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From: <sfr...@us...> - 2011-12-16 02:33:48
|
Revision: 1006
http://treebase.svn.sourceforge.net/treebase/?rev=1006&view=rev
Author: sfrgpiel
Date: 2011-12-16 02:33:42 +0000 (Fri, 16 Dec 2011)
Log Message:
-----------
Updating the splash screen with an RSS feed
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2011-12-13 20:14:19 UTC (rev 1005)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2011-12-16 02:33:42 UTC (rev 1006)
@@ -2,7 +2,13 @@
<div class="gutter">
<h1>Welcome to TreeBASE</h1>
<p>
- TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using a special access code. </p>
+ TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using a special access code.</p>
+ <p>Some recent additions:</p>
+ <script language="JavaScript" src="http://landmark-project.com/feed2js/feed2js.php?src=http%3A%2F%2Fpipes.yahoo.com%2Fpipes%2Fpipe.run%3F_id%3D41dc2d1544150c1b8e69367059f26950%26_render%3Drss&date=y&utf=y" charset="UTF-8" type="text/javascript">
+ </script>
+ <noscript>
+ <a href="http://landmark-project.com/feed2js/feed2js.php?src=http%3A%2F%2Fpipes.yahoo.com%2Fpipes%2Fpipe.run%3F_id%3D41dc2d1544150c1b8e69367059f26950%26_render%3Drss&date=y&utf=y&html=y">View RSS feed</a>
+ </noscript>
<p>The current release includes a host of new features and improvements over the previous TreeBASE prototype. New features include:</p>
<ul>
<li>Richer annotation of metadata (journal DOIs, specimen georeferences, Genbank accession numbers, etc) </li>
@@ -13,8 +19,6 @@
<li>Data are delivered in several serializations, including <a href="http:/hackathon.nescent.org/Supporting_NEXUS_Documentation" target="_blank">NEXUS</a> and <a href="http://www.nexml.org" target="_blank">NeXML</a></li>
<li> A special URL gives journal editors and reviewers anonymous advanced access to data</li>
<li>Programmatic access to the data using the <a href="http://evoinfo.nescent.org/PhyloWS" target="_blank">PhyloWS API</a>. Queries are expressed in URLs using PhyloWS syntax and can return results in RDF as RSS 1.0 feeds, which means that users can set their favorite RSS Reader to fetch all new TreeBASE studies that satisfy a particular query (e.g. return all studies published in "Systematic Biology," or return all trees that include "Homo sapiens," etc)</li>
- </ul>
- <p>
- As of early 2010, TreeBASE contains 6,500 trees in 2,500 publications written by 4,500 different authors. These trees have 135,000 distinct taxon labels that map to approximately 60,000 distinct taxa. </p>
- </div>
+ </ul>
+ <p>As of December 2011, TreeBASE contains 2,946 publications written by 6,106 different authors. These studies analyzed 5,717 matrices and resulted in 8,462 trees with 465,762 taxon labels that mapped to 82,043 distinct taxa.</p> </div>
</div>
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|
|
From: <rv...@us...> - 2011-12-13 20:14:25
|
Revision: 1005
http://treebase.svn.sourceforge.net/treebase/?rev=1005&view=rev
Author: rvos
Date: 2011-12-13 20:14:19 +0000 (Tue, 13 Dec 2011)
Log Message:
-----------
Changed header from "Downloaded on..." to "Generated on..." because of Apache level caching, so that pre-generated files don't have confusing time stamps.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2011-12-12 18:21:28 UTC (rev 1004)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2011-12-13 20:14:19 UTC (rev 1005)
@@ -519,7 +519,7 @@
public static void attachStudyHeader(Study pStudy, StringBuilder pBuilder) {
pBuilder
.append(
- "[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.\n\n\nDownloaded on "
+ "[!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file.\n\n\nGenerated on "
+ getTimeAndDateAtGMT()).append(TreebaseUtil.LINESEP).append(
"\nTreeBASE (cc) 1994-2008").append(TreebaseUtil.LINESEP);
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|
|
From: <rv...@us...> - 2011-12-12 18:21:34
|
Revision: 1004
http://treebase.svn.sourceforge.net/treebase/?rev=1004&view=rev
Author: rvos
Date: 2011-12-12 18:21:28 +0000 (Mon, 12 Dec 2011)
Log Message:
-----------
Typo fix, s/overseas/oversees/
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-12-12 18:01:09 UTC (rev 1003)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-12-12 18:21:28 UTC (rev 1004)
@@ -29,7 +29,7 @@
<li>Provide an overview of access and sharing. For your TreeBASE-submitted data, you can state that TreeBASE makes all data and metadata freely available to the public once the manuscript under review has been accepted by a peer-review publication. TreeBASE will allow data embargo periods according to the policies of the journal, but once data are public they are assumed to be released to the public domain without any restrictions on reuse. We recommend that you state that you will provide TreeBASE's resolvable globally unique identifiers (GUIDs) for your deposited data in future progress reports to NSF, in relevant publications, and in your lab's web page. </li>
<li>State that you will flag your submissions to TreeBASE as data subject to your data management plan so as to receive special attention by TreeBASE staff to help ensure that the data are richly annotated and fully compliant for reuse in accordance with community standards in phylogenetics. </li>
</ul>
-<p>TreeBASE suggests that for each submission of data from sponsored research you contribute at least $100 towards defraying the costs of storage and dissemination, as well as in support of the additional scrutiny by TreeBASE staff for NSF data management compliance. This fee is collected by the Phyloinformatics Research Foundation, which overseas TreeBASE activities. Anticipated costs can be budgeted under publication expenses in your grant proposal's budget. </p>
+<p>TreeBASE suggests that for each submission of data from sponsored research you contribute at least $100 towards defraying the costs of storage and dissemination, as well as in support of the additional scrutiny by TreeBASE staff for NSF data management compliance. This fee is collected by the Phyloinformatics Research Foundation, which oversees TreeBASE activities. Anticipated costs can be budgeted under publication expenses in your grant proposal's budget. </p>
<hr /></p>
<table width="100%" border="0">
<tr>
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From: <hs...@us...> - 2011-12-12 18:01:15
|
Revision: 1003
http://treebase.svn.sourceforge.net/treebase/?rev=1003&view=rev
Author: hshyket
Date: 2011-12-12 18:01:09 +0000 (Mon, 12 Dec 2011)
Log Message:
-----------
Fixing issue where the numbering of the translation table in the tree string was not converting properly
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java 2011-12-09 16:23:11 UTC (rev 1002)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java 2011-12-12 18:01:09 UTC (rev 1003)
@@ -260,7 +260,7 @@
return getTitle();
}
- private void sortByTaxonLabel(List<TaxonLabel> tList)
+ public void sortByTaxonLabel(List<TaxonLabel> tList)
{
java.util.Collections.sort(tList, new Comparator<TaxonLabel>() {
@@ -273,4 +273,16 @@
});
}
+
+ public void sortByTaxonLabelLength(List<TaxonLabel> tList)
+ {
+ java.util.Collections.sort(tList, new Comparator<TaxonLabel>() {
+
+ public int compare(TaxonLabel pObject1, TaxonLabel pObject2) {
+ return pObject2.getTaxonLabel().length() - pObject1.getTaxonLabel().length();
+ }
+
+ });
+
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-12-09 16:23:11 UTC (rev 1002)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-12-12 18:01:09 UTC (rev 1003)
@@ -244,11 +244,18 @@
}
String tmpnewick, newick = atree.getNewickString();
+ List<TaxonLabel> txnlbllistclone = new ArrayList<TaxonLabel>(txnlbllist);
+ tlSet.sortByTaxonLabelLength(txnlbllistclone);
+ HashMap<String, Integer> txnOrder = new HashMap<String, Integer>();
+ for (int y = 0; y < numoftxnlbls; y++) {
+ txnOrder.put(txnlbllist.get(y).getTaxonLabel(), y);
+ }
for (int z = 0; z < numoftxnlbls; z++) {
- String label = StringUtil.tokenize(txnlbllist.get(z).getTaxonLabel());
- tmpnewick = newick.replace(label, String.valueOf(z + 1));
+ String label = StringUtil.tokenize(txnlbllistclone.get(z).getTaxonLabel());
+ tmpnewick = newick.replace(label, String.valueOf(txnOrder.get(txnlbllistclone.get(z).getTaxonLabel())+1));
newick = tmpnewick;
}
+ txnlbllistclone = null;
// out.append(atree.getNewickString());
pBuilder.append(newick);
pBuilder.append("\n");
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java 2011-12-09 16:23:11 UTC (rev 1002)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/taxon/TaxonLabelTest.java 2011-12-12 18:01:09 UTC (rev 1003)
@@ -2,6 +2,7 @@
import java.util.ArrayList;
import java.util.Collection;
+import java.util.List;
import org.apache.log4j.Logger;
import org.cipres.treebase.dao.AbstractDAOTest;
@@ -112,17 +113,49 @@
}
assertTrue(matricesOkay);
}
+
+ public void testTaxonLabelLengthSorting() {
+ int x = 0;
+ boolean isTaxonSorted = false;
+
+ List<TaxonLabel> res = (List<TaxonLabel>) findHomoSapiensTL();
+ LOGGER.info("Homo matrices: " + res.size() + " result(s)");
+ assertNotNull(res);
+ TaxonLabel newTaxon = new TaxonLabel();
+ newTaxon.setTaxonLabel("Homo Sapiens ABCD");
+ res.add(newTaxon);
+ //res.get(1).setTaxonLabel("Homo Sapiens ABCD");
+ TaxonLabelSet tlSet = new TaxonLabelSet();
+ tlSet.sortByTaxonLabelLength(res);
+
+ //for (TaxonLabel tLabel : res) {
+ for (x = 0; x < res.size(); x++) {
+ if (x > 0) {
+ if (res.get(x-1).getTaxonLabel().length() >= res.get(x).getTaxonLabel().length()) {
+ isTaxonSorted = true;
+ }
+ else {
+ LOGGER.debug("Taxon Labels are not sorted");
+ isTaxonSorted = false;
+ break;
+ }
+ }
+ }
+ assertTrue(isTaxonSorted);
+ }
private Collection<TaxonLabel> findHomoSapiensTL() {
return getTaxonLabelHome().findByExactString("Homo sapiens");
}
-
+
private TaxonVariant findHomoSapiensTV() {
Collection<TaxonVariant> hSap = getTaxonLabelHome().findTaxonVariantByFullName("Homo sapiens");
if (hSap == null) return null;
if (hSap.isEmpty()) return null;
return hSap.iterator().next();
}
+
+
}
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|
|
From: <hs...@us...> - 2011-12-09 16:23:20
|
Revision: 1002
http://treebase.svn.sourceforge.net/treebase/?rev=1002&view=rev
Author: hshyket
Date: 2011-12-09 16:23:11 +0000 (Fri, 09 Dec 2011)
Log Message:
-----------
Fixing error with last commit. Needed to set the study in the matrix before it saved to the database.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-12-09 15:00:21 UTC (rev 1001)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-12-09 16:23:11 UTC (rev 1002)
@@ -692,10 +692,10 @@
sub.getStudy().getTaxonLabelSets().addAll(data.getTaxonLabelSets());
// Store matrice:
- getMatrixHome().persistAll(data.getMatrices());
for (Matrix uploadMatrix : data.getMatrices()) {
uploadMatrix.setStudy(sub.getStudy());
}
+ getMatrixHome().persistAll(data.getMatrices());
sub.addMatrices(data.getMatrices());
getMatrixHome().flush();
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|
|
From: <hs...@us...> - 2011-12-09 15:00:30
|
Revision: 1001
http://treebase.svn.sourceforge.net/treebase/?rev=1001&view=rev
Author: hshyket
Date: 2011-12-09 15:00:21 +0000 (Fri, 09 Dec 2011)
Log Message:
-----------
Setting the study id for matrices on upload and setting the database creation script to have NOT NULL for the study id in the matrix table
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-12-08 22:15:08 UTC (rev 1000)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/SubmissionServiceImpl.java 2011-12-09 15:00:21 UTC (rev 1001)
@@ -693,6 +693,9 @@
// Store matrice:
getMatrixHome().persistAll(data.getMatrices());
+ for (Matrix uploadMatrix : data.getMatrices()) {
+ uploadMatrix.setStudy(sub.getStudy());
+ }
sub.addMatrices(data.getMatrices());
getMatrixHome().flush();
Modified: trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
===================================================================
--- trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2011-12-08 22:15:08 UTC (rev 1000)
+++ trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2011-12-09 15:00:21 UTC (rev 1001)
@@ -526,7 +526,7 @@
casesensitive smallint,
matrixdatatype_id bigint,
matrixkind_id bigint,
- study_id bigint,
+ study_id bigint NOT NULL,
taxonlabelset_id bigint,
ancstateset_id bigint,
codonpositionset_id bigint,
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From: <hs...@us...> - 2011-12-08 22:15:15
|
Revision: 1000
http://treebase.svn.sourceforge.net/treebase/?rev=1000&view=rev
Author: hshyket
Date: 2011-12-08 22:15:08 +0000 (Thu, 08 Dec 2011)
Log Message:
-----------
Overriding fetch mode of matrix (to join) so that we can pull whether the study is published in the PhyloWSMatrixController
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java 2011-12-08 16:27:56 UTC (rev 999)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java 2011-12-08 22:15:08 UTC (rev 1000)
@@ -23,6 +23,8 @@
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
@@ -320,6 +322,7 @@
*/
@ManyToOne(cascade = {CascadeType.MERGE, CascadeType.PERSIST}, fetch = FetchType.LAZY)
@JoinColumn(name = "STUDY_ID")
+ @Fetch(FetchMode.JOIN)
public Study getStudy() {
return mStudy;
}
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|
From: <sfr...@us...> - 2011-12-08 16:28:06
|
Revision: 999
http://treebase.svn.sourceforge.net/treebase/?rev=999&view=rev
Author: sfrgpiel
Date: 2011-12-08 16:27:56 +0000 (Thu, 08 Dec 2011)
Log Message:
-----------
nuts. will need to issue a new one.
Modified Paths:
--------------
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql
Modified: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql 2011-12-07 21:59:47 UTC (rev 998)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql 2011-12-08 16:27:56 UTC (rev 999)
@@ -1,5 +1,5 @@
-- psql -U treebase_app -d treebasedev -h treebasedb-dev.nescent.org
--- qLoMjwRz
+--
12037
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From: <hs...@us...> - 2011-12-07 21:59:53
|
Revision: 998
http://treebase.svn.sourceforge.net/treebase/?rev=998&view=rev
Author: hshyket
Date: 2011-12-07 21:59:47 +0000 (Wed, 07 Dec 2011)
Log Message:
-----------
When downloading a study will loop through taxon block to check for duplicate blocks
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java 2011-12-06 21:59:41 UTC (rev 997)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java 2011-12-07 21:59:47 UTC (rev 998)
@@ -1,5 +1,8 @@
package org.cipres.treebase.web.controllers;
+import java.util.ArrayList;
+import java.util.List;
+
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
@@ -8,6 +11,7 @@
import org.cipres.treebase.domain.matrix.Matrix;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.StudyService;
+import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelSet;
import org.cipres.treebase.domain.tree.TreeBlock;
import org.springframework.web.servlet.ModelAndView;
@@ -51,15 +55,35 @@
// taxa:
//set a unique number for each block when the title is Taxa
- Integer taxa = 1;
+ Integer taxaCount = 1;
+ List<List <TaxonLabel>> taxonCompare = new ArrayList<List <TaxonLabel>>();
for ( TaxonLabelSet tls : study.getTaxonLabelSets() ) {
- if (tls.getTitle().equals("Taxa")) {
- tls.setTitle(tls.getTitle() + taxa.toString());
- taxa++;
+ Boolean isDuplicateTaxa = false;
+ Integer taxaCompareCount = 1;
+
+ List<TaxonLabel> taxonLblSet = tls.getTaxonLabelsReadOnly();
+ if (taxonCompare != null) {
+ for (List<TaxonLabel> lstTls : taxonCompare) {
+ if (taxonLblSet.equals(lstTls)) {
+ isDuplicateTaxa = true;
+ break;
+ }
+ else {
+ taxaCompareCount++;
+ }
+ }
}
- // one taxon label per line, no line number.
- tls.buildNexusBlockTaxa(builder, true, false);
+ if (isDuplicateTaxa) {
+ tls.setTitle("Taxa" + taxaCompareCount.toString());
+ }
+ else {
+ tls.setTitle("Taxa" + taxaCount.toString());
+ taxaCount++;
+ // one taxon label per line, no line number.
+ tls.buildNexusBlockTaxa(builder, true, false);
+ taxonCompare.add(taxonLblSet);
+ }
}
// matrices::
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|
|
From: <hs...@us...> - 2011-12-06 21:59:47
|
Revision: 997
http://treebase.svn.sourceforge.net/treebase/?rev=997&view=rev
Author: hshyket
Date: 2011-12-06 21:59:41 +0000 (Tue, 06 Dec 2011)
Log Message:
-----------
Fixing Matrix check of whether a study was published from PURL redirect.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java 2011-12-06 21:01:56 UTC (rev 996)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java 2011-12-06 21:59:41 UTC (rev 997)
@@ -45,7 +45,7 @@
throw new ObjectNotFoundException("Can't find study for matrix "+objectId);
}
- checkAccess(study.isPublished());
+ checkAccess(matrix.getStudy().isPublished());
Map<String,String> params = new HashMap<String,String>();
params.put("id", ""+study.getId());
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|
|
From: <sfr...@us...> - 2011-12-06 21:02:02
|
Revision: 996
http://treebase.svn.sourceforge.net/treebase/?rev=996&view=rev
Author: sfrgpiel
Date: 2011-12-06 21:01:56 +0000 (Tue, 06 Dec 2011)
Log Message:
-----------
Fix problem where matrix records lack a study_id value
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2011-12-06_matrix_nullstudyid_fix/
trunk/treebase-core/db/cleaning/2011-12-06_matrix_nullstudyid_fix/fix_matrix_study_id_null.sql
Added: trunk/treebase-core/db/cleaning/2011-12-06_matrix_nullstudyid_fix/fix_matrix_study_id_null.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_matrix_nullstudyid_fix/fix_matrix_study_id_null.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_matrix_nullstudyid_fix/fix_matrix_study_id_null.sql 2011-12-06 21:01:56 UTC (rev 996)
@@ -0,0 +1,25 @@
+begin work;
+
+-- check to see how many matrices lack a study_id
+SELECT count(*) FROM matrix WHERE study_id IS NULL;
+
+-- for those matrices that lack a study_id,
+-- update the study_id based on the study_id
+-- value found in the related taxonlabelset
+
+UPDATE matrix SET study_id = tls.study_id
+FROM matrix mx JOIN taxonlabelset tls USING (taxonlabelset_id)
+WHERE mx.study_id IS NULL
+AND tls.study_id IS NOT NULL
+AND matrix.matrix_id = mx.matrix_id;
+
+-- check to see how many trees still lack a study_id
+SELECT count(*) FROM matrix WHERE study_id IS NULL;
+
+-- if no more trees lack a study_id, we can now apply a new
+-- constraint to ensure that trees always have a study_id
+
+ALTER TABLE matrix
+ALTER COLUMN study_id SET NOT NULL;
+
+commit;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hs...@us...> - 2011-12-06 19:31:55
|
Revision: 995
http://treebase.svn.sourceforge.net/treebase/?rev=995&view=rev
Author: hshyket
Date: 2011-12-06 19:31:48 +0000 (Tue, 06 Dec 2011)
Log Message:
-----------
Fixing issues where deleting a tree block would not delete new orphaned taxon label sets
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java 2011-12-06 19:24:05 UTC (rev 994)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/tree/PhyloTreeDAO.java 2011-12-06 19:31:48 UTC (rev 995)
@@ -125,9 +125,9 @@
block.removePhyloTree(pTree);
if (block.isEmpty()) {
- TaxonLabelSet tSet=block.getTaxonLabelSet();
+ //TaxonLabelSet tSet=block.getTaxonLabelSet();
deleteTreeBlock(block);
- getTaxonLabelHome().clean(tSet);
+ //getTaxonLabelHome().clean(tSet);
}
}
@@ -172,7 +172,9 @@
*/
public void deleteTreeBlock(TreeBlock pTreeBlock) {
if (pTreeBlock != null && pTreeBlock.getId() != null) {
-
+
+ TaxonLabelSet tSet=pTreeBlock.getTaxonLabelSet();
+
// bi-directional relationships:
// * submission -> treeblock
Submission sub = getSubmissionHome().findByTreeBlock(pTreeBlock);
@@ -187,7 +189,9 @@
realDelete(tree);
}
- getHibernateTemplate().delete(pTreeBlock);
+ ;getHibernateTemplate().delete(pTreeBlock);
+
+ getTaxonLabelHome().clean(tSet);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2011-12-06 19:24:14
|
Revision: 994
http://treebase.svn.sourceforge.net/treebase/?rev=994&view=rev
Author: sfrgpiel
Date: 2011-12-06 19:24:05 +0000 (Tue, 06 Dec 2011)
Log Message:
-----------
PERL script to clean the database of orphaned taxonlabelsets.
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql
trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/README 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,18 @@
+The script delete_orphaned_taxonlabelsets.pl is intended to delete orphaned taxonlabelsets.
+
+As of Dec 6 2012, orphans were being generated as a result of a bug. Our delete treeblock
+function inadvertently failed to include a cleanup step to delete related, but now orphaned,
+taxonlabelset records. The result is studies that (sometimes) generate a "yikes" error when
+you try to get a list of taxa.
+
+For example, this page generates a Yikes:
+
+http://treebase.org/treebase-web/search/study/taxa.html?id=12037
+
+While this page (after fixing the data with delete_orphaned_taxonlabelsets.pl) does not:
+
+http://treebase-dev.nescent.org/treebase-web/search/study/taxa.html?id=12037
+
+To run the script, first edit lines 12-15 to point to production, then execute. It takes no
+parameters. Example output is provided with "output.txt".
+
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/affected_studies.sql 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,361 @@
+
+SELECT DISTINCT ON (tls.study_id) tls.taxonlabelset_id, tls.study_id, ss.description
+FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE
+mx.matrix_id IS NULL
+AND
+tb.treeblock_id IS NULL
+
+-- 345 studies are affected
+
+-- 1394 22 In Progress
+-- 4810 23 In Progress
+-- 9450 44 In Progress
+-- 11200 1019 Published
+-- 13335 1919 Published
+-- 14190 2264 In Progress
+-- 16071 10215 In Progress
+-- 16132 10317 Published
+-- 16464 10335 Published
+-- 16188 10339 In Progress
+-- 18753 10347 In Progress
+-- 16228 10356 In Progress
+-- 16280 10367 In Progress
+-- 16399 10399 Published
+-- 16402 10400 Published
+-- 16434 10413 In Progress
+-- 16456 10424 In Progress
+-- 16466 10425 In Progress
+-- 16477 10429 Published
+-- 16567 10431 In Progress
+-- 16484 10433 Published
+-- 16501 10434 In Progress
+-- 16507 10435 Published
+-- 18799 10436 Published
+-- 16514 10438 Published
+-- 16545 10449 In Progress
+-- 16554 10452 In Progress
+-- 16668 10462 In Progress
+-- 16784 10464 Published
+-- 16633 10468 In Progress
+-- 16638 10469 Published
+-- 16643 10470 In Progress
+-- 16653 10474 In Progress
+-- 16749 10485 Published
+-- 16757 10486 In Progress
+-- 16702 10489 Published
+-- 16696 10492 Published
+-- 16700 10493 Published
+-- 16731 10504 Published
+-- 16734 10507 Published
+-- 16738 10508 In Progress
+-- 16772 10511 Published
+-- 21310 10512 Published
+-- 16860 10529 In Progress
+-- 16888 10530 In Progress
+-- 16940 10536 Published
+-- 16972 10541 Published
+-- 16969 10542 Published
+-- 17064 10553 Published
+-- 17057 10569 In Progress
+-- 17076 10570 Published
+-- 17093 10583 In Progress
+-- 17289 10589 In Progress
+-- 17293 10593 Published
+-- 17206 10603 Published
+-- 17138 10604 In Progress
+-- 18665 10605 In Progress
+-- 17671 10608 Published
+-- 17174 10613 Published
+-- 17192 10623 Published
+-- 17237 10635 Published
+-- 17255 10639 In Progress
+-- 17379 10644 Published
+-- 17291 10648 Published
+-- 17338 10652 Published
+-- 22206 10653 Published
+-- 17347 10654 Published
+-- 17355 10658 Published
+-- 17468 10665 Published
+-- 18527 10673 In Progress
+-- 17453 10679 Published
+-- 17568 10680 Published
+-- 17429 10684 Published
+-- 17463 10689 Published
+-- 17471 10692 Published
+-- 17514 10698 In Progress
+-- 17528 10699 In Progress
+-- 17572 10703 Published
+-- 17584 10711 In Progress
+-- 22854 10713 Published
+-- 17605 10714 Published
+-- 18102 10724 Published
+-- 17643 10727 Published
+-- 17659 10732 Published
+-- 17669 10733 In Progress
+-- 17740 10736 Published
+-- 17752 10740 In Progress
+-- 17784 10749 Published
+-- 17821 10759 In Progress
+-- 17836 10766 Published
+-- 17850 10772 Published
+-- 17856 10774 Published
+-- 17895 10786 In Progress
+-- 17950 10795 In Progress
+-- 17992 10797 Published
+-- 17987 10803 Published
+-- 17997 10812 In Progress
+-- 18004 10814 In Progress
+-- 20216 10817 In Progress
+-- 18030 10821 Published
+-- 18044 10828 In Progress
+-- 18748 10830 Published
+-- 18138 10831 In Progress
+-- 18123 10847 Published
+-- 18216 10859 In Progress
+-- 18286 10861 In Progress
+-- 18238 10870 In Progress
+-- 18244 10876 Published
+-- 18346 10888 Published
+-- 18283 10898 Published
+-- 18366 10902 In Progress
+-- 18566 10904 In Progress
+-- 21995 10905 Published
+-- 18410 10908 Published
+-- 18478 10927 Published
+-- 18564 10938 Published
+-- 18580 10940 Published
+-- 18509 10942 Published
+-- 18591 10950 Published
+-- 18593 10951 Published
+-- 18619 10961 In Progress
+-- 18638 10963 Published
+-- 18633 10966 Published
+-- 18657 10971 In Progress
+-- 18673 10977 In Progress
+-- 18683 10983 Published
+-- 18687 10984 Published
+-- 18737 10996 Published
+-- 18726 10999 In Progress
+-- 18760 11009 Published
+-- 18822 11020 Published
+-- 22845 11021 Published
+-- 18826 11022 Published
+-- 18887 11032 Published
+-- 18983 11056 In Progress
+-- 19367 11058 Published
+-- 19007 11061 Published
+-- 19045 11078 In Progress
+-- 19055 11079 Published
+-- 19062 11080 Published
+-- 19077 11083 Published
+-- 19095 11088 Published
+-- 19107 11089 In Progress
+-- 19104 11090 Published
+-- 19429 11091 In Progress
+-- 19127 11093 Published
+-- 19126 11097 Published
+-- 19160 11111 Published
+-- 19173 11112 Published
+-- 19186 11114 Published
+-- 19191 11115 Published
+-- 19199 11116 Ready
+-- 19394 11117 In Progress
+-- 19205 11118 Published
+-- 19213 11122 Published
+-- 19260 11126 Published
+-- 19274 11128 Published
+-- 19318 11132 Published
+-- 19337 11136 In Progress
+-- 19359 11140 Published
+-- 21258 11159 In Progress
+-- 19424 11161 Published
+-- 19454 11174 Published
+-- 19462 11177 In Progress
+-- 19494 11181 In Progress
+-- 19497 11183 Published
+-- 19503 11184 Published
+-- 19513 11192 Published
+-- 19523 11197 Published
+-- 19540 11200 Published
+-- 20145 11204 Published
+-- 19682 11210 Published
+-- 19576 11211 Published
+-- 19601 11216 Published
+-- 19662 11219 In Progress
+-- 19654 11226 Published
+-- 19793 11252 In Progress
+-- 19828 11260 Published
+-- 19829 11261 In Progress
+-- 19844 11267 Published
+-- 19854 11269 Published
+-- 19883 11273 In Progress
+-- 19893 11276 In Progress
+-- 19918 11284 Published
+-- 19942 11289 Published
+-- 19962 11294 In Progress
+-- 19979 11296 In Progress
+-- 20000 11298 Published
+-- 20317 11303 Published
+-- 20140 11312 Published
+-- 20142 11313 Published
+-- 20177 11327 In Progress
+-- 20207 11331 Published
+-- 20190 11333 In Progress
+-- 20222 11336 Published
+-- 20252 11346 In Progress
+-- 20258 11348 In Progress
+-- 20284 11352 In Progress
+-- 20283 11355 Published
+-- 22141 11367 In Progress
+-- 20338 11369 In Progress
+-- 20802 11378 Published
+-- 20375 11380 In Progress
+-- 20520 11383 In Progress
+-- 20424 11391 Published
+-- 20419 11392 Published
+-- 20468 11397 In Progress
+-- 22095 11398 In Progress
+-- 20503 11404 Published
+-- 22263 11409 In Progress
+-- 20610 11415 Published
+-- 23182 11416 Published
+-- 20628 11417 In Progress
+-- 20631 11418 Published
+-- 20670 11439 Published
+-- 20719 11448 In Progress
+-- 21327 11461 In Progress
+-- 20964 11465 In Progress
+-- 21181 11468 Published
+-- 21278 11472 Published
+-- 21062 11476 Published
+-- 20901 11480 Published
+-- 21036 11487 In Progress
+-- 20941 11489 Published
+-- 20962 11499 In Progress
+-- 20976 11504 In Progress
+-- 21067 11512 Published
+-- 21052 11517 Published
+-- 21141 11524 In Progress
+-- 21513 11527 In Progress
+-- 21106 11535 Published
+-- 21112 11536 In Progress
+-- 21135 11537 In Progress
+-- 21188 11552 Published
+-- 22436 11557 Published
+-- 21216 11561 In Progress
+-- 21673 11563 Published
+-- 21343 11568 In Progress
+-- 21243 11570 Published
+-- 21246 11571 In Progress
+-- 21264 11575 Published
+-- 21273 11586 Published
+-- 21305 11593 Published
+-- 21320 11596 Published
+-- 21413 11600 In Progress
+-- 21349 11601 In Progress
+-- 21340 11607 In Progress
+-- 21345 11608 In Progress
+-- 21369 11616 Published
+-- 21380 11619 In Progress
+-- 21390 11623 Published
+-- 21387 11625 In Progress
+-- 22145 11644 Published
+-- 21461 11651 Published
+-- 21568 11652 In Progress
+-- 21520 11654 In Progress
+-- 21485 11659 In Progress
+-- 21750 11662 Published
+-- 21611 11670 In Progress
+-- 21696 11681 In Progress
+-- 21712 11683 In Progress
+-- 22040 11687 In Progress
+-- 21762 11689 Published
+-- 21774 11692 In Progress
+-- 21999 11695 Published
+-- 22004 11705 In Progress
+-- 22019 11711 In Progress
+-- 22027 11713 Published
+-- 22052 11719 In Progress
+-- 22089 11729 In Progress
+-- 22153 11747 Published
+-- 22170 11756 In Progress
+-- 22183 11759 Published
+-- 22225 11768 In Progress
+-- 22636 11779 Published
+-- 22256 11780 In Progress
+-- 22293 11798 Published
+-- 22348 11815 Published
+-- 22362 11822 Published
+-- 22390 11823 In Progress
+-- 22374 11825 In Progress
+-- 22387 11829 In Progress
+-- 22405 11832 In Progress
+-- 22450 11848 In Progress
+-- 22480 11849 Published
+-- 22706 11852 In Progress
+-- 22494 11863 In Progress
+-- 22489 11864 In Progress
+-- 22519 11865 Published
+-- 22496 11866 In Progress
+-- 22514 11868 Published
+-- 22529 11872 Published
+-- 22600 11876 Published
+-- 22551 11878 Published
+-- 22574 11891 Published
+-- 22581 11892 Published
+-- 22661 11893 In Progress
+-- 22608 11906 Published
+-- 23365 11908 Published
+-- 22632 11911 In Progress
+-- 22638 11914 In Progress
+-- 22652 11917 In Progress
+-- 22723 11918 Published
+-- 22727 11936 In Progress
+-- 22883 11943 In Progress
+-- 22872 11949 Published
+-- 22828 11950 Published
+-- 22876 11956 In Progress
+-- 23160 11959 In Progress
+-- 22895 11960 In Progress
+-- 23072 11963 In Progress
+-- 22914 11975 Published
+-- 22930 11980 In Progress
+-- 23021 11985 Published
+-- 23399 11988 Published
+-- 23539 11991 Published
+-- 22979 11995 In Progress
+-- 22996 12003 Published
+-- 23012 12006 In Progress
+-- 23061 12009 Published
+-- 23080 12029 In Progress
+-- 23095 12034 In Progress
+-- 23146 12036 Published
+-- 23102 12037 Published
+-- 23203 12043 In Progress
+-- 23158 12048 In Progress
+-- 23174 12050 In Progress
+-- 23200 12055 In Progress
+-- 23211 12057 Published
+-- 23226 12065 In Progress
+-- 23247 12072 In Progress
+-- 23274 12079 Published
+-- 23290 12087 In Progress
+-- 23292 12088 In Progress
+-- 23342 12096 In Progress
+-- 23357 12101 In Progress
+-- 23401 12120 In Progress
+-- 23408 12121 In Progress
+-- 23428 12128 In Progress
+-- 23491 12145 In Progress
+-- 23509 12149 In Progress
+-- 23606 12153 In Progress
+-- 23532 12160 Published
+-- 23590 12162 Published
+-- 23608 12167 In Progress
+
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/delete_orphaned_taxonlabelsets.pl 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,97 @@
+#!/usr/bin/perl
+
+use strict;
+use DBI;
+
+# This script is intended to delete orphaned taxonlabelsets. As of Dec 6 2012, orphans
+# were being generated as a result of a bug. When our delete-treeblock function inadvertently
+# failed to include a cleanup step to delete related, but now orphaned, taxonlabelset records.
+# The result are studies that generate a "yikes" error when you try to get a list of taxa.
+
+
+my $database = "treebasedev";
+my $username = "treebase_app";
+my $password = "";
+my $host = "treebasedb-dev.nescent.org";
+
+
+my $dbh = &ConnectToPg($database, $username, $password, $host);
+
+# start by asking how many taxonlabelset records are orphaned
+
+my $recs = "SELECT count(*) FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE mx.matrix_id IS NULL
+AND tb.treeblock_id IS NULL ";
+my $totRec = $dbh->selectrow_array ($recs);
+
+print "$totRec orphaned taxonlabelset records need to be deleted\n\n";
+
+# get a list of all these taxonlabelset IDs
+
+my $statement = "SELECT tls.taxonlabelset_id FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE mx.matrix_id IS NULL
+AND tb.treeblock_id IS NULL ";
+
+my @orphaned;
+my $orphanedlist = $dbh->prepare($statement) or die "Can't prepare $statement: $dbh->errstr\n";
+$orphanedlist->execute;
+while(my @row = $orphanedlist->fetchrow_array) {
+ push(@orphaned, $row[0]);
+}
+
+foreach my $orph ( @orphaned ) {
+ print "preparing to delete $orph\n";
+
+ # run the whole thing in a single transaction
+ eval {
+
+ # First delete the records that reference this taxonlabelset
+ $dbh->do( "DELETE FROM taxonlabelset_taxonlabel WHERE taxonlabelset_id = ?", undef, $orph );
+
+ # Next delete the taxonlabelset
+ $dbh->do( "DELETE FROM taxonlabelset WHERE taxonlabelset_id = ?", undef, $orph );
+
+ # If no errors so far, let's commit
+ $dbh->commit();
+ };
+
+ if ($@) {
+ warn "Failed to delete taxonlabelset_id $orph: $@\n";
+ $dbh->rollback();
+ print "rollback!!\n";
+ }
+
+}
+
+$totRec = $dbh->selectrow_array ($recs);
+
+print "\n$totRec orphaned taxonlabelset records need to be deleted\n";
+
+exit;
+
+
+
+# Connect to Postgres using DBI
+#==============================================================
+sub ConnectToPg {
+
+ my ($cstr, $user, $pass, $host) = @_;
+
+ $cstr = "DBI:Pg:dbname="."$cstr";
+ $cstr .= ";host=$host" if ($host);
+
+ my $dbh = DBI->connect($cstr, $user, $pass, {AutoCommit => 0, PrintError => 1, RaiseError => 1});
+ $dbh || &error("DBI connect failed : ",$dbh->errstr);
+
+ return($dbh);
+}
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/fixing_orphaned_taxonlabelsets.sql 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,405 @@
+-- psql -U treebase_app -d treebasedev -h treebasedb-dev.nescent.org
+-- qLoMjwRz
+
+
+12037
+
+SELECT tls.taxonlabelset_id, count(tt.*)
+FROM
+taxonlabelset tls JOIN
+taxonlabelset_taxonlabel tt USING (taxonlabelset_id) JOIN
+taxonlabel tl USING (taxonlabel_id)
+WHERE tls.study_id = 12037
+GROUP BY tls.taxonlabelset_id
+
+23165 55
+23161 100
+23102 94
+
+Set 23102 is probably orphaned
+
+SELECT tls.*, mx.matrix_id, tb.treeblock_id
+FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id)
+WHERE
+tls.taxonlabelset_id IN (23165, 23161, 23102)
+
+SELECT DISTINCT ON (tls.study_id) tls.taxonlabelset_id, tls.study_id, ss.description
+FROM
+taxonlabelset tls LEFT JOIN
+matrix mx ON (tls.taxonlabelset_id = mx.taxonlabelset_id) LEFT JOIN
+treeblock tb ON (tls.taxonlabelset_id = tb.taxonlabelset_id) JOIN
+study s ON (tls.study_id = s.study_id) JOIN
+studystatus ss USING (studystatus_id)
+WHERE
+mx.matrix_id IS NULL
+AND
+tb.treeblock_id IS NULL
+
+-- 345 studies are affected
+
+-- 1394 22 In Progress
+-- 4810 23 In Progress
+-- 9450 44 In Progress
+-- 11200 1019 Published
+-- 13335 1919 Published
+-- 14190 2264 In Progress
+-- 16071 10215 In Progress
+-- 16132 10317 Published
+-- 16464 10335 Published
+-- 16188 10339 In Progress
+-- 18753 10347 In Progress
+-- 16228 10356 In Progress
+-- 16280 10367 In Progress
+-- 16399 10399 Published
+-- 16402 10400 Published
+-- 16434 10413 In Progress
+-- 16456 10424 In Progress
+-- 16466 10425 In Progress
+-- 16477 10429 Published
+-- 16567 10431 In Progress
+-- 16484 10433 Published
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+-- 23539 11991 Published
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+-- 23290 12087 In Progress
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+-- 23532 12160 Published
+-- 23590 12162 Published
+-- 23608 12167 In Progress
+
+
+SELECT tb.treeblock_id, stb.submission_id, pt.study_id
+FROM treeblock tb LEFT JOIN
+sub_treeblock stb USING (treeblock_id) LEFT JOIN
+phylotree pt ON (tb.treeblock_id = pt.treeblock_id)
+WHERE tb.taxonlabelset_id IS NULL
+
+-- 4781 66
+-- 4782 67
+-- 4783 68
+-- 4784 69
+-- 4785 70
+-- 4786 71
+-- 4787 72
+-- 4788 73
+
+
Added: trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-12-06_orphaned_taxonlabelsets/output.txt 2011-12-06 19:24:05 UTC (rev 994)
@@ -0,0 +1,5102 @@
+5098 orphaned taxonlabelset records need to be deleted
+
+preparing to delete 81
+preparing to delete 82
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...
[truncated message content] |
|
From: <hs...@us...> - 2011-12-02 20:12:21
|
Revision: 993
http://treebase.svn.sourceforge.net/treebase/?rev=993&view=rev
Author: hshyket
Date: 2011-12-02 20:12:15 +0000 (Fri, 02 Dec 2011)
Log Message:
-----------
Checking to make sure that studies that have been cached but then removed from being published do not redirect from the PURL link to the cached object. Cached object may still remain in the Apache frontend cache and possibly be served to a user directly hitting the URL.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSStudyController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSTreeController.java
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
trunk/treebase-web/src/main/webapp/common/meta.jsp
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 2011-11-30 20:48:02 UTC (rev 992)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java 2011-12-02 20:12:15 UTC (rev 993)
@@ -10,10 +10,14 @@
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;
+import org.cipres.treebase.web.exceptions.NoStudySpecifiedError;
+
import org.cipres.treebase.NamespacedGUID;
import org.cipres.treebase.TreebaseIDString;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.TreebaseIDString.MalformedTreebaseIDString;
+import org.cipres.treebase.domain.study.Study;
+import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.web.Constants;
/**
@@ -58,6 +62,8 @@
public abstract class PhyloWSController implements Controller {
private static final long serialVersionUID = 1L;
private static String searchBase = "/treebase-web/search/";
+
+ private boolean redirectDownload = true;
/**
* Child classes return the display page for the focal type
@@ -108,7 +114,10 @@
// output format is something else, re-direct to download services
else {
- url = createDownloadUrl(tbID.getId(),serializationFormat,req);
+ url = createDownloadUrl(tbID.getId(),serializationFormat,req);
+ if (!redirectDownload) {
+ url = "/treebase-web/accessviolation.html";
+ }
}
}
@@ -122,6 +131,7 @@
res.sendError(HttpServletResponse.SC_NOT_FOUND, "Object not found: " + e.getMessage());
}
}
+
if ( ! TreebaseUtil.isEmpty(url) ) {
res.setContentType("text/plain");
@@ -274,5 +284,9 @@
super(message);
}
}
+
+ public void checkAccess(boolean isPublished) {
+ redirectDownload = isPublished;
+ }
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java 2011-11-30 20:48:02 UTC (rev 992)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSMatrixController.java 2011-12-02 20:12:15 UTC (rev 993)
@@ -40,9 +40,13 @@
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);
}
+
+ checkAccess(study.isPublished());
+
Map<String,String> params = new HashMap<String,String>();
params.put("id", ""+study.getId());
params.put("matrixid", ""+objectId);
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSStudyController.java 2011-11-30 20:48:02 UTC (rev 992)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSStudyController.java 2011-12-02 20:12:15 UTC (rev 993)
@@ -35,9 +35,13 @@
@Override
Map<String,String> getObjectQueryParameters(Long objectId) throws ObjectNotFoundException {
Study study = getStudyService().findByID(objectId);
+
if ( study == null ) {
throw new ObjectNotFoundException("Can't find study " + objectId);
- }
+ }
+
+ checkAccess(study.isPublished());
+
Map<String,String> params = new HashMap<String,String>();
params.put("id", ""+objectId);
return params;
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSTreeController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSTreeController.java 2011-11-30 20:48:02 UTC (rev 992)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSTreeController.java 2011-12-02 20:12:15 UTC (rev 993)
@@ -40,9 +40,13 @@
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);
}
+
+ checkAccess(study.isPublished());
+
Map<String,String> params = new HashMap<String,String>();
params.put("id",""+study.getId());
params.put("treeid", ""+objectId);
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-30 20:48:02 UTC (rev 992)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-12-02 20:12:15 UTC (rev 993)
@@ -82,19 +82,11 @@
<url-pattern>/search/study/anyObjectAsRDF.rdf</url-pattern>
</filter-mapping>
-
<filter-mapping>
<filter-name>CacheFilter</filter-name>
- <url-pattern>/search/study/summary.html</url-pattern>
- </filter-mapping>
-
-
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
<url-pattern>/search/downloadANexusFile.html</url-pattern>
</filter-mapping>
-
<filter-mapping>
<filter-name>CacheFilter</filter-name>
<url-pattern>/search/downloadAMatrix.html</url-pattern>
@@ -105,11 +97,6 @@
<url-pattern>/search/downloadATree.html</url-pattern>
</filter-mapping>
- <filter-mapping>
- <filter-name>CacheFilter</filter-name>
- <url-pattern>/search/downloadATree.html</url-pattern>
- </filter-mapping>
-
<!-- =================================================================== -->
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-30 20:48:02 UTC (rev 992)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-12-02 20:12:15 UTC (rev 993)
@@ -1,19 +1,10 @@
-<%@page import="java.util.Date" %>
-<%@page import="java.util.Calendar" %>
-<%@page import="java.text.SimpleDateFormat;" %>
<!-- HTTP 1.1 -->
<meta http-equiv="Cache-Control" content="no-store"/>
<!-- HTTP 1.0 -->
<meta http-equiv="Pragma" content="no-cache"/>
<!-- Prevents caching at the Proxy Server -->
-<% Calendar expires = Calendar.getInstance();
- expires.add(Calendar.DATE,7);
- SimpleDateFormat expiresFormat = new SimpleDateFormat("E, dd MMM yyyy kk:mm:ss");
- if (request.getRequestURI().equals("/treebase-web/search/study/summary.html")) {
-%><meta http-equiv="Expires" content="<%=expiresFormat.format(expires.getTime())%> GMT"/>
-<%}else {
-%><meta http-equiv="Expires" content="0"/>
-<% } %><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
+<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" />
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|
|
From: <hs...@us...> - 2011-11-30 20:48:08
|
Revision: 992
http://treebase.svn.sourceforge.net/treebase/?rev=992&view=rev
Author: hshyket
Date: 2011-11-30 20:48:02 +0000 (Wed, 30 Nov 2011)
Log Message:
-----------
Adding leading number for day in meta expires
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/meta.jsp
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-30 20:29:42 UTC (rev 991)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-30 20:48:02 UTC (rev 992)
@@ -8,7 +8,7 @@
<!-- Prevents caching at the Proxy Server -->
<% Calendar expires = Calendar.getInstance();
expires.add(Calendar.DATE,7);
- SimpleDateFormat expiresFormat = new SimpleDateFormat("E, d MMM yyyy kk:mm:ss");
+ SimpleDateFormat expiresFormat = new SimpleDateFormat("E, dd MMM yyyy kk:mm:ss");
if (request.getRequestURI().equals("/treebase-web/search/study/summary.html")) {
%><meta http-equiv="Expires" content="<%=expiresFormat.format(expires.getTime())%> GMT"/>
<%}else {
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|
|
From: <hs...@us...> - 2011-11-30 20:29:48
|
Revision: 991
http://treebase.svn.sourceforge.net/treebase/?rev=991&view=rev
Author: hshyket
Date: 2011-11-30 20:29:42 +0000 (Wed, 30 Nov 2011)
Log Message:
-----------
Adding expires header of 1 week to any search summary page
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/meta.jsp
Modified: trunk/treebase-web/src/main/webapp/common/meta.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-30 18:22:48 UTC (rev 990)
+++ trunk/treebase-web/src/main/webapp/common/meta.jsp 2011-11-30 20:29:42 UTC (rev 991)
@@ -1,3 +1,6 @@
+<%@page import="java.util.Date" %>
+<%@page import="java.util.Calendar" %>
+<%@page import="java.text.SimpleDateFormat;" %>
<!-- HTTP 1.1 -->
<meta http-equiv="Cache-Control" content="no-store"/>
<!-- HTTP 1.0 -->
@@ -3,6 +6,12 @@
<meta http-equiv="Pragma" content="no-cache"/>
<!-- Prevents caching at the Proxy Server -->
-<meta http-equiv="Expires" content="0"/>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
+<% Calendar expires = Calendar.getInstance();
+ expires.add(Calendar.DATE,7);
+ SimpleDateFormat expiresFormat = new SimpleDateFormat("E, d MMM yyyy kk:mm:ss");
+ if (request.getRequestURI().equals("/treebase-web/search/study/summary.html")) {
+%><meta http-equiv="Expires" content="<%=expiresFormat.format(expires.getTime())%> GMT"/>
+<%}else {
+%><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" />
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|
|
From: <hs...@us...> - 2011-11-30 18:22:55
|
Revision: 990
http://treebase.svn.sourceforge.net/treebase/?rev=990&view=rev
Author: hshyket
Date: 2011-11-30 18:22:48 +0000 (Wed, 30 Nov 2011)
Log Message:
-----------
Adding URL patterns for caching
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-28 15:43:15 UTC (rev 989)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-30 18:22:48 UTC (rev 990)
@@ -76,6 +76,40 @@
<filter-name>CacheFilter</filter-name>
<url-pattern>/search/downloadAStudy.html</url-pattern>
</filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/study/anyObjectAsRDF.rdf</url-pattern>
+ </filter-mapping>
+
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/study/summary.html</url-pattern>
+ </filter-mapping>
+
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadANexusFile.html</url-pattern>
+ </filter-mapping>
+
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadAMatrix.html</url-pattern>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadATree.html</url-pattern>
+ </filter-mapping>
+
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadATree.html</url-pattern>
+ </filter-mapping>
+
<!-- =================================================================== -->
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|
|
From: <hs...@us...> - 2011-11-28 15:43:26
|
Revision: 989
http://treebase.svn.sourceforge.net/treebase/?rev=989&view=rev
Author: hshyket
Date: 2011-11-28 15:43:15 +0000 (Mon, 28 Nov 2011)
Log Message:
-----------
Adding a read timeout when uBio takes too long to respond
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java 2011-11-23 21:43:54 UTC (rev 988)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java 2011-11-28 15:43:15 UTC (rev 989)
@@ -372,4 +372,6 @@
*/
Set<TaxonVariant> findTaxonVariantByName(String s);
+ boolean getuBioTimeOutError();
+
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java 2011-11-23 21:43:54 UTC (rev 988)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java 2011-11-28 15:43:15 UTC (rev 989)
@@ -6,6 +6,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.InterruptedIOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
@@ -52,18 +53,22 @@
private static final String NMBKID = "namebankID";
private static final String NAMESTR = "nameString";
private static final int TIMEOUT = 10000;
+ private static final int READTIMEOUT = 30000;
private static final String VALUETAG = "value";
private static final String DETAILSSERVICEURLPART = "http://www.ubio.org/browser/details.php?namebankID=";
private TaxonLabelHome mTaxonLabelHome;
private PhyloTreeHome mPhyloTreeHome;
private TaxonHome mTaxonHome;
+
+ private boolean muBioTimeOutError;
/**
* constructor.
*/
public TaxonLabelServiceImpl() {
super();
+ setuBioTimeOutError(false);
}
/**
@@ -459,7 +464,7 @@
booleanplaceholder bph = new booleanplaceholder();
longplaceholder lph = new longplaceholder();
TaxonVariant firstVariant = null;
-
+
// XXX 1. Turn label into tri- or binomial, no var./ex./etc.
testString = normalizeLabelString(pTaxonLabel.getTaxonLabel());
@@ -468,6 +473,9 @@
String result = getStringFromURL(taxonFinderFullURL, null, null);
// XXX 3. Process TaxonFinder result
+ if (getuBioTimeOutError()) {
+ return null;
+ }
if (result == null || result.indexOf(NMBKID) < 0 || result.indexOf(testString) < 0 || result.indexOf(NAMESTR) < 0) {
LOGGER.warn("Problem: uBio result is garbled or doesn't contain our testString");
return null;
@@ -755,6 +763,7 @@
URL url = new URL(urlString);
URLConnection urlconn = url.openConnection();
urlconn.setConnectTimeout(TIMEOUT);
+ urlconn.setReadTimeout(READTIMEOUT);
BufferedReader in = new BufferedReader(new InputStreamReader(urlconn.getInputStream()));
StringBuilder results = new StringBuilder();
String str;
@@ -780,7 +789,11 @@
return results.toString();
} catch (MalformedURLException mfe) {
mfe.printStackTrace();
- } catch (IOException ioe) {
+ } catch (InterruptedIOException iioe) {
+ iioe.printStackTrace();
+ setuBioTimeOutError(true);
+ }
+ catch (IOException ioe) {
ioe.printStackTrace();
}
return null;
@@ -808,6 +821,14 @@
}
return result.substring(start + 1, end);
}
+
+ public boolean getuBioTimeOutError() {
+ return muBioTimeOutError;
+ }
+
+ public void setuBioTimeOutError(Boolean pTimeOutError) {
+ muBioTimeOutError = pTimeOutError;
+ }
/**
* @return the taxonHome
@@ -1019,5 +1040,5 @@
@Override
public Class defaultResultClass() {
return TaxonLabel.class;
- }
+ }
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java 2011-11-23 21:43:54 UTC (rev 988)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java 2011-11-28 15:43:15 UTC (rev 989)
@@ -148,11 +148,20 @@
// no variants were found by uBio
if ( variant == null ) {
- ubioResultMessages.add(taxonlabel.getTaxonLabel() + " is **UNRECOGNIZED**.");
- ubioResultErrors.add(taxonlabel.getTaxonLabel()
- + " is **UNRECOGNIZED** try <a href=" + UBIOSEARCHTAXONLABEL
- + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
- + " target=_blank>UBIO</a> site.");
+ if (getTaxonLabelService().getuBioTimeOutError()) {
+ ubioResultMessages.add("uBio service was unavailable when checking " + taxonlabel.getTaxonLabel() + ".");
+ ubioResultErrors.add("uBio service was unavailable when checking " + taxonlabel.getTaxonLabel() +
+ " try <a href=" + UBIOSEARCHTAXONLABEL
+ + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
+ + " target=_blank>UBIO</a> site.");
+ }
+ else {
+ ubioResultMessages.add(taxonlabel.getTaxonLabel() + " is **UNRECOGNIZED**.");
+ ubioResultErrors.add(taxonlabel.getTaxonLabel()
+ + " is **UNRECOGNIZED** try <a href=" + UBIOSEARCHTAXONLABEL
+ + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
+ + " target=_blank>UBIO</a> site.");
+ }
}
// variants stored by uBio,TODO now check for homonyms
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|
|
From: <hs...@us...> - 2011-11-23 21:44:00
|
Revision: 988
http://treebase.svn.sourceforge.net/treebase/?rev=988&view=rev
Author: hshyket
Date: 2011-11-23 21:43:54 +0000 (Wed, 23 Nov 2011)
Log Message:
-----------
Missing leading slash in previous commit
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-23 21:40:13 UTC (rev 987)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-23 21:43:54 UTC (rev 988)
@@ -74,7 +74,7 @@
<filter-mapping>
<filter-name>CacheFilter</filter-name>
- <url-pattern>search/downloadAStudy.html</url-pattern>
+ <url-pattern>/search/downloadAStudy.html</url-pattern>
</filter-mapping>
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|
|
From: <hs...@us...> - 2011-11-23 21:40:19
|
Revision: 987
http://treebase.svn.sourceforge.net/treebase/?rev=987&view=rev
Author: hshyket
Date: 2011-11-23 21:40:13 +0000 (Wed, 23 Nov 2011)
Log Message:
-----------
Updating filter mapping for caching
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-22 20:38:26 UTC (rev 986)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-23 21:40:13 UTC (rev 987)
@@ -74,7 +74,7 @@
<filter-mapping>
<filter-name>CacheFilter</filter-name>
- <url-pattern>/search/downloadAStudy.html*</url-pattern>
+ <url-pattern>search/downloadAStudy.html</url-pattern>
</filter-mapping>
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|
|
From: <hs...@us...> - 2011-11-22 20:38:32
|
Revision: 986
http://treebase.svn.sourceforge.net/treebase/?rev=986&view=rev
Author: hshyket
Date: 2011-11-22 20:38:26 +0000 (Tue, 22 Nov 2011)
Log Message:
-----------
Adding OSCache with expiration time so that Apache can cache study downloads
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2011-11-18 22:22:51 UTC (rev 985)
+++ trunk/treebase-web/pom.xml 2011-11-22 20:38:26 UTC (rev 986)
@@ -419,6 +419,12 @@
</exclusion>
</exclusions>
</dependency>
+
+ <dependency>
+ <groupId>opensymphony</groupId>
+ <artifactId>oscache</artifactId>
+ <version>2.4.1</version>
+ </dependency>
</dependencies>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-18 22:22:51 UTC (rev 985)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-22 20:38:26 UTC (rev 986)
@@ -58,8 +58,26 @@
<listener>
<listener-class>net.bull.javamelody.SessionListener</listener-class>
</listener>
-
+
+ <filter>
+ <filter-name>CacheFilter</filter-name>
+ <filter-class>com.opensymphony.oscache.web.filter.CacheFilter</filter-class>
+ <init-param>
+ <param-name>expires</param-name>
+ <param-value>time</param-value>
+ </init-param>
+ <init-param>
+ <param-name>time</param-name>
+ <param-value>2592000</param-value> <!-- one month -->
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>CacheFilter</filter-name>
+ <url-pattern>/search/downloadAStudy.html*</url-pattern>
+ </filter-mapping>
+
+
<!-- =================================================================== -->
<!-- Declarations of JNDI Resources expected from the Tomcat container -->
<!-- =================================================================== -->
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|
|
From: <hs...@us...> - 2011-11-18 22:22:58
|
Revision: 985
http://treebase.svn.sourceforge.net/treebase/?rev=985&view=rev
Author: hshyket
Date: 2011-11-18 22:22:51 +0000 (Fri, 18 Nov 2011)
Log Message:
-----------
Removing RDF download functionality and links to RDF
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
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 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAMatrixController.java 2011-11-18 22:22:51 UTC (rev 985)
@@ -90,18 +90,18 @@
Study pStudy = ControllerUtil.findStudy(request, getStudyService());
Matrix matrix = getMatrixService().findByID(objectId);
TaxonLabelSet taxa = matrix.getTaxa();
- if ( getFormat(request) == FORMAT_NEXML ) {
+ if ( getFormat(request) == FORMAT_NEXML || getFormat(request) == FORMAT_RDF ) {
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
return getNexmlService().serialize(pNexusDataSet,getDefaultProperties(request),matrix.getStudy());
}
- else if ( getFormat(request) == FORMAT_RDF ) {
+ /*else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet pNexusDataSet = new NexusDataSet();
pNexusDataSet.getTaxonLabelSets().add(taxa);
pNexusDataSet.getMatrices().add(matrix);
return getRdfaService().serialize(pNexusDataSet,getDefaultProperties(request),matrix.getStudy());
- }
+ }*/
else { // FORMAT_NEXUS or none
StringBuilder matrixContent = new StringBuilder();
matrixContent.append("#NEXUS\n");
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAStudyController.java 2011-11-18 22:22:51 UTC (rev 985)
@@ -35,12 +35,12 @@
@Override
protected String getFileContent(long pStudyID, HttpServletRequest request) {
Study study = getStudyService().findByID(pStudyID);
- if ( getFormat(request) == FORMAT_NEXML ) {
+ if ( getFormat(request) == FORMAT_NEXML || getFormat(request) == FORMAT_RDF ) {
return getNexmlService().serialize(study,getDefaultProperties(request));
}
- else if ( getFormat(request) == FORMAT_RDF ) {
+ /*else if ( getFormat(request) == FORMAT_RDF ) {
return getRdfaService().serialize(study,getDefaultProperties(request));
- }
+ }*/
else {
StringBuilder builder = new StringBuilder();
builder.append("#NEXUS\n\n");
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeBlockController.java 2011-11-18 22:22:51 UTC (rev 985)
@@ -98,18 +98,18 @@
@Override
protected String getFileContent(long blockid, HttpServletRequest request) {
TreeBlock treeBlock = getPhyloTreeHome().findTreeBlockById(blockid);
- if ( getFormat(request) == FORMAT_NEXML ) {
+ if ( getFormat(request) == FORMAT_NEXML || getFormat(request) == FORMAT_RDF ) {
NexusDataSet nexusDataSet = new NexusDataSet();
nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
nexusDataSet.getTreeBlocks().add(treeBlock);
return getNexmlService().serialize(nexusDataSet,getDefaultProperties(request));
}
- else if ( getFormat(request) == FORMAT_RDF ) {
+ /*else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet nexusDataSet = new NexusDataSet();
nexusDataSet.getTaxonLabelSets().add(treeBlock.getTaxonLabelSet());
nexusDataSet.getTreeBlocks().add(treeBlock);
return getRdfaService().serialize(nexusDataSet,getDefaultProperties(request));
- }
+ }*/
else {
StringBuilder bldr = new StringBuilder("#NEXUS\n\n");
treeBlock.generateAFileDynamically(bldr);
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadATreeController.java 2011-11-18 22:22:51 UTC (rev 985)
@@ -89,7 +89,7 @@
tree = getPhyloTreeService().resurrect(tree);
TreeBlock enclosingTreeBlock = getPhyloTreeService().resurrect(tree.getTreeBlock());
TaxonLabelSet tls = getPhyloTreeService().resurrect(enclosingTreeBlock.getTaxonLabelSet());
- if ( getFormat(request) == FORMAT_NEXML ) {
+ if ( getFormat(request) == FORMAT_NEXML || getFormat(request) == FORMAT_RDF ) {
NexusDataSet nds = new NexusDataSet();
nds.getTaxonLabelSets().add(tls);
TreeBlock treeBlock = new TreeBlock();
@@ -98,7 +98,7 @@
nds.getTreeBlocks().add(treeBlock);
return getNexmlService().serialize(nds,getDefaultProperties(request),tree.getStudy());
}
- else if ( getFormat(request) == FORMAT_RDF ) {
+ /*else if ( getFormat(request) == FORMAT_RDF ) {
NexusDataSet nds = new NexusDataSet();
nds.getTaxonLabelSets().add(tls);
TreeBlock treeBlock = new TreeBlock();
@@ -106,7 +106,7 @@
treeBlock.addPhyloTree(tree);
nds.getTreeBlocks().add(treeBlock);
return getRdfaService().serialize(nds,getDefaultProperties(request),tree.getStudy());
- }
+ } */
else {
StringBuilder builder = new StringBuilder();
builder.append("#NEXUS\n\n");
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp 2011-11-18 22:22:51 UTC (rev 985)
@@ -58,12 +58,12 @@
<dc:format>text/plain</dc:format>
</item>
</c:if>
- <c:if test="${hasRdf}">
+<%-- <c:if test="${hasRdf}">
<item rdf:about="${baseURL}${phyloWSPath}?format=rdf">
<title>RDF file</title>
<link>${baseURL}${phyloWSPath}?format=rdf</link>
<description>An RDF/XML serialization of the resource</description>
<dc:format>application/rdf+xml</dc:format>
</item>
- </c:if>
+ </c:if> --%>
</rdf:RDF>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrices.jsp 2011-11-18 22:22:51 UTC (rev 985)
@@ -77,7 +77,7 @@
</a>
</display:column>
- <display:column
+ <%--<display:column
sortable="false"
class="iconColumn"
headerClass="iconColumn">
@@ -89,7 +89,7 @@
title="<fmt:message key="download.rdf"/>"
alt="<fmt:message key="download.rdf"/>"/>
</a>
- </display:column>
+ </display:column> --%>
<display:column
sortable="false"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/summary.jsp 2011-11-18 22:22:51 UTC (rev 985)
@@ -103,14 +103,15 @@
alt="<fmt:message key="download.nexml"/>"/>
NeXML
</a>
- <a href="${baseLink}?format=rdf">
+ <%
+ /* <a href="${baseLink}?format=rdf">
<img
class="iconButton"
src="<fmt:message key="icons.rdf"/>"
title="<fmt:message key="download.rdf"/>"
alt="<fmt:message key="download.rdf"/>"/>
RDF
- </a>
+ </a> */ %>
</li>
</ul>
<h3>BibTeX reference</h3>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2011-11-18 18:18:06 UTC (rev 984)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/trees.jsp 2011-11-18 22:22:51 UTC (rev 985)
@@ -77,7 +77,7 @@
</a>
</display:column>
- <display:column
+ <%--<display:column
sortable="false"
class="iconColumn"
headerClass="iconColumn">
@@ -89,7 +89,7 @@
title="<fmt:message key="download.rdf"/>"
alt="<fmt:message key="download.rdf"/>"/>
</a>
- </display:column>
+ </display:column> --%>
<display:column
sortable="false"
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|
From: <hs...@us...> - 2011-11-18 18:18:12
|
Revision: 984
http://treebase.svn.sourceforge.net/treebase/?rev=984&view=rev
Author: hshyket
Date: 2011-11-18 18:18:06 +0000 (Fri, 18 Nov 2011)
Log Message:
-----------
Setting systems-action-enabled to false until we get password protection for monitoring set up on the servers
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-18 17:29:17 UTC (rev 983)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-18 18:18:06 UTC (rev 984)
@@ -48,7 +48,7 @@
-->
<init-param>
<param-name>system-actions-enabled</param-name>
- <param-value>true</param-value>
+ <param-value>false</param-value>
</init-param>
</filter>
<filter-mapping>
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|
From: <hs...@us...> - 2011-11-18 17:29:23
|
Revision: 983
http://treebase.svn.sourceforge.net/treebase/?rev=983&view=rev
Author: hshyket
Date: 2011-11-18 17:29:17 +0000 (Fri, 18 Nov 2011)
Log Message:
-----------
Updating web.xml to have JavaMelody work
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-17 21:45:53 UTC (rev 982)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-18 17:29:17 UTC (rev 983)
@@ -37,6 +37,27 @@
<param-name>javax.servlet.jsp.jstl.fmt.fallbackLocale</param-name>
<param-value>en</param-value>
</context-param>
+
+ <filter>
+ <filter-name>monitoring</filter-name>
+ <filter-class>net.bull.javamelody.MonitoringFilter</filter-class>
+ <!-- Allows a user who can connect to the monitoring page to perform system-level actions such as:
+ * Run the Garbage Collector
+ * Invalidate HTTP sessions (individually and in bulk)
+ * Kill server threads
+ -->
+ <init-param>
+ <param-name>system-actions-enabled</param-name>
+ <param-value>true</param-value>
+ </init-param>
+ </filter>
+ <filter-mapping>
+ <filter-name>monitoring</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
+ <listener>
+ <listener-class>net.bull.javamelody.SessionListener</listener-class>
+ </listener>
<!-- =================================================================== -->
@@ -113,14 +134,7 @@
<filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
</filter>
- <filter>
- <filter-name>monitoring</filter-name>
- <filter-class>net.bull.javamelody.MonitoringFilter</filter-class>
- <init-param>
- <param-name>system-actions-enabled</param-name>
- <param-value>true</param-value>
- </init-param>
- </filter>
+
@@ -210,12 +224,8 @@
<filter-name>UrlRewriteFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
+
- <filter-mapping>
- <filter-name>monitoring</filter-name>
- <url-pattern>/*</url-pattern>
- </filter-mapping>
-
@@ -231,9 +241,6 @@
<listener>
<listener-class>net.sf.navigator.menu.MenuContextListener</listener-class>
</listener>
- <listener>
- <listener-class>net.bull.javamelody.SessionListener</listener-class>
- </listener>
<!-- listener>
<listener-class>org.cipres.treebase.web.listeners.EventListener</listener-class>
</listener -->
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|
From: <hs...@us...> - 2011-11-17 21:46:00
|
Revision: 982
http://treebase.svn.sourceforge.net/treebase/?rev=982&view=rev
Author: hshyket
Date: 2011-11-17 21:45:53 +0000 (Thu, 17 Nov 2011)
Log Message:
-----------
Updating the error message for when no study is found (and also handling no Taxa found). Adding JavaMelody monitoring system
Modified Paths:
--------------
trunk/treebase-web/pom.xml
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/pom.xml 2011-11-17 21:45:53 UTC (rev 982)
@@ -393,6 +393,33 @@
<version>1.0</version>
</dependency>
+<!-- javamelody-core -->
+ <dependency>
+ <groupId>net.bull.javamelody</groupId>
+ <artifactId>javamelody-core</artifactId>
+ <version>1.32.1</version>
+ </dependency>
+ <!-- itext, option to add PDF export -->
+ <dependency>
+ <groupId>com.lowagie</groupId>
+ <artifactId>itext</artifactId>
+ <version>2.1.7</version>
+ <exclusions>
+ <exclusion>
+ <artifactId>bcmail-jdk14</artifactId>
+ <groupId>bouncycastle</groupId>
+ </exclusion>
+ <exclusion>
+ <artifactId>bcprov-jdk14</artifactId>
+ <groupId>bouncycastle</groupId>
+ </exclusion>
+ <exclusion>
+ <artifactId>bctsp-jdk14</artifactId>
+ <groupId>bouncycastle</groupId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+
</dependencies>
</project>
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchSummaryController.java 2011-11-17 21:45:53 UTC (rev 982)
@@ -50,6 +50,7 @@
import org.cipres.treebase.web.util.AnalyzedDataComparator;
import org.cipres.treebase.web.util.ControllerUtil;
+import org.cipres.treebase.web.exceptions.NoStudySpecifiedError;
import org.springframework.validation.BindException;
import org.springframework.web.servlet.ModelAndView;
@@ -71,7 +72,6 @@
String defaultPage = null;
private static final Logger LOGGER = Logger.getLogger(SearchSummaryController.class);
- class NoStudySpecifiedError extends Error { }
class UnknownStudyError extends Error { }
class RestrictedStudyError extends Error { }
@@ -90,7 +90,7 @@
theStudy = null;
{
Long studyID = getIDParam(param, "id");
- if (studyID == null) { throw new NoStudySpecifiedError(); }
+ if (studyID == null) { throw new NoStudySpecifiedError("No study was found"); }
theStudy = getStudyService().findByID(studyID);
if (theStudy == null) { throw new UnknownStudyError(); }
LOGGER.debug("formBackingObject found study " + theStudy);
@@ -268,7 +268,17 @@
*/
private Long getIDParam(Map<String, String []> params, String paramName) {
String [] IDParam = params.get(paramName);
- return IDParam.length == 0 ? null : Long.parseLong(IDParam[0]);
+ if (IDParam == null || IDParam.length == 0) {
+ return null;
+ }
+ else {
+ try {
+ return Long.parseLong(IDParam[0]);
+ }
+ catch(Exception e) {
+ return null;
+ }
+ }
}
@Override
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java 2011-11-17 21:45:53 UTC (rev 982)
@@ -239,7 +239,7 @@
switch(namingAuthority) {
case TREEBASE :
LOGGER.debug("Going to search for TreeBASE IDs");
- if ( ! index.endsWith(".tb1") ) {
+ if (null != index && ! index.endsWith(".tb1") ) {
TreebaseIDString idstr;
try {
idstr = new TreebaseIDString(identifier, Taxon.class, true);
@@ -261,7 +261,7 @@
addMessage(request, "Ignoring malformed TreeBASE1 ID string '" + identifier + "', because: " + e.getMessage());
LOGGER.error("Couldn't parse legacy ID: "+e.getMessage());
}
- if ( null != tb1LegacyId && index.matches(".*taxonVariant.*") ) {
+ if ( null != tb1LegacyId && null != index && index.matches(".*taxonVariant.*") ) {
TaxonVariant tv = getTaxonHome().findVariantByTB1LegacyId(tb1LegacyId);
LOGGER.debug("Found taxon variant: " + tv.getId());
if ( null != tv.getTaxon() ) {
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/exceptions/NoStudySpecifiedError.java 2011-11-17 21:45:53 UTC (rev 982)
@@ -0,0 +1,19 @@
+
+package org.cipres.treebase.web.exceptions;
+
+/**
+ * EmptySubmissionException.java
+ *
+ * Created on Jun 7, 2006
+ * @author lcchan
+ *
+ */
+public class NoStudySpecifiedError extends RuntimeException {
+
+ /**
+ * Constructor.
+ */
+ public NoStudySpecifiedError(String s) {
+ super(s);
+ }
+}
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/errors/itemNotFound.jsp 2011-11-17 21:45:53 UTC (rev 982)
@@ -0,0 +1,3 @@
+<%@ include file="/common/taglibs.jsp" %>
+
+${requestScope.exception.message}
\ 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 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-11-17 21:45:53 UTC (rev 982)
@@ -1112,7 +1112,8 @@
<props>
<prop key="org.springframework.dao.DataAccessException">/errors/dataAccessFailure</prop>
<prop key="org.springframework.transaction.TransactionException">/errors/dataAccessFailure</prop>
- <prop key="org.cipres.treebase.web.exceptions.EmptyStudyException">/errors/studyAccessFailure</prop>
+ <prop key="org.cipres.treebase.web.exceptions.EmptyStudyException">/errors/studyAccessFailure</prop>
+ <prop key="org.cipres.treebase.web.exceptions.NoStudySpecifiedError">/errors/itemNotFound</prop>
</props>
</property>
</bean>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-16 17:08:00 UTC (rev 981)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2011-11-17 21:45:53 UTC (rev 982)
@@ -111,7 +111,17 @@
<filter>
<filter-name>UrlRewriteFilter</filter-name>
<filter-class>org.tuckey.web.filters.urlrewrite.UrlRewriteFilter</filter-class>
- </filter>
+ </filter>
+
+ <filter>
+ <filter-name>monitoring</filter-name>
+ <filter-class>net.bull.javamelody.MonitoringFilter</filter-class>
+ <init-param>
+ <param-name>system-actions-enabled</param-name>
+ <param-value>true</param-value>
+ </init-param>
+ </filter>
+
@@ -200,6 +210,12 @@
<filter-name>UrlRewriteFilter</filter-name>
<url-pattern>/*</url-pattern>
</filter-mapping>
+
+ <filter-mapping>
+ <filter-name>monitoring</filter-name>
+ <url-pattern>/*</url-pattern>
+ </filter-mapping>
+
@@ -215,6 +231,9 @@
<listener>
<listener-class>net.sf.navigator.menu.MenuContextListener</listener-class>
</listener>
+ <listener>
+ <listener-class>net.bull.javamelody.SessionListener</listener-class>
+ </listener>
<!-- listener>
<listener-class>org.cipres.treebase.web.listeners.EventListener</listener-class>
</listener -->
@@ -356,6 +375,10 @@
<exception-type>java.lang.Exception</exception-type>
<location>/WEB-INF/pages/errors/uncaughtException.jsp</location>
</error-page>
+ <error-page>
+ <exception-type>java.lang.Exception</exception-type>
+ <location>/WEB-INF/pages/errors/uncaughtException.jsp</location>
+ </error-page>
<!-- Internal Server Error -->
<error-page>
<error-code>500</error-code>
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