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[Treebase-guts] SF.net SVN: treebase:[714] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/Taxon.java

From: <rv...@us...> - 2010-06-04 11:26:39

Revision: 714
          http://treebase.svn.sourceforge.net/treebase/?rev=714&view=rev
Author:   rvos
Date:     2010-06-04 11:26:33 +0000 (Fri, 04 Jun 2010)

Log Message:
-----------
Adding annotation of tb:identifier.taxon.tb1

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-06-04 11:25:52 UTC (rev 713)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/Taxon.java	2010-06-04 11:26:33 UTC (rev 714)
@@ -261,6 +261,9 @@
 				annotations.add(new Annotation(Constants.SKOSURI,"skos:exactMatch",Constants.uBioBase + getUBioNamebankId()));
 				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.ubio", getUBioNamebankId()));				
 			}
+			if ( null != getTB1LegacyId() ) {
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxon.tb1", getTB1LegacyId()));
+			}
 		} catch ( Exception e ) {
 			e.printStackTrace();
 		}


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[Treebase-guts] SF.net SVN: treebase:[713] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/taxon/TaxonVariant.java

From: <rv...@us...> - 2010-06-04 11:25:58

Revision: 713
          http://treebase.svn.sourceforge.net/treebase/?rev=713&view=rev
Author:   rvos
Date:     2010-06-04 11:25:52 +0000 (Fri, 04 Jun 2010)

Log Message:
-----------
Adding annotation of tb:identifier.taxonVariant.tb1

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonVariant.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonVariant.java	2010-06-04 11:25:16 UTC (rev 712)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonVariant.java	2010-06-04 11:25:52 UTC (rev 713)
@@ -1,6 +1,8 @@
 
 package org.cipres.treebase.domain.taxon;
 
+import java.util.List;
+
 import javax.persistence.AttributeOverride;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -18,7 +20,9 @@
 import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.Index;
 
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.domain.AbstractPersistedObject;
+import org.cipres.treebase.domain.Annotation;
 import org.cipres.treebase.domain.TBPersistable;
 
 /**
@@ -178,4 +182,17 @@
 	public String getLabel() {
 		return getFullName();
 	}
+	
+	@Transient
+	public List<Annotation> getAnnotations() {
+		List<Annotation> annotations = super.getAnnotations();
+		try {
+			if ( null != getTB1LegacyId() ) {
+				annotations.add(new Annotation(Constants.TBTermsURI, "tb:identifier.taxonVariant.tb1", getTB1LegacyId()));
+			}
+		} catch ( Exception e ) {
+			e.printStackTrace();
+		}
+		return annotations;
+	}	
 }


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[Treebase-guts] SF.net SVN: treebase:[712] trunk/treebase-core/src/main/resources/treebase. owl

From: <rv...@us...> - 2010-06-04 11:25:22

Revision: 712
          http://treebase.svn.sourceforge.net/treebase/?rev=712&view=rev
Author:   rvos
Date:     2010-06-04 11:25:16 +0000 (Fri, 04 Jun 2010)

Log Message:
-----------
Adding CQL search predicate ontology.

Added Paths:
-----------
    trunk/treebase-core/src/main/resources/treebase.owl

Added: trunk/treebase-core/src/main/resources/treebase.owl
===================================================================
--- trunk/treebase-core/src/main/resources/treebase.owl	                        (rev 0)
+++ trunk/treebase-core/src/main/resources/treebase.owl	2010-06-04 11:25:16 UTC (rev 712)
@@ -0,0 +1,251 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+    <!ENTITY owl2 "http://www.w3.org/2006/12/owl2#" >
+    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+    <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
+    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+]>
+
+
+<rdf:RDF xmlns="http://purl.org/phylo/treebase/2.0/terms#"
+     xml:base="http://purl.org/phylo/treebase/2.0/terms#"
+     xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:owl2="http://www.w3.org/2006/12/owl2#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:owl="http://www.w3.org/2002/07/owl#">
+    <owl:Ontology rdf:about="">
+        <owl:imports rdf:resource="http://dublincore.org/2008/01/14/dcterms.rdf"/>
+    </owl:Ontology>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://purl.org/dc/elements/1.1/identifier -->
+
+    <owl:ObjectProperty rdf:about="http://purl.org/dc/elements/1.1/identifier"/>
+    
+
+
+    <!-- http://purl.org/dc/terms/extent -->
+
+    <owl:ObjectProperty rdf:about="http://purl.org/dc/terms/extent"/>
+    
+
+
+    <!-- http://purl.org/dc/terms/title -->
+
+    <owl:ObjectProperty rdf:about="http://purl.org/dc/terms/title"/>
+    
+
+
+    <!-- http://purl.org/dc/terms/type -->
+
+    <owl:ObjectProperty rdf:about="http://purl.org/dc/terms/type"/>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.matrix -->
+
+    <owl:ObjectProperty rdf:about="identifier.matrix">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.ncbi -->
+
+    <owl:ObjectProperty rdf:about="identifier.ncbi">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.study -->
+
+    <owl:ObjectProperty rdf:about="identifier.study">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.study.tb1 -->
+
+    <owl:ObjectProperty rdf:about="identifier.study.tb1">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.taxon -->
+
+    <owl:ObjectProperty rdf:about="identifier.taxon">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.taxon.tb1 -->
+
+    <owl:ObjectProperty rdf:about="identifier.taxon.tb1">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>    
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.taxonLabel -->
+
+    <owl:ObjectProperty rdf:about="identifier.taxonLabel">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.taxonVariant -->
+
+    <owl:ObjectProperty rdf:about="identifier.taxonVariant">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+    
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.taxonVariant.tb1 -->
+
+    <owl:ObjectProperty rdf:about="identifier.taxonVariant.tb1">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.tree -->
+
+    <owl:ObjectProperty rdf:about="identifier.tree">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#identifier.ubio -->
+
+    <owl:ObjectProperty rdf:about="identifier.ubio">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/identifier"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#kind.tree -->
+
+    <owl:ObjectProperty rdf:about="kind.tree">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/type"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#nchar.matrix -->
+
+    <owl:ObjectProperty rdf:about="nchar.matrix">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/extent"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#ntax.matrix -->
+
+    <owl:ObjectProperty rdf:about="ntax.matrix">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/extent"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#ntax.tree -->
+
+    <owl:ObjectProperty rdf:about="ntax.tree">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/extent"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#quality.tree -->
+
+    <owl:ObjectProperty rdf:about="quality.tree">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/type"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#title.matrix -->
+
+    <owl:ObjectProperty rdf:about="title.matrix">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/title"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#title.study -->
+
+    <owl:ObjectProperty rdf:about="title.study">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/title"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#title.taxon -->
+
+    <owl:ObjectProperty rdf:about="title.taxon">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/title"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#title.taxonLabel -->
+
+    <owl:ObjectProperty rdf:about="title.taxonLabel">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/title"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#title.taxonVariant -->
+
+    <owl:ObjectProperty rdf:about="title.taxonVariant">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/title"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#title.tree -->
+
+    <owl:ObjectProperty rdf:about="title.tree">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/title"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#type.matrix -->
+
+    <owl:ObjectProperty rdf:about="type.matrix">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/type"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- http://purl.org/phylo/treebase/2.0/terms#type.tree -->
+
+    <owl:ObjectProperty rdf:about="type.tree">
+        <rdfs:subPropertyOf rdf:resource="http://purl.org/dc/terms/type"/>
+    </owl:ObjectProperty>
+</rdf:RDF>


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[Treebase-guts] SF.net SVN: treebase:[711] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/AbstractPersistedObject.java

From: <rv...@us...> - 2010-06-03 17:16:17

Revision: 711
          http://treebase.svn.sourceforge.net/treebase/?rev=711&view=rev
Author:   rvos
Date:     2010-06-03 17:16:11 +0000 (Thu, 03 Jun 2010)

Log Message:
-----------
Where available, now adds rdfs:isDefinedBy annotations that point to the containing context (e.g. for a tree, the study in which it is published). This is on the recommendation of the SADI bunch, and at @rdmpage's request.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.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	2010-06-03 17:14:46 UTC (rev 710)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/AbstractPersistedObject.java	2010-06-03 17:16:11 UTC (rev 711)
@@ -115,6 +115,11 @@
 		List<Annotation> annotations = new ArrayList<Annotation>();
 		URI uri = URI.create(TreebaseUtil.getPurlBase()+getPhyloWSPath());
 		annotations.add(new Annotation(Constants.OWLURI,"owl:sameAs",uri));
+		TBPersistable context = getContext();
+		if ( null != context ) {
+			URI contextUri = URI.create(TreebaseUtil.getPurlBase()+context.getPhyloWSPath());
+			annotations.add(new Annotation(Constants.RDFSURI, "rdfs:isDefinedBy",contextUri));
+		}
 		return annotations;
 	}
 


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[Treebase-guts] SF.net SVN: treebase:[710] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceRDFa.java

From: <rv...@us...> - 2010-06-03 17:14:52

Revision: 710
          http://treebase.svn.sourceforge.net/treebase/?rev=710&view=rev
Author:   rvos
Date:     2010-06-03 17:14:46 +0000 (Thu, 03 Jun 2010)

Log Message:
-----------
Now changes local URIs into global ones, based on the owl:sameAs value

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	2010-06-03 17:13:16 UTC (rev 709)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-06-03 17:14:46 UTC (rev 710)
@@ -6,17 +6,23 @@
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
 import java.util.Properties;
 
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.apache.log4j.Logger;
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.domain.nexus.NexusDataSet;
 import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
 import org.cipres.treebase.domain.study.Study;
 import org.dom4j.DocumentException;
+import org.dom4j.Node;
 import org.dom4j.QName;
 import org.dom4j.io.DocumentResult;
 import org.dom4j.io.DocumentSource;
@@ -72,42 +78,50 @@
 	}
 	
 	/**
-	 * 
+	 * Changes local URIs into global ones, based on owl:sameAs annotations
 	 * @param cdaoDoc
 	 */
 	private void normalizeCdaoDoc (org.dom4j.Document cdaoDoc) {
+		Map<String,String> resourceForId = new HashMap<String,String>();
+		QName rdfAboutQName = QName.get("about", "rdf", Constants.RDFURI.toString());
+		QName rdfResourceQName = QName.get("resource", "rdf", Constants.RDFURI.toString());
+		QName rdfIDQName = QName.get("ID", "rdf", Constants.RDFURI.toString());
 		
 		LOGGER.info("inside normalizeCdaoDoc");
-		Iterator<org.dom4j.Element> parentIterator = cdaoDoc.getRootElement().elementIterator();
-		while ( parentIterator.hasNext() ) {
-			org.dom4j.Element parent = parentIterator.next();
-			QName rdfIDQName = QName.get("ID", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
-			String rdfID = parent.attributeValue(rdfIDQName);
-			if ( ! TreebaseUtil.isEmpty(rdfID) ) {
-				
-				LOGGER.info("going to flatten ID "+rdfID);
-				Iterator<org.dom4j.Element> childIterator = cdaoDoc.getRootElement().elementIterator();
-				while ( childIterator.hasNext() ) {
-					org.dom4j.Element child = childIterator.next();
-					QName rdfAboutQName = QName.get("about", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
-					String rdfAbout = child.attributeValue(rdfAboutQName);
-					
-					if ( ! TreebaseUtil.isEmpty(rdfAbout) && rdfAbout.equals("#"+rdfID) ) {
-						
-						LOGGER.info("found referencing element");
-						Iterator<org.dom4j.Element> grandChildIterator = child.elementIterator();
-						while ( grandChildIterator.hasNext() ) {
-							org.dom4j.Element grandChild = grandChildIterator.next();
-							grandChild.detach();
-							parent.add(grandChild);
-						}
-						
-						childIterator.remove();
-					}
-
-				}
+		List<org.dom4j.Element> sameAsObjects = cdaoDoc.selectNodes("//owl:sameAs[@rdf:resource]");
+		for ( org.dom4j.Element sameAsElt : sameAsObjects ) {
+			org.dom4j.Element subjectElt = sameAsElt.getParent();
+			String id = subjectElt.attributeValue(rdfAboutQName).substring(1); // remove #
+			String resource = sameAsElt.attributeValue(rdfResourceQName);
+			resourceForId.put(id, resource);			
+			subjectElt.detach();
+		}
+		
+		// replace ID attributes
+		List<org.dom4j.Element> identifiableObjects = cdaoDoc.selectNodes("//rdf:Description[@rdf:ID]");
+		for ( org.dom4j.Element identifiableObject : identifiableObjects ) {
+			String rdfID = identifiableObject.attributeValue(rdfIDQName);
+			if ( resourceForId.containsKey(rdfID) ) {
+				org.dom4j.Attribute idAttr = identifiableObject.attribute(rdfIDQName);
+				identifiableObject.remove(idAttr);
+				identifiableObject.addAttribute(rdfAboutQName, resourceForId.get(rdfID));					
 			}
 		}
+		
+		// replace about and resource references
+		for ( String rdfID : resourceForId.keySet() ) {
+			List<org.dom4j.Element> referencingObjects = cdaoDoc.selectNodes("//rdf:Description[@rdf:about='#"+rdfID+"']");
+			referencingObjects.addAll(cdaoDoc.selectNodes("//*[@rdf:resource='#"+rdfID+"']"));
+			for ( org.dom4j.Element referencingObject : referencingObjects ) {
+				org.dom4j.Attribute attr = referencingObject.attribute(rdfAboutQName);
+				if ( null == attr ) {
+					attr = referencingObject.attribute(rdfResourceQName);
+				}
+				if ( null != attr ) {
+					attr.setValue(resourceForId.get(rdfID));
+				}										
+			}	
+		}		
 
 	}
 	


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[Treebase-guts] SF.net SVN: treebase:[709] trunk/treebase-core/src/main/java/org/cipres/ treebase/Constants.java

From: <rv...@us...> - 2010-06-03 17:13:23

Revision: 709
          http://treebase.svn.sourceforge.net/treebase/?rev=709&view=rev
Author:   rvos
Date:     2010-06-03 17:13:16 +0000 (Thu, 03 Jun 2010)

Log Message:
-----------
Adding RDF and RDF-schema namespaces for CDAO generation. Changed the template for NCBI (UniProt) URIs to remove the rdf suffix, as per @rdmpage's recommendation.

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java	2010-06-02 14:42:42 UTC (rev 708)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/Constants.java	2010-06-03 17:13:16 UTC (rev 709)
@@ -13,8 +13,10 @@
 	public static final URI BaseURI = URI.create("http://purl.org/PHYLO/TREEBASE/PHYLOWS/");
 	public static final URI OWLURI = URI.create("http://www.w3.org/2002/07/owl#");	
 	public static final URI SKOSURI = URI.create("http://www.w3.org/2004/02/skos/core#");
+	public static final URI RDFSURI = URI.create("http://www.w3.org/2000/01/rdf-schema#");
+	public static final URI RDFURI = URI.create("http://www.w3.org/1999/02/22-rdf-syntax-ns#");
 	public static final String NCBITaxonomyBase = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=";
 	public static final String uBioBase = "http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:";
-	public static final String NCBITaxonomyFormat = "http://purl.uniprot.org/taxonomy/%s.rdf";
+	public static final String NCBITaxonomyFormat = "http://purl.uniprot.org/taxonomy/%s";
 }
 


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[Treebase-guts] [ treebase-Bugs-2992932 ] Exact match "==" does not work in PhyloWS query

From: SourceForge.net <no...@so...> - 2010-06-02 14:51:44

Bugs item #2992932, was opened at 2010-04-27 13:08
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992932&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: 7
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Rutger Vos (rvos)
Summary: Exact match "==" does not work in PhyloWS query

Initial Comment:
This query:

http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName==Evolution

...results in many journals that are not just "Evolution" but have the word "Evolution" in them (e.g. "Molecular Phylogenetics and Evolution"). So our PhyloWS is not recognizing "==" as an exact match search.


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

>Comment By: Rutger Vos (rvos)
Date: 2010-06-02 14:51

Message:
Exact matching on journal titles now works.

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

Comment By: Rutger Vos (rvos)
Date: 2010-06-02 14:51

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


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992932&group_id=248804

[Treebase-guts] SF.net SVN: treebase:[708] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers

From: <rv...@us...> - 2010-06-02 14:42:52

Revision: 708
          http://treebase.svn.sourceforge.net/treebase/?rev=708&view=rev
Author:   rvos
Date:     2010-06-02 14:42:42 +0000 (Wed, 02 Jun 2010)

Log Message:
-----------
Fixes for issue 2992932

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -71,21 +73,7 @@
 		LOGGER.info("formName is '" + formName + "'");
 		
 		if ( ! TreebaseUtil.isEmpty(query) ) {
-			/*
-			CQLParser parser = new CQLParser();
-			CQLNode root = parser.parse(query);
-			root = normalizeParseTree(root);
-			Set<Matrix> queryResults = doCQLQuery(root, new HashSet<Matrix>(),request, response, errors);
-			MatrixSearchResults tsr = new MatrixSearchResults(queryResults);
-			saveSearchResults(request, tsr);
-			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
-				return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, tsr); 			
-			}
-			else {
-				return this.searchResultsAsRDF(tsr, request, root);
-			}
-			*/
-			return this.handleQueryRequest(request, response, errors);
+			return this.handleQueryRequest(request, response, errors, query);
 		}		
 		
 		if (formName.equals("matrixSimple")) {
@@ -180,27 +168,8 @@
 		}
 		logger.debug(node);
 		return results;		
-	}		
+	}
 	
-	private CQLNode normalizeParseTree(CQLNode node) {
-		if ( node instanceof CQLBooleanNode ) {
-			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
-			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
-			return node;
-		}
-		else if ( node instanceof CQLTermNode ) {
-			String index = ((CQLTermNode)node).getIndex();
-			String term = ((CQLTermNode)node).getTerm();
-			CQLRelation relation = ((CQLTermNode)node).getRelation();
-			index = index.replaceAll("dcterms.title", "tb.title.matrix");
-			index = index.replaceAll("dcterms.identifier", "tb.identifier.matrix");
-			index = index.replaceAll("dcterms.extent", "tb.ntax.matrix");
-			return new CQLTermNode(index,relation,term);
-		}
-		logger.debug(node);
-		return node;
-	}	
-	
 	@SuppressWarnings("unchecked")
 	private Collection<Matrix> doSearch(
 			HttpServletRequest request,
@@ -209,20 +178,6 @@
 			BindException errors,
 			String searchTerm) throws InstantiationException {
 
-//		String searchTerm = convertStars(request.getParameter("searchTerm"));
-//		String keywordSearchTerm = "%" + searchTerm + "%";
-//	 	SearchMessageSetter mSetter = new RequestMessageSetter(request);
-		
-//		MatrixSearchResults oldRes;	
-//		{
-//			SearchResults<?> sr = searchResults(request);
-//			if (sr != null) {
-//				oldRes = (MatrixSearchResults) sr.convertToMatrices();
-//			} else {
-//				oldRes = new MatrixSearchResults ();   // TODO: Convert existing search results to new type	
-//			}
-//		}
-
 		Collection<Matrix> matches = null;
 		MatrixService matrixService = getSearchService().getMatrixService();	
 
@@ -271,13 +226,6 @@
 		}
 		matches.removeAll(orphanedMatrices);
 		return matches;
-		
-//		SearchResults<Matrix> newRes = intersectSearchResults(oldRes, 
-//				new MatrixSearchResults(matches), mSetter, "No matching matrices found");
-//
-//		saveSearchResults(request, newRes);
-//		
-//		return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, newRes); 
 
 	}
 
@@ -291,8 +239,8 @@
 	}
 
 	@Override
-	protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors) throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");				
+	protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors, String query) throws CQLParseException, IOException, InstantiationException {
+		//String query = request.getParameter("query");				
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -322,4 +270,13 @@
 		}
 	}
 
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.matrix");
+		mapping.put("dcterms.identifier", "tb.identifier.matrix");
+		mapping.put("dcterms.extent", "tb.ntax.matrix");
+		return mapping;
+	}
+
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -35,8 +35,11 @@
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.view.RedirectView;
+import org.z3950.zing.cql.CQLBooleanNode;
 import org.z3950.zing.cql.CQLNode;
 import org.z3950.zing.cql.CQLParseException;
+import org.z3950.zing.cql.CQLRelation;
+import org.z3950.zing.cql.CQLTermNode;
 
 
 /**
@@ -46,14 +49,51 @@
 	/**
 	 * Logger for this class
 	 */
-	private static final Logger LOGGER = Logger.getLogger(SearchController.class);
-	
+	private static final Logger LOGGER = Logger.getLogger(SearchController.class);	
 	protected SearchService searchService;
 	protected String formView;
-
 	private TaxonLabelService mTaxonLabelService;
 	
-	protected abstract ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors) throws CQLParseException, IOException, InstantiationException;	
+	protected abstract ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors,String query) throws CQLParseException, IOException, InstantiationException;
+	
+	/**
+	 * Recursively traverses a CQL parse tree (presumably starting from its
+	 * root node), replacing the observed indices with ones suggested by the map
+	 * returned by getPredicateMapping(). The function of this is to allow concrete
+	 * subclasses to create specific mappings from more general ones, e.g. when a
+	 * study search query refers to the index "dcterms.identifier", the StudySearchController
+	 * can specify that within its context this index is understood to mean "tb.identifier.study",
+	 * i.e. the study ID.
+	 * @param node
+	 * @return
+	 */
+	protected CQLNode normalizeParseTree(CQLNode node) {
+		if ( node instanceof CQLBooleanNode ) {
+			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
+			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
+			return node;
+		}
+		else if ( node instanceof CQLTermNode ) {
+			String index = ((CQLTermNode)node).getIndex();
+			String term = ((CQLTermNode)node).getTerm();
+			CQLRelation relation = ((CQLTermNode)node).getRelation();
+			Map<String,String> mapping = getPredicateMapping();
+			for ( String key : mapping.keySet() ) {
+				index = index.replaceAll(key, mapping.get(key));
+			}
+			return new CQLTermNode(index,relation,term);
+		}
+		logger.debug(node);
+		return node;
+	}	
+	
+	/**
+	 * Returns a mapping between more general search indices (e.g. "dcterms.identifier")
+	 * and the specific indices (e.g. "tb.identifier.study") that are understood to be used 
+	 * by the concrete subclass
+	 * @return
+	 */
+	protected abstract Map<String,String> getPredicateMapping();
 
 	protected ModelAndView onSubmit(
 			HttpServletRequest request,
@@ -399,7 +439,7 @@
 		String query = request.getParameter("query");
 		if ( query != null && ! TreebaseUtil.isEmpty(query) ) {
 			LOGGER.info("query is '"+ query +"'");
-			return this.handleQueryRequest(request, response, bindException);
+			return this.handleQueryRequest(request, response, bindException, query);
 		}
 		String action = request.getParameter("action");
 		if (action != null && action.equals("discard") && request.getMethod().equals("GET")) {

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -96,7 +98,7 @@
 		
 		if ( ! TreebaseUtil.isEmpty(query) && ! query.equals("")) {
 			LOGGER.info("query is '" + query + "'");
-			return this.handleQueryRequest(request, response, errors);
+			return this.handleQueryRequest(request, response, errors, query);
 		}		
 		
 		if (formName.equals("searchKeyword")) {
@@ -129,7 +131,9 @@
 			} else {
 				throw new Error("Unknown search button name '" + buttonName + "'");
 			}
-			Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm);	
+			// XXX we now never do an exact match with terms provided through the web app. We can change
+			// this, e.g. by adding a check box whose value is the boolean argument of doSearch()
+			Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm,false);	
 			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {				
 				SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches), 
 				new RequestMessageSetter(request), "No matching studies found");	
@@ -139,7 +143,8 @@
 			else {
 				return this.searchResultsAsRDF(new StudySearchResults(matches), request, null,"study","study");
 			}
-		} else {
+		} 
+		else {
 			return super.onSubmit(request, response, command, errors);
 		}
 	}
@@ -177,23 +182,24 @@
 		}		
 		else if ( node instanceof CQLTermNode ) {
 			CQLTermNode term = (CQLTermNode)node;
+			boolean exactMatch = term.getRelation().getBase().equals("==");
 			String index = term.getIndex();
 			if ( index.startsWith("tb.title") ) {
-				results.addAll(doSearch(request, response, SearchType.byTitle, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byTitle, errors, term.getTerm(),exactMatch));
 			} else if ( index.equals("tb.identifier.study") ) {
-				results.addAll(doSearch(request, response, SearchType.byID, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byID, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.contributor") ) {
-				results.addAll(doSearch(request, response, SearchType.byAuthorName, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byAuthorName, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.abstract") ) {
-				results.addAll(doSearch(request, response, SearchType.inAbstract, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.inAbstract, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.subject") ) {
-				results.addAll(doSearch(request, response, SearchType.byKeyword, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byKeyword, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.bibliographicCitation") ) {
-				results.addAll(doSearch(request, response, SearchType.inCitation, errors, term.getTerm()));				
+				results.addAll(doSearch(request, response, SearchType.inCitation, errors, term.getTerm(),exactMatch));				
 			} else if ( index.equals("tb.identifier.study.tb1") ) {
-				results.addAll(doSearch(request, response, SearchType.byLegacyID, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byLegacyID, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("prism.publicationName") ) {
-				results.addAll(doSearch(request, response, SearchType.byJournal, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byJournal, errors, term.getTerm(),exactMatch));
 			} else {
 				// issue warnings
 				addMessage(request, "Unsupported index: " + index);
@@ -201,48 +207,18 @@
 		}
 		logger.debug(node);
 		return results;		
-	}		
+	}	
 	
-	private CQLNode normalizeParseTree(CQLNode node) {
-		if ( node instanceof CQLBooleanNode ) {
-			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
-			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
-			return node;
-		}
-		else if ( node instanceof CQLTermNode ) {
-			String index = ((CQLTermNode)node).getIndex();
-			String term = ((CQLTermNode)node).getTerm();
-			CQLRelation relation = ((CQLTermNode)node).getRelation();
-			index = index.replaceAll("dcterms.title", "tb.title.study");
-			index = index.replaceAll("dcterms.identifier", "tb.identifier.study");
-			return new CQLTermNode(index,relation,term);
-		}
-		logger.debug(node);
-		return node;
-	}		
-	
 	@SuppressWarnings("unchecked")
 	protected Collection<Study> doSearch(
 			HttpServletRequest request,
 			HttpServletResponse response,
 			SearchType searchType,
 			BindException errors,
-			String searchTerm) throws InstantiationException {
+			String searchTerm,
+			boolean exactMatch) throws InstantiationException {
 		
-//		String searchTerm = convertStars(request.getParameter("searchTerm"));
 		String keywordSearchTerm = "%" + searchTerm + "%";
-//		StudySearchResults oldRes;	
-//
-//		{
-//			SearchResults<?> sr = searchResults(request);
-//			if (sr != null) {
-//				oldRes = (StudySearchResults) sr.convertToStudies();
-//			} else {
-//				oldRes = new StudySearchResults ();   // TODO: Convert existing search results to new type	
-//			}
-//		}
-//		
-//		LOGGER.info("doSearch old results contained " + oldRes.size() + " item(s)");
 		Collection<Study> matches;
 		StudyService studyService = getSearchService().getStudyService();	
 				
@@ -283,79 +259,21 @@
 				matches = studyService.findByKeyword(keywordSearchTerm);
 				break;
 			case byJournal:
-				matches = studyService.findByJournal(keywordSearchTerm, false);
+			{
+				if ( exactMatch ) {
+					matches = studyService.findByJournal(searchTerm, exactMatch);
+				} else {
+					matches = studyService.findByJournal(keywordSearchTerm, exactMatch);
+				}
 				break;
+			}
 			default:
 				throw new Error ("Unknown search type '" + searchType + "'");
 		}
 		
 		return matches;
-//		SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches), 
-//				new RequestMessageSetter(request), "No matching studies found");
-//		
-//		saveSearchResults(request, newRes);
-//
-//		return new ModelAndView("search/studySearch", Constants.RESULT_SET, newRes); 
 	}
 
-	/*
-	private void validateTaxonSet(HttpServletRequest request,
-			HttpServletResponse response, String searchTerm,
-			BindException errors) {
-		String[] taxonStrings = getTaxonStrings(searchTerm);
-		List<String> unrecognizedTaxa = new LinkedList<String> ();
-		List<String> recognizedTaxa = new LinkedList<String> ();
-
-		Collection<TaxonLabel> taxonLabels = stringsToTaxonLabels(taxonStrings);
-		request.setAttribute("taxonLabelSetOverride", taxonLabels);
-		
-		for (TaxonLabel tl : taxonLabels) {
-			TaxonVariant variant = getTaxonLabelService().findTaxonVariant(tl);
-			if (variant == null) {
-				variant = getTaxonLabelService().createFromUBIOService(tl);
-				if (variant == null) {
-					unrecognizedTaxa.add(tl.getTaxonLabel());
-				} else {
-					recognizedTaxa.add(tl.getTaxonLabel());
-				}
-			} else {
-				recognizedTaxa.add(variant.getName());
-			}
-		}
-		
-		LOGGER.info("validateTaxonSet: of " 
-				+ taxonStrings.length 
-				+ " entered taxa, "
-				+ unrecognizedTaxa.size()
-				+ " was/were unrecognized: "
-				+ unrecognizedTaxa.toString());
-		
-		request.setAttribute("unrecognizedTaxa", unrecognizedTaxa);
-		request.setAttribute("taxonLabels", joinStrings(recognizedTaxa));
-		return;
-	}
-
-	private String joinStrings(Collection<String> strings) {
-		String result = "";
-		for (String s : strings) {
-			result = result + s + "\n";
-		}
-		return result;
-	}
-
-	private Collection<TaxonLabel> stringsToTaxonLabels(String[] taxonStrings) {
-		Collection<TaxonLabel> tls = new LinkedList<TaxonLabel>();
-		for (String s : taxonStrings) {
-			tls.add(new TaxonLabel(titleCase(s)));
-		}
-		return tls;
-	}
-
-	private String titleCase(String s) {
-		return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
-	}
-	*/
-
 	@Override
 	SearchResultsType currentSearchType() {
 		return SearchResultsType.STUDY;
@@ -368,9 +286,9 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors,String query)
 			throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");						
+		//String query = request.getParameter("query");						
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -399,4 +317,12 @@
 			return this.searchResultsAsRDF(res, request, root, schema, "study");
 		}		
 	}
+
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.study");
+		mapping.put("dcterms.identifier", "tb.identifier.study");
+		return mapping;
+	}
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -54,21 +56,7 @@
 		String formName = request.getParameter("formName");
 		String query = request.getParameter("query");
 		if ( ! TreebaseUtil.isEmpty(query) ) {
-			/*
-			CQLParser parser = new CQLParser();
-			CQLNode root = parser.parse(query);
-			root = normalizeParseTree(root);
-			Set<Taxon> queryResults = doCQLQuery(root, new HashSet<Taxon>(),request);
-			TaxonSearchResults tsr = new TaxonSearchResults(queryResults);
-			saveSearchResults(request, tsr);
-			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
-				return samePage(request);
-			}
-			else {
-				return this.searchResultsAsRDF(tsr, request, root);
-			}
-			*/
-			return this.handleQueryRequest(request, response, errors);
+			return this.handleQueryRequest(request, response, errors, query);
 		}
 		if (formName.equals("searchByTaxonLabel")) {
 			SearchCommand newSearchCommand = (SearchCommand)searchCommand;
@@ -109,24 +97,6 @@
 		}
 	}
 	
-	private CQLNode normalizeParseTree(CQLNode node) {
-		if ( node instanceof CQLBooleanNode ) {
-			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
-			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
-			return node;
-		}
-		else if ( node instanceof CQLTermNode ) {
-			String index = ((CQLTermNode)node).getIndex();
-			String term = ((CQLTermNode)node).getTerm();
-			CQLRelation relation = ((CQLTermNode)node).getRelation();
-			index = index.replaceAll("dcterms.title", "tb.title.taxon");
-			index = index.replaceAll("dcterms.identifier", "tb.identifier.taxon");
-			return new CQLTermNode(index,relation,term);
-		}
-		logger.debug(node);
-		return node;
-	}
-	
 	private Set<Taxon> doCQLQuery(CQLNode node, Set<Taxon> results, HttpServletRequest request) {
 		if ( node instanceof CQLBooleanNode ) {
 			Set<Taxon> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request);
@@ -401,9 +371,9 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");
+		//String query = request.getParameter("query");
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -432,4 +402,12 @@
 			return this.searchResultsAsRDF(res, request, root,schema,"taxon");
 		}
 	}
+
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.taxon");
+		mapping.put("dcterms.identifier", "tb.identifier.taxon");		
+		return mapping;
+	}
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -69,21 +71,7 @@
 		LOGGER.info("formName is '" + formName + "'");
 		
 		if ( ! TreebaseUtil.isEmpty(query) ) {
-			/*
-			CQLParser parser = new CQLParser();
-			CQLNode root = parser.parse(query);
-			root = normalizeParseTree(root);
-			Set<PhyloTree> queryResults = doCQLQuery(root, new HashSet<PhyloTree>(),request, response, errors);
-			TreeSearchResults tsr = new TreeSearchResults(queryResults);
-			saveSearchResults(request, tsr);
-			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {			
-				return new ModelAndView("search/treeSearch", Constants.RESULT_SET, tsr);
-			}
-			else {
-				return this.searchResultsAsRDF(tsr, request, root);
-			}
-			*/
-			return this.handleQueryRequest(request, response, errors);
+			return this.handleQueryRequest(request, response, errors, query);
 		}
 		
 		if (formName.equals("treeSimple")) {
@@ -180,25 +168,6 @@
 		logger.debug(node);
 		return results;		
 	}	
-	
-	private CQLNode normalizeParseTree(CQLNode node) {
-		if ( node instanceof CQLBooleanNode ) {
-			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
-			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
-			return node;
-		}
-		else if ( node instanceof CQLTermNode ) {
-			String index = ((CQLTermNode)node).getIndex();
-			String term = ((CQLTermNode)node).getTerm();
-			CQLRelation relation = ((CQLTermNode)node).getRelation();
-			index = index.replaceAll("dcterms.title", "tb.title.tree");
-			index = index.replaceAll("dcterms.identifier", "tb.identifier.tree");
-			index = index.replaceAll("dcterms.extent", "tb.ntax.tree");
-			return new CQLTermNode(index,relation,term);
-		}
-		logger.debug(node);
-		return node;
-	}	
 
 	@SuppressWarnings("unchecked")
 	private Collection<PhyloTree> doSearch(
@@ -208,18 +177,6 @@
 			BindException errors,
 			String searchTerm) throws InstantiationException {
 
-//		String searchTerm = convertStars(request.getParameter("searchTerm"));
-//		String keywordSearchTerm = "%" + searchTerm + "%";
-//		TreeSearchResults oldRes;	
-//		{
-//			SearchResults<?> sr = searchResults(request);
-//			if (sr != null) {
-//				oldRes = (TreeSearchResults) sr.convertToTrees();
-//			} else {
-//				oldRes = new TreeSearchResults ();   // TODO: Convert existing search results to new type	
-//			}
-//		}
-
 		Collection<PhyloTree> matches = null;
 		PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();	
 
@@ -279,9 +236,9 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");
+		//String query = request.getParameter("query");
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -311,4 +268,13 @@
 		}
 	}
 
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.tree");
+		mapping.put("dcterms.identifier", "tb.identifier.tree");
+		mapping.put("dcterms.extent", "tb.ntax.tree");		
+		return mapping;
+	}
+
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -5,6 +5,7 @@
 import java.util.Collection;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -20,6 +21,7 @@
 import org.cipres.treebase.web.Constants;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLNode;
 import org.z3950.zing.cql.CQLParseException;
 
 /**
@@ -189,10 +191,22 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
 		// TODO Auto-generated method stub
 		return null;
 	}
 
+	@Override
+	protected CQLNode normalizeParseTree(CQLNode node) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }


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[Treebase-guts] SF.net SVN: treebase:[707] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/study/StudyServiceImpl.java

From: <rv...@us...> - 2010-06-02 13:28:03

Revision: 707
          http://treebase.svn.sourceforge.net/treebase/?rev=707&view=rev
Author:   rvos
Date:     2010-06-02 13:27:57 +0000 (Wed, 02 Jun 2010)

Log Message:
-----------
Now properly dispatches to getStudyHome().findByJournal(pJournal,pCaseSensitive), i.e. the method with the boolean flag, as opposed to the one without it (which only does fuzzy matching).

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java	2010-06-02 13:26:16 UTC (rev 706)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java	2010-06-02 13:27:57 UTC (rev 707)
@@ -533,6 +533,6 @@
 
 	public Collection<Study> findByJournal(String pJournal,
 			boolean pCaseSensitive) {
-		return getStudyHome().findByJournal(pJournal);
+		return getStudyHome().findByJournal(pJournal,pCaseSensitive);
 	}
 }


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[Treebase-guts] SF.net SVN: treebase:[706] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/study/StudyHome.java

From: <rv...@us...> - 2010-06-02 13:26:24

Revision: 706
          http://treebase.svn.sourceforge.net/treebase/?rev=706&view=rev
Author:   rvos
Date:     2010-06-02 13:26:16 +0000 (Wed, 02 Jun 2010)

Log Message:
-----------
Added interface of findByJournal(String pJournal, boolean pExactMatch), so that we can do exact matching against journal names - and then deliver them as RSS, so that journals can have feeds with treebase publications.

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java	2010-06-02 13:25:28 UTC (rev 705)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java	2010-06-02 13:26:16 UTC (rev 706)
@@ -53,6 +53,15 @@
 	 * @return Collection<Study>
 	 */
 	Collection<Study> findByJournal(String pJournal);
+	
+	/**
+	 * Find studies by journal name, with exact matching
+	 * 
+	 * @param pJournal
+	 * @param pExactMatch
+	 * @return Collection<Study>
+	 */
+	Collection<Study> findByJournal(String pJournal, boolean pExactMatch);
 
 	/**
 	 * Find studies submitted by an user. Return an empty set if no match is found.


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[Treebase-guts] SF.net SVN: treebase:[705] trunk/treebase-core/src/main/java/org/cipres/ treebase/dao/study/StudyDAO.java

From: <rv...@us...> - 2010-06-02 13:25:35

Revision: 705
          http://treebase.svn.sourceforge.net/treebase/?rev=705&view=rev
Author:   rvos
Date:     2010-06-02 13:25:28 +0000 (Wed, 02 Jun 2010)

Log Message:
-----------
Added implementation of findByJournal(String pJournal, boolean pExactMatch), so that we can do exact matching against journal names - and then deliver them as RSS, so that journals can have feeds with treebase publications.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java	2010-06-02 12:42:58 UTC (rev 704)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java	2010-06-02 13:25:28 UTC (rev 705)
@@ -22,6 +22,7 @@
 import org.hibernate.Query;
 import org.hibernate.SQLQuery;
 import org.hibernate.criterion.Expression;
+import org.hibernate.criterion.MatchMode;
 import org.hibernate.criterion.Restrictions;
 
 /**
@@ -379,5 +380,24 @@
 		return returnVal;
 	}
 
+	/*
+	 * (non-Javadoc)
+	 * @see org.cipres.treebase.domain.study.StudyHome#findByJournal(java.lang.String, boolean)
+	 */
+	public Collection<Study> findByJournal(String pJournal, boolean pExactMatch) {
+		if ( pExactMatch == false ) {
+			return findByJournal(pJournal);
+		}		
+		if (LOGGER.isInfoEnabled()) {
+			LOGGER.info("Going to do an exact journal name match for "+pJournal);  
+		}		
+		Collection<Study> studies = new ArrayList<Study>();
+		Criteria studyCrit = getSession().createCriteria(Study.class).createAlias("citation", "cit");
+		//studyCrit.add(Restrictions.like("cit.journal", pJournal.trim(), MatchMode.EXACT));
+		studyCrit.add(Restrictions.eq("cit.journal", pJournal));
+		studies = (Collection<Study>) studyCrit.list();
+		return studies;
+	}
 
+
 }


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[Treebase-guts] SF.net SVN: treebase:[704] trunk/treebase-core/db/cleaning

From: <sfr...@us...> - 2010-06-02 12:43:04

Revision: 704
          http://treebase.svn.sourceforge.net/treebase/?rev=704&view=rev
Author:   sfrgpiel
Date:     2010-06-02 12:42:58 +0000 (Wed, 02 Jun 2010)

Log Message:
-----------
This is the solution recommended by Rutger for fixing issue 2992022, which is an inability to view study 2164

Added Paths:
-----------
    trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/
    trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/README.txt
    trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/fix_S2164.sql

Added: trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/README.txt	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/README.txt	2010-06-02 12:42:58 UTC (rev 704)
@@ -0,0 +1,36 @@
+To apply, run fix_S2164.sql
+
+--------
+
+Hi all,
+
+I'm trying to fix issue 2992022, which was hypothesised to be a
+character encoding problem. This is not the case, it has nothing to do
+with UTF-8 handling. It's a database inconsistency:
+
+* in the person table, there's both an entry for "Balázs Tímea",
+person_id=3971 and for "Tímea Balázs", person_id=5609
+
+* in the latter record, first and last name are in the correct order,
+but the author's email address is missing, and the author order index
+is 5, on a three-author paper. In the former record, the first and
+last name are switched around, but everything else is in the correct
+order. It looks like the nullpointer exception is thrown because there
+is no author 4 (see:
+http://www.mycologia.org/cgi/content/abstract/101/2/247).
+
+* here's my suggested fix: correct the name order in record 3971,
+purge record 5609 from person and from citation_author, i.e.:
+
+update person set firstname='Tímea', lastname='Balázs' where person_id=3971;
+delete from citation_author where authors_person_id=5609;
+delete from person where person_id=5609;
+
+On the test instance this fixes the exception, the citation is
+serialised correctly. Can someone fix this on the production instance?
+I re-assigned this bug to Bill, but whoever has access to the prod
+server can run those SQL snippets and everything should be OK.
+
+Cheers,
+
+Rutger
\ No newline at end of file

Added: trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/fix_S2164.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/fix_S2164.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-06-02_fix_S2164/fix_S2164.sql	2010-06-02 12:42:58 UTC (rev 704)
@@ -0,0 +1,13 @@
+-- beware that the inspection tool to apply these statements needs to be 
+-- utf-8 aware
+
+BEGIN WORK;
+
+UPDATE person SET firstname='Tímea', lastname='Balázs' WHERE person_id=3971;
+
+DELETE FROM citation_author WHERE authors_person_id=5609;
+
+DELETE FROM person WHERE person_id=5609;
+
+COMMIT;
+


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[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

From: SourceForge.net <no...@so...> - 2010-06-01 20:57:00

Bugs item #2798604, was opened at 2009-05-29 21:21
Message generated for change (Settings changed) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&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: data
Group: None
Status: Open
Priority: 2
Private: No
Submitted By: Blaise Li (blaiseli)
>Assigned to: Nobody/Anonymous (nobody)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

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

>Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:56

Message:
OK, I am assigning this to "None". It is pointless to pretend that this is
a fixable bug. To be able to read MrBayes trees we will have to switch to a
newer mesquite. This is not a task that is properly assigned to me. I will
not do this.

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

Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:56

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


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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 16:13

Message:
We won't fix this directly because we can't support all variants of NEXUS.
However, we should better document which NEXUS versions we do support, and
at some point we may also switch out Mesquite as the NEXUS parser to
another one, e.g., NCL. (Though no NEXUS parser can be expected to support
all flavors.)

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

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 11:11

Message:
I think this needs to be closed: there is simply no way we will ever
support all nexus variants. It is a feature of treebase that we support
mesquite-compatible files. We state this very clearly. If people decide to
upload files that are not compatible with mesquite there's not much we can
do.

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

Comment By: Rutger Vos (rvos)
Date: 2009-11-18 18:23

Message:
This has been downgraded. We can't fix this unless mesquite gets fixed. If
people want to upload mrbayes files they will have to run them through
mesquite first on their own machines.

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

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 07:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

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

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

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

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 14:29

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


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2798604&group_id=248804

[Treebase-guts] [ treebase-Bugs-2972133 ] Add to connotea, del.icio.us etc broken due to absolute URL

From: SourceForge.net <no...@so...> - 2010-06-01 20:54:16

Bugs item #2972133, was opened at 2010-03-17 18:52
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2972133&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: 7
Private: No
Submitted By: Hilmar Lapp (hlapp)
Assigned to: Rutger Vos (rvos)
Summary: Add to connotea, del.icio.us etc broken due to absolute URL

Initial Comment:
The code uses an absolute path, which results in things like http://localhost.localdomain:8280/treebase-web/search/study/summary.html?id=1021, which obviously won't work.

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

>Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:54

Message:
Removed hardcoding, now using the purl instead.

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

Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:54

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


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

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 11:07

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


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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-03-17 19:02

Message:
Turns out I do have a CiteULike account. The code adds an entry to the
library but w/o a link back to the TreeBASE URL (or the article URL). Is
that intended?

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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-03-17 18:57

Message:
This may only affect Connotea actually. The add to Del.icio.us code works,
can't test CiteULike as a I don't have an account. 

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

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[Treebase-guts] SF.net SVN: treebase:[703] trunk/treebase-web/src/main/webapp/WEB-INF/pages /search/study/nav.jsp

From: <rv...@us...> - 2010-06-01 20:53:52

Revision: 703
          http://treebase.svn.sourceforge.net/treebase/?rev=703&view=rev
Author:   rvos
Date:     2010-06-01 20:53:46 +0000 (Tue, 01 Jun 2010)

Log Message:
-----------
Removed hardcoding of url, using purl instead. This fixes issue 2972133.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp	2010-06-01 20:05:30 UTC (rev 702)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/nav.jsp	2010-06-01 20:53:46 UTC (rev 703)
@@ -82,17 +82,16 @@
 		
 		<!-- save to connotea -->
                 <!-- commented out temporarily because this uses the absolute path, which won't work due to proxying - SF Bug 2972133 --> 
-       <%--
 		<form method="post" id="connotea" action="http://www.connotea.org/add" enctype="application/x-www-form-urlencoded" name="edit">
 		
 		    <input 
 		        name="uri" 
-		        value="<%= request.getScheme() %>://<%= request.getLocalName() %>:<%= request.getLocalPort() %>/treebase-web/search/study/summary.html?id=<c:out value="${study.id}"/>" 
+		        value="${baseLink}?format=html" 
 		        type="hidden"/>
 		
 		    <input 
 		        name="uri" 
-		        value="<%= request.getScheme() %>://<%= request.getLocalName() %>:<%= request.getLocalPort() %>/treebase-web/search/study/summary.html?id=<c:out value="${study.id}"/>" 
+		        value="${baseLink}?format=html" 
 		        type="hidden"/>
 		
 		    <input name="ctitle" value="<c:out value="${cit.title}"/>"  type="hidden"/>		        
@@ -174,7 +173,7 @@
 				<img src="/treebase-web/images/connotea.gif" alt="Connotea" class="iconButton"/>
 				Connotea
 			</a>
-		--%> <!-- end of commenting out connotea -->
+		<!-- end of commenting out connotea -->
 		<div id="notice"></div>
 	</fieldset>
 </div>


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[Treebase-guts] [ treebase-Bugs-3005716 ] Tree URI results in Yikes

From: SourceForge.net <no...@so...> - 2010-06-01 20:16:45

Bugs item #3005716, was opened at 2010-05-22 15:25
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3005716&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: data
Group: None
>Status: Closed
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Rutger Vos (rvos)
Summary: Tree URI results in Yikes

Initial Comment:
If I follow a URI for a tree, instead of getting an RSS feed I get a Yikes error.

http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6031

Yikes!

javax.servlet.jsp.el.ELException: An error occurred while getting property "phyloWSPath" from an instance of class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$9d782eec
	at org.apache.commons.el.Logger.logError(Logger.java:484)
	at org.apache.commons.el.Logger.logError(Logger.java:588)
	at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318)
	at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190)
	at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fout_005f1(anyObjectAsRDF_jsp.java:224)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fif_005f0(anyObjectAsRDF_jsp.java:199)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspService(anyObjectAsRDF_jsp.java:100)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	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 com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39)
	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.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
	at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
	at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239)
	at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879)
	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.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
	at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
	at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
	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.Http11Processor.process(Http11Processor.java:873)
	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
	at java.lang.Thread.run(Thread.java:636)


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

>Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:16

Message:
Issue #2974771 and this bug had the same cause. Both are now fixed. For
details, see 2974771.

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

Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:16

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


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3005716&group_id=248804

[Treebase-guts] [ treebase-Bugs-2974771 ] Accessing phyloWS URLs yields exception for HTML view

From: SourceForge.net <no...@so...> - 2010-06-01 20:11:15

Bugs item #2974771, was opened at 2010-03-22 18:59
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974771&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: 8
Private: No
Submitted By: Hilmar Lapp (hlapp)
Assigned to: Rutger Vos (rvos)
Summary: Accessing phyloWS URLs yields exception for HTML view

Initial Comment:
For example the following works:

http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6917?format=rdf

whereas removing the format= parameter (i.e., the HTML view) results in the following YIKES. I suspect that this means that depending on the path from which you access a page, the phyloWSPath (and possibly other page or request parameters) are not properly initialized.

javax.servlet.jsp.el.ELException: An error occurred while getting property "phyloWSPath" from an instance of class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$4d099cbc
	at org.apache.commons.el.Logger.logError(Logger.java:484)
	at org.apache.commons.el.Logger.logError(Logger.java:588)
	at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318)
	at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190)
	at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fout_005f1(anyObjectAsRDF_jsp.java:224)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fif_005f0(anyObjectAsRDF_jsp.java:199)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspService(anyObjectAsRDF_jsp.java:100)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	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 com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39)
	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.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
	at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
	at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239)
	at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879)
	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 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.Http11Processor.process(Http11Processor.java:873)
	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
	at java.lang.Thread.run(Thread.java:636)

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

>Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:11

Message:
We are getting an ELException when getting phyloWSPath of the context
object that defines the focal object (e.g. the containing study for a focal
tree). 

The idea is that, when serializing an object such as a tree to RDF, we
might want to add rdfs:isDefinedBy which points to the resource identifier
of the containing object (the study). We have implemented this with the
getContext() method, which for any focal AbstractPersistedObject should
return the context object, or null.

We get the exception because in some situations the context object might
not yet have been initialized, so we can't yet ask it for its phyloWSPath
(which is needed to construct its resource address).

This is addressed by adding the @Fetch(FetchMode.JOIN) annotation, which I
have added to all implementors of getContext().

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

Comment By: Rutger Vos (rvos)
Date: 2010-06-01 20:11

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


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

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 11:06

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


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974771&group_id=248804

[Treebase-guts] SF.net SVN: treebase:[702] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain

From: <rv...@us...> - 2010-06-01 20:05:39

Revision: 702
          http://treebase.svn.sourceforge.net/treebase/?rev=702&view=rev
Author:   rvos
Date:     2010-06-01 20:05:30 +0000 (Tue, 01 Jun 2010)

Log Message:
-----------
Fixes for issue 2974771, ELException when getting phyloWSPath of the context object that defines the focal object (e.g. the containing study). This is addressed by adding the @Fetch(FetchMode.JOIN) annotation.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java	2010-06-01 17:11:18 UTC (rev 701)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixColumn.java	2010-06-01 20:05:30 UTC (rev 702)
@@ -18,6 +18,8 @@
 import org.hibernate.annotations.BatchSize;
 import org.hibernate.annotations.Cache;
 import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.Index;
 
 import org.cipres.treebase.domain.AbstractPersistedObject;
@@ -78,6 +80,7 @@
 	// the nullable = false cause the add error code -407, the matrix column is null!
 	// @JoinColumn(name = "MATRIX_ID", insertable = false, updatable = false, nullable = false)
 	@Index(name = "COLUMN_M_IDX")
+	@Fetch(FetchMode.JOIN)
 	public CharacterMatrix getMatrix() {
 		return mMatrix;
 	}

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java	2010-06-01 17:11:18 UTC (rev 701)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/MatrixElement.java	2010-06-01 20:05:30 UTC (rev 702)
@@ -20,6 +20,8 @@
 import javax.persistence.Transient;
 
 import org.hibernate.annotations.BatchSize;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.Index;
 
 import org.cipres.treebase.domain.AbstractPersistedObject;
@@ -119,6 +121,7 @@
 	@ManyToOne
 	@JoinColumn(name = "MATRIXCOLUMN_ID", nullable = true)
 	@Index(name = "Element_COL_IDX")
+	@Fetch(FetchMode.JOIN)
 	public MatrixColumn getColumn() {
 		return mColumn;
 	}

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java	2010-06-01 17:11:18 UTC (rev 701)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java	2010-06-01 20:05:30 UTC (rev 702)
@@ -458,6 +458,7 @@
 	 */
 	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "STUDY_ID")
+	@Fetch(FetchMode.JOIN)
 	public Study getStudy() {
 		return mStudy;
 	}
@@ -813,6 +814,7 @@
 	@Override
 	@Transient
 	public Study getContext() {
+		// org.hibernate.LazyInitializationException
 		return getStudy();
 	}
 

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2010-06-01 17:11:18 UTC (rev 701)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTreeNode.java	2010-06-01 20:05:30 UTC (rev 702)
@@ -17,6 +17,8 @@
 import org.hibernate.annotations.BatchSize;
 import org.hibernate.annotations.Cache;
 import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.Index;
 
 import org.cipres.treebase.TreebaseUtil;
@@ -168,6 +170,7 @@
 	@ManyToOne(fetch = FetchType.LAZY)
 	@JoinColumn(name = "PHYLOTREE_ID", nullable = false)
 	@Index(name = "TNODE_TREE_IDX")
+	@Fetch(FetchMode.JOIN)
 	public PhyloTree getTree() {
 		return mTree;
 	}


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[Treebase-guts] [ treebase-Bugs-2992022 ] Yikes when viewing 2164: UTF8 handling problem?

From: SourceForge.net <no...@so...> - 2010-06-01 17:31:54

Bugs item #2992022, was opened at 2010-04-25 16:04
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&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: 8
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: William Piel (sfrgpiel)
Summary: Yikes when viewing 2164: UTF8 handling problem?

Initial Comment:

An error is thrown when users try to browse to S2164. This *may* be an issue with UTF8 character set rendering, seeing as this study is from Hungarian authors. 

http://www.treebase.org/treebase-web/search/study/summary.html?id=2164

Yikes!

javax.servlet.jsp.el.ELException: An error occurred while getting property "bibtexReference" from an instance of class org.cipres.treebase.domain.study.ArticleCitation
	at org.apache.commons.el.Logger.logError(Logger.java:484)
	at org.apache.commons.el.Logger.logError(Logger.java:588)
	at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318)
	at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190)
	at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924)
	at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspx_meth_c_005fout_005f0(nav_jsp.java:285)
	at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspService(nav_jsp.java:89)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	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.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:584)
	at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:497)
	at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:965)
	at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspService(summary_jsp.java:109)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	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 com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39)
	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.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
	at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
	at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239)
	at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879)
	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.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
	at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
	at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	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.Http11Processor.process(Http11Processor.java:873)
	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
	at java.lang.Thread.run(Thread.java:636)
	

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

>Comment By: Rutger Vos (rvos)
Date: 2010-06-01 17:31

Message:
This has nothing to do with UTF-8 handling. It's a database inconsistency:

* in the person table, there's both an entry for "Balázs Tímea",
person_id=3971 and for "Tímea Balázs", person_id=5609

* in the latter record, first and last name are in the correct order, but
the author's email address is missing, and the author order index is 5, on
a three-author paper. In the former record, the first and last name are
switched around, but everything else is in the correct order.

* here's my suggested fix: correct the name order in record 3971, purge
record 5609 from person and from citation_author, i.e.:

update person set firstname='Tímea', lastname='Balázs' where
person_id=3971;

delete from citation_author where authors_person_id=5609;

delete from person where person_id=5609;

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

Comment By: Rutger Vos (rvos)
Date: 2010-06-01 17:31

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


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

Comment By: Rutger Vos (rvos)
Date: 2010-04-27 16:27

Message:
Also test this with issue 2669366

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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 15:36

Message:
This may indicate a larger problem with UTF8 handling.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&group_id=248804

[Treebase-guts] SF.net SVN: treebase:[701] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/study/Citation.java

From: <rv...@us...> - 2010-06-01 17:11:24

Revision: 701
          http://treebase.svn.sourceforge.net/treebase/?rev=701&view=rev
Author:   rvos
Date:     2010-06-01 17:11:18 +0000 (Tue, 01 Jun 2010)

Log Message:
-----------
Wrapped author name concatenation in try/catch block

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java	2010-06-01 16:28:03 UTC (rev 700)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java	2010-06-01 17:11:18 UTC (rev 701)
@@ -475,26 +475,31 @@
 	public String getAuthorsCitationStyleWithoutHtml() {
 
 		StringBuilder authorsCitationStyle = new StringBuilder();
-		List<Person> authors = getAuthors();
-		int size = authors.size();
-
-		if (size > 0) {
-
-			for (int i = 0; i < size; i++) {
-
-				authorsCitationStyle.append(authors.get(i).getFullNameCitationStyle());
-
-				if (size > 1 && i == size - 2) {
-					authorsCitationStyle.append(", & ");
-				} else if (size > 1 && i < size - 2) {
-					authorsCitationStyle.append(", ");
+		try {
+			List<Person> authors = getAuthors();
+			int size = authors.size();
+	
+			if (size > 0) {
+	
+				for (int i = 0; i < size; i++) {
+	
+					authorsCitationStyle.append(authors.get(i).getFullNameCitationStyle());
+	
+					if (size > 1 && i == size - 2) {
+						authorsCitationStyle.append(", & ");
+					} else if (size > 1 && i < size - 2) {
+						authorsCitationStyle.append(", ");
+					}
 				}
+	
 			}
-
+	
+			authorsCitationStyle.append(" ").append(getPublishYear());
+			getDetailedPublicationInformation(authorsCitationStyle, false);
 		}
-
-		authorsCitationStyle.append(" ").append(getPublishYear());
-		getDetailedPublicationInformation(authorsCitationStyle, false);
+		catch ( Exception e ) {
+			e.printStackTrace();
+		}
 		return authorsCitationStyle.toString();
 	}
 	
@@ -525,65 +530,70 @@
 	@Transient
 	public String getRisReference () {
 		StringBuilder ris = new StringBuilder(), sub = new StringBuilder();
-		String citationType = this.getRealCitationType(), cls = "\n";
-		boolean isArticle = false, isBook = false, isInBook = false;		
-		if ( citationType.equals(ArticleCitation.CITATION_TYPE_ARTICLE) ) {
-			ris.append("TY  - JOUR\n");
-			sub.append("JF  - ").append(appendMe(((ArticleCitation)this).getJournal())).append(cls);
-			sub.append("VL  - ").append(appendMe(((ArticleCitation)this).getVolume())).append(cls);
-			sub.append("IS  - ").append(appendMe(((ArticleCitation)this).getIssue())).append(cls);
-			isArticle = true;
-		}
-		else if ( citationType.equals(BookCitation.CITATION_TYPE_BOOK) ) {
-			ris.append("TY  - BOOK\n");
-			isBook = true;
-		}	
-		else if ( citationType.equals(InBookCitation.CITATION_TYPE_BOOKSECTION) ) {
-			ris.append("TY  - CHAP\n");
-			sub.append("TI  - ").append(appendMe(((InBookCitation)this).getBookTitle())).append(cls);
-			isInBook = true;
-		}	
-		if ( isBook || isInBook) {
-			sub.append("SN  - ISBN ").append(appendMe(((BookCitation)this).getISBN())).append(cls);
-			sub.append("PB  - ").append(appendMe(((BookCitation)this).getPublisher())).append(cls);
-			sub.append("CY  - ").append(appendMe(((BookCitation)this).getCity())).append(cls);
-			catPersonsRis(sub,"ED - ",((BookCitation)this).getEditors());			
-		}
-		if ( isInBook || isArticle ) {
-			String pages = getPages();
-			if ( pages != null && pages.matches("^\\d+-\\d+$") ) {
-				String[] pageRange = pages.split("-");
-				sub.append("SP  - ").append(pageRange[0]).append(cls);
-				sub.append("EP  - ").append(pageRange[1]).append(cls);
+		try {
+			String citationType = this.getRealCitationType(), cls = "\n";
+			boolean isArticle = false, isBook = false, isInBook = false;		
+			if ( citationType.equals(ArticleCitation.CITATION_TYPE_ARTICLE) ) {
+				ris.append("TY  - JOUR\n");
+				sub.append("JF  - ").append(appendMe(((ArticleCitation)this).getJournal())).append(cls);
+				sub.append("VL  - ").append(appendMe(((ArticleCitation)this).getVolume())).append(cls);
+				sub.append("IS  - ").append(appendMe(((ArticleCitation)this).getIssue())).append(cls);
+				isArticle = true;
 			}
-		}
-		ris.append("ID  - ").append(getId()).append(cls);	
-		catPersonsRis(ris,"AU  - ",getAuthors());		
-		ris.append("T1  - ").append(appendMe(getTitle())).append(cls);		
-		ris.append("PY  - ").append(appendMe(getPublishYear())).append(cls);
-		String keyWords = getKeywords();
-		if ( keyWords != null ) {
-			String[] words = keyWords.split(",\\s*");
-			for ( int i = 0; i < words.length; i++ ) {
-				ris.append("KW  - ").append(appendMe(words[i])).append(cls);
+			else if ( citationType.equals(BookCitation.CITATION_TYPE_BOOK) ) {
+				ris.append("TY  - BOOK\n");
+				isBook = true;
+			}	
+			else if ( citationType.equals(InBookCitation.CITATION_TYPE_BOOKSECTION) ) {
+				ris.append("TY  - CHAP\n");
+				sub.append("TI  - ").append(appendMe(((InBookCitation)this).getBookTitle())).append(cls);
+				isInBook = true;
+			}	
+			if ( isBook || isInBook) {
+				sub.append("SN  - ISBN ").append(appendMe(((BookCitation)this).getISBN())).append(cls);
+				sub.append("PB  - ").append(appendMe(((BookCitation)this).getPublisher())).append(cls);
+				sub.append("CY  - ").append(appendMe(((BookCitation)this).getCity())).append(cls);
+				catPersonsRis(sub,"ED - ",((BookCitation)this).getEditors());			
 			}
+			if ( isInBook || isArticle ) {
+				String pages = getPages();
+				if ( pages != null && pages.matches("^\\d+-\\d+$") ) {
+					String[] pageRange = pages.split("-");
+					sub.append("SP  - ").append(pageRange[0]).append(cls);
+					sub.append("EP  - ").append(pageRange[1]).append(cls);
+				}
+			}
+			ris.append("ID  - ").append(getId()).append(cls);	
+			catPersonsRis(ris,"AU  - ",getAuthors());		
+			ris.append("T1  - ").append(appendMe(getTitle())).append(cls);		
+			ris.append("PY  - ").append(appendMe(getPublishYear())).append(cls);
+			String keyWords = getKeywords();
+			if ( keyWords != null ) {
+				String[] words = keyWords.split(",\\s*");
+				for ( int i = 0; i < words.length; i++ ) {
+					ris.append("KW  - ").append(appendMe(words[i])).append(cls);
+				}
+			}
+			String url = getURL(), doi = getDoi(), pmid = getPMID();
+			String theUrl = null;
+			if ( url != null && ! url.equals("http://") ) {
+				theUrl = url;
+			}
+			else if ( doi != null ) {
+				theUrl = "http://dx.doi.org/" + doi;
+			}
+			else if ( pmid != null ) {
+				theUrl = "http://pmid.us/" + pmid;
+			}
+			ris.append("UR  - ").append(appendMe(theUrl)).append(cls);
+			ris.append("N2  - ").append(appendMe(getAbstract())).append(cls);		
+			ris.append("L3  - ").append(appendMe(getDoi())).append(cls);
+			ris.append(sub);
+			ris.append("ER  - ").append(cls);
 		}
-		String url = getURL(), doi = getDoi(), pmid = getPMID();
-		String theUrl = null;
-		if ( url != null && ! url.equals("http://") ) {
-			theUrl = url;
+		catch ( Exception e ) {
+			e.printStackTrace();
 		}
-		else if ( doi != null ) {
-			theUrl = "http://dx.doi.org/" + doi;
-		}
-		else if ( pmid != null ) {
-			theUrl = "http://pmid.us/" + pmid;
-		}
-		ris.append("UR  - ").append(appendMe(theUrl)).append(cls);
-		ris.append("N2  - ").append(appendMe(getAbstract())).append(cls);		
-		ris.append("L3  - ").append(appendMe(getDoi())).append(cls);
-		ris.append(sub);
-		ris.append("ER  - ").append(cls);
 		return ris.toString();		
 	}
 	
@@ -603,44 +613,49 @@
 	@Transient
 	public String getBibtexReference () {
 		StringBuilder bib = new StringBuilder(), sub = new StringBuilder();
-		String citationType = this.getRealCitationType(), cls = "},";
-		boolean isArticle = false, isBook = false, isInBook = false;		
-		if ( citationType.equals(ArticleCitation.CITATION_TYPE_ARTICLE) ) {
-			bib.append("@ARTICLE{");
-			sub.append("\n\t journal = {").append(appendMe(((ArticleCitation)this).getJournal())).append(cls);
-			sub.append("\n\t volume = {").append(appendMe(((ArticleCitation)this).getVolume())).append(cls);
-			sub.append("\n\t number = {").append(appendMe(((ArticleCitation)this).getIssue())).append(cls);
-			isArticle = true;
+		try {
+			String citationType = this.getRealCitationType(), cls = "},";
+			boolean isArticle = false, isBook = false, isInBook = false;		
+			if ( citationType.equals(ArticleCitation.CITATION_TYPE_ARTICLE) ) {
+				bib.append("@ARTICLE{");
+				sub.append("\n\t journal = {").append(appendMe(((ArticleCitation)this).getJournal())).append(cls);
+				sub.append("\n\t volume = {").append(appendMe(((ArticleCitation)this).getVolume())).append(cls);
+				sub.append("\n\t number = {").append(appendMe(((ArticleCitation)this).getIssue())).append(cls);
+				isArticle = true;
+			}
+			else if ( citationType.equals(BookCitation.CITATION_TYPE_BOOK) ) {
+				bib.append("@BOOK{");
+				isBook = true;
+			}
+			else if ( citationType.equals(InBookCitation.CITATION_TYPE_BOOKSECTION) ) {
+				bib.append("@INCOLLECTION{");
+				sub.append("\n\t booktitle = {").append(appendMe(((InBookCitation)this).getBookTitle())).append(cls);
+				isInBook = true;
+			}
+			if ( isBook || isInBook) {
+				sub.append("\n\t isbn = {").append(appendMe(((BookCitation)this).getISBN())).append(cls);
+				sub.append("\n\t publisher = {").append(appendMe(((BookCitation)this).getPublisher())).append(cls);
+				sub.append("\n\t address = {").append(appendMe(((BookCitation)this).getCity())).append(cls);
+				sub.append("\n\t editor = {").append(appendMe(catPersonsBibtex(((BookCitation)this).getEditors()))).append(cls);			
+			}
+			if ( isInBook || isArticle ) {
+				sub.append("\n\t pages = {").append(appendMe(getPages()).replaceFirst("\\-", "--")).append(cls);
+			}		
+			bib.append("TreeBASE2Ref").append(getId()).append(",");		
+			bib.append("\n\t author = {").append(appendMe(catPersonsBibtex(getAuthors()))).append(cls);		
+			bib.append("\n\t title = {").append(appendMe(getTitle())).append(cls);		
+			bib.append("\n\t year = {").append(appendMe(getPublishYear())).append(cls);
+			bib.append("\n\t keywords = {").append(appendMe(getKeywords())).append(cls);
+			bib.append("\n\t doi = {").append(appendMe(getDoi())).append(cls);
+			bib.append("\n\t url = {").append(appendMe(getURL())).append(cls);
+			bib.append("\n\t pmid = {").append(appendMe(getPMID())).append(cls);
+			bib.append(sub);
+			bib.append("\n\t abstract = {").append(appendMe(getAbstract())).append("}");		
+			bib.append("\n}");
 		}
-		else if ( citationType.equals(BookCitation.CITATION_TYPE_BOOK) ) {
-			bib.append("@BOOK{");
-			isBook = true;
+		catch ( Exception e ) {
+			e.printStackTrace();
 		}
-		else if ( citationType.equals(InBookCitation.CITATION_TYPE_BOOKSECTION) ) {
-			bib.append("@INCOLLECTION{");
-			sub.append("\n\t booktitle = {").append(appendMe(((InBookCitation)this).getBookTitle())).append(cls);
-			isInBook = true;
-		}
-		if ( isBook || isInBook) {
-			sub.append("\n\t isbn = {").append(appendMe(((BookCitation)this).getISBN())).append(cls);
-			sub.append("\n\t publisher = {").append(appendMe(((BookCitation)this).getPublisher())).append(cls);
-			sub.append("\n\t address = {").append(appendMe(((BookCitation)this).getCity())).append(cls);
-			sub.append("\n\t editor = {").append(appendMe(catPersonsBibtex(((BookCitation)this).getEditors()))).append(cls);			
-		}
-		if ( isInBook || isArticle ) {
-			sub.append("\n\t pages = {").append(appendMe(getPages()).replaceFirst("\\-", "--")).append(cls);
-		}		
-		bib.append("TreeBASE2Ref").append(getId()).append(",");		
-		bib.append("\n\t author = {").append(appendMe(catPersonsBibtex(getAuthors()))).append(cls);		
-		bib.append("\n\t title = {").append(appendMe(getTitle())).append(cls);		
-		bib.append("\n\t year = {").append(appendMe(getPublishYear())).append(cls);
-		bib.append("\n\t keywords = {").append(appendMe(getKeywords())).append(cls);
-		bib.append("\n\t doi = {").append(appendMe(getDoi())).append(cls);
-		bib.append("\n\t url = {").append(appendMe(getURL())).append(cls);
-		bib.append("\n\t pmid = {").append(appendMe(getPMID())).append(cls);
-		bib.append(sub);
-		bib.append("\n\t abstract = {").append(appendMe(getAbstract())).append("}");		
-		bib.append("\n}");
 		return bib.toString();
 	}
 	


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[Treebase-guts] SF.net SVN: treebase:[700] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/AbstractDownloadController.java

From: <rv...@us...> - 2010-06-01 16:28:09

Revision: 700
          http://treebase.svn.sourceforge.net/treebase/?rev=700&view=rev
Author:   rvos
Date:     2010-06-01 16:28:03 +0000 (Tue, 01 Jun 2010)

Log Message:
-----------
Added UTF-8 specifier in content-type header

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java	2010-05-28 08:03:51 UTC (rev 699)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AbstractDownloadController.java	2010-06-01 16:28:03 UTC (rev 700)
@@ -26,8 +26,8 @@
 	private NexusService mNexmlService;	
 	private NexusService mRdfaService;	
 	private SubmissionService mSubmissionService;
-	private static String mNexmlContentType = "application/xml";
-	private static String mRdfContentType = "application/rdf+xml";
+	private static String mNexmlContentType = "application/xml; charset=UTF-8";
+	private static String mRdfContentType = "application/rdf+xml; charset=UTF-8";
 
 	/**
 	 * Return the StudyService field.


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[Treebase-guts] SF.net SVN: treebase:[699] trunk/treebase-web/src/main/webapp/WEB-INF/pages /searchResultsAsRDF.jsp

From: <rv...@us...> - 2010-05-28 08:03:58

Revision: 699
          http://treebase.svn.sourceforge.net/treebase/?rev=699&view=rev
Author:   rvos
Date:     2010-05-28 08:03:51 +0000 (Fri, 28 May 2010)

Log Message:
-----------
Specified content-type (utf-8) in http header

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp	2010-05-28 07:59:14 UTC (rev 698)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp	2010-05-28 08:03:51 UTC (rev 699)
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <%@ include file="/common/taglibs.jsp"%>
-<% response.setContentType("application/rss+xml"); %>
+<% response.setContentType("application/rss+xml; charset=UTF-8"); %>
 <rdf:RDF
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:dcterms="http://purl.org/dc/terms/"


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[Treebase-guts] SF.net SVN: treebase:[698] trunk/treebase-web/src/main/webapp/WEB-INF/pages /anyObjectAsRDF.jsp

From: <rv...@us...> - 2010-05-28 07:59:21

Revision: 698
          http://treebase.svn.sourceforge.net/treebase/?rev=698&view=rev
Author:   rvos
Date:     2010-05-28 07:59:14 +0000 (Fri, 28 May 2010)

Log Message:
-----------
Specified content-type (utf-8) in http header

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp	2010-05-24 16:54:27 UTC (rev 697)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp	2010-05-28 07:59:14 UTC (rev 698)
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <%@ include file="/common/taglibs.jsp"%>
-<% response.setContentType("application/rss+xml"); %>
+<% response.setContentType("application/rss+xml; charset=UTF-8"); %>
 <rdf:RDF
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"


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[Treebase-guts] SF.net SVN: treebase:[697] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchSummaryController.java

From: <hl...@us...> - 2010-05-24 16:54:34

Revision: 697
          http://treebase.svn.sourceforge.net/treebase/?rev=697&view=rev
Author:   hlapp
Date:     2010-05-24 16:54:27 +0000 (Mon, 24 May 2010)

Log Message:
-----------
Fix for the null pointer exception in TaxonLabelByLabelComparator.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-05-01 15:13:17 UTC (rev 696)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java	2010-05-24 16:54:27 UTC (rev 697)
@@ -547,7 +547,11 @@
 
 	private class TaxonLabelByLabelComparator implements Comparator<TaxonLabel> {
 		public int compare(TaxonLabel a, TaxonLabel b) {
-			return a.getTaxonLabel().compareTo(b.getTaxonLabel());
+                    String l1 = (a == null) ? "" : a.getTaxonLabel();
+                    String l2 = (b == null) ? "" : b.getTaxonLabel();
+                    if (l1 == null) l1 = "";
+                    if (l2 == null) l2 = "";
+                    return l1.compareTo(l2);
 		}	
 	}
 }
\ No newline at end of file


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[Treebase-guts] [ treebase-Bugs-3005716 ] Tree URI results in Yikes

From: SourceForge.net <no...@so...> - 2010-05-22 15:25:49

Bugs item #3005716, was opened at 2010-05-22 11:25
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3005716&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: data
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Rutger Vos (rvos)
Summary: Tree URI results in Yikes

Initial Comment:
If I follow a URI for a tree, instead of getting an RSS feed I get a Yikes error.

http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr6031

Yikes!

javax.servlet.jsp.el.ELException: An error occurred while getting property "phyloWSPath" from an instance of class org.cipres.treebase.domain.study.Study$$EnhancerByCGLIB$$9d782eec
	at org.apache.commons.el.Logger.logError(Logger.java:484)
	at org.apache.commons.el.Logger.logError(Logger.java:588)
	at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318)
	at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190)
	at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fout_005f1(anyObjectAsRDF_jsp.java:224)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspx_meth_c_005fif_005f0(anyObjectAsRDF_jsp.java:199)
	at org.apache.jsp.WEB_002dINF.pages.anyObjectAsRDF_jsp._jspService(anyObjectAsRDF_jsp.java:100)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	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 com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39)
	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.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
	at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
	at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239)
	at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879)
	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.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
	at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
	at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
	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.Http11Processor.process(Http11Processor.java:873)
	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
	at java.lang.Thread.run(Thread.java:636)


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