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From: <rv...@us...> - 2011-05-12 12:07:15
|
Revision: 841
http://treebase.svn.sourceforge.net/treebase/?rev=841&view=rev
Author: rvos
Date: 2011-05-12 12:07:09 +0000 (Thu, 12 May 2011)
Log Message:
-----------
implemented getter and setter for submissionService
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/service/search/SearchServiceImpl.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/search/SearchServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/search/SearchServiceImpl.java 2011-05-12 12:06:17 UTC (rev 840)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/search/SearchServiceImpl.java 2011-05-12 12:07:09 UTC (rev 841)
@@ -8,6 +8,7 @@
import org.cipres.treebase.domain.search.SearchService;
import org.cipres.treebase.domain.search.UnknownSearchResultsTypeError;
import org.cipres.treebase.domain.study.StudyService;
+import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.domain.taxon.TaxonLabelService;
import org.cipres.treebase.domain.tree.PhyloTreeService;
import org.cipres.treebase.service.AbstractService;
@@ -22,6 +23,7 @@
MatrixService matrixService;
PhyloTreeService phyloTreeService;
TaxonLabelService taxonLabelService;
+ SubmissionService mSubmissionService;
@SuppressWarnings("serial")
public class UnimplementedLayerException extends RuntimeException {
@@ -88,6 +90,14 @@
return null;
}
+ public SubmissionService getSubmissionService() {
+ return mSubmissionService;
+ }
+ public void setSubmissionService(SubmissionService submissionService) {
+ mSubmissionService = submissionService;
+ }
+
+
}
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|
|
From: <rv...@us...> - 2011-05-12 12:06:23
|
Revision: 840
http://treebase.svn.sourceforge.net/treebase/?rev=840&view=rev
Author: rvos
Date: 2011-05-12 12:06:17 +0000 (Thu, 12 May 2011)
Log Message:
-----------
added interface for findByPublicationDateRange
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java 2011-05-12 12:05:46 UTC (rev 839)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java 2011-05-12 12:06:17 UTC (rev 840)
@@ -3,6 +3,7 @@
import java.io.File;
import java.util.Collection;
+import java.util.Date;
import java.util.Set;
import org.cipres.treebase.domain.admin.UserRole.TBPermission;
@@ -125,6 +126,14 @@
String generateReconstructedNexusFile(Long pSubmissionId, String pFileName);
/**
+ * Find studies whose citation publication date is within the range
+ * @param from - a starting date
+ * @param until - a closing date
+ * @return
+ */
+ Collection<Study> findByPublicationDateRange(Date from, Date until);
+
+ /**
* Find studies whose text contains the keyword anywhere
* @param keyword - target word
* @return a collection of matching studies
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|
|
From: <rv...@us...> - 2011-05-12 12:05:52
|
Revision: 839
http://treebase.svn.sourceforge.net/treebase/?rev=839&view=rev
Author: rvos
Date: 2011-05-12 12:05:46 +0000 (Thu, 12 May 2011)
Log Message:
-----------
added interface for findByPublicationDateRange
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java 2011-05-12 12:05:19 UTC (rev 838)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java 2011-05-12 12:05:46 UTC (rev 839)
@@ -2,6 +2,7 @@
package org.cipres.treebase.domain.study;
import java.util.Collection;
+import java.util.Date;
import java.util.Set;
import org.cipres.treebase.domain.DomainHome;
@@ -108,4 +109,13 @@
* @author mjd 20080813
*/
Collection<Study> findByTaxonLabelName(String taxonLabel);
+
+ /**
+ * Find the studies that were published within the specified date range
+ * @param from
+ * @param until
+ * @return
+ */
+ Collection<Study> findByPublicationDateRange(Date from, Date until);
+
}
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|
|
From: <rv...@us...> - 2011-05-12 12:05:25
|
Revision: 838
http://treebase.svn.sourceforge.net/treebase/?rev=838&view=rev
Author: rvos
Date: 2011-05-12 12:05:19 +0000 (Thu, 12 May 2011)
Log Message:
-----------
tb:lastModifiedDate is now inserted as a study annotation in the NeXML output
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2011-05-12 12:04:32 UTC (rev 837)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Study.java 2011-05-12 12:05:19 UTC (rev 838)
@@ -27,7 +27,6 @@
import org.apache.log4j.Logger;
import org.cipres.treebase.Constants;
-import org.cipres.treebase.ContextManager;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.AbstractPersistedObject;
import org.cipres.treebase.domain.Annotation;
@@ -41,8 +40,6 @@
import org.cipres.treebase.domain.taxon.TaxonVariant;
import org.cipres.treebase.domain.tree.PhyloTree;
import org.cipres.treebase.domain.tree.TreeBlock;
-import org.hibernate.Session;
-import org.hibernate.SessionFactory;
import org.hibernate.annotations.BatchSize;
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -51,7 +48,6 @@
import org.hibernate.annotations.Index;
import org.hibernate.annotations.IndexColumn;
import org.jdom.Element;
-import org.nexml.model.Document;
@Entity
@Table(name = "STUDY")
@@ -722,6 +718,9 @@
if ( null != getReleaseDate() ) {
annotations.add(new Annotation(Constants.DCURI,"dc:date",getReleaseDate().toString()));
}
+ if ( null != getLastModifiedDate() ) {
+ annotations.add(new Annotation(Constants.TBTermsURI, "tb:lastModifiedDate", getLastModifiedDate().toString()));
+ }
if ( null != getSubmission() ) {
if ( null != getSubmission().getSubmitter() ) {
// annotations.add(new Annotation(Constants.DCURI,"dc:creator",getSubmission().getSubmitter().getPerson().getFullNameCitationStyle()));
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|
|
From: <rv...@us...> - 2011-05-12 12:04:38
|
Revision: 837
http://treebase.svn.sourceforge.net/treebase/?rev=837&view=rev
Author: rvos
Date: 2011-05-12 12:04:32 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Added getter and setter for submissionService
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchService.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchService.java 2011-05-12 12:03:54 UTC (rev 836)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/SearchService.java 2011-05-12 12:04:32 UTC (rev 837)
@@ -3,6 +3,7 @@
import org.cipres.treebase.domain.matrix.MatrixService;
import org.cipres.treebase.domain.study.StudyService;
+import org.cipres.treebase.domain.study.SubmissionService;
import org.cipres.treebase.domain.taxon.TaxonLabelService;
import org.cipres.treebase.domain.tree.PhyloTreeService;
import org.cipres.treebase.service.AbstractService;
@@ -14,6 +15,8 @@
public interface SearchService extends AbstractService {
public StudyService getStudyService();
public void setStudyService(StudyService studyService);
+ public SubmissionService getSubmissionService();
+ public void setSubmissionService(SubmissionService submissionService);
public PhyloTreeService getPhyloTreeService();
public void setPhyloTreeService(PhyloTreeService phyloTreeService);
public MatrixService getMatrixService();
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|
|
From: <rv...@us...> - 2011-05-12 12:04:00
|
Revision: 836
http://treebase.svn.sourceforge.net/treebase/?rev=836&view=rev
Author: rvos
Date: 2011-05-12 12:03:54 +0000 (Thu, 12 May 2011)
Log Message:
-----------
implemented findByPublicationDateRange
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java 2011-05-12 12:03:04 UTC (rev 835)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java 2011-05-12 12:03:54 UTC (rev 836)
@@ -3,6 +3,7 @@
import java.util.ArrayList;
import java.util.Collection;
+import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -12,6 +13,7 @@
import org.cipres.treebase.dao.AbstractDAO;
import org.cipres.treebase.domain.admin.Person;
import org.cipres.treebase.domain.admin.User;
+import org.cipres.treebase.domain.study.Citation;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.StudyCriteria;
import org.cipres.treebase.domain.study.StudyHome;
@@ -399,5 +401,18 @@
return studies;
}
+ public Collection<Study> findByPublicationDateRange(Date from, Date until) {
+ Query q = getSession().createQuery(
+ "from Citation where publishyear between :begin and :end");
+ q.setInteger("begin", from.getYear());
+ q.setInteger("end", until.getYear());
+ Collection<Citation> citations = q.list();
+ Set<Study> results = new HashSet<Study>();
+ for ( Citation citation : citations ) {
+ results.add(citation.getStudy());
+ }
+ return results;
+ }
+
}
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|
|
From: <rv...@us...> - 2011-05-12 12:03:10
|
Revision: 835
http://treebase.svn.sourceforge.net/treebase/?rev=835&view=rev
Author: rvos
Date: 2011-05-12 12:03:04 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Added submissionService parameter to the searchService bean configuration
Modified Paths:
--------------
trunk/treebase-core/src/main/resources/applicationContext-service.xml
Modified: trunk/treebase-core/src/main/resources/applicationContext-service.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-service.xml 2011-05-12 12:02:01 UTC (rev 834)
+++ trunk/treebase-core/src/main/resources/applicationContext-service.xml 2011-05-12 12:03:04 UTC (rev 835)
@@ -285,7 +285,8 @@
<property name="phyloTreeService" ref="phyloTreeService"/>
<property name="matrixService" ref="matrixService"/>
<property name="studyService" ref="studyService"/>
- <property name="taxonLabelService" ref="taxonLabelService"/>
+ <property name="taxonLabelService" ref="taxonLabelService"/>
+ <property name="submissionService" ref="submissionService"/>
</bean>
</property>
</bean>
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|
|
From: <rv...@us...> - 2011-05-12 12:02:07
|
Revision: 834
http://treebase.svn.sourceforge.net/treebase/?rev=834&view=rev
Author: rvos
Date: 2011-05-12 12:02:01 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Added stub to satisfy the interface
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java 2011-05-12 12:01:22 UTC (rev 833)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java 2011-05-12 12:02:01 UTC (rev 834)
@@ -362,6 +362,12 @@
// TODO Auto-generated method stub
return null;
}
+
+ public Collection<Study> findByPublicationDateRange(Date from,
+ Date until) {
+ // TODO Auto-generated method stub
+ return null;
+ }
}
}
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|
|
From: <rv...@us...> - 2011-05-12 12:01:28
|
Revision: 833
http://treebase.svn.sourceforge.net/treebase/?rev=833&view=rev
Author: rvos
Date: 2011-05-12 12:01:22 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Added test to make sure the submission service is properly assigned to the search service bean.
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/search/SearchResultsTest.java
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/search/SearchResultsTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/search/SearchResultsTest.java 2011-05-11 13:35:26 UTC (rev 832)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/search/SearchResultsTest.java 2011-05-12 12:01:22 UTC (rev 833)
@@ -51,6 +51,7 @@
assertNotNull(ssr.getSearchService());
assertNotNull(ssr.getSearchService().getStudyService());
assertNotNull(ssr.getStudyService());
+ assertNotNull(ssr.getSearchService().getSubmissionService());
assertNotNull(tsr.getSearchService());
assertNotNull(tsr.getSearchService().getPhyloTreeService());
assertNotNull(tsr.getPhyloTreeService());
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From: SourceForge.net <no...@so...> - 2011-05-12 03:08:55
|
Bugs item #3300808, was opened at 2011-05-11 23:08 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3300808&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: Submission notes can break javascript Initial Comment: Sometimes the yellow highlights do not show up on Tool Box items that have errors or have not been visited. Often editing the submission notes field solves the problem -- it looks as though extra return keys in the text are responsible for the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3300808&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-12 02:38:37
|
Bugs item #3267613, was opened at 2011-04-01 12:11 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3267613&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Downloading original file problem Initial Comment: TreeBASE retains the original uploaded NEXUS files so that users can see what the submitter originally uploaded. However, if a submitter uploads several files with exactly the same file name, only the oldest version is available for download. One solution is to prefix or suffix the file name with a time/date stamp, or a count (plus 1) of the number of files already uploaded. This will insure that each filename is unique and available for download. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3267613&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-12 02:37:34
|
Bugs item #3284494, was opened at 2011-04-11 10:17 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3284494&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: When too many trees are uploaded they cannot be deleted Initial Comment: Although the verbiage on our upload page (http://www.treebase.org/treebase-web/user/uploadFile.html) clearly states that submitters should limit the number of trees that they upload, they continue to ignore this warning. When 1000+ trees are uploaded the problem is twofold: (1) the user-experience is swamped by way too many trees for the same basic dataset, and (2) it is impossible to delete the trees, probably because of a database time-out. Let's implement two solutions: (1) only the first 30 trees from an incoming tree block will be parsed and stored -- the others ignored. (2) if possible, modify the delete-tree-block function (ie http://www.treebase.org/treebase-web/user/deleteATreeBlock.html?treeblockid=xyz) so that each time a tree inside this treeblock is deleted, the database does a commit. That way even if there is a time-out, the database won't completely rollback all the trees that were successfully deleted. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2011-05-11 22:37 Message: Let's just stick with solution (1), and then manually delete the existing uploads that have too many trees. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3284494&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-12 02:35:10
|
Bugs item #3291519, was opened at 2011-04-22 12:38 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3291519&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Charsets not tokenized and treeblocks not inked to taxa bloc Initial Comment: With regard's to Mark Holder's complaint (below), we need to ensure that the titles of charsets are properly tokenized (see /treebase/domain/matrix/UserDefinedCharSet.java) and that tree blocks properly reference the correct Taxon Block title using the "LINK TAXA" command. For the Link Taxa issue, the solution may be to edit line 229 in treebase/domain/tree/TreeBlock.java to add the following: pBuilder.append("\tLINK TAXA = " + StringUtil.tokenize(taxaTitle.replaceAll("Input|Output", "")) + ";").append(TreebaseUtil.LINESEP); ...which is the solution used on line 437 of treebase/domain/matrix/Matrix.java, and is somewhat similar to the solution on line 561 of treebase/domain/tree/PhyloTree.java For the LINK TAXA issue, the trick is to get the result of: http://purl.org/phylo/treebase/phylows/study/TB2:S2012?format=nexml To look like a fusion of these two files: http://treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=4172&id=2012 http://treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=4173&id=2012 On Apr 21, 2011, at 11:09 PM, Mark Holder wrote: >Hi, > I just downloaded S2012.nex (I can send it along if needed, but I > won't clutter your inboxes unless it is needed. The url is > http://purl.org/phylo/treebase/phylows/study/TB2:S2012 ). > > My NEXUS parser is choking on a couple of things: > 1. The names of the CHARSET commands in the SETS block have spaces, > but the names have not been "escaped" to convert them to single NEXUS > tokens. > > 2. There are multiple TAXA blocks but the TREES blocks do not use > the LINK command to disambiguate. Mesquite is smart enough to figure > out which TAXA block is correct. I suppose I could add taxa-block-detection > code to NCL (the NEXUS parsing library that I use), but it would > be much easier if TreeBase used LINK to clarify the connections. > > all the best, > Mark ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3291519&group_id=248804 |
|
From: <sfr...@us...> - 2011-05-11 13:35:36
|
Revision: 832
http://treebase.svn.sourceforge.net/treebase/?rev=832&view=rev
Author: sfrgpiel
Date: 2011-05-11 13:35:26 +0000 (Wed, 11 May 2011)
Log Message:
-----------
Slight fixes to the text
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-05-10 19:34:26 UTC (rev 831)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-05-11 13:35:26 UTC (rev 832)
@@ -7,13 +7,13 @@
<content tag="heading">Create New Submission</content>
<p>Please provide a brief title for your study. Usually this is the same title as the title of your pubication.</p>
<p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
- <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
+ <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:when>
<c:otherwise>
<content tag="heading">Update Submission</content>
<p>Please update the following submission information as needed.</p>
<p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
- <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
+ <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:otherwise>
</c:choose>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp 2011-05-10 19:34:26 UTC (rev 831)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/uploadFile.jsp 2011-05-11 13:35:26 UTC (rev 832)
@@ -25,10 +25,10 @@
<body id="submissions"/>
<p>Use the following form to upload your Nexus files for <b>submission ${studyMap['id']} - ${studyMap['name']}</b><br>
-Please limit the number of trees you upload for parsing to ~30, otherwise large numbers of trees resulting from the
+Please note that only the first ~30 trees will be parsed, otherwise large numbers of trees resulting from the
same analysis will overwhelm the user experience in TreeBASE's search interface with what are largely redundant trees.
-If you have a large number of trees, please either select a few preferred trees and upload those for parsing, or upload
-a consensus tree. For information on making large numbers of trees available to users, please see the help
+If you have a large number of trees, please put your preferred trees, or a consensus tree, within the first ~30
+trees in the tree block. For more information, please see the help
<a href="#" class="openHelp" onclick="openHelp('uploadFile')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>.</p>
<!--form method="post" enctype="multipart/form-data" onsubmit="setTimeout('queryStatus()', 200);"-->
<!-- Line above is needed to show the actal amount of data uploaded using Ajax -->
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|
From: <hs...@us...> - 2011-05-10 19:34:32
|
Revision: 831
http://treebase.svn.sourceforge.net/treebase/?rev=831&view=rev
Author: hshyket
Date: 2011-05-10 19:34:26 +0000 (Tue, 10 May 2011)
Log Message:
-----------
Adding in Link Taxa to Trees in Nexus file
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java
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 2011-05-05 20:31:14 UTC (rev 830)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/TreeBlock.java 2011-05-10 19:34:26 UTC (rev 831)
@@ -226,7 +226,7 @@
}
pBuilder.append("BEGIN TREES;\n");
pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
- //pBuilder.append(" LINK TAXA = " + StringUtil.tokenize(getTaxobLabelSetTitle()) + ";\n");
+ pBuilder.append(" LINK TAXA = " + StringUtil.tokenize(tlSet.getTitle().replaceAll("Input|Output", "")) + ";\n");
pBuilder.append(" TRANSLATE\n");
tlSet.buildTaxonWithLineNumber(pBuilder);
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From: SourceForge.net <no...@so...> - 2011-05-05 21:22:16
|
Bugs item #3295057, was opened at 2011-04-29 14:26 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3295057&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Session not set correctly when changing to readystate Initial Comment: When a submitter clicks on the "Change to Ready State" button (http://treebase-dev.nescent.org/treebase-web/user/readyState.html?submissionid=xxxxx) the Tool Box may o rmay not appear, and if it does appear it may not have the correct warning messages. This is because the session is not set properly -- ie it is not being set the way it is set for edit submission (http://treebase-dev.nescent.org/treebase-web/user/summary.html?id=xxxxxx). ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3295057&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-05 20:48:12
|
Bugs item #2992022, was opened at 2010-04-25 12:04 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: William Piel (sfrgpiel) Summary: Yikes when viewing 2164: UTF8 handling problem? Initial Comment: An error is thrown when users try to browse to S2164. This *may* be an issue with UTF8 character set rendering, seeing as this study is from Hungarian authors. http://www.treebase.org/treebase-web/search/study/summary.html?id=2164 Yikes! javax.servlet.jsp.el.ELException: An error occurred while getting property "bibtexReference" from an instance of class org.cipres.treebase.domain.study.ArticleCitation at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspx_meth_c_005fout_005f0(nav_jsp.java:285) at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspService(nav_jsp.java:89) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:584) at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:497) at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:965) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspService(summary_jsp.java:109) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2011-05-05 16:48 Message: I just tested the SQL fix with DEV, and it works: DELETE FROM citation_author WHERE citation_id = 2101 AND authors_person_id = 3971; ... and then: DELETE FROM person WHERE person_id = 3971; Now reintroduce the last author using the web page UI: Tímea Balázs t.b...@gm... ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-06-01 13:31 Message: This has nothing to do with UTF-8 handling. It's a database inconsistency: * in the person table, there's both an entry for "Balázs Tímea", person_id=3971 and for "Tímea Balázs", person_id=5609 * in the latter record, first and last name are in the correct order, but the author's email address is missing, and the author order index is 5, on a three-author paper. In the former record, the first and last name are switched around, but everything else is in the correct order. * here's my suggested fix: correct the name order in record 3971, purge record 5609 from person and from citation_author, i.e.: update person set firstname='Tímea', lastname='Balázs' where person_id=3971; delete from citation_author where authors_person_id=5609; delete from person where person_id=5609; ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-06-01 13:31 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-04-27 12:27 Message: Also test this with issue 2669366 ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-04-27 11:36 Message: This may indicate a larger problem with UTF8 handling. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&group_id=248804 |
|
From: <hs...@us...> - 2011-05-05 20:31:20
|
Revision: 830
http://treebase.svn.sourceforge.net/treebase/?rev=830&view=rev
Author: hshyket
Date: 2011-05-05 20:31:14 +0000 (Thu, 05 May 2011)
Log Message:
-----------
Fixing issue where menu was not displaying when choosing "Change to Ready State" if "Update Treebase Submission" had not been visited
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ReadyStateController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ReadyStateController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ReadyStateController.java 2011-05-05 19:43:04 UTC (rev 829)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ReadyStateController.java 2011-05-05 20:31:14 UTC (rev 830)
@@ -13,10 +13,13 @@
import org.springframework.web.bind.ServletRequestUtils;
import org.springframework.web.servlet.ModelAndView;
+import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.domain.admin.UserRole.TBPermission;
+import org.cipres.treebase.domain.study.ArticleCitation;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.study.StudyService;
import org.cipres.treebase.domain.study.SubmissionService;
+import org.cipres.treebase.web.util.ControllerUtil;
/**
* ReadyStateController.java
@@ -87,7 +90,47 @@
protected Object formBackingObject(HttpServletRequest request) throws ServletException {
String subid = ServletRequestUtils.getStringParameter(request, "submissionid", null);
+
+ String username = request.getRemoteUser();
+ Study study;
+ if (TreebaseUtil.isEmpty(subid)) {
+ study = ControllerUtil.findStudy(request, mStudyService);
+ LOGGER.info("setAuthorizationChecked(true)");
+ setAuthorizationChecked(true);// This is needed in case one is clicking at Summary
+ // link at the bottom of the menu list on the right hand
+ // side.
+ } else {
+ study = mStudyService.findBySubmissionID(Long.parseLong(subid));
+ }
+ if (!TreebaseUtil.isEmpty(subid)) {
+ TBPermission perm2 = getSubmissionService().getPermission(
+ username,
+ Long.parseLong(subid));
+ if (perm2 == TBPermission.WRITE || perm2 == TBPermission.READ_ONLY
+ || perm2 == TBPermission.SUBMITTED_WRITE) {
+ LOGGER.info("setAuthorizationChecked(true)");
+ setAuthorizationChecked(true);
+ } else {
+ LOGGER.info("setAuthorizationChecked(false)");
+ setAuthorizationChecked(false);
+ return new ArticleCitation();
+ }
+
+ ControllerUtil.saveStudy(request, study); // user has made selection
+ // Added by Madhu to set the session variables
+ if (study.isReady()) {
+ request.getSession().setAttribute("publicationState", "Ready");
+ } else if (study.isPublished()) {
+ request.getSession().setAttribute("publicationState", "Published");
+ } else {
+ request.getSession().setAttribute("publicationState", "NotReady");
+ }
+
+ } else {
+ request.getSession().setAttribute("publicationState", "NotReady");
+ }
+
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("VALUE OF SUBMISSION ID in FORM BACKING =" + subid);
}
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|
From: SourceForge.net <no...@so...> - 2011-05-05 20:16:30
|
Bugs item #3293398, was opened at 2011-04-26 19:57 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3293398&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Users can search on embargoed trees and matrices Initial Comment: Data that are not yet available to the public should not be searchable. This is working for Study ID 10381: if you search on study_id = 10381, you won't get any results. However, the matrices that belong to study 10381 are, in fact, searchable. For example, you can search on matrices 5123 and 5124, and you can search on trees 7581 and 7582. You can also search on the taxon "Melpomene firma", then click on the Trees tab and see that Tree 7582 is in the results set. Although it is true that if you try to download these trees and matrices, you can't do that -- it would be better if they did not even appear in the results set. Course, in adding this requirement that only non-embargoed data can be returned in the results of a query, we need to be cautious that this added search criterion does not sacrifice on performance. Once this is fixed in the interface, let's check that it's okay in the API. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3293398&group_id=248804 |
|
From: <sfr...@us...> - 2011-05-05 19:43:10
|
Revision: 829
http://treebase.svn.sourceforge.net/treebase/?rev=829&view=rev
Author: sfrgpiel
Date: 2011-05-05 19:43:04 +0000 (Thu, 05 May 2011)
Log Message:
-----------
Some minor edits as a result of feedback from the PRF board
Modified Paths:
--------------
trunk/treebase-web/src/main/resources/ApplicationResources.properties
trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2011-05-05 14:29:07 UTC (rev 828)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2011-05-05 19:43:04 UTC (rev 829)
@@ -79,7 +79,7 @@
nav.search=Search
nav.search.treebase=Search TreeBASE
nav.submit=Submit
-nav.dataman=NSF Data Management Plan
+nav.dataman=NSF Data Management
nav.stats=Stats
nav.referee=Referee
nav.urlapi= URL API
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-05-05 14:29:07 UTC (rev 828)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-05-05 19:43:04 UTC (rev 829)
@@ -33,8 +33,8 @@
<hr /></p>
<table width="100%" border="0">
<tr>
- <td width="50%" valign="top">Data storage contribution for sponsored research:</td>
- <td width="50%" valign="top">Alternatively, please consider a donation towards TreeBASE activities:</td>
+ <td width="50%" valign="top">Data storage fee for submissions resulting from sponsored research where TreeBASE provides added validation to help with data preparation and to ensure compliance with NSF directives:</td>
+ <td width="50%" valign="top">Alternatively, for sponsored research that had not budgeted for data sharing with TreeBASE, please consider making a voluntary donation:</td>
</tr>
<tr>
<td><form target="paypal" action="https://www.paypal.com/cgi-bin/webscr" method="post">
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-05-05 14:29:07 UTC (rev 828)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-05-05 19:43:04 UTC (rev 829)
@@ -5,11 +5,15 @@
<c:choose>
<c:when test="${empty study.submission.id}">
<content tag="heading">Create New Submission</content>
- <p>Please complete the following submission information </p>
+ <p>Please provide a brief title for your study. Usually this is the same title as the title of your pubication.</p>
+ <p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
+ <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:when>
<c:otherwise>
<content tag="heading">Update Submission</content>
- <p>Please update the following submission information </p>
+ <p>Please update the following submission information as needed.</p>
+ <p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
+ <p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:otherwise>
</c:choose>
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|
|
From: <hs...@us...> - 2011-05-05 14:29:14
|
Revision: 828
http://treebase.svn.sourceforge.net/treebase/?rev=828&view=rev
Author: hshyket
Date: 2011-05-05 14:29:07 +0000 (Thu, 05 May 2011)
Log Message:
-----------
Fixing issue where matrices and trees were appearing that had unpublished studies. This was happening after doing a taxa search and moving over to the matrix or tree search tabs.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TaxonSearchResults.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TaxonSearchResults.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TaxonSearchResults.java 2011-05-04 18:02:23 UTC (rev 827)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/search/TaxonSearchResults.java 2011-05-05 14:29:07 UTC (rev 828)
@@ -34,6 +34,17 @@
for (Taxon m : getResults()) {
matrices.addAll(getTaxonLabelService().findMatrices(m));
}
+
+ // XXX need to filter out orphaned matrices or matrices whose studies are unpublished
+ Collection<Matrix> orphanedMatrices = new HashSet<Matrix>();
+ for ( Matrix mat : matrices ) {
+ if ( mat.getStudy() == null || (mat.getStudy().isPublished() == false) ) {
+ orphanedMatrices.add(mat);
+ }
+ }
+
+ matrices.removeAll(orphanedMatrices);
+
return new MatrixSearchResults(matrices);
}
@@ -60,6 +71,17 @@
for (Taxon t : getResults()) {
trees.addAll(getTaxonLabelService().findTrees(t));
}
+
+ // XXX need to filter out orphaned matrices or matrices whose studies are unpublished
+ Collection<PhyloTree> orphanedTrees = new HashSet<PhyloTree>();
+ for ( PhyloTree tree : trees ) {
+ if (tree.getStudy() == null || (tree.getStudy().isPublished() == false)){
+ orphanedTrees.add(tree);
+ }
+ }
+
+ trees.removeAll(orphanedTrees);
+
return new TreeSearchResults(trees);
}
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From: <hs...@us...> - 2011-05-04 18:02:29
|
Revision: 827
http://treebase.svn.sourceforge.net/treebase/?rev=827&view=rev
Author: hshyket
Date: 2011-05-04 18:02:23 +0000 (Wed, 04 May 2011)
Log Message:
-----------
Updating matrix search so that no matrices appear whose studies are not published. Doing the same thing for tree search with the addition of not displaying any orphaned trees.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java 2011-05-03 19:21:24 UTC (rev 826)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java 2011-05-04 18:02:23 UTC (rev 827)
@@ -223,12 +223,12 @@
}
- // XXX need to filter out orphaned matrices
+ // XXX need to filter out orphaned matrices or matrices whose studies are unpublished
Collection<Matrix> orphanedMatrices = new HashSet<Matrix>();
for ( Matrix m : matches ) {
- if ( m.getStudy() == null ) {
+ if ( m.getStudy() == null || (m.getStudy().isPublished() == false) ) {
orphanedMatrices.add(m);
- }
+ }
}
matches.removeAll(orphanedMatrices);
return matches;
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java 2011-05-03 19:21:24 UTC (rev 826)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java 2011-05-04 18:02:23 UTC (rev 827)
@@ -14,6 +14,7 @@
import org.apache.log4j.Logger;
import org.cipres.treebase.TreebaseUtil;
import org.cipres.treebase.RangeExpression.MalformedRangeExpression;
+import org.cipres.treebase.domain.matrix.Matrix;
import org.cipres.treebase.domain.search.SearchResults;
import org.cipres.treebase.domain.search.SearchResultsType;
import org.cipres.treebase.domain.search.TreeSearchResults;
@@ -101,6 +102,16 @@
} else {
throw new Error("Unknown search button name '" + buttonName + "'");
}
+
+ // XXX need to filter out orphaned matrices or matrices whose studies are unpublished
+ Collection<PhyloTree> orphanedTrees = new HashSet<PhyloTree>();
+ for ( PhyloTree t : matches ) {
+ if (t.getStudy() == null || (t.getStudy().isPublished() == false)){
+ orphanedTrees.add(t);
+ }
+ }
+ matches.removeAll(orphanedTrees);
+
SearchResults<PhyloTree> newRes = intersectSearchResults(oldRes, new TreeSearchResults(matches),
new RequestMessageSetter(request), "No matching trees found");
saveSearchResults(request, newRes);
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From: SourceForge.net <no...@so...> - 2011-05-04 12:11:04
|
Bugs item #3293404, was opened at 2011-04-26 20:15 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3293404&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Row Segment Metadata not displaying properly Initial Comment: When the user wants to view some matrix row metadata, the lat/longs are not being displayed. e.g.: http://www.treebase.org/treebase-web/search/study/rowSegments.html?id=11020&matrixid=8689&matrixrowid=604519 ... should show the lat/long in addition to the locality. Also, how about we do something a little fancier, like if there is a lat long pair, offer a hyperlink to a Google map in a new window showing the point, or a hyperlink to a geohack like this: http://toolserver.org/~geohack/geohack.php?params=48.8583_N_2.2945_E Also, we really need a way to download all metadata at the level of the matrix. For example, when you are at this page: http://www.treebase.org/treebase-web/search/study/matrix.html?matrixid=8689&id=11020 There should be a button that says "Download all Row Segment Metadata" for this particular matrix (if this data exists). The button should result in a download some basic format, e.g. tab-separated text or CSV. (And here again is an opportunity to create a outlink to a Google maps page with all the points for the matrix displayed) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3293404&group_id=248804 |
|
From: <hs...@us...> - 2011-05-03 19:21:31
|
Revision: 826
http://treebase.svn.sourceforge.net/treebase/?rev=826&view=rev
Author: hshyket
Date: 2011-05-03 19:21:24 +0000 (Tue, 03 May 2011)
Log Message:
-----------
Fixing issue where Specimen Labels for Latitude and Longitude were not displaying properly. Also adding in Google Maps link to table with row segment data. Adding in functionality to download all row segment metadata if any row segment data exists.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/SpecimenLabel.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrix.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/rowSegments.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
Added Paths:
-----------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadRowSegmentDataController.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/SpecimenLabel.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/SpecimenLabel.java 2011-05-01 00:57:43 UTC (rev 825)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/SpecimenLabel.java 2011-05-03 19:21:24 UTC (rev 826)
@@ -217,7 +217,7 @@
@Transient
public String getLongitudeString() {
if (mLongitude == null) return "";
- else return abs(mLongitude) + mLongitude < 0 ? "S" : "N";
+ else return abs(mLongitude) + (mLongitude < 0 ? "S" : "N");
}
/**
@@ -245,7 +245,7 @@
@Transient
public String getLatitudeString() {
if (mLatitude == null) return "";
- else return abs(mLatitude) + mLatitude < 0 ? "W" : "E";
+ else return abs(mLatitude) + (mLatitude < 0 ? "W" : "E");
}
/**
Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadRowSegmentDataController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadRowSegmentDataController.java (rev 0)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadRowSegmentDataController.java 2011-05-03 19:21:24 UTC (rev 826)
@@ -0,0 +1,104 @@
+
+
+
+package org.cipres.treebase.web.controllers;
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.Map;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.mvc.Controller;
+
+import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.matrix.RowSegmentService;
+import org.cipres.treebase.web.util.WebUtil;
+
+
+/**
+ *
+ * @author Madhu
+ *
+ * Created on May 15, 2008
+ *
+ * For exporting the tab delimited row segment data for a particular matrix.
+ *
+ */
+public class DownloadRowSegmentDataController implements Controller {
+
+ private RowSegmentService mRowSegmentService;
+
+ /**
+ * @return the rowSegmentService
+ */
+ public RowSegmentService getRowSegmentService() {
+ return mRowSegmentService;
+ }
+
+ /**
+ * @param pRowSegmentService the rowSegmentService to set
+ */
+ public void setRowSegmentService(RowSegmentService pRowSegmentService) {
+ mRowSegmentService = pRowSegmentService;
+ }
+
+ public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
+ throws Exception {
+
+ Map<String,String []> param = request.getParameterMap();
+
+
+ //String matrixId = (String) request.getSession().getAttribute("MATRIX_ID");
+ String matrixId = param.get("matrixid")[0];
+ String data = null;
+ if (!TreebaseUtil.isEmpty(matrixId)) {
+ data = getRowSegmentService().generateRowSegmentTextTSV(Long.parseLong(matrixId));
+ }
+
+ String downloadDir = request.getSession().getServletContext().getRealPath(
+ TreebaseUtil.FILESEP + "RowSegmentDownload")
+ + TreebaseUtil.FILESEP + "temp_rowsegment";
+
+ String fileName = "RowSegmentData_" + matrixId + ".tsv";
+
+ File dirPath = new File(downloadDir);
+ if (!dirPath.exists()) {
+ dirPath.mkdirs();
+ }
+
+ String rowsegmentFile = downloadDir + TreebaseUtil.FILESEP + fileName;
+
+ try {
+
+ File file = new File(rowsegmentFile);
+ FileWriter out = new FileWriter(file);
+
+ out.write(data);
+
+ out.close();
+ // File did not exist and was created
+ // } else {
+ // File already exists
+ // }
+
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ WebUtil.downloadFile(response, downloadDir, fileName);
+
+ File rowFile = new File(rowsegmentFile);
+
+ if (rowFile.exists()) {
+ rowFile.delete();
+ }
+
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrix.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrix.jsp 2011-05-01 00:57:43 UTC (rev 825)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/matrix.jsp 2011-05-03 19:21:24 UTC (rev 826)
@@ -10,9 +10,10 @@
</c:url>
<c:url var="matricesURL" value="matrices.html">
<c:param name="id" value="${study.id}"/>
+</c:url>
+<c:url var="rowSegmentsTSV" value="rowSegmentsTSV.html">
+ <c:param name="matrixid" value="${matrix.id}" />
</c:url>
-
-
<title>Matrix ${matrix.id} of study ${study.id}</title>
<body id="s-matrix"/>
@@ -23,7 +24,19 @@
<c:if test="${ not empty matrix.description }">
<p><strong>Description</strong>: ${matrix.description}</p>
-</c:if>
+</c:if>
+
+<c:set var="rowSegmentCount" value="false" />
+
+<c:forEach var="row" items="${matrix.rowsReadOnly}" varStatus="status">
+ <c:if test="${fn:length(row.segmentsReadOnly) gt 0}">
+ <c:set var="rowSegmentCount" value="true" />
+ </c:if>
+</c:forEach>
+
+<c:if test="${rowSegmentCount}">
+ <a href="${rowSegmentsTSV}">Download all Row Segment Metadata</a>
+</c:if>
<h2>Rows</h2>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/rowSegments.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/rowSegments.jsp 2011-05-01 00:57:43 UTC (rev 825)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/rowSegments.jsp 2011-05-03 19:21:24 UTC (rev 826)
@@ -19,6 +19,7 @@
<c:param name="id" value="${study.id}" />
<c:param name="matrixid" value="${matrix.id}" />
</c:url>
+
<c:forEach var="row" items="${matrix.rowsReadOnly}" varStatus="status">
<c:if test="${row.id == matrixrow.id}">
<c:set var="rownum" value="${status.count}"/>
@@ -61,7 +62,28 @@
sortable="true"
style="text-align:left; font-family:Courier; width:20%;">
${seg.specimenInfo}
- </display:column>
+ </display:column>
+
+ <display:column title="Google Map"
+ style="text-align:left; font-family:Courier; width:20%;">
+ <c:if test="${not empty(seg.specimenLabel.latitude) && not empty(seg.specimenLabel.longitude)}">
+ <c:url var="googleMapURL" value="http://www.google.com/maps">
+ <c:param name="f" value="q" />
+ <c:param name="source" value="s_q" />
+ <c:param name="hl" value="en" />
+ <c:param name="geocode" value="" />
+ <c:param name="q" value="${seg.specimenLabel.latitude},${seg.specimenLabel.longitude}" />
+ <c:param name="sll" value="${seg.specimenLabel.latitude},${seg.specimenLabel.longitude}" />
+ <c:param name="aq" value="" />
+ <c:param name="sspn" value="0.199959,0.445976" />
+ <c:param name="ie" value="UTF8" />
+ <c:param name="z" value="16" />
+ </c:url>
+ <a href='<c:out value="${googleMapURL}"/>' target="_blank">View Map</a>
+ </c:if>
+ </display:column>
+
+
<%--
<display:column title="Segment data" property="segmentData"
sortable="false"
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-05-01 00:57:43 UTC (rev 825)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2011-05-03 19:21:24 UTC (rev 826)
@@ -254,6 +254,10 @@
<property name="phyloTreeService"><ref bean="phyloTreeService"></ref></property>
<property name="analysisService"><ref bean="analysisService"></ref></property>
<property name="taxonLabelService"><ref bean="taxonLabelService"></ref></property>
+ </bean>
+
+ <bean id="downloadRowSegmentDataController" class="org.cipres.treebase.web.controllers.DownloadRowSegmentDataController">
+ <property name="rowSegmentService"><ref bean="rowSegmentService"></ref></property>
</bean>
<!-- MultiActionController to display sumbissions by different criteria -->
@@ -1023,7 +1027,8 @@
<prop key="/search/study/matrix.html">searchSummaryController</prop>
<prop key="/search/study/analysis.html">searchSummaryController</prop>
<prop key="/search/study/taxa.html">searchSummaryController</prop>
- <prop key="/search/study/rowSegments.html">searchSummaryController</prop>
+ <prop key="/search/study/rowSegments.html">searchSummaryController</prop>
+ <prop key="/search/study/rowSegmentsTSV.html">downloadRowSegmentDataController</prop>
<prop key="/search/study/anyObjectAsRDF.rdf">anyObjectAsRDFController</prop>
<prop key="/search/searchResultsAsRDF.rdf">searchResultsAsRDFController</prop>
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|
|
From: <sfr...@us...> - 2011-05-01 00:57:51
|
Revision: 825
http://treebase.svn.sourceforge.net/treebase/?rev=825&view=rev
Author: sfrgpiel
Date: 2011-05-01 00:57:43 +0000 (Sun, 01 May 2011)
Log Message:
-----------
Additional modifications to the data management plan text
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-04-30 22:03:40 UTC (rev 824)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/dataMan.jsp 2011-05-01 00:57:43 UTC (rev 825)
@@ -4,26 +4,33 @@
<div class="gutter">
<h1>NSF Data Management Plan</h1>
-<p>To foster the sharing and dissemination of data produced by sponsored research, the National Science Foundation requires a data management plan for all proposals. At a minimum, these data consist of whatever is necessary to validate research findings by the scientific community, which includes (1) analyzed data, and metadata that (2) provide provenance and (3) define how the data were generated. </p>
-<h2>Data Ingest and Storage</h2>
-<p>The three kinds of data required by NSF are accepted by TreeBASE, whether submitted directly to TreeBASE or indirectly by way of <a href="http://datadryad.org/" target="_blank">Dryad</a>. For (1), we accept NEXUS character block data with datatypes standard, continuous, DNA, RNA, and protein, and non-reticulating phylogenetic trees with branch lengths and clade support values. For (2) we parse and store character labels and state labels in submitted NEXUS files and we map taxon labels to NCBI and uBio external taxonomies. Additionally, we accept the following metadata: museum specimen numbers in accordance with the Registry of Biological Repositories (<a href="http://www.biorepositories.org" target="_blank">RBR</a>), Genbank accession numbers, other accession numbers, and Darwin Core compatible specimen metadata: collecting date, collector, latitude/longitude, elevation, country, state, and locality. For (3), we store and share the original uploaded NEXUS files (including any program-specific command blocks that can define substitution models and search parameters) as well as offer metadata files in analysis description records for annotating software, algorithm, and commands used. TreeBASE only shares data that are linked to a manuscript that is accepted by a peer reviewed publication (e.g. journal article, reviewed book or book section, academic thesis accepted by a thesis committee, etc). </p>
+<p>To foster the sharing and dissemination of data produced by sponsored research, the National Science Foundation requires a data management plan for all proposals. The kinds of data that must be shared generally include whatever the scientific community needs to validate research findings. In particular, researchers must present a plan to share (1) analyzed data, (2) metadata that provide provenance information, and (3) metadata that describe how the data were generated. </p>
+<h2>Data Submission and Storage</h2>
+<p>For phylogenetics, the three kinds of data mentioned above and required by NSF are all accepted by TreeBASE, whether submitted directly to TreeBASE or indirectly by way of <a href="http://datadryad.org/" target="_blank">Dryad</a>. For data type (1), we accept NEXUS formatted data with characters of datatype standard, continuous, DNA, RNA, and protein, and non-reticulating phylogenetic trees with branch lengths and clade support values. For metadata type (2) we parse and store morphological character labels and state labels in submitted NEXUS files and we map taxon labels to NCBI and uBio external taxonomies. Additionally, we accept the following metadata: museum specimen numbers in accordance with the Registry of Biological Repositories (<a href="http://www.biorepositories.org" target="_blank">RBR</a>), Genbank accession numbers, other accession numbers, and Darwin Core compatible specimen metadata: collecting date, collector, latitude/longitude, elevation, country, state, and locality. For metadata type (3), we store and share the original uploaded NEXUS files (including any program-specific command blocks that can define substitution models and search parameters) as well as provide data entry fields to describe software, algorithm, and commands used. TreeBASE only shares data that are linked to a manuscript that is accepted by a peer reviewed publication (e.g. journal article, reviewed book or book section, or academic thesis approved by a thesis committee). </p>
<h2>Data Integrity and Verification</h2>
-<p>TreeBASE helps to certify data integrity by: (A) only accepting NEXUS data that are successfully parsed by a server-side headless version of <a href="http://mesquiteproject.org/" target="_blank">Mesquite</a>, (B) verifying that taxon labels in matrices and relevant trees are consistent, (C) verifying that data objects are not 'orphaned' (i.e. unlinked to an analysis), and (D) verifying that taxon labels are recognizable by biologists, spelled correctly, and mapped to external taxonomies whenever possible. TreeBASE provides a special advanced access URL for anonymous reviewers and referees to provide additional quality control. Although additional NSF requirements relating to provenance and how data were generated are not normally required or scrutinized by TreeBASE, submitters who flag their submission as NSF-sponsored data will receive special attention by our staff. In these cases, TreeBASE staff will check to make sure that provenance and analysis metadata are adequately provided, and, as needed, communicate with the submitter and assist in properly formatting and ingesting these data. </p>
+<p>TreeBASE helps to certify data integrity by: </p>
+<ul>
+ <li>Validating submitted NEXUS files by parsing them with <a href="http://mesquiteproject.org/" target="_blank">Mesquite</a> on the TreeBASE server</li>
+ <li>Verifying that taxon labels in matrices and relevant trees are consistent</li>
+ <li>Verifying that data objects are not 'orphaned' (i.e. unlinked to an analysis)</li>
+ <li>Verifying that taxon labels are recognizable by biologists, spelled correctly, and mapped to external taxonomies whenever possible</li>
+</ul>
+<p>TreeBASE provides an advanced access URL for anonymous reviewers and referees to provide additional quality control before the data are made public. Although additional NSF requirements relating to provenance and how data were generated are not normally required or scrutinized by TreeBASE staff, submitters who flag their submission (in the submission notes section) as NSF-sponsored data will receive special attention by our staff. In these cases, TreeBASE staff will check to make sure that provenance and analysis metadata are adequately provided, and, as needed, communicate with the submitter and assist in properly formatting and ingesting these data. </p>
<h2>Data Standards and Dissemination</h2>
-<p>TreeBASE plans to remain in compliance with the emerging, but still evolving, standard of Minimal Information for a Phylogenetic Analysis (<a href="http://www.nescent.org/sites/evoio/MIAPA" target="_blank">MIAPA</a>). In addition, TreeBASE publishes persistant and resolvable globally unique identifiers for all major data objects and disseminates data and metadata using commonly accepted standards. A Restful <a href="http://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS" target="_blank">PhyloWS</a> API exposes metadata using RSS feeds in RDF; a <a href="http://www.nexml.org/" target="_blank">NeXML</a> serialization exposes data marked up with metadata using published vocabularies and fully qualified URIs in compliance with <a href="http://linkeddata.org/" target="_blank">Linked Data</a> standards. Basic record metadata are published through an OIA-PMH service and records are mirrored by Dryad, which provides a secondary Dryad <a href="http://www.datacite.org" target="_blank">DataCite DOI</a>. However, for most people in the scientific community, data will be retrieved using the web user interface and downloaded in the NEXUS format, and metadata will be downloaded in tab-separated text format. </p>
+<p>TreeBASE plans to remain in compliance with the emerging, but still evolving, standard of Minimal Information for a Phylogenetic Analysis (<a href="http://www.nescent.org/sites/evoio/MIAPA" target="_blank">MIAPA</a>). In addition, TreeBASE publishes persistant and resolvable globally unique identifiers (GUIDs) for all major data objects and disseminates data and metadata using commonly accepted standards. A Restful <a href="http://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS" target="_blank">PhyloWS</a> API exposes metadata using RSS feeds in RDF; a <a href="http://www.nexml.org/" target="_blank">NeXML</a> serialization exposes data marked up with metadata using published vocabularies and fully qualified URIs in compliance with <a href="http://linkeddata.org/" target="_blank">Linked Data</a> standards. Basic record metadata are published through an OIA-PMH service, and TreeBASE records are mirrored by Dryad, which provides a secondary Dryad <a href="http://www.datacite.org" target="_blank">DataCite DOI</a>. However, for most people in the scientific community, data will be retrieved using the web user interface and downloaded in the NEXUS format, while metadata can be downloaded separately in a tab-separated text format. </p>
<h2>Data Persistance</h2>
-<p>Although no data service can guarantee indefinite persistance, TreeBASE will make every effort to preserve it services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specifies that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
+<p>Although no data service can guarantee indefinite persistance, TreeBASE will make every effort to preserve its services as long as possible. Additionally, the Articles of Incorporation of the <a href="http://www.phylofoundation.org" target="_blank">Phyloinformatics Research Foundation</a>, which oversees TreeBASE activities, specify that if dissolution is ever required the assets will be transferred to a similar entity with a comparable mission. </p>
<h2>Preparing a Data Management Plan for NSF</h2>
-<p>Scientists are welcome to designate TreeBASE as their selected repository and dissemination service for phylogenetic data generated by sponsored research. In this document, the following should be mentioned:</p>
+<p>Scientists are welcome to designate TreeBASE as their selected repository and dissemination service for phylogenetic data generated by sponsored research. In their Data Management Plan, we suggest that the following be mentioned:</p>
<ul>
- <li>Specify the name(s) of the person(s) responsible for preparing the data matrices, trees, and metadata for submission to TreeBASE.</li>
- <li>Identify the kinds of data that will be submitted, including provenance and analysis metadata as outlined above. For metadata not accepted by TreeBASE (e.g. digital images of specimens), identify other repositories where these will be stored (e.g. <a href="http://www.morphbank.net/" target="_blank">Morphbank</a> or <a href="http://www.morphobank.org/" target="_blank">Morphobank</a>), and indicate how these data objects will be linked between TreeBASE data and the other repository (e.g. using shared specimen catalog numbers). </li>
- <li>For your phylogenetic data, you can report that your data will be serialized using TreeBASE's data formats: NEXUS, for character and tree data alone, and NeXML for these data plus marked up with supplied metadata (e.g. basic Dublin Core publication data, basic Darwin Core specimen information, RBR collection codes and catalog numbers, uBio and NCBI taxon identification numbers, and Genbank accession numbers).</li>
- <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-reviewed publisher. TreeBASE will allow for 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 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 maximum reuse in accordance with community standards in phylogenetics. </li>
+ <li>Specify the name(s) of person(s) responsible for preparing the data matrices, trees, and metadata for submission to TreeBASE.</li>
+ <li>Identify the kinds of data that will be submitted, including provenance and analysis metadata as outlined above. For metadata not accepted by TreeBASE (e.g. digital images of specimens), identify other repositories where these will be stored (e.g. <a href="http://www.morphbank.net/" target="_blank">Morphbank</a> or <a href="http://www.morphobank.org/" target="_blank">Morphobank</a>), and indicate how entities in TreeBASE and in the other repository will be linked (e.g. using shared specimen catalog numbers). </li>
+ <li>For data standards, you can state that your data will be serialized using TreeBASE's data formats: NEXUS, for character and tree data alone, and NeXML for character and tree data with additional metadata (e.g. basic Dublin Core publication data, Darwin Core specimen information, RBR collection codes and catalog numbers, uBio and NCBI taxon identification numbers, and Genbank accession numbers).</li>
+ <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 $50 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 cost can be budgeted under publication expenses on your grant proposal's budget. </p>
-<p><hr /></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 overseas 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>
<td width="50%" valign="top">Data storage contribution for sponsored research:</td>
@@ -48,4 +55,5 @@
</tr>
</table>
+
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2011-04-30 22:03:40 UTC (rev 824)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2011-05-01 00:57:43 UTC (rev 825)
@@ -14,6 +14,7 @@
<li><a href="<c:url value="/reference.html"/>"><fmt:message key="nav.references"/></a></li>
</ul>
</li>
+ <li><a href="<c:url value="/dataMan.html"/>"><fmt:message key="nav.dataman"/></a></li>
<li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
<li><a href="<c:url value="/journal.html"/>"><fmt:message key="nav.journals"/></a></li>
<li><a href="<c:url value="/contact.html"/>"><fmt:message key="nav.contact"/></a></li>
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