountered
java.lang.NoClassDefFoundError: Could not initialize class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$3a7ae697 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at net.sf.cglib.proxy.Enhancer.setCallbacksHelper(Enhancer.java:616) at net.sf.cglib.proxy.Enhancer.setThreadCallbacks(Enhancer.java:609) at net.sf.cglib.proxy.Enhancer.registerCallbacks(Enhancer.java:578) at org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.getProxyInstance(CGLIBLazyInitializer.java:110) at org.hibernate.proxy.pojo.cglib.CGLIBLazyInitializer.getProxy(CGLIBLazyInitializer.java:93) at org.hibernate.proxy.pojo.cglib.CGLIBProxyFactory.getProxy(CGLIBProxyFactory.java:49) at org.hibernate.tuple.entity.AbstractEntityTuplizer.createProxy(AbstractEntityTuplizer.java:379) at org.hibernate.persister.entity.AbstractEntityPersister.createProxy(AbstractEntityPersister.java:3460) at org.hibernate.event.def.DefaultLoadEventListener.createProxyIfNecessary(DefaultLoadEventListener.java:257) at org.hibernate.event.def.DefaultLoadEventListener.proxyOrLoad(DefaultLoadEventListener.java:191) at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:103) at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:878) at org.hibernate.impl.SessionImpl.internalLoad(SessionImpl.java:846) at org.hibernate.type.EntityType.resolveIdentifier(EntityType.java:557) at org.hibernate.type.EntityType.resolve(EntityType.java:379) at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:120) at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:854) at org.hibernate.loader.Loader.doQuery(Loader.java:729) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.doList(Loader.java:2213) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104) at org.hibernate.loader.Loader.list(Loader.java:2099) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569) at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283) at org.hibernate.impl.CriteriaImpl.uniqueResult(CriteriaImpl.java:305) at org.cipres.treebase.dao.AbstractDAO.findPersistedObjectByID(AbstractDAO.java:118) at sun.reflect.GeneratedMethodAccessor139.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy64.findPersistedObjectByID(Unknown Source) at org.cipres.treebase.service.taxon.TaxonLabelServiceImpl.findByID(TaxonLabelServiceImpl.java:106) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy81.findByID(Unknown Source) at org.cipres.treebase.web.controllers.EditTaxonLabelController.formBackingObject(EditTaxonLabelController.java:283) at org.springframework.web.servlet.mvc.AbstractFormController.getErrorsForNewForm(AbstractFormController.java:358) at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm(AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:278) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: itemToHighlight=[http%3A//treebasedb-dev.nescent.org%3A6666/treebase-web/user/taxaList.html] JSESSIONID=[D8DBFE309A8CE8933D7C825D25810660] __utma=[53240375.1924499357.1236724314.1263756485.1264137469.40] __utmz=[53240375.1263756485.39.6.utmccn]

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