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From: SourceForge.net <no...@so...> - 2009-07-23 19:36:45
|
Bugs item #2826165, was opened at 2009-07-23 15:36 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2826165&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Reviewer/Referee Access Initial Comment: I'm making this a priority of 9 only because it is needed before TreeBASE2 can be made public. We need to make sure that reviewers or referees can have access to datasets that are "in progress" and associated with a manuscript that is in the review process of a journal. Jin Ruan initially created a user role called "reviewer" which gives someone read-only access to the private sections of the database. We decided that this is a bad solution because it requires that each reviewer get a login name and password, which implies a huge amount of admin overhead. A better solution is to auto-generate a long random string which can be used in an URL to give someone a read-only access to the submission page. But however which way we do this, it is needed because some journals depend on this as part of their review process. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2826165&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-07-22 13:23:44
|
Bugs item #2825363, was opened at 2009-07-22 09:23 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2825363&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: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Analysis falsely reports taxon mismatch when tree in+out Initial Comment: when creating an analysis step that has trees as input and trees as output, software reports that the taxon labels among the input objects do not match with those in the output objects, when in fact they do. example is here: http://8ball.sdsc.edu:6666/treebase-web/user/summary.html?id=2383 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2825363&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2009-07-16 19:02:51
|
Bugs item #2822673, was opened at 2009-07-16 15:02 Message generated for change (Tracker Item Submitted) made by mjdominus You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2822673&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: easy Status: Open Priority: 5 Private: No Submitted By: Mark Dominus (mjdominus) Assigned to: Rutger Vos (rvos) Summary: Failed search behavior seems confusing Initial Comment: Suppose I do a search and get 17 results. Then I do a second search. These results are intersected with the first 17 to produce a final result, *unless* the result is empty, in which case the original 17 are retained. The retention behavior is correct, but is not explained quite clearly enough. The resulting search page displays two messages: No matching items found Your search has yielded 1 item: which appear contradictory. The language should be changed here; instead of "your search has yielded 1 item" it should perhaps say something like "Previous search results retained". ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2822673&group_id=248804 |
|
From: <mjd...@us...> - 2009-07-15 19:10:46
|
Revision: 181
http://treebase.svn.sourceforge.net/treebase/?rev=181&view=rev
Author: mjdominus
Date: 2009-07-15 19:09:55 +0000 (Wed, 15 Jul 2009)
Log Message:
-----------
new utility to exercise findByTopology3() function
Added Paths:
-----------
trunk/treebase-core/src/main/java/org/cipres/treebase/util/TreeQuery.java
Added: trunk/treebase-core/src/main/java/org/cipres/treebase/util/TreeQuery.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/util/TreeQuery.java (rev 0)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/util/TreeQuery.java 2009-07-15 19:09:55 UTC (rev 181)
@@ -0,0 +1,40 @@
+package org.cipres.treebase.util;
+
+import java.util.Set;
+
+import org.cipres.treebase.ContextManager;
+import org.cipres.treebase.domain.taxon.TaxonLabelService;
+import org.cipres.treebase.domain.taxon.TaxonVariant;
+import org.cipres.treebase.domain.tree.PhyloTree;
+import org.cipres.treebase.domain.tree.PhyloTreeService;
+
+public class TreeQuery extends AbstractStandalone {
+ public static void main(String[] args) {
+ setupContext();
+ PhyloTreeService treeServ = ContextManager.getPhyloTreeService();
+ TaxonLabelService tlServ = ContextManager.getTaxonLabelService();
+
+ Set<TaxonVariant>[] tvSet = new Set[3];
+ for (int i=0; i<3; i++) {
+ tvSet[i] = tlServ.findTaxonVariantByName(args[i]);
+ warn(args[i] + " yields " + tvSet[i].size() + " matches");
+ }
+
+ TaxonVariant[] tv = new TaxonVariant[3];
+ for (int i=0; i<3; i++) {
+ tv[i] = tvSet[i].iterator().next();
+ tvShow(tv[i]);
+ }
+
+ Set<PhyloTree> trees = treeServ.findByTopology3(tv[0], tv[1], tv[2]);
+ warn("Found " + trees.size() + " trees.");
+
+ for (PhyloTree t : trees) {
+ System.out.println(t.getId());
+ }
+ }
+
+ public static void tvShow(TaxonVariant tv) {
+ warn("Tv" + tv.getId() + ": " + tv.getName());
+ }
+}
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|
|
From: <mjd...@us...> - 2009-07-15 18:15:53
|
Revision: 180
http://treebase.svn.sourceforge.net/treebase/?rev=180&view=rev
Author: mjdominus
Date: 2009-07-15 18:14:59 +0000 (Wed, 15 Jul 2009)
Log Message:
-----------
add zing cql-java to .classpath
Modified Paths:
--------------
trunk/treebase-web/.classpath
Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath 2009-07-07 09:05:13 UTC (rev 179)
+++ trunk/treebase-web/.classpath 2009-07-15 18:14:59 UTC (rev 180)
@@ -106,6 +106,6 @@
<classpathentry kind="var" path="M2_REPO/org/nexml/model/nexml/1.5-SNAPSHOT/nexml-1.5-SNAPSHOT.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v5.5"/>
- <!-- classpathentry combineaccessrules="false" exported="true" kind="src" path="/nexml"/ -->
+ <classpathentry kind="var" path="M2_REPO/zing/z3950/org/cql-java/1.0/cql-java-1.0.jar"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
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|
|
From: <rv...@us...> - 2009-07-07 09:05:25
|
Revision: 179
http://treebase.svn.sourceforge.net/treebase/?rev=179&view=rev
Author: rvos
Date: 2009-07-07 09:05:13 +0000 (Tue, 07 Jul 2009)
Log Message:
-----------
NPE prevention changes
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2009-07-06 10:04:34 UTC (rev 178)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2009-07-07 09:05:13 UTC (rev 179)
@@ -84,11 +84,21 @@
if ( null != phyloTree.getLabel() ) {
xmlTree.setLabel(phyloTree.getLabel());
}
- xmlTree.addAnnotationValue("tb:identifier.tree", mTBTermsURI, phyloTree.getId());
- xmlTree.addAnnotationValue("tb:kind.tree", mTBTermsURI, phyloTree.getKindDescription());
- xmlTree.addAnnotationValue("tb:type.tree", mTBTermsURI, phyloTree.getTypeDescription());
- xmlTree.addAnnotationValue("tb:quality.tree", mTBTermsURI, phyloTree.getQualityDescription());
- xmlTree.addAnnotationValue("tb:ntax.tree", mTBTermsURI, phyloTree.getnTax());
+ if ( null != phyloTree.getId() ) {
+ xmlTree.addAnnotationValue("tb:identifier.tree", mTBTermsURI, phyloTree.getId());
+ }
+ if ( null != phyloTree.getKindDescription() ) {
+ xmlTree.addAnnotationValue("tb:kind.tree", mTBTermsURI, phyloTree.getKindDescription());
+ }
+ if ( null != phyloTree.getTypeDescription() ) {
+ xmlTree.addAnnotationValue("tb:type.tree", mTBTermsURI, phyloTree.getTypeDescription());
+ }
+ if ( null != phyloTree.getQualityDescription() ) {
+ xmlTree.addAnnotationValue("tb:quality.tree", mTBTermsURI, phyloTree.getQualityDescription());
+ }
+ if ( null != phyloTree.getnTax() ) {
+ xmlTree.addAnnotationValue("tb:ntax.tree", mTBTermsURI, phyloTree.getnTax());
+ }
attachTreeBaseID(xmlTree, phyloTree,PhyloTree.class);
copyTreeBaseTree(phyloTree, xmlTree);
return xmlTree;
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|
|
From: <rv...@us...> - 2009-07-06 10:04:40
|
Revision: 178
http://treebase.svn.sourceforge.net/treebase/?rev=178&view=rev
Author: rvos
Date: 2009-07-06 10:04:34 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Removed invalid textarea contents
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp 2009-07-06 08:44:02 UTC (rev 177)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp 2009-07-06 10:04:34 UTC (rev 178)
@@ -20,7 +20,7 @@
<a href="/treebase-web/help/urlAPI.jsp">TreeBASE help page about searching</a>.
</p>
<div>
- <textarea name="query" style="width:100%">Try CQL query here</textarea><br/>
+ <textarea name="query" style="width:100%"></textarea><br/>
<input type="submit" style="width:100%" value="Evaluate query"/>
</div>
</fieldset>
\ No newline at end of file
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|
|
From: <rv...@us...> - 2009-07-06 08:44:03
|
Revision: 177
http://treebase.svn.sourceforge.net/treebase/?rev=177&view=rev
Author: rvos
Date: 2009-07-06 08:44:02 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Added xml 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 2009-07-06 08:43:00 UTC (rev 176)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp 2009-07-06 08:44:02 UTC (rev 177)
@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
<%@ include file="/common/taglibs.jsp"%>
<% response.setContentType("application/rdf+xml"); %>
<rdf:RDF
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|
From: <rv...@us...> - 2009-07-06 08:43:01
|
Revision: 176
http://treebase.svn.sourceforge.net/treebase/?rev=176&view=rev
Author: rvos
Date: 2009-07-06 08:43:00 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Added xml 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 2009-07-06 08:41:02 UTC (rev 175)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp 2009-07-06 08:43:00 UTC (rev 176)
@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
<%@ include file="/common/taglibs.jsp"%>
<% response.setContentType("application/rss+xml"); %>
<rdf:RDF
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|
From: <rv...@us...> - 2009-07-06 08:41:03
|
Revision: 175
http://treebase.svn.sourceforge.net/treebase/?rev=175&view=rev
Author: rvos
Date: 2009-07-06 08:41:02 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Now throws 404 instead of NPE when study not found
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-07-06 08:37:02 UTC (rev 174)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2009-07-06 08:41:02 UTC (rev 175)
@@ -162,6 +162,9 @@
throw new ObjectNotFoundException("Can't find matrix " + objectId);
}
Study study = matrix.getStudy();
+ if ( study == null ) {
+ throw new ObjectNotFoundException("Can't find study for matrix "+objectId);
+ }
return base
.append("/downloadAMatrix.html?id=")
.append(study.getId())
@@ -177,6 +180,9 @@
throw new ObjectNotFoundException("Can't find tree " + objectId);
}
Study study = phyloTree.getStudy();
+ if ( study == null ) {
+ throw new ObjectNotFoundException("Can't find study for tree "+objectId);
+ }
return base
.append("/downloadATree.html?id=")
.append(study.getId())
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|
From: <rv...@us...> - 2009-07-06 08:37:03
|
Revision: 174
http://treebase.svn.sourceforge.net/treebase/?rev=174&view=rev
Author: rvos
Date: 2009-07-06 08:37:02 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Made uBio namebank ID and NCBI taxon ID sortable columns in taxon labels list.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/taxonLabels.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/taxonLabels.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/taxonLabels.jsp 2009-07-06 08:35:26 UTC (rev 173)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/taxonLabels.jsp 2009-07-06 08:37:02 UTC (rev 174)
@@ -39,14 +39,14 @@
<display:column sortable="true" property="taxonVariant.fullName" titleKey="taxon.name" />
- <display:column titleKey="taxon.ncbiTaxID">
+ <display:column titleKey="taxon.ncbiTaxID" sortable="true">
<c:if test="${userList.taxonVariant!=null}">
<c:set var="ncbiTaxoURL" value="${ncbiTaxonomyURL}${userList.ncbiTaxID}"/>
<a href="${ncbiTaxoURL}" target="_blank">${userList.ncbiTaxID}</a>
</c:if>
</display:column>
- <display:column titleKey="taxon.uBioTaxID">
+ <display:column titleKey="taxon.uBioTaxID" sortable="true">
<c:if test="${userList.taxonVariant!=null}">
<c:set var="ubioTaxoURL" value="${uBioTaxonomyURL}${userList.taxonVariant.namebankID}"/>
<a href="${ubioTaxoURL}" target="_blank">${userList.taxonVariant.namebankID}</a>
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|
From: <rv...@us...> - 2009-07-06 08:35:27
|
Revision: 173
http://treebase.svn.sourceforge.net/treebase/?rev=173&view=rev
Author: rvos
Date: 2009-07-06 08:35:26 +0000 (Mon, 06 Jul 2009)
Log Message:
-----------
Removed javascript debug alert on taxon label editor.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp 2009-07-02 22:52:46 UTC (rev 172)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/editTaxonLabel.jsp 2009-07-06 08:35:26 UTC (rev 173)
@@ -80,7 +80,6 @@
and here is the namebank id:
<script type="text/javascript">
function selectRadio(textBoxRadio) {
- alert($(textBoxRadio));
$(textBoxRadio).checked = true;
}
</script>
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|
From: <rv...@us...> - 2009-07-03 09:06:49
|
Revision: 157
http://treebase.svn.sourceforge.net/treebase/?rev=157&view=rev
Author: rvos
Date: 2009-07-02 10:39:17 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Interface needed to change, added method stub.
Modified Paths:
--------------
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/TreeTopSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java 2009-07-02 10:38:23 UTC (rev 156)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java 2009-07-02 10:39:17 UTC (rev 157)
@@ -20,6 +20,7 @@
package org.cipres.treebase.web.controllers;
+import java.io.IOException;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
@@ -38,6 +39,7 @@
import org.cipres.treebase.web.Constants;
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLParseException;
/**
* TreeTopSearchController.java
@@ -204,4 +206,12 @@
return "treeTopSearch.html";
}
+ @Override
+ protected ModelAndView handleQueryRequest(HttpServletRequest request,
+ HttpServletResponse response, BindException errors)
+ throws CQLParseException, IOException, InstantiationException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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|
From: <rv...@us...> - 2009-07-02 22:52:48
|
Revision: 172
http://treebase.svn.sourceforge.net/treebase/?rev=172&view=rev
Author: rvos
Date: 2009-07-02 22:52:46 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Adding template to represent SearchResults objects in RSS1.0
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp 2009-07-02 22:52:46 UTC (rev 172)
@@ -0,0 +1,33 @@
+<%@ include file="/common/taglibs.jsp"%>
+<% response.setContentType("application/rdf+xml"); %>
+<rdf:RDF
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:dcterms="http://purl.org/dc/terms/"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns="http://purl.org/rss/1.0/">
+ <channel rdf:about="${baseURL}/${phyloWSPath}?query=<c:out value="${normalizedCQLQuery}" escapeXml="true"/>&format=${format}&recordSchema=${recordSchema}">
+ <title>${phyloWSPath}</title>
+ <link>${baseURL}</link>
+ <description>${searchResultsThawed.description}</description>
+ <image rdf:resource="${domainAddress}<fmt:message key="icons.treebase.16px"/>"/>
+ <items>
+ <rdf:Seq>
+ <c:forEach var="result" items="${searchResultsThawed.results}" varStatus="status">
+ <rdf:li rdf:resource="${baseURL}/<c:out value="${result.phyloWSPath}"/>"/>
+ </c:forEach>
+ </rdf:Seq>
+ </items>
+ </channel>
+ <image rdf:about="${domainAddress}<fmt:message key="icons.treebase.16px"/>">
+ <title>${phyloWSPath}</title>
+ <link>${baseURL}</link>
+ <url>${domainAddress}<fmt:message key="icons.treebase.16px"/></url>
+ </image>
+ <c:forEach var="result" items="${searchResultsThawed.results}" varStatus="status">
+ <item rdf:about="${baseURL}/<c:out value="${result.phyloWSPath}"/>">
+ <title><c:out value="${result.namespacedGUID}"/></title>
+ <link>${baseURL}/<c:out value="${result.phyloWSPath}"/></link>
+ <description><c:out value="${result.namespacedGUID}"/></description>
+ </item>
+ </c:forEach>
+</rdf:RDF>
\ No newline at end of file
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|
From: <rv...@us...> - 2009-07-02 22:51:35
|
Revision: 171
http://treebase.svn.sourceforge.net/treebase/?rev=171&view=rev
Author: rvos
Date: 2009-07-02 22:51:34 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added CQL search facility to main search pages
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2009-07-02 22:49:58 UTC (rev 170)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2009-07-02 22:51:34 UTC (rev 171)
@@ -17,4 +17,5 @@
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
</fieldset>
+ <jsp:include page="querySearchBox.jsp"/>
</form>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2009-07-02 22:49:58 UTC (rev 170)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2009-07-02 22:51:34 UTC (rev 171)
@@ -19,4 +19,5 @@
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
</fieldset>
+ <jsp:include page="querySearchBox.jsp"/>
</form>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearchForm.jsp 2009-07-02 22:49:58 UTC (rev 170)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/taxonSearchForm.jsp 2009-07-02 22:51:34 UTC (rev 171)
@@ -24,25 +24,29 @@
else {
$('searchTermLegend').textContent = 'Enter names (one per line)';
}
- $('searchTerm').disabled = true;
}
- function toggleTextArea(button) {
- var noneChecked = true;
- var siblings = $(button.parentNode).getElementsByClassName('selectionNeeded');
- for ( var i = 0; i < siblings.length; i++ ) {
- if ( siblings[i].checked ) {
- noneChecked = false;
+ function validateForm() {
+ if ( $('searchTerm').value != "" ) {
+ if ( $('IdentifiersRadio').checked ) {
+ if ( $('TreeBASERadio').checked || $('NCBIRadio').checked || $('uBioRadio').checked ) {
+ return $('searchByTaxonLabel').submit();
+ }
+ alert("Please select either TreeBASE, NCBI or uBio");
}
+ else if ( $('TextSearchRadio').checked ) {
+ if ( $('taxonLabelRadio').checked || $('taxonVariantRadio').checked || $('taxonRadio').checked ) {
+ return $('searchByTaxonLabel').submit();
+ }
+ alert("Please select at least one of Taxon label, Taxon variant or Taxon");
+ }
+ else {
+ alert("Please select what to search on (identifiers or text)");
+ }
}
- $('searchTerm').disabled = noneChecked;
- }
- function toggleSubmit(textarea) {
- if ( textarea.value != "" ) {
- $('submitSearch').disabled = false;
- }
else {
- $('submitSearch').disabled = true;
+ alert("Please enter search terms in the text area");
}
+ return false;
}
</script>
@@ -53,25 +57,25 @@
<input type="hidden" name="searchType" value="${searchType }"/>
<fieldset id="Identifiers">
<legend>
- <input onclick="toggleFieldSet('TextSearch','Identifiers')" type="radio" name="searchOn" value="Identifiers"/>Identifiers
+ <input onclick="toggleFieldSet('TextSearch','Identifiers')" type="radio" id="IdentifiersRadio" name="searchOn" value="Identifiers"/>Identifiers
<a href="#" class="openHelp" onclick="openHelp('taxonSearchIdentifiers')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
</legend>
- <input type="radio" name="objectIdentifier" class="selectionNeeded" onchange="toggleTextArea(this)" value="TreeBASE" disabled="disabled"/>TreeBASE taxon ID
- <input type="radio" name="objectIdentifier" class="selectionNeeded" onchange="toggleTextArea(this)" value="NCBI" disabled="disabled"/> NCBI taxon ID
- <input type="radio" name="objectIdentifier" class="selectionNeeded" onchange="toggleTextArea(this)" value="uBio" disabled="disabled"/> uBio nameBankID
+ <input type="radio" name="objectIdentifier" class="selectionNeeded" id="TreeBASERadio" value="TreeBASE" disabled="disabled"/>TreeBASE taxon ID
+ <input type="radio" name="objectIdentifier" class="selectionNeeded" id="NCBIRadio" value="NCBI" disabled="disabled"/> NCBI taxon ID
+ <input type="radio" name="objectIdentifier" class="selectionNeeded" id="uBioRadio" value="uBio" disabled="disabled"/> uBio nameBankID
</fieldset>
<fieldset id="TextSearch">
<legend>
- <input onclick="toggleFieldSet('Identifiers','TextSearch')" type="radio" name="searchOn" value="TextSearch"/>Text search
+ <input onclick="toggleFieldSet('Identifiers','TextSearch')" type="radio" name="searchOn" id="TextSearchRadio" value="TextSearch"/>Text search
<a href="#" class="openHelp" onclick="openHelp('taxonSearchTextSearch')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
</legend>
- <input type="checkbox" name="stringProperty" class="selectionNeeded" onchange="toggleTextArea(this)" value="taxonLabel" disabled="disabled"/> Taxon label
- <input type="checkbox" name="stringProperty" class="selectionNeeded" onchange="toggleTextArea(this)" value="taxonVariant" disabled="disabled"/> Taxon variant
- <input type="checkbox" name="stringProperty" class="selectionNeeded" onchange="toggleTextArea(this)" value="taxon" disabled="disabled"/> Taxon
+ <input type="checkbox" name="stringProperty" class="selectionNeeded" id="taxonLabelRadio" value="taxonLabel" disabled="disabled"/> Taxon label
+ <input type="checkbox" name="stringProperty" class="selectionNeeded" id="taxonVariantRadio" value="taxonVariant" disabled="disabled"/> Taxon variant
+ <input type="checkbox" name="stringProperty" class="selectionNeeded" id="taxonRadio" value="taxon" disabled="disabled"/> Taxon
<hr style="border: 1px solid #cccccc" />
<input type="checkbox" name="stringModifier" value="caseSensitive" disabled="disabled"/> Case sensitive
<input type="checkbox" name="stringModifier" value="exactMatch" disabled="disabled"/> Exact match
@@ -83,9 +87,12 @@
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
</legend>
- <textarea name="searchTerm" id="searchTerm" style="width:100%" onchange="toggleSubmit(this)" disabled="disabled">${searchTerm}</textarea>
+ <textarea name="searchTerm" id="searchTerm" style="width:100%">${searchTerm}</textarea>
</fieldset>
- <input type=submit name="Action" id="submitSearch" value="Search" disabled="disabled"/>
+ <input type="hidden" name="Action" value="Search"/>
+ <input type="button" name="Action" id="submitSearch" onclick="validateForm()" value="Search"/>
+
+ <jsp:include page="querySearchBox.jsp"/>
</fieldset>
</form>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2009-07-02 22:49:58 UTC (rev 170)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2009-07-02 22:51:34 UTC (rev 171)
@@ -18,4 +18,5 @@
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
</fieldset>
+ <jsp:include page="querySearchBox.jsp"/>
</form>
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|
|
From: <rv...@us...> - 2009-07-02 22:49:59
|
Revision: 170
http://treebase.svn.sourceforge.net/treebase/?rev=170&view=rev
Author: rvos
Date: 2009-07-02 22:49:58 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Adding CQL search box page fragment
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/querySearchBox.jsp 2009-07-02 22:49:58 UTC (rev 170)
@@ -0,0 +1,26 @@
+<%@ include file="/common/taglibs.jsp"%>
+
+<a onclick="TreeBASE.collapseExpand('CQLBox','block',this)"
+ style="border:none"
+ title="collapse">
+ <img
+ class="iconButton"
+ src="<fmt:message key="icons.expand"/>"
+ style="vertical-align:middle"
+ alt="collapse" /> Advanced search...
+</a>
+<fieldset id="CQLBox" style="display:none">
+ <legend>
+ CQL query testing
+ </legend>
+ <p>
+ The TreeBASE website can be searched using a subset of constructs from the
+ <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> specification. For
+ more information on how this is used, visit the
+ <a href="/treebase-web/help/urlAPI.jsp">TreeBASE help page about searching</a>.
+ </p>
+ <div>
+ <textarea name="query" style="width:100%">Try CQL query here</textarea><br/>
+ <input type="submit" style="width:100%" value="Evaluate query"/>
+ </div>
+</fieldset>
\ No newline at end of file
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|
|
From: <rv...@us...> - 2009-07-02 21:18:20
|
Revision: 169
http://treebase.svn.sourceforge.net/treebase/?rev=169&view=rev
Author: rvos
Date: 2009-07-02 21:18:18 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added configuration for searchResultsAsRDFController
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2009-07-02 21:15:21 UTC (rev 168)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2009-07-02 21:18:18 UTC (rev 169)
@@ -16,7 +16,7 @@
<bean id="processUserController" class="org.cipres.treebase.web.controllers.ProcessUserController"/>
<bean id="anyObjectAsRDFController" class="org.cipres.treebase.web.controllers.AnyObjectAsRDFController"/>
-
+ <bean id="searchResultsAsRDFController" class="org.cipres.treebase.web.controllers.SearchResultsAsRDFController"/>
<bean id="appletInteractionController" class="org.cipres.treebase.web.controllers.AppletInteractionController">
<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
@@ -930,6 +930,7 @@
<prop key="/search/study/taxa.html">searchSummaryController</prop>
<prop key="/search/study/rowSegments.html">searchSummaryController</prop>
<prop key="/search/study/anyObjectAsRDF.html">anyObjectAsRDFController</prop>
+ <prop key="/search/searchResultsAsRDF.html">searchResultsAsRDFController</prop>
<prop key="/search/matrixRowList.html">listMatrixRowController</prop>
<prop key="/search/taxonList.html">listTaxaSearchController</prop>
<prop key="/search/downloadAStudy.html">downloadAStudyController</prop>
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|
|
From: <rv...@us...> - 2009-07-02 21:15:27
|
Revision: 168
http://treebase.svn.sourceforge.net/treebase/?rev=168&view=rev
Author: rvos
Date: 2009-07-02 21:15:21 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added document describing URL API
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/help/urlAPI.jsp
Modified: trunk/treebase-web/src/main/webapp/help/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/help/urlAPI.jsp 2009-07-02 21:12:18 UTC (rev 167)
+++ trunk/treebase-web/src/main/webapp/help/urlAPI.jsp 2009-07-02 21:15:21 UTC (rev 168)
@@ -78,11 +78,11 @@
an asterisk</a> can be used in statements in the site section they apply to, such that, for example
a taxon can be retrieved by its ncbi ID like so:
<div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb:identifier.ncbi=<em><ncbi taxon id></em></strong>
+ <strong>taxon/find?query=tb.identifier.ncbi=<em><ncbi taxon id></em></strong>
</div>
or by its name like so:
<div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb:title.taxon=<em><name></em></strong>
+ <strong>taxon/find?query=tb.title.taxon=<em><name></em></strong>
</div>
or using an exact match
(<strong>==</strong>) or a case-insensitive one (<strong>=/ignoreCase</strong>). These statements
@@ -103,7 +103,7 @@
By default, all these queries return a web page, but with a <strong>format=rss1</strong> argument
the search results are listed in an RDF compatible RSS1.0 file, i.e.:
<div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb:title.taxon=<em><name></em>&format=rss1</strong>
+ <strong>taxon/find?query=tb.title.taxon=<em><name></em>&format=rss1</strong>
</div>
The returned results in RSS1.0 use the short urls of the form <strong><section>/<id></strong>, whose
returned resource descriptions (like <a href="/treebase-web/phylows/tree/TB2:Tr2227">
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|
|
From: <rv...@us...> - 2009-07-02 21:12:19
|
Revision: 167
http://treebase.svn.sourceforge.net/treebase/?rev=167&view=rev
Author: rvos
Date: 2009-07-02 21:12:18 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added link to page describing URL API
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2009-07-02 21:10:13 UTC (rev 166)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2009-07-02 21:12:18 UTC (rev 167)
@@ -10,7 +10,7 @@
<li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>
<li><a href="#"><fmt:message key="nav.stats"/></a></li>
<li><a href="#"><fmt:message key="nav.referee"/></a></li>
- <li><a href="#"><fmt:message key="nav.urlapi"/></a></li>
+ <li><a href="/treebase-web/help/urlAPI.jsp"><fmt:message key="nav.urlapi"/></a></li>
</ul>
</div>
</div>
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|
|
From: <rv...@us...> - 2009-07-02 21:10:13
|
Revision: 166
http://treebase.svn.sourceforge.net/treebase/?rev=166&view=rev
Author: rvos
Date: 2009-07-02 21:10:13 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added dom4j dependency
Modified Paths:
--------------
trunk/treebase-core/pom.xml
Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml 2009-07-02 21:09:43 UTC (rev 165)
+++ trunk/treebase-core/pom.xml 2009-07-02 21:10:13 UTC (rev 166)
@@ -244,6 +244,11 @@
<artifactId>slf4j-jdk14</artifactId>
</exclusion>
</exclusions>
+ </dependency>
+ <dependency>
+ <groupId>dom4j</groupId>
+ <artifactId>dom4j</artifactId>
+ <version>1.6.1</version>
</dependency>
<!--dependency>
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|
|
From: <rv...@us...> - 2009-07-02 21:09:46
|
Revision: 165
http://treebase.svn.sourceforge.net/treebase/?rev=165&view=rev
Author: rvos
Date: 2009-07-02 21:09:43 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added cql-java dependency
Modified Paths:
--------------
trunk/treebase-web/pom.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2009-07-02 21:08:10 UTC (rev 164)
+++ trunk/treebase-web/pom.xml 2009-07-02 21:09:43 UTC (rev 165)
@@ -376,6 +376,11 @@
<artifactId>saaj-api</artifactId>
<version>1.3</version>
<scope>runtime</scope>
+ </dependency>
+ <dependency>
+ <groupId>zing.z3950.org</groupId>
+ <artifactId>cql-java</artifactId>
+ <version>1.0</version>
</dependency>
<!--commented on April 23, 2008 Madhu-->
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|
|
From: <rv...@us...> - 2009-07-02 21:08:10
|
Revision: 164
http://treebase.svn.sourceforge.net/treebase/?rev=164&view=rev
Author: rvos
Date: 2009-07-02 21:08:10 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added namespace prefixes for NCBI and UBIO
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/NamespacedGUID.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/NamespacedGUID.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/NamespacedGUID.java 2009-07-02 21:06:34 UTC (rev 163)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/NamespacedGUID.java 2009-07-02 21:08:10 UTC (rev 164)
@@ -12,6 +12,8 @@
private String mMamespacedIDString;
public static final String NAMING_AUTHORITY_PREFIX_TB1 = "TB1";
public static final String NAMING_AUTHORITY_PREFIX_TB2 = "TB2";
+ public static final String NAMING_AUTHORITY_PREFIX_NCBI = "NCBI";
+ public static final String NAMING_AUTHORITY_PREFIX_UBIO = "uBio";
public static final String GUID_DELIMITER = ":";
/**
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|
|
From: <rv...@us...> - 2009-07-02 21:06:35
|
Revision: 163
http://treebase.svn.sourceforge.net/treebase/?rev=163&view=rev
Author: rvos
Date: 2009-07-02 21:06:34 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Changed convertToMatrices to prevent NPEs.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TreeSearchResults.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TreeSearchResults.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TreeSearchResults.java 2009-07-02 21:02:07 UTC (rev 162)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TreeSearchResults.java 2009-07-02 21:06:34 UTC (rev 163)
@@ -77,34 +77,37 @@
// need to resurrect the study, otherwise we get a LazyInitializationException
Study resurrectedStudy = getStudyService().resurrect(study);
- Collection<AnalysisStep> analysisStepCollection = resurrectedStudy.getAnalysisSteps();
- // for the study we need to iterate over all analysis steps
- for ( AnalysisStep analysisStep : analysisStepCollection ) {
- Collection<AnalyzedData> analyzedDataCollection = analysisStep.getDataSetReadOnly();
- boolean treeIsOutput = false;
-
- // now we have to check any trees in the analyzedData...
- for ( AnalyzedData analyzedData : analyzedDataCollection ) {
- PhyloTree analyzedTree = analyzedData.getTreeData();
- String inputOutput = analyzedData.getInputOutput();
-
- // if the datum is a tree, and it's an output, and it's our focal tree...
- if ( inputOutput.equals("output") && analyzedTree != null && analyzedTree.getId() == phyloTree.getId() ) {
- treeIsOutput = true;
- }
- }
- // ...then...
- if ( treeIsOutput ) {
+ if ( resurrectedStudy != null ) {
+ Collection<AnalysisStep> analysisStepCollection = resurrectedStudy.getAnalysisSteps();
+
+ // for the study we need to iterate over all analysis steps
+ for ( AnalysisStep analysisStep : analysisStepCollection ) {
+ Collection<AnalyzedData> analyzedDataCollection = analysisStep.getDataSetReadOnly();
+ boolean treeIsOutput = false;
+
+ // now we have to check any trees in the analyzedData...
for ( AnalyzedData analyzedData : analyzedDataCollection ) {
- Matrix analyzedMatrix = analyzedData.getMatrixData();
- String inputOutput = analyzedData.getInputOutput();
+ PhyloTree analyzedTree = analyzedData.getTreeData();
+ String inputOutput = analyzedData.getInputOutput();
- // collect all input matrices
- if ( inputOutput.equals("input") && analyzedMatrix != null ) {
- pResults.add(analyzedMatrix);
- }
+ // if the datum is a tree, and it's an output, and it's our focal tree...
+ if ( inputOutput.equals("output") && analyzedTree != null && analyzedTree.getId() == phyloTree.getId() ) {
+ treeIsOutput = true;
+ }
}
+ // ...then...
+ if ( treeIsOutput ) {
+ for ( AnalyzedData analyzedData : analyzedDataCollection ) {
+ Matrix analyzedMatrix = analyzedData.getMatrixData();
+ String inputOutput = analyzedData.getInputOutput();
+
+ // collect all input matrices
+ if ( inputOutput.equals("input") && analyzedMatrix != null ) {
+ pResults.add(analyzedMatrix);
+ }
+ }
+ }
}
}
}
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|
|
From: <rv...@us...> - 2009-07-02 21:02:24
|
Revision: 162
http://treebase.svn.sourceforge.net/treebase/?rev=162&view=rev
Author: rvos
Date: 2009-07-02 21:02:07 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Added treebase term annotations
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2009-07-02 10:48:31 UTC (rev 161)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2009-07-02 21:02:07 UTC (rev 162)
@@ -95,8 +95,9 @@
* @param document
*/
private void copyCitationMetadata(Citation citation,Document document) {
+ attachAnnotation("dcterms.bibliographicCitation",citation.getAuthorsCitationStyleWithoutHtml(),mDCURI,document);
if ( null != citation.getTitle() ) {
- attachAnnotation("dc:title",citation.getTitle(),mPrismURI,document);
+ attachAnnotation("tb:title.study",citation.getTitle(),mTBTermsURI,document);
}
if ( null != citation.getPublishYear() ) {
attachAnnotation("prism:publicationDate",citation.getPublishYear().toString(),mPrismURI,document);
@@ -115,7 +116,7 @@
if ( null != citation.getKeywords() ) {
String[] keywords = citation.getKeywords().split(", ");
for ( int i = 0; i < keywords.length; i++ ) {
- attachAnnotation("prism:keyword",keywords[i],mPrismURI,document);
+ attachAnnotation("dcterms:subject",keywords[i],mDCURI,document);
}
}
if ( citation instanceof ArticleCitation ) {
@@ -162,12 +163,14 @@
private void copyMetadata(Study pStudy) {
attachTreeBaseID(getDocument(), pStudy,Study.class);
+ attachAnnotation("tb:identifier.study",pStudy.getId().toString(), mTBTermsURI, getDocument());
+ attachAnnotation("tb:identifier.study.tb1",pStudy.getTB1StudyID(), mTBTermsURI, getDocument());
if ( null != pStudy.getName() ) {
- attachAnnotation("dc:title", pStudy.getName(), mDCURI, getDocument());
+ attachAnnotation("tb:title.study", pStudy.getName(), mTBTermsURI, getDocument());
}
for ( Person person : pStudy.getAuthors() ) {
String personName = person.getFullNameCitationStyle();
- attachAnnotation("dc:contributor",personName,mDCURI,getDocument());
+ attachAnnotation("dcterms:contributor",personName,mDCURI,getDocument());
}
if ( null != pStudy.getReleaseDate() ) {
attachAnnotation("prism:embargoDate",pStudy.getReleaseDate().toString(),mPrismURI,getDocument());
@@ -175,7 +178,7 @@
if ( null != pStudy.getSubmission() ) {
if ( null != pStudy.getSubmission().getSubmitter() ) {
attachAnnotation(
- "dc:creator",
+ "dcterms:creator",
pStudy.getSubmission().getSubmitter().getPerson().getFullNameCitationStyle(),
mDCURI,
getDocument()
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2009-07-02 10:48:31 UTC (rev 161)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2009-07-02 21:02:07 UTC (rev 162)
@@ -178,7 +178,7 @@
xmlState.setLabel(tbState.getDescription());
}
if ( null != tbState.getNotes() ) {
- ((Annotatable)xmlState).addAnnotationValue("dc:description", mDCURI, tbState.getNotes());
+ ((Annotatable)xmlState).addAnnotationValue("dcterms:description", mDCURI, tbState.getNotes());
}
attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
}
@@ -220,7 +220,7 @@
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
PhyloChar tbCharacter = tbColumn.getCharacter();
if ( null != tbCharacter.getDescription() && ! tbCharacter.getDescription().equals(tbDataType) ) {
- ((Annotatable)xmlCharacter).addAnnotationValue("dc:description", mDCURI, tbCharacter.getDescription());
+ ((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", mDCURI, tbCharacter.getDescription());
}
if ( null != tbCharacter.getId() && tbCharacter.getId() != 2 ) { // XXX is PhyloChar.id 2 some sort of magic number?
attachTreeBaseID((Annotatable)xmlCharacter,tbCharacter,PhyloChar.class);
@@ -243,7 +243,7 @@
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
PhyloChar tbCharacter = tbColumn.getCharacter();
if ( null != tbCharacter.getDescription() ) {
- ((Annotatable)xmlCharacter).addAnnotationValue("dc:description", mDCURI, tbCharacter.getDescription());
+ ((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", mDCURI, tbCharacter.getDescription());
}
attachTreeBaseID((Annotatable)xmlCharacter,tbCharacter,PhyloChar.class);
}
@@ -273,6 +273,10 @@
}
xmlMatrix.setLabel(tbMatrix.getTitle());
attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix,Matrix.class);
+ ((Annotatable)xmlMatrix).addAnnotationValue("tb:type.matrix", mTBTermsURI, tbMatrix.getDataType().getDescription());
+ ((Annotatable)xmlMatrix).addAnnotationValue("tb:ntax.matrix", mTBTermsURI, tbMatrix.getnTax());
+ ((Annotatable)xmlMatrix).addAnnotationValue("tb:nchar.matrix", mTBTermsURI, tbMatrix.getnChar());
+ ((Annotatable)xmlMatrix).addAnnotationValue("tb:identifier.matrix", mTBTermsURI, tbMatrix.getId());
return xmlMatrix;
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2009-07-02 10:48:31 UTC (rev 161)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2009-07-02 21:02:07 UTC (rev 162)
@@ -85,6 +85,10 @@
StringBuilder urlString = new StringBuilder(getDocument().getBaseURI().toString());
taxonLabel.getPhyloWSPath().getPath(urlString).append("NCBI:").append(taxonLabel.getNcbiTaxID());
xmlOTU.addAnnotationValue("dc:relation", mDCURI, URI.create(urlString.toString()));
+ xmlOTU.addAnnotationValue("tb:identifier.ncbi", mTBTermsURI, "NCBI:" + taxonLabel.getNcbiTaxID());
+ xmlOTU.addAnnotationValue("tb:identifier.taxon", mTBTermsURI, taxonLabel.getTaxonVariant().getTaxon().getId());
+ xmlOTU.addAnnotationValue("tb:identifier.taxonLabel", mTBTermsURI, taxonLabel.getId());
+ xmlOTU.addAnnotationValue("tb:title.taxon", mTBTermsURI, taxonLabel.getTaxonVariant().getTaxon().getName());
}
TaxonVariant tv = taxonLabel.getTaxonVariant();
if ( null != tv ) {
@@ -92,6 +96,9 @@
StringBuilder urlString = new StringBuilder(getDocument().getBaseURI().toString());
taxonLabel.getPhyloWSPath().getPath(urlString).append("uBio:").append(tv.getNamebankID());
xmlOTU.addAnnotationValue("dc:relation", mDCURI, URI.create(urlString.toString()));
+ xmlOTU.addAnnotationValue("tb:identifier.ubio", mTBTermsURI, "uBio:" + tv.getNamebankID());
+ xmlOTU.addAnnotationValue("tb:identifier.taxonVariant", mTBTermsURI, tv.getId());
+ xmlOTU.addAnnotationValue("tb:title.taxonVariant", mTBTermsURI, tv.getFullName());
}
}
return xmlOTU;
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2009-07-02 10:48:31 UTC (rev 161)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java 2009-07-02 21:02:07 UTC (rev 162)
@@ -23,11 +23,13 @@
public class NexmlObjectConverter extends AbstractNexusConverter {
protected static URI mDCURI;
protected static URI mPrismURI;
+ protected static URI mTBTermsURI;
protected URI mBaseURI;
- private static String mDCURIString = "http://purl.org/dc/elements/1.1/";
+ private static String mTBTermsString = "http://treebase.org/terms#";
+ private static String mDCURIString = "http://purl.org/dc/terms/";
private static String mPrismURIString = "http://prismstandard.org/namespaces/1.2/basic/";
private static String mBaseURIString = "http://purl.org/PHYLO/TREEBASE/PHYLOWS/";
- private static String mDCIdentifier = "dc:identifier";
+ private static String mDCIdentifier = "dcterms:identifier";
public static String TreeBASE2Prefix = "TreeBASE2";
private Document mDocument;
@@ -40,6 +42,7 @@
try {
mDCURI = new URI(mDCURIString);
mPrismURI = new URI(mPrismURIString);
+ mTBTermsURI = new URI(mTBTermsString);
if ( null != baseURI ) {
mBaseURI = new URI(baseURI);
}
@@ -81,7 +84,7 @@
if ( null != tbPersistable.getId() ) {
//attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);
String uriString = getDocument().getBaseURI().toString() + tbPersistable.getPhyloWSPath().toString();
- annotatable.addAnnotationValue("dc:relation",mDCURI, URI.create(uriString));
+ annotatable.addAnnotationValue("dcterms:relation",mDCURI, URI.create(uriString));
}
}
@@ -108,7 +111,7 @@
// dc:identifier predicate in a nexml meta annotation,
// e.g. <meta property="dc:identifier" content="TB2:Tr231"/>
// this will return something that stringifies to TB2:Tr231
- Set<Object> dublinCoreRelationObjects = annotatable.getRelValues("dc:relation");
+ Set<Object> dublinCoreRelationObjects = annotatable.getRelValues("dcterms:relation");
Iterator<Object> objectIterator = dublinCoreRelationObjects.iterator();
while ( objectIterator.hasNext() ) {
URI relationURI = (URI)objectIterator.next();
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2009-07-02 10:48:31 UTC (rev 161)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2009-07-02 21:02:07 UTC (rev 162)
@@ -84,6 +84,11 @@
if ( null != phyloTree.getLabel() ) {
xmlTree.setLabel(phyloTree.getLabel());
}
+ xmlTree.addAnnotationValue("tb:identifier.tree", mTBTermsURI, phyloTree.getId());
+ xmlTree.addAnnotationValue("tb:kind.tree", mTBTermsURI, phyloTree.getKindDescription());
+ xmlTree.addAnnotationValue("tb:type.tree", mTBTermsURI, phyloTree.getTypeDescription());
+ xmlTree.addAnnotationValue("tb:quality.tree", mTBTermsURI, phyloTree.getQualityDescription());
+ xmlTree.addAnnotationValue("tb:ntax.tree", mTBTermsURI, phyloTree.getnTax());
attachTreeBaseID(xmlTree, phyloTree,PhyloTree.class);
copyTreeBaseTree(phyloTree, xmlTree);
return xmlTree;
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|
|
From: <rv...@us...> - 2009-07-02 10:48:37
|
Revision: 161
http://treebase.svn.sourceforge.net/treebase/?rev=161&view=rev
Author: rvos
Date: 2009-07-02 10:48:31 +0000 (Thu, 02 Jul 2009)
Log Message:
-----------
Adding cql-java.jar, a parser library for CQL queries (http://zing.z3950.org/cql/java/)
Added Paths:
-----------
trunk/treebase-web/lib/cql-java.jar
Added: trunk/treebase-web/lib/cql-java.jar
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/lib/cql-java.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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