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From: <rv...@us...> - 2011-06-08 13:59:24
|
Revision: 901
http://treebase.svn.sourceforge.net/treebase/?rev=901&view=rev
Author: rvos
Date: 2011-06-08 13:59:18 +0000 (Wed, 08 Jun 2011)
Log Message:
-----------
I don't need to see all the HQL clogging my console, let's just turn that log level up to warn, performance gets a bit better that way as well.
Modified Paths:
--------------
trunk/treebase-core/src/main/resources/log4j.xml
Modified: trunk/treebase-core/src/main/resources/log4j.xml
===================================================================
--- trunk/treebase-core/src/main/resources/log4j.xml 2011-06-06 14:18:19 UTC (rev 900)
+++ trunk/treebase-core/src/main/resources/log4j.xml 2011-06-08 13:59:18 UTC (rev 901)
@@ -50,7 +50,7 @@
<!-- show SQL statement -->
<logger name="org.hibernate.SQL">
- <level value="debug"/>
+ <level value="warn"/>
</logger>
<!-- show jdbc -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2011-06-07 14:08:33
|
Bugs item #3313183, was opened at 2011-06-07 10:08 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3313183&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: hshyket (hshyket) Summary: Links to download trees don't use purl.org base Initial Comment: In the matrix page, the matrix download links all use purls. e.g. if you go here: http://treebase.org/treebase-web/search/study/matrices.html?id=11618 You can see these links, where purl is used whenever referencing a phylows object: http://purl.org/phylo/treebase/phylows/matrix/TB2:M9145?format=nexml http://purl.org/phylo/treebase/phylows/matrix/TB2:M9145?format=rdf http://purl.org/phylo/treebase/phylows/matrix/TB2:M9145?format=nexus However, the equivalent download links that reference tree objects are not using purl, e.g.: http://treebase.org/treebase-web/phylows/tree/TB2:Tr46502?format=nexml http://treebase.org/treebase-web/phylows/tree/TB2:Tr46502?format=rdf http://treebase.org/treebase-web/phylows/tree/TB2:Tr46502?format=nexus This will cause, for example, Google to try to index these pages, which I don't think would be wise. But also, we want to use purl to encourage people to recognize these as stable URIs to objects in TreeBASE. It is just a matter of changing the above tree links to: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr46502?format=nexml [etc] And note that on dev, this should be the following: http://purl.org/phylo/treebase/dev/phylows/tree/TB2:Tr46502?format=nexml ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3313183&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-06-07 13:59:07
|
Bugs item #3313176, was opened at 2011-06-07 09:59 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3313176&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: hshyket (hshyket) Summary: Taxon blocks do not have unique titles Initial Comment: This is a new bug introduced after fixing bug 3291519. The combined NEXUS download properly creates distinct taxon blocks for each analysis, and it properly links each tree block and character block with it's corresponding taxon block. The only problem here is that the title given to each taxon block is the same -- which will confuse Mesquite when reading the file. Each taxa block title must be unique, and perhaps the logical solution is to name it according to the Analysis ID (currently it is probably named according to the original name in the uploaded NEXUS). So, for example, this study has six taxon blocks, all called "Taxa": http://purl.org/phylo/treebase/phylows/study/TB2:S11618?format=nexus ... But perhaps they should be given titles like the analysis IDs shown in the analysis downloads, e.g. this one in the same study: http://treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=7476&id=11618 ... which is "TaxaForAnalysisStep7476". (but perhaps better to write "Taxa_For_Analysis_Step_7476"). bp ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3313176&group_id=248804 |
|
From: <rv...@us...> - 2011-06-06 14:18:26
|
Revision: 900
http://treebase.svn.sourceforge.net/treebase/?rev=900&view=rev
Author: rvos
Date: 2011-06-06 14:18:19 +0000 (Mon, 06 Jun 2011)
Log Message:
-----------
This is pretty much how to convert treebase matrices to nexml ones.
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-04 03:36:27 UTC (rev 899)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-06 14:18:19 UTC (rev 900)
@@ -1,18 +1,20 @@
package org.cipres.treebase.domain.nexus;
+import java.util.List;
+
import junit.framework.Assert;
import org.cipres.treebase.dao.AbstractDAOTest;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
-import org.cipres.treebase.domain.matrix.Matrix;
-import org.cipres.treebase.domain.matrix.StandardMatrix;
-import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
-import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.nexml.model.CategoricalMatrix;
+import org.nexml.model.ContinuousMatrix;
import org.nexml.model.DocumentFactory;
import org.nexml.model.Document;
+import org.nexml.model.Matrix;
+import org.nexml.model.MolecularMatrix;
public class NexmlMatrixConverterTest extends AbstractDAOTest {
private TaxonLabelHome mTaxonLabelHome;
@@ -29,30 +31,26 @@
long studyId = 1787;
Study study = (Study)loadObject(Study.class, studyId);
- NexusDataSet nexusDataSet = new NexusDataSet();
Document doc = DocumentFactory.safeCreateDocument();
NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),doc);
- NexmlMatrixConverter nmc = new NexmlMatrixConverter (study,getTaxonLabelHome(),ndc.fromTreeBaseToXml(study));
- nexusDataSet = ndc.fromXmlToTreeBase(doc);
- nexusDataSet.setNexmlProject(doc);
-
- for (org.cipres.treebase.domain.matrix.Matrix matrix : nexusDataSet.getMatrices() ) {
- if ( matrix instanceof CharacterMatrix ) {
- //fromTreeBaseToXml(CharacterMatrix) is main method being tested here--it uses populateXmlMatrix() function
- String xml = ((Document) nmc.fromTreeBaseToXml((CharacterMatrix)matrix)).getXmlString();
- System.out.println(xml);
- Assert.assertNotNull(xml);
+ Document document = ndc.fromTreeBaseToXml(study);
+ List<Matrix<?>> matrices = document.getMatrices();
+ Assert.assertTrue(matrices.size() != 0 );
+ for ( Matrix<?> matrix : matrices ) {
+ if ( matrix instanceof MolecularMatrix ) {
+ System.out.println(matrix.getId() + " is a molecular character state matrix");
}
+ else if ( matrix instanceof ContinuousMatrix ) {
+ System.out.println(matrix.getId() + " is a continuous-valued character matrix");
+ }
+ else if ( matrix instanceof CategoricalMatrix ) {
+ System.out.println(matrix.getId() + " is a categorical character state matrix");
+ }
else {
- System.out.println("im not working");
+ System.out.println("This should not ever happen.");
}
}
-
- //signal that test is over
- if (logger.isInfoEnabled()) {
- logger.info(testName + " - end ");
- }
}
/**
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|
|
From: <sfr...@us...> - 2011-06-04 03:36:33
|
Revision: 899
http://treebase.svn.sourceforge.net/treebase/?rev=899&view=rev
Author: sfrgpiel
Date: 2011-06-04 03:36:27 +0000 (Sat, 04 Jun 2011)
Log Message:
-----------
Updating the list of journals that require TreeBASE
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/journal_files/aliso.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/bry.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/ima.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/jfwm.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/myc.jpg
trunk/treebase-web/src/main/webapp/images/journal_files/naf.gif
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-06-03 18:53:51 UTC (rev 898)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-06-04 03:36:27 UTC (rev 899)
@@ -28,6 +28,23 @@
</tr>
<tr>
<td>
+ <p><a href="http://www.rsabg.org/research-department/scientific-publications"
+ title="Aliso">
+ <img class="journal"
+ src="images/journal_files/aliso.jpg" alt="Aliso"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22"
+ title="Find records in TreeBASE for articles published in Aliso">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.amjbot.org/"
title="American Journal of Botany">
<img class="journal"
@@ -45,6 +62,23 @@
</tr>
<tr>
<td>
+ <p><a href="http://192.104.39.110/bryologist.html"
+ title="The Bryologist">
+ <img class="journal"
+ src="images/journal_files/bry.jpg" alt="Bryologist"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22"
+ title="Find records in TreeBASE for articles published in The Bryologist">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
title="Evolution">
<img class="journal"
@@ -99,6 +133,24 @@
<tr>
<td>
<p>
+ <a
+ href="http://www.imafungus.org/">
+ <img class="journal"
+ src="images/journal_files/ima.jpg" alt="IMA Fungus"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22"
+ title="Find records in TreeBASE for articles published in IMA Fungus">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p>
<a href="http://www.publish.csiro.au/nid/120.htm">
<img class="journal"
src="images/journal_files/image004.gif"
@@ -116,6 +168,24 @@
</tr>
<tr>
<td>
+ <p>
+ <a href="http://www.fws.gov/science/jfwm.html">
+ <img class="journal"
+ src="images/journal_files/jfwm.jpg"
+ alt="Journal of Fish and Wildlife Management" />
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22"
+ title="Find records in TreeBASE for articles published in Journal of Fish and Wildlife Management">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22
+ </a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
<p><a href="http://www.blackwellpublishing.com/journal.asp?ref=0962-1083">
<img class="journal" src="images/journal_files/image021.jpg" alt="Molecular Ecology" /></a></p>
</td>
@@ -173,6 +243,21 @@
<tr>
<td>
<p><a
+ href="http://www.tandf.co.uk/journals/journal.asp?issn=2150-1203">
+ <img class="journal"
+ src="images/journal_files/myc.jpg" alt="Mycology"/>
+ </a></p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22"
+ title="Find records in TreeBASE for articles published in Mycology">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
href="http://www.springer.com/life+sciences/microbiology/journal/10267">
<img class="journal"
src="images/journal_files/image008.gif" alt="Mycoscience"/></a></p>
@@ -199,6 +284,21 @@
<tr>
<td>
<p><a
+ href="http://www.fws.gov/science/naf.html">
+ <img class="journal"
+ src="images/journal_files/naf.gif"
+ alt="North American Fauna"/></a></p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22"
+ title="Find records in TreeBASE for articles published in North American Fauna">
+ <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22</a></p>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <p><a
href="http://www.elsevier.com/wps/find/journaldescription.cws_home/701789/description#description">
<img class="journal"
src="images/journal_files/image010.gif"
Added: trunk/treebase-web/src/main/webapp/images/journal_files/aliso.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/aliso.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/bry.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/bry.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ima.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ima.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/jfwm.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/jfwm.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/myc.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/myc.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/naf.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/naf.gif
___________________________________________________________________
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.
|
|
From: <hs...@us...> - 2011-06-03 18:53:57
|
Revision: 898
http://treebase.svn.sourceforge.net/treebase/?rev=898&view=rev
Author: hshyket
Date: 2011-06-03 18:53:51 +0000 (Fri, 03 Jun 2011)
Log Message:
-----------
Fixing sitemap so that it doesn't point to the PURL links but to the actual study URLs in TreeBASE. Google was not able to index the PURL links because it went to an external source
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java 2011-06-02 19:55:32 UTC (rev 897)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java 2011-06-03 18:53:51 UTC (rev 898)
@@ -11,6 +11,7 @@
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
+import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.study.Submission;
import org.cipres.treebase.domain.study.SubmissionService;
@@ -37,7 +38,10 @@
Collection<Submission> submissions = mSubmissionService.findPublishedSubmissions();
for ( Submission submission : submissions ) {
- phyloURL.add(submission.getStudy().getPhyloWSPath().getPurl().toString());
+ //Google web crawler does not like external links in the sitemap
+ //phyloURL.add(submission.getStudy().getPhyloWSPath().getPurl().toString());
+ phyloURL.add(TreebaseUtil.getSiteUrl() + "search/study/summary.html?id=" + submission.getStudy().getId().toString());
+
}
return new ModelAndView("sitemap", "phyloURL", phyloURL);
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp 2011-06-02 19:55:32 UTC (rev 897)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp 2011-06-03 18:53:51 UTC (rev 898)
@@ -4,7 +4,7 @@
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
<c:forEach var="url" items="${phyloURL}" varStatus="status">
<url>
- <loc><c:out value="${url}"/>?format=html</loc>
+ <loc><c:out value="${url}"/></loc>
</url>
</c:forEach>
</urlset>
\ No newline at end of file
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|
|
From: <lol...@us...> - 2011-06-02 19:55:38
|
Revision: 897
http://treebase.svn.sourceforge.net/treebase/?rev=897&view=rev
Author: loloyohe
Date: 2011-06-02 19:55:32 +0000 (Thu, 02 Jun 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
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 2011-06-02 19:55:09 UTC (rev 896)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-06-02 19:55:32 UTC (rev 897)
@@ -340,15 +340,31 @@
xmlMatrix.setSeq(seq,xmlOTU);
}
for ( RowSegment tbSegment : tbSegments ) {
+ String accessionNumber = tbSegment.getSpecimenLabel().getGenBankAccession();
Double latitude = tbSegment.getSpecimenLabel().getLatitude();
Double longitude = tbSegment.getSpecimenLabel().getLongitude();
+ Double elevation = tbSegment.getSpecimenLabel().getElevation();
+ String collector = tbSegment.getSpecimenLabel().getCollector();
+ String country = tbSegment.getSpecimenLabel().getCountry();
+ if ( null != accessionNumber) {
+ xmlOTU.addAnnotationValue("DwC:StringGenbankAcessionNumber", Constants.DwCURI, accessionNumber);
+ }
if ( null != latitude ) {
xmlOTU.addAnnotationValue("DwC:DecimalLatitude", Constants.DwCURI, latitude);
}
if ( null != longitude ) {
xmlOTU.addAnnotationValue("DwC:DecimalLongitude", Constants.DwCURI, longitude);
}
- }
+ if ( null != elevation ) {
+ xmlOTU.addAnnotationValue("DwC:DecimalElevation", Constants.DwCURI, elevation);
+ }
+ if ( null != collector ) {
+ xmlOTU.addAnnotationValue("DwC:StringCollector", Constants.DwCURI, collector);
+ }
+ if ( null != country ) {
+ xmlOTU.addAnnotationValue("DwC:StringCountry", Constants.DwCURI, country);
+ }
+ }
}
}
@@ -378,16 +394,32 @@
}
Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
for ( RowSegment tbSegment : tbSegments ) {
+ String accessionNumber = tbSegment.getSpecimenLabel().getGenBankAccession();
Double latitude = tbSegment.getSpecimenLabel().getLatitude();
Double longitude = tbSegment.getSpecimenLabel().getLongitude();
+ Double elevation = tbSegment.getSpecimenLabel().getElevation();
+ String collector = tbSegment.getSpecimenLabel().getCollector();
+ String country = tbSegment.getSpecimenLabel().getCountry();
+ if ( null != accessionNumber) {
+ xmlOTU.addAnnotationValue("DwC:StringGenbankAcessionNumber", Constants.DwCURI, accessionNumber);
+ }
if ( null != latitude ) {
xmlOTU.addAnnotationValue("DwC:DecimalLatitude", Constants.DwCURI, latitude);
}
if ( null != longitude ) {
xmlOTU.addAnnotationValue("DwC:DecimalLongitude", Constants.DwCURI, longitude);
}
- }
+ if ( null != elevation ) {
+ xmlOTU.addAnnotationValue("DwC:DecimalElevation", Constants.DwCURI, elevation);
+ }
+ if ( null != collector ) {
+ xmlOTU.addAnnotationValue("DwC:StringCollector", Constants.DwCURI, collector);
+ }
+ if ( null != country ) {
+ xmlOTU.addAnnotationValue("DwC:StringCountry", Constants.DwCURI, country);
+ }
+ }
}
}
-
+
}
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|
|
From: <lol...@us...> - 2011-06-02 19:55:15
|
Revision: 896
http://treebase.svn.sourceforge.net/treebase/?rev=896&view=rev
Author: loloyohe
Date: 2011-06-02 19:55:09 +0000 (Thu, 02 Jun 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-02 15:58:44 UTC (rev 895)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-02 19:55:09 UTC (rev 896)
@@ -4,7 +4,10 @@
import org.cipres.treebase.dao.AbstractDAOTest;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.matrix.Matrix;
+import org.cipres.treebase.domain.matrix.StandardMatrix;
import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
+import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
import org.cipres.treebase.domain.nexus.NexusDataSet;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -29,8 +32,11 @@
NexusDataSet nexusDataSet = new NexusDataSet();
Document doc = DocumentFactory.safeCreateDocument();
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),doc);
+ NexmlMatrixConverter nmc = new NexmlMatrixConverter (study,getTaxonLabelHome(),ndc.fromTreeBaseToXml(study));
+ nexusDataSet = ndc.fromXmlToTreeBase(doc);
nexusDataSet.setNexmlProject(doc);
- NexmlMatrixConverter nmc = new NexmlMatrixConverter(study,getTaxonLabelHome(),doc);
+
for (org.cipres.treebase.domain.matrix.Matrix matrix : nexusDataSet.getMatrices() ) {
if ( matrix instanceof CharacterMatrix ) {
//fromTreeBaseToXml(CharacterMatrix) is main method being tested here--it uses populateXmlMatrix() function
@@ -38,7 +44,11 @@
System.out.println(xml);
Assert.assertNotNull(xml);
}
+ else {
+ System.out.println("im not working");
+ }
}
+
//signal that test is over
if (logger.isInfoEnabled()) {
logger.info(testName + " - end ");
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|
|
From: <hs...@us...> - 2011-06-02 17:24:12
|
Revision: 895
http://treebase.svn.sourceforge.net/treebase/?rev=895&view=rev
Author: hshyket
Date: 2011-06-02 15:58:44 +0000 (Thu, 02 Jun 2011)
Log Message:
-----------
Adding in meta tags so that Google, Yahoo! and Bing can verify the site through their webmaster tools. Adding in functionality to generate a sitemap.xml so that the bots can index the submissions.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
trunk/treebase-web/src/main/webapp/common/meta.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SiteMapController.java 2011-06-02 15:58:44 UTC (rev 895)
@@ -0,0 +1,55 @@
+
+
+
+package org.cipres.treebase.web.controllers;
+
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.cipres.treebase.domain.study.Submission;
+import org.cipres.treebase.domain.study.SubmissionService;
+
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.Controller;
+
+
+
+/**
+ * @author mjd 20080701
+ */
+public class SiteMapController implements Controller{
+ /**
+ * Logger for this class
+ */
+ //private static final Logger LOGGER = Logger.getLogger(SearchController.class);
+ private SubmissionService mSubmissionService;
+
+ public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
+ throws Exception {
+
+ List<String> phyloURL = new ArrayList<String>();
+
+ Collection<Submission> submissions = mSubmissionService.findPublishedSubmissions();
+
+ for ( Submission submission : submissions ) {
+ phyloURL.add(submission.getStudy().getPhyloWSPath().getPurl().toString());
+ }
+
+ return new ModelAndView("sitemap", "phyloURL", phyloURL);
+ }
+
+ public SubmissionService getSubmissionService() {
+ return mSubmissionService;
+ }
+
+ public void setSubmissionService(SubmissionService pNewSubmissionService) {
+ mSubmissionService = pNewSubmissionService;
+ }
+}
+
+
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/sitemap.jsp 2011-06-02 15:58:44 UTC (rev 895)
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<%@ include file="/common/taglibs.jsp"%>
+<% response.setContentType("application/xml; charset=UTF-8"); %>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+ <c:forEach var="url" items="${phyloURL}" varStatus="status">
+ <url>
+ <loc><c:out value="${url}"/>?format=html</loc>
+ </url>
+ </c:forEach>
+</urlset>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-06-01 18:47:29 UTC (rev 894)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-06-02 15:58:44 UTC (rev 895)
@@ -190,6 +190,11 @@
<property name="submissionService"><ref bean="submissionService"></ref></property>
</bean>
+ <!-- View SiteMap -->
+ <bean id="siteMapController" class="org.cipres.treebase.web.controllers.SiteMapController">
+ <property name="submissionService"><ref bean="submissionService"></ref></property>
+ </bean>
+
<!-- View Taxa -->
<bean id="listTaxaController" class="org.cipres.treebase.web.controllers.ListTaxaController">
<property name="studyService"><ref bean="studyService"></ref></property>
@@ -1040,8 +1045,10 @@
<prop key="/search/downloadAMatrix.html">downloadAMatrixController</prop>
<prop key="/search/downloadAnAnalysisStep.html">downloadAnAnalysisStepController</prop>
<prop key="/search/downloadANexusFile.html">downloadANexusFileController</prop>
- <prop key="/search/downloadANexusRCTFile.html">downloadANexusRCTFileController</prop>
+ <prop key="/search/downloadANexusRCTFile.html">downloadANexusRCTFileController</prop>
+ <prop key="/sitemap.xml">siteMapController</prop>
+
<!-- SUBMISSION SECTION -->
<prop key="/user/updateProfile.html">userFormController</prop>
<prop key="/user/submissionList.html">listSubmissionController</prop>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-06-01 18:47:29 UTC (rev 894)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-06-02 15:58:44 UTC (rev 895)
@@ -276,6 +276,10 @@
</servlet-mapping>
<servlet-mapping>
<servlet-name>treebase</servlet-name>
+ <url-pattern>*.xml</url-pattern>
+ </servlet-mapping>
+ <servlet-mapping>
+ <servlet-name>treebase</servlet-name>
<url-pattern>*.rdf</url-pattern>
</servlet-mapping>
<servlet-mapping>
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-06-01 18:47:29 UTC (rev 894)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-06-02 15:58:44 UTC (rev 895)
@@ -6,6 +6,9 @@
<meta http-equiv="Expires" content="0"/>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
<meta name="author" content="Rutger A. Vos (rut...@gm...)"/>
+<meta name="google-site-verification" content="9Lr7BwyD6VMDIk5dENnSt_2YsUdpq_aEhnee0mMTxrw" />
+<META name="y_key" content="8c736195266b5ebb" />
+<meta name="msvalidate.01" content="D931446190993D0D2D719F2978AC44EB" />
<link rel="icon" href="<c:url value="/images/favicon.ico"/>"/>
<%
String ua = request.getHeader( "User-Agent" );
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|
|
From: <lol...@us...> - 2011-06-01 18:47:35
|
Revision: 894
http://treebase.svn.sourceforge.net/treebase/?rev=894&view=rev
Author: loloyohe
Date: 2011-06-01 18:47:29 +0000 (Wed, 01 Jun 2011)
Log Message:
-----------
Test for NexmlMatrixConverter class for function fromTreeBaseToXml(CharacterMatrix). This is the function that calls the poplulateXmlMatrix() function
Added Paths:
-----------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
Added: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java (rev 0)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-01 18:47:29 UTC (rev 894)
@@ -0,0 +1,64 @@
+package org.cipres.treebase.domain.nexus;
+
+import junit.framework.Assert;
+
+import org.cipres.treebase.dao.AbstractDAOTest;
+import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
+import org.cipres.treebase.domain.nexus.NexusDataSet;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.nexml.model.DocumentFactory;
+import org.nexml.model.Document;
+
+public class NexmlMatrixConverterTest extends AbstractDAOTest {
+ private TaxonLabelHome mTaxonLabelHome;
+
+ /**
+ * Test for {@link org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter#fromTreeBaseToXml(CharacterMatrix)}.
+ */
+ public void testNexmlMatrixConverter() {
+ String testName = "testNexmlMatrixConverter";
+ //signal beginning of test
+ if (logger.isInfoEnabled()) {
+ logger.info("\n\t\tRunning Test: " + testName);
+ }
+
+ long studyId = 1787;
+ Study study = (Study)loadObject(Study.class, studyId);
+ NexusDataSet nexusDataSet = new NexusDataSet();
+
+ Document doc = DocumentFactory.safeCreateDocument();
+ nexusDataSet.setNexmlProject(doc);
+ NexmlMatrixConverter nmc = new NexmlMatrixConverter(study,getTaxonLabelHome(),doc);
+ for (org.cipres.treebase.domain.matrix.Matrix matrix : nexusDataSet.getMatrices() ) {
+ if ( matrix instanceof CharacterMatrix ) {
+ //fromTreeBaseToXml(CharacterMatrix) is main method being tested here--it uses populateXmlMatrix() function
+ String xml = ((Document) nmc.fromTreeBaseToXml((CharacterMatrix)matrix)).getXmlString();
+ System.out.println(xml);
+ Assert.assertNotNull(xml);
+ }
+ }
+ //signal that test is over
+ if (logger.isInfoEnabled()) {
+ logger.info(testName + " - end ");
+ }
+ }
+
+ /**
+ * Return the TaxonLabelHome field.
+ *
+ * @return TaxonLabelHome mTaxonLabelHome
+ */
+ public TaxonLabelHome getTaxonLabelHome() {
+ return mTaxonLabelHome;
+ }
+
+ /**
+ * Set the TaxonLabelHome field.
+ */
+ public void setTaxonLabelHome(TaxonLabelHome pNewTaxonLabelHome) {
+ mTaxonLabelHome = pNewTaxonLabelHome;
+ }
+
+}
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|
|
From: <hs...@us...> - 2011-05-27 20:02:44
|
Revision: 893
http://treebase.svn.sourceforge.net/treebase/?rev=893&view=rev
Author: hshyket
Date: 2011-05-27 20:02:37 +0000 (Fri, 27 May 2011)
Log Message:
-----------
Checks to make sure that trees exist in the analysis when displaying message before deleting.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeBlockController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeBlockController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeBlockController.java 2011-05-27 14:55:09 UTC (rev 892)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeBlockController.java 2011-05-27 20:02:37 UTC (rev 893)
@@ -3,6 +3,7 @@
import java.util.Collection;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
@@ -14,6 +15,10 @@
import org.springframework.web.servlet.view.RedirectView;
import org.cipres.treebase.domain.admin.UserRole.TBPermission;
+import org.cipres.treebase.domain.study.Analysis;
+import org.cipres.treebase.domain.study.AnalysisStep;
+import org.cipres.treebase.domain.study.AnalyzedData;
+import org.cipres.treebase.domain.study.AnalyzedTree;
import org.cipres.treebase.domain.study.SubmissionHome;
import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.domain.tree.PhyloTree;
@@ -140,9 +145,9 @@
TreeBlock pTreeBlock = getPhyloTreeHome().findTreeBlockById(treeBlockID);
Collection<PhyloTree> pTreeCollection = pTreeBlock.getTreeList();
-
+
for (PhyloTree pTree : pTreeCollection) {
- if (pTree.getStudy() != null) { // It means this tree is tied to analysis step
+ /*if (pTree.getStudy() != null) { // It means this tree is tied to analysis step
setTestVariable(true);
referenceMap
.put(
@@ -150,6 +155,29 @@
"Either this TreeBlock or atleast one of the Tree in this Block is tied to an Analysis Step.");
break; // Even if one tree of the block is ties to Analysis step, we can exit the
// for loop.
+ }*/
+
+ for (Analysis analysis : pTree.getStudy().getAnalyses()) {
+
+ List<AnalysisStep> analysisStepList = analysis.getAnalysisStepsReadOnly();
+
+ for (AnalysisStep analysisStep : analysisStepList) {
+
+ List<AnalyzedData> analyzedDataSet = analysisStep.getDataSetReadOnly();
+
+ for (AnalyzedData analyzedData : analyzedDataSet) {
+
+ if (analyzedData instanceof AnalyzedTree) {
+
+ if ( pTreeCollection.contains(((AnalyzedTree) analyzedData).getTree())) {
+
+ referenceMap.put("generalmessage", "Either this TreeBlock or at least one of the Tree in this Block is tied to an Analysis Step.");
+ break; // Even if one tree of the block is ties to Analysis step, we can exit the
+ }
+ }
+ }
+
+ }
}
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeController.java 2011-05-27 14:55:09 UTC (rev 892)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DeleteATreeController.java 2011-05-27 20:02:37 UTC (rev 893)
@@ -4,6 +4,7 @@
package org.cipres.treebase.web.controllers;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import javax.servlet.http.HttpServletRequest;
@@ -14,6 +15,10 @@
import org.springframework.web.servlet.ModelAndView;
import org.cipres.treebase.domain.admin.UserRole.TBPermission;
+import org.cipres.treebase.domain.study.Analysis;
+import org.cipres.treebase.domain.study.AnalysisStep;
+import org.cipres.treebase.domain.study.AnalyzedData;
+import org.cipres.treebase.domain.study.AnalyzedTree;
import org.cipres.treebase.domain.study.SubmissionHome;
import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.domain.tree.PhyloTree;
@@ -114,8 +119,31 @@
Long treeID = Long.parseLong(request.getParameter("treeid"));
PhyloTree pTree = getPhyloTreeService().findByID(treeID);
- if (pTree.getStudy() != null) { // It means this tree is tied to analysis step
+ /*if (pTree.getStudy() != null) { // It means this tree is tied to analysis step
referenceMap.put("generalmessage", "This PhyloTree is tied to an Analysis Step.");
+ }*/
+
+ for (Analysis analysis : pTree.getStudy().getAnalyses()) {
+
+ List<AnalysisStep> analysisStepList = analysis.getAnalysisStepsReadOnly();
+
+ for (AnalysisStep analysisStep : analysisStepList) {
+
+ List<AnalyzedData> analyzedDataSet = analysisStep.getDataSetReadOnly();
+
+ for (AnalyzedData analyzedData : analyzedDataSet) {
+
+ if (analyzedData instanceof AnalyzedTree) {
+
+ if (pTree.getId() == ((AnalyzedTree) analyzedData).getTree().getId()) {
+
+ referenceMap.put("generalmessage", "This PhyloTree is tied to an Analysis Step.");
+ }
+ }
+ }
+
+ }
+
}
referenceMap.put("deleteid", "Tree ID : " + treeID);
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|
|
From: <hs...@us...> - 2011-05-27 14:55:15
|
Revision: 892
http://treebase.svn.sourceforge.net/treebase/?rev=892&view=rev
Author: hshyket
Date: 2011-05-27 14:55:09 +0000 (Fri, 27 May 2011)
Log Message:
-----------
Fixing issue with NeXML and RDF not displaying for matrices
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2011-05-27 13:37:32 UTC (rev 891)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2011-05-27 14:55:09 UTC (rev 892)
@@ -94,13 +94,13 @@
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
- return getNexmlService().serialize(pNexusDataSet,getDefaultProperties(request));
+ return getNexmlService().serialize(pNexusDataSet,getDefaultProperties(request),matrix.getStudy());
}
else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
- return getRdfaService().serialize(pNexusDataSet,getDefaultProperties(request));
+ return getRdfaService().serialize(pNexusDataSet,getDefaultProperties(request),matrix.getStudy());
}
else { // FORMAT_NEXUS or none
StringBuilder matrixContent = new StringBuilder();
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|
|
From: <rv...@us...> - 2011-05-27 13:37:39
|
Revision: 891
http://treebase.svn.sourceforge.net/treebase/?rev=891&view=rev
Author: rvos
Date: 2011-05-27 13:37:32 +0000 (Fri, 27 May 2011)
Log Message:
-----------
Updated some of the default values for CLI tomcat deployment. I still like using this script, for some reason I can't get eclipse to be happy about my maven/tomcat/spring configuration, but this seems to work
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/misc/publish
Modified: trunk/treebase-core/src/main/perl/misc/publish
===================================================================
--- trunk/treebase-core/src/main/perl/misc/publish 2011-05-26 19:38:18 UTC (rev 890)
+++ trunk/treebase-core/src/main/perl/misc/publish 2011-05-27 13:37:32 UTC (rev 891)
@@ -25,6 +25,8 @@
WEBAPPS="$CATALINA_HOME/webapps"
TARGET_DIR="treebase-web"
IP_ADDR=`curl -s checkip.dyndns.org | grep -Eo '[0-9\.]+'`
+PORT_NUMBER=8080
+PHYLOWIDGET=$HOME/PhyloWidget.jar
# Flag to suppress sourre update and rebuilding
update_sources=true
@@ -32,7 +34,7 @@
update_sources=false
fi
-TOMCAT_URL=http://$IP_ADDR:6666/treebase-web/
+TOMCAT_URL=http://${IP_ADDR}:${PORT_NUMBER}/treebase-web/
VERSIONFILE=${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java
# Rebuild the application WAR file, if requested
@@ -87,7 +89,7 @@
while [ '!' -d $phyloWidgetTarget ]; do
sleep 1;
done
-cp -pv $HOME/PhyloWidget.jar $phyloWidgetTarget || warn "Couldn't install phyloWidget"
+cp -pv $PHYLOWIDGET $phyloWidgetTarget || warn "Couldn't install phyloWidget"
echo "Publish operation complete"
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|
|
From: <rv...@us...> - 2011-05-26 19:38:24
|
Revision: 890
http://treebase.svn.sourceforge.net/treebase/?rev=890&view=rev
Author: rvos
Date: 2011-05-26 19:38:18 +0000 (Thu, 26 May 2011)
Log Message:
-----------
Adding some more class path entries for dealing with TAR archives, multipart messages and REST services, all as used by the Dryad importer, without actually being specified in the .classpath previously for some reason.
Modified Paths:
--------------
trunk/treebase-web/.classpath
Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath 2011-05-26 19:37:41 UTC (rev 889)
+++ trunk/treebase-web/.classpath 2011-05-26 19:38:18 UTC (rev 890)
@@ -107,5 +107,8 @@
<classpathentry kind="con" path="org.eclipse.jst.server.core.container/org.eclipse.jst.server.tomcat.runtimeTarget/Apache Tomcat v5.5"/>
<classpathentry kind="var" path="M2_REPO/zing/z3950/org/cql-java/1.0/cql-java-1.0.jar"/>
<classpathentry kind="var" path="M2_REPO/postgresql/postgresql/8.3-603.jdbc3/postgresql-8.3-603.jdbc3.jar"/>
+ <classpathentry kind="var" path="M2_REPO/org/apache/ant/ant/1.8.0/ant-1.8.0.jar"/>
+ <classpathentry kind="var" path="M2_REPO/com/sun/jersey/contribs/jersey-multipart/1.1.0-ea/jersey-multipart-1.1.0-ea.jar"/>
+ <classpathentry kind="var" path="M2_REPO/javax/ws/rs/jsr311-api/1.0/jsr311-api-1.0.jar"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>
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|
|
From: <rv...@us...> - 2011-05-26 19:37:48
|
Revision: 889
http://treebase.svn.sourceforge.net/treebase/?rev=889&view=rev
Author: rvos
Date: 2011-05-26 19:37:41 +0000 (Thu, 26 May 2011)
Log Message:
-----------
Adding some more dependencies for dealing with TAR archives, multipart messages and REST services, all as used by the Dryad importer, without actually being specified in the pom for some reason.
Modified Paths:
--------------
trunk/treebase-web/pom.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2011-05-26 19:36:28 UTC (rev 888)
+++ trunk/treebase-web/pom.xml 2011-05-26 19:37:41 UTC (rev 889)
@@ -162,6 +162,12 @@
<artifactId>commons-lang</artifactId>
<version>2.3</version>
</dependency>
+
+ <dependency>
+ <groupId>commons-digester</groupId>
+ <artifactId>commons-digester</artifactId>
+ <version>1.5</version>
+ </dependency>
<dependency>
<groupId>taglibs</groupId>
@@ -368,6 +374,25 @@
<artifactId>jsr311-api</artifactId>
<version>1.0</version>
</dependency>
+
+<dependency>
+ <groupId>org.apache.ant</groupId>
+ <artifactId>ant</artifactId>
+ <version>1.8.0</version>
+</dependency>
+
+<dependency>
+ <groupId>com.sun.jersey.contribs</groupId>
+ <artifactId>jersey-multipart</artifactId>
+ <version>1.1.0-ea</version>
+</dependency>
+
+<dependency>
+ <groupId>javax.ws.rs</groupId>
+ <artifactId>jsr311-api</artifactId>
+ <version>1.0</version>
+</dependency>
+
</dependencies>
</project>
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|
From: <rv...@us...> - 2011-05-26 19:36:34
|
Revision: 888
http://treebase.svn.sourceforge.net/treebase/?rev=888&view=rev
Author: rvos
Date: 2011-05-26 19:36:28 +0000 (Thu, 26 May 2011)
Log Message:
-----------
This class was using the wrong DateFormat, we're using the one from java.text.* instead
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
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 2011-05-26 19:06:26 UTC (rev 887)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2011-05-26 19:36:28 UTC (rev 888)
@@ -38,7 +38,7 @@
import org.z3950.zing.cql.CQLRelation;
import org.z3950.zing.cql.CQLTermNode;
-import com.ibm.icu.text.DateFormat;
+import java.text.DateFormat;
/**
* StudySearchController.java
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|
From: <rv...@us...> - 2011-05-26 19:06:32
|
Revision: 887
http://treebase.svn.sourceforge.net/treebase/?rev=887&view=rev
Author: rvos
Date: 2011-05-26 19:06:26 +0000 (Thu, 26 May 2011)
Log Message:
-----------
We're not actually using the cipres framework jar (whatever that was), so I removed it from the .classpath
Modified Paths:
--------------
trunk/treebase-web/.classpath
Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath 2011-05-26 19:06:07 UTC (rev 886)
+++ trunk/treebase-web/.classpath 2011-05-26 19:06:26 UTC (rev 887)
@@ -41,7 +41,6 @@
<classpathentry kind="var" path="M2_REPO/net/sf/ehcache/ehcache/1.2.3/ehcache-1.2.3.jar"/>
<classpathentry kind="var" path="M2_REPO/org/hibernate/ejb3-persistence/1.0.1.GA/ejb3-persistence-1.0.1.GA.jar"/>
<classpathentry kind="var" path="M2_REPO/com/sun/xml/fastinfoset/FastInfoset/1.2.2/FastInfoset-1.2.2.jar"/>
- <classpathentry kind="var" path="M2_REPO/org/cipres/framework/1.0.1/framework-1.0.1.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-activation_1.1_spec/1.0.2/geronimo-activation_1.1_spec-1.0.2.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-annotation_1.0_spec/1.1.1/geronimo-annotation_1.0_spec-1.1.1.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-javamail_1.4_spec/1.3/geronimo-javamail_1.4_spec-1.3.jar"/>
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|
From: <rv...@us...> - 2011-05-26 19:06:13
|
Revision: 886
http://treebase.svn.sourceforge.net/treebase/?rev=886&view=rev
Author: rvos
Date: 2011-05-26 19:06:07 +0000 (Thu, 26 May 2011)
Log Message:
-----------
The maven nature inside eclipse is giving me nothing but grief, I don't know what's up with m2eclipse. Anyway, as long as we set up our local repo the way it is described on the wiki we can just remove it here and use the paths as in .classpath with an M2_REPO variable without having to deal with maven in here at all.
Modified Paths:
--------------
trunk/treebase-web/.project
Modified: trunk/treebase-web/.project
===================================================================
--- trunk/treebase-web/.project 2011-05-26 19:03:42 UTC (rev 885)
+++ trunk/treebase-web/.project 2011-05-26 19:06:07 UTC (rev 886)
@@ -21,14 +21,8 @@
<arguments>
</arguments>
</buildCommand>
- <buildCommand>
- <name>org.maven.ide.eclipse.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
</buildSpec>
<natures>
- <nature>org.maven.ide.eclipse.maven2Nature</nature>
<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
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|
From: <rv...@us...> - 2011-05-26 19:03:47
|
Revision: 885
http://treebase.svn.sourceforge.net/treebase/?rev=885&view=rev
Author: rvos
Date: 2011-05-26 19:03:42 +0000 (Thu, 26 May 2011)
Log Message:
-----------
The maven nature inside eclipse is giving me nothing but grief, I don't know what's up with m2eclipse. Anyway, as long as we set up our local repo the way it is described on the wiki we can just remove it here and use the paths as in .classpath with an M2_REPO variable without having to deal with maven in here at all.
Modified Paths:
--------------
trunk/treebase-core/.project
Modified: trunk/treebase-core/.project
===================================================================
--- trunk/treebase-core/.project 2011-05-26 19:01:33 UTC (rev 884)
+++ trunk/treebase-core/.project 2011-05-26 19:03:42 UTC (rev 885)
@@ -20,14 +20,8 @@
<arguments>
</arguments>
</buildCommand>
- <buildCommand>
- <name>org.maven.ide.eclipse.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
</buildSpec>
<natures>
- <nature>org.maven.ide.eclipse.maven2Nature</nature>
<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
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|
From: <rv...@us...> - 2011-05-26 19:01:39
|
Revision: 884
http://treebase.svn.sourceforge.net/treebase/?rev=884&view=rev
Author: rvos
Date: 2011-05-26 19:01:33 +0000 (Thu, 26 May 2011)
Log Message:
-----------
We're not actually using the cipres framework jar (whatever that was), so I removed it from the .classpath
Modified Paths:
--------------
trunk/treebase-core/.classpath
Modified: trunk/treebase-core/.classpath
===================================================================
--- trunk/treebase-core/.classpath 2011-05-26 19:00:34 UTC (rev 883)
+++ trunk/treebase-core/.classpath 2011-05-26 19:01:33 UTC (rev 884)
@@ -34,7 +34,6 @@
<classpathentry kind="var" path="M2_REPO/net/sf/ehcache/ehcache/1.2.3/ehcache-1.2.3.jar"/>
<classpathentry kind="var" path="M2_REPO/org/hibernate/ejb3-persistence/1.0.1.GA/ejb3-persistence-1.0.1.GA.jar"/>
<classpathentry kind="var" path="M2_REPO/com/sun/xml/fastinfoset/FastInfoset/1.2.2/FastInfoset-1.2.2.jar"/>
- <classpathentry kind="var" path="M2_REPO/org/cipres/framework/1.0.1/framework-1.0.1.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-activation_1.1_spec/1.0.2/geronimo-activation_1.1_spec-1.0.2.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-annotation_1.0_spec/1.1.1/geronimo-annotation_1.0_spec-1.1.1.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/geronimo/specs/geronimo-javamail_1.4_spec/1.3/geronimo-javamail_1.4_spec-1.3.jar"/>
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|
From: <rv...@us...> - 2011-05-26 19:00:41
|
Revision: 883
http://treebase.svn.sourceforge.net/treebase/?rev=883&view=rev
Author: rvos
Date: 2011-05-26 19:00:34 +0000 (Thu, 26 May 2011)
Log Message:
-----------
Adding scripts to create and test DBIx::Class ORM mapping generation
Added Paths:
-----------
trunk/treebase-core/src/main/perl/orm/
trunk/treebase-core/src/main/perl/orm/maketreebase.pl
trunk/treebase-core/src/main/perl/orm/testtreebase.pl
Added: trunk/treebase-core/src/main/perl/orm/maketreebase.pl
===================================================================
--- trunk/treebase-core/src/main/perl/orm/maketreebase.pl (rev 0)
+++ trunk/treebase-core/src/main/perl/orm/maketreebase.pl 2011-05-26 19:00:34 UTC (rev 883)
@@ -0,0 +1,21 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use DBIx::Class::Schema::Loader qw/make_schema_at/;
+
+my $dbname = 'treebasedev';
+my $host = 'treebasedb-dev.nescent.org';
+my $user = 'treebase_app';
+my $pass = 'tim5tema';
+make_schema_at(
+ 'Bio::Phylo::TreeBASE',
+ {
+ 'debug' => 1,
+ 'dump_directory' => './lib',
+ },
+ [
+ "dbi:Pg:dbname=$dbname;host=$host",
+ $user,
+ $pass,
+ ],
+);
\ No newline at end of file
Added: trunk/treebase-core/src/main/perl/orm/testtreebase.pl
===================================================================
--- trunk/treebase-core/src/main/perl/orm/testtreebase.pl (rev 0)
+++ trunk/treebase-core/src/main/perl/orm/testtreebase.pl 2011-05-26 19:00:34 UTC (rev 883)
@@ -0,0 +1,85 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+use Bio::Phylo::TreeBASE;
+use Bio::Phylo::Util::Logger ':levels';
+use Bio::Phylo::Factory;
+use Data::Dumper;
+
+my $fac = Bio::Phylo::Factory->new;
+my $logger = Bio::Phylo::Util::Logger->new;
+
+my $dbname = 'treebasedev';
+my $host = 'treebasedb-dev.nescent.org';
+my $user = 'treebase_app';
+my $pass = 'tim5tema';
+
+my $tb = Bio::Phylo::TreeBASE->connect(
+ "dbi:Pg:dbname=$dbname;host=$host",
+ $user,
+ $pass,
+ { AutoCommit => 0 },
+);
+
+my @matrices = $tb->resultset('Matrix')->search_literal(
+ 'ntax > ? AND nchar > ?', qw/3 20/);
+
+my ( @studies, %seen_tree );
+MATRIX: for my $matrix ( @matrices ) {
+ my $matrix_id = $matrix->matrix_id;
+ my $type = $matrix->get_type;
+ if ( $type ne 'Dna' ) {
+ warn "Matrix $matrix_id is ${type}, not Dna";
+ next MATRIX;
+ }
+ if ( -e "nexus/${matrix_id}.nex" ) {
+ warn "Matrix $matrix_id has already been written out";
+ next MATRIX;
+ }
+ for my $data ( $matrix->analyzeddatas ) {
+ if ( $data->input ) {
+ my $step = $data->analysisstep;
+ for my $other_data ( $step->analyzeddatas ) {
+ if ( not $other_data->input ) {
+ if ( $other_data->type eq 'T' ) {
+ my $tree = $other_data->phylotree;
+ my $tree_id = $tree->phylotree_id;
+ if ( not $seen_tree{ $tree_id } ) {
+ $seen_tree{ $tree_id } = 1;
+ write_study($matrix_id,$tree_id);
+ warn "found tree $tree_id";
+ }
+ else {
+ warn "already seen tree $tree_id";
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+sub write_study {
+ my ( $matrix_id, $tree_id ) = @_;
+ my $template = 'http://purl.org/phylo/treebase/phylows/%s/TB2:%s?format=nexus';
+
+ # download tree
+ my $tree_file = "nexus/M${matrix_id}-Tr${tree_id}.tre";
+ my $tree_url = sprintf($template,"tree","Tr${tree_id}");
+ if ( system('wget','-O',$tree_file,$tree_url) == 0 ) {
+ warn "downloaded $tree_file from $tree_url";
+ }
+ else {
+ warn "problem: $?";
+ }
+
+ # download matrix
+ my $matrix_file = "nexus/M${matrix_id}.nex";
+ my $matrix_url = sprintf($template,"matrix","M${matrix_id}");
+ if ( system('wget','-O',$matrix_file,$matrix_url) == 0 ) {
+ warn "downloaded $matrix_file from $matrix_url";
+ }
+ else {
+ warn "problem: $?";
+ }
+}
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From: <rv...@us...> - 2011-05-26 18:59:48
|
Revision: 882
http://treebase.svn.sourceforge.net/treebase/?rev=882&view=rev
Author: rvos
Date: 2011-05-26 18:59:42 +0000 (Thu, 26 May 2011)
Log Message:
-----------
This test was using the wrong DateFormat class.
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java 2011-05-24 15:15:27 UTC (rev 881)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/dao/study/StudyDAOTest.java 2011-05-26 18:59:42 UTC (rev 882)
@@ -15,7 +15,7 @@
import org.cipres.treebase.domain.study.StudyStatus;
import org.cipres.treebase.domain.study.StudyStatusHome;
-import com.ibm.icu.text.DateFormat;
+import java.text.DateFormat;
/**
* The class <code>StudyDAOTest</code> contains tests for the class {@link <code>StudyDAO</code>}
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From: <hs...@us...> - 2011-05-24 15:15:34
|
Revision: 881
http://treebase.svn.sourceforge.net/treebase/?rev=881&view=rev
Author: hshyket
Date: 2011-05-24 15:15:27 +0000 (Tue, 24 May 2011)
Log Message:
-----------
Changing Google Analytics tracking to track outgoing links, downloads and emails as events instead of pageviews
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
Modified: trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js 2011-05-20 14:19:47 UTC (rev 880)
+++ trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js 2011-05-24 15:15:27 UTC (rev 881)
@@ -23,7 +23,7 @@
var path = hrefs[l].pathname + hrefs[l].search;
var isDoc = path.match(/\.(?:doc|eps|jpg|png|svg|xls|ppt|pdf|xls|zip|txt|vsd|vxd|js|css|rar|exe|wma|mov|avi|wmv|mp3|nex)($|\&|\?)/);
if (isDoc) {
- startListening(hrefs[l],"click",trackExternalLinks);
+ startListening(hrefs[l],"click",trackDownloads);
}
} else if (hrefs[l].hostname != location.hostname) {
startListening(hrefs[l],"click",trackExternalLinks);
@@ -46,7 +46,7 @@
function trackMailto (evnt) {
var href = (evnt.srcElement) ? evnt.srcElement.href : this.href;
var mailto = "/mailto/" + href.substring(7);
- if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackPageview(mailto);
+ if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackEvent("Email",mailto);
}
function trackExternalLinks (evnt) {
@@ -57,5 +57,16 @@
var lnk = (e.pathname.charAt(0) == "/") ? e.pathname : "/" + e.pathname;
if (e.search && e.pathname.indexOf(e.search) == -1) lnk += e.search;
if (e.hostname != location.hostname) lnk = e.hostname + lnk;
- if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackPageview(lnk);
+ if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackEvent("Outgoing Links",lnk);
+}
+
+function trackDownloads (evnt) {
+ var e = (evnt.srcElement) ? evnt.srcElement : this;
+ while (e.tagName != "A") {
+ e = e.parentNode;
+ }
+ var lnk = (e.pathname.charAt(0) == "/") ? e.pathname : "/" + e.pathname;
+ if (e.search && e.pathname.indexOf(e.search) == -1) lnk += e.search;
+ if (e.hostname != location.hostname) lnk = e.hostname + lnk;
+ if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackEvent("Downloads", lnk);
}
\ No newline at end of file
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From: <hs...@us...> - 2011-05-20 14:19:53
|
Revision: 880
http://treebase.svn.sourceforge.net/treebase/?rev=880&view=rev
Author: hshyket
Date: 2011-05-20 14:19:47 +0000 (Fri, 20 May 2011)
Log Message:
-----------
Making it so that any action that calls doAction in Javascript removes the URL parameters
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp 2011-05-20 14:08:08 UTC (rev 879)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp 2011-05-20 14:19:47 UTC (rev 880)
@@ -45,7 +45,7 @@
<script type="text/javascript">
function doAction(action) {
$('action').value = action;
- if (!(location.search == "") && action == 'discardResults')
+ if (!(location.search == ""))
{
var url = location.href;
var url_parts = url.split('?');
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From: <hs...@us...> - 2011-05-20 14:08:14
|
Revision: 879
http://treebase.svn.sourceforge.net/treebase/?rev=879&view=rev
Author: hshyket
Date: 2011-05-20 14:08:08 +0000 (Fri, 20 May 2011)
Log Message:
-----------
Fixing issue where javascript would to a post to discard the results, but the results would still be there since it was pulling the parameters from the URL
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp 2011-05-19 21:28:17 UTC (rev 878)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/searchResultsList.jsp 2011-05-20 14:08:08 UTC (rev 879)
@@ -43,9 +43,14 @@
<div id="output"></div>
<script type="text/javascript">
-
- function doAction(action) {
+ function doAction(action) {
$('action').value = action;
+ if (!(location.search == "") && action == 'discardResults')
+ {
+ var url = location.href;
+ var url_parts = url.split('?');
+ $('resultsActionForm').writeAttribute('action', url_parts[0]);
+ }
$('resultsActionForm').submit();
}
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