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[Treebase-guts] SF.net SVN: treebase:[771] trunk/treebase-core/db/cleaning

From: <sfr...@us...> - 2011-01-19 19:59:08

Revision: 771
          http://treebase.svn.sourceforge.net/treebase/?rev=771&view=rev
Author:   sfrgpiel
Date:     2011-01-19 19:59:02 +0000 (Wed, 19 Jan 2011)

Log Message:
-----------
SQL for fixing the records where study.releasedate IS NULL.

Added Paths:
-----------
    trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/
    trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/README.txt
    trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/fix_releasedate.sql

Added: trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/README.txt	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/README.txt	2011-01-19 19:59:02 UTC (rev 771)
@@ -0,0 +1,16 @@
+To apply, execute the queries in fix_releasedate.sql
+
+--------
+
+Studies that lack a study.releasedate value fail to return a <pubDate> in the PhyloWS RSS, 
+and this causes Safari's RSS reader to subsitute this value with a last-checked timestamp. 
+The result is that these records appear to be new additions to the database, when in fact 
+they are quite old. The NULL values in study.releasedate is an artefact of the data migration 
+from TB1. Fix the releasedate and lastmodifieddate for studies that were migrated from TB1 
+by using the submission.createdate.
+
+To see how the effect, use Safari to compare the "fixed" data in treebase-dev:
+http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=dcterms.contributor=Huelsenbeck&format=rss1
+
+with the results from the same request on production here:
+http://purl.org/phylo/treebase/phylows/study/find?query=dcterms.contributor=Huelsenbeck&format=rss1

Added: trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/fix_releasedate.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/fix_releasedate.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2011-01-19_releasedate_fix/fix_releasedate.sql	2011-01-19 19:59:02 UTC (rev 771)
@@ -0,0 +1,38 @@
+-- Studies that lack a study.releasedate value fail to return 
+-- a <pubDate> in the PhyloWS RSS, and this causes Safari's 
+-- RSS reader to subsitute this value with a last-checked timestamp. 
+-- The result is that these records appear to be new additions
+-- to the database, when in fact they are quite old. The NULL 
+-- values in study.releasedate is an artefact of the data migration 
+-- from TB1. Fix the releasedate and lastmodifieddate for studies 
+-- that were migrated from TB1 by using the submission.createdate.
+
+-- To see how the effect, use Safari to compare the "fixed" data in treebase-dev:
+-- http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=dcterms.contributor=Huelsenbeck&format=rss1
+-- with the results from the same request on production here:
+-- http://purl.org/phylo/treebase/phylows/study/find?query=dcterms.contributor=Huelsenbeck&format=rss1
+
+-- Test to count the number of records with a NULL value in study.releasedate
+SELECT count(*) FROM study st LEFT JOIN submission sb USING (study_id) 
+WHERE st.studystatus_id = 3 
+AND st.releasedate IS NULL;
+
+-- should result in a largish number like "2282"
+
+begin work;
+
+UPDATE study SET releasedate = sb.createdate, lastmodifieddate = sb.createdate 
+FROM submission sb 
+WHERE study.studystatus_id = 3 
+AND study.releasedate IS NULL 
+AND study.study_id = sb.study_id 
+
+-- now let's check this again
+
+SELECT count(*) FROM study st LEFT JOIN submission sb USING (study_id) 
+WHERE st.studystatus_id = 3 
+AND st.releasedate IS NULL;
+
+-- result should be zero
+-- if so:
+commit;


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[Treebase-guts] SF.net SVN: treebase:[770] trunk/treebase-curation/S2493

From: <hs...@us...> - 2010-12-15 19:39:36

Revision: 770
          http://treebase.svn.sourceforge.net/treebase/?rev=770&view=rev
Author:   hshyket
Date:     2010-12-15 19:39:30 +0000 (Wed, 15 Dec 2010)

Log Message:
-----------
Renaming item to ensure that this file works on windows

Added Paths:
-----------
    trunk/treebase-curation/S2493/50-taxon, combined cpDNA-nrDNA

Removed Paths:
-------------
    trunk/treebase-curation/S2493/50-taxon, combined cpDNA:nrDNA

Copied: trunk/treebase-curation/S2493/50-taxon, combined cpDNA-nrDNA (from rev 769, trunk/treebase-curation/S2493/50-taxon, combined cpDNA:nrDNA)
===================================================================
--- trunk/treebase-curation/S2493/50-taxon, combined cpDNA-nrDNA	                        (rev 0)
+++ trunk/treebase-curation/S2493/50-taxon, combined cpDNA-nrDNA	2010-12-15 19:39:30 UTC (rev 770)
@@ -0,0 +1,152 @@

@@ Diff output truncated at 100000 characters. @@

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[Treebase-guts] SF.net SVN: treebase:[769] trunk/treebase-web/src/main/webapp/WEB-INF/pages /people.jsp

From: <sfr...@us...> - 2010-12-10 18:58:17

Revision: 769
          http://treebase.svn.sourceforge.net/treebase/?rev=769&view=rev
Author:   sfrgpiel
Date:     2010-12-10 18:58:11 +0000 (Fri, 10 Dec 2010)

Log Message:
-----------
Adding Harry, moving Youjun, redirecting PRF inc

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

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp	2010-12-10 18:56:12 UTC (rev 768)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp	2010-12-10 18:58:11 UTC (rev 769)
@@ -16,11 +16,6 @@
 					<br/>Deployment Maintainer
 				</td>
 				<td>
-					<img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
-					<br/><strong>Youjun Guo</strong>
-					<br/>Developer
-				</td>			
-				<td>
 					<img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
 					<br/><strong>Hilmar Lapp</strong>
 					<br/>Deployment Manager
@@ -32,18 +27,23 @@
 					<br/>Prototype Dev
 				</td>
 				<td>
-					<img src="http://www.treebase.org/treebase-web/images/people/jping.jpg" width="81" height="108" alt="Junli Ping"/>
+					<img src="images/people/jping.jpg" width="81" height="108" alt="Junli Ping"/>
 					<br/><strong>Junli Ping</strong>
 					<br/>Metadata Editor
 				</td>
-			</tr>
-			<tr>
 				<td>
-					<img src="http://www.treebase.org/treebase-web/images/people/mplaza.jpg" width="81" height="108" alt="Melanie Plaza"/>
+					<img src="images/people/mplaza.jpg" width="81" height="108" alt="Melanie Plaza"/>
 					<br/><strong>Melanie Plaza</strong>
 					<br/>Metadata Editor
 				</td>
+			</tr>
+			<tr>
 				<td>
+					<img src="images/people/hshyket.gif" width="81" height="108" alt="Harry Shyket"/>
+					<br/><strong>Harry Shyket</strong>
+					<br/>Developer
+				</td>
+				<td>
 					<img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
 					<br/><strong>Val Tannen</strong>
 					<br/>Development Leader
@@ -107,6 +107,11 @@
 			</td>
 		</tr>
 		<tr>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+					<br/><strong>Youjun Guo</strong>
+					<br/>Developer
+				</td>			
 			<td>
 				<img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
 				<br/><strong>Chris Henze</strong>
@@ -133,19 +138,43 @@
 				<br/><strong>Can van Tran</strong>
 				<br/>Developer
 			</td>
+		</tr>
+		<tr>
 			<td>
 				<img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
 				<br/><strong>Tracy Zhao</strong>
 				<br/>Developer
 			</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+					<br/><strong>Volunteeers?</strong>
+					<br/>Please sign up!
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+					<br/><strong>Volunteeers?</strong>
+					<br/>Please sign up!
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+					<br/><strong>Volunteeers?</strong>
+					<br/>Please sign up!
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+					<br/><strong>Volunteeers?</strong>
+					<br/>Please sign up!
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Volunteeers"/>
+					<br/><strong>Volunteeers?</strong>
+					<br/>Please sign up!
+				</td>
 		</tr>
 	</table>
 	
 	<h2>Phyloinformatics Research Foundation Inc, Board</h2>
 	<ul>
-		<li>Michael Donoghue</li>
-		<li>David Maddison</li>
-		<li>William Piel</li>
-		<li>Val Tannen</li>		
+		<li>See <a href="http://www.phylorf.org" title="Phyloinformatics Research Foundation Inc">here</a> for the list of officers and members of the board.</li>		
 	</ul>
 </div>
\ No newline at end of file


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[Treebase-guts] SF.net SVN: treebase:[768] trunk/treebase-web/src/main/webapp/images/people /hshyket.gif

From: <sfr...@us...> - 2010-12-10 18:56:18

Revision: 768
          http://treebase.svn.sourceforge.net/treebase/?rev=768&view=rev
Author:   sfrgpiel
Date:     2010-12-10 18:56:12 +0000 (Fri, 10 Dec 2010)

Log Message:
-----------
adding gif for Harry

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/people/hshyket.gif

Added: trunk/treebase-web/src/main/webapp/images/people/hshyket.gif
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/hshyket.gif
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


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[Treebase-guts] SF.net SVN: treebase:[767] trunk/treebase-web/src/main/webapp/WEB-INF/pages /about.jsp

From: <sfr...@us...> - 2010-12-08 17:36:44

Revision: 767
          http://treebase.svn.sourceforge.net/treebase/?rev=767&view=rev
Author:   sfrgpiel
Date:     2010-12-08 17:36:38 +0000 (Wed, 08 Dec 2010)

Log Message:
-----------
Update link to phylorf.org

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

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp	2010-12-08 17:28:29 UTC (rev 766)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp	2010-12-08 17:36:38 UTC (rev 767)
@@ -60,8 +60,8 @@
 		Computational Phylogenetics"). 
 	</p>
 	<p>
-		TreeBASE was released in March 2010 as one of the main products of The 
-		Phyloinformatics Research Foundation, Inc., a Connecticut non-profit 
+		TreeBASE was released in March 2010 as one of the main products of <a href="http://www.phylorf.org" title="Phyloinformatics Research Foundation, Inc.">The 
+		Phyloinformatics Research Foundation, Inc.</a>, a Connecticut non-profit 
 		corporation. The Foundation provides direction, governance, and continuity for 
 		software, data sharing, and communication standards to promote phyloinformatic 
 		research for the scientific community.


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[Treebase-guts] SF.net SVN: treebase:[766] trunk/treebase-web/src/main/webapp/WEB-INF/pages /urlAPI.jsp

From: <sfr...@us...> - 2010-12-08 17:28:35

Revision: 766
          http://treebase.svn.sourceforge.net/treebase/?rev=766&view=rev
Author:   sfrgpiel
Date:     2010-12-08 17:28:29 +0000 (Wed, 08 Dec 2010)

Log Message:
-----------
Added link to OAI-PMH wiki

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

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp	2010-12-06 19:09:26 UTC (rev 765)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp	2010-12-08 17:28:29 UTC (rev 766)
@@ -22,11 +22,12 @@
 			title="PhyloWS">PhyloWS</a> RESTful API. A detailed description
 			of <a href="https://sourceforge.net/apps/mediawiki/treebase/index.php?title=API"
 			title="TreeBASE's PhyloWS implementation">TreeBASE's PhyloWS
-			implementation</a> is at the TreeBASE wiki.
+			implementation</a> is on the TreeBASE wiki.
 		</li>
 		<li>
 			<a href="http://www.openarchives.org/pmh/" title="OAI-PMH">OAI-PMH</a>
-			harvesting interface, coming soon.
+			metadata harvesting interface is available, though under development. 
+			A detailed description is on the <a href="http://sourceforge.net/apps/mediawiki/treebase/index.php?title=OAI-PMH" title="OAI-PMH">TreeBASE wiki</a>.
 		</li>
 		<li>SQL data dumps, coming soon.</li>
 	</ul>


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[Treebase-guts] SF.net SVN: treebase:[765] trunk/treebase-web/src/main/webapp/WEB-INF/pages /journal.jsp

From: <sfr...@us...> - 2010-12-06 19:09:32

Revision: 765
          http://treebase.svn.sourceforge.net/treebase/?rev=765&view=rev
Author:   sfrgpiel
Date:     2010-12-06 19:09:26 +0000 (Mon, 06 Dec 2010)

Log Message:
-----------
Update of list of journals that require treebase submission

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

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2010-12-06 19:03:51 UTC (rev 764)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp	2010-12-06 19:09:26 UTC (rev 765)
@@ -99,6 +99,19 @@
 		</tr>
 		<tr>
 			<td>
+			<p><a href="http://www.blackwellpublishing.com/journal.asp?ref=0962-1083"> 
+			<img class="journal" src="images/journal_files/image021.jpg" alt="Molecular Ecology" /></a></p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
+				title="Find records in TreeBASE for articles published in Molecular Ecology">
+			<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22</a>
+			</p>
+			</td>
+		</tr>
+		<tr>
+			<td>
 			<p><a href="http://www.msafungi.org/"> 
 			<img class="journal" src="images/journal_files/image005.gif" alt="Mycologia" /></a></p>
 			</td>
@@ -226,6 +239,19 @@
 		</tr>
 		<tr>
 			<td>
+			<p><a href="http://currents.plos.org/treeoflife"><img
+				class="journal"
+				src="images/journal_files/image020.jpg" alt="PLoS Currents ToL"/></a></p>
+			</td>
+			<td>
+			<p><a
+				href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS+Currents:+Tree+of+Life%22"
+				title="Find records in TreeBASE for articles published in PLoS Currents: Tree of Life">
+			<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS+Currents:+Tree+of+Life%22</a></p>
+			</td>
+		</tr>
+		<tr>
+			<td>
 			<p><a href="http://www.rhodora.org/Rhodora.html"><img
 				class="journal"
 				src="images/journal_files/image014.gif" alt="Rhodora"/></a></p>
@@ -330,8 +356,6 @@
 		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Biology+and+Evolution%22"
 		title="Molecular Biology and Evolution">Molecular Biology and
 	Evolution</a>; <a
-		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Ecology%22"
-		title="Molecular Ecology">Molecular Ecology</a>; <a
 		href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular+Phylogenetics+and+Evolution%22"
 		title="Molecular Phylogenetics and Evolution">Molecular
 	Phylogenetics and Evolution</a>; <a


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[Treebase-guts] SF.net SVN: treebase:[764] trunk/treebase-web/src/main/webapp/images/ journal_files/image021.jpg

From: <sfr...@us...> - 2010-12-06 19:03:57

Revision: 764
          http://treebase.svn.sourceforge.net/treebase/?rev=764&view=rev
Author:   sfrgpiel
Date:     2010-12-06 19:03:51 +0000 (Mon, 06 Dec 2010)

Log Message:
-----------
New jpg for Molecular Ecology

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/journal_files/image021.jpg

Added: trunk/treebase-web/src/main/webapp/images/journal_files/image021.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image021.jpg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


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[Treebase-guts] SF.net SVN: treebase:[763] trunk/treebase-web/src/main/webapp/images/ journal_files/image020.jpg

From: <sfr...@us...> - 2010-12-06 18:43:05

Revision: 763
          http://treebase.svn.sourceforge.net/treebase/?rev=763&view=rev
Author:   sfrgpiel
Date:     2010-12-06 18:42:59 +0000 (Mon, 06 Dec 2010)

Log Message:
-----------
New jpg for PLoS Currents: ToL

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/images/journal_files/image020.jpg

Added: trunk/treebase-web/src/main/webapp/images/journal_files/image020.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/image020.jpg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


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[Treebase-guts] [ treebase-Bugs-3127413 ] confusing: progressive search + missing "discard" button

From: SourceForge.net <no...@so...> - 2010-12-04 15:03:31

Bugs item #3127413, was opened at 2010-12-04 10:03
Message generated for change (Tracker Item Submitted) made by astoltzfus
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3127413&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: APIs
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Arlin Stoltzfus (astoltzfus)
Assigned to: Nobody/Anonymous (nobody)
Summary: confusing: progressive search + missing "discard" button

Initial Comment:
I think the web-based search interface is misleading in a way that will frustrate users. The search is progressive, but this isn't advertised, and users are not accustomed to it. If a newbie issues a query, gets some results, and realizes from the results that she is searching for the wrong thing, then she is going to enter a new query value and try to search again. She'll see either a) a yellow warning bar saying "No matching studies found", followed by the list of studies that were found (in the previous query), or b) a result list that is only a subset of what she really wants, because its a subset of the earlier botched query.

This isn't an imaginary example. It happened to me when I first tried the new query interface. Then it happened to me again because I forgot what I had learned the first time.

I didn't see the "Discard all Results" button because I wasn't looking for it, and because its at the bottom of the list, which means that if you get more than 3 or 4 hits, its going to be below the browser pane and invisible.

I would suggest to make each search independent, i.e., clear the results with each new query, rather than using a progressive search. Alternatively, the messages could be more informative and the "discard" button could be put at the top of the list. In any case, it wouldn't hurt to widen the layout and abbreviate the titles so that the results list takes up less space.

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

You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3127413&group_id=248804

[Treebase-guts] [ treebase-Bugs-3116660 ] Dryad Import missing help popup

From: SourceForge.net <no...@so...> - 2010-11-23 15:09:19

Bugs item #3116660, was opened at 2010-11-23 07:09
Message generated for change (Tracker Item Submitted) made by ksclarke
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3116660&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: 5
Private: No
Submitted By: Kevin S. Clarke (ksclarke)
Assigned to: Nobody/Anonymous (nobody)
Summary: Dryad Import missing help popup

Initial Comment:
This was reported in Dryad's FogBugz, but it's a missing help message in TreeBASE.  See the attached screenshot.

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

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[Treebase-guts] [ treebase-Bugs-3089438 ] Find journal name in Dryad bagit metadata

From: SourceForge.net <no...@so...> - 2010-11-18 20:28:57

Bugs item #3089438, was opened at 2010-10-17 21:04
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
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including the initial issue submission, for this request,
not just the latest update.
Category: APIs
Group: None
>Status: Closed
Priority: 7
Private: No
Submitted By: Kevin S. Clarke (ksclarke)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: Find journal name in Dryad bagit metadata

Initial Comment:
Dryad returns to TreeBASE information about a submission in the bagit format.  This format contains a data/dryadpub.xml record that contains a metadata element with journal information.  The element is <bibo:Journal>  Bill Piel has mentioned that the TreeBASE side is not finding the journal information.  TreeBASE code needs to be updated to look in the data/dryadpub.xml record (after unpacking the bagit format) for this information.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-18 15:28

Message:
The data extraction code on the Treebase side was not aware of the
bibo=http://purl.org/ontology/bibo/ namespace. 
Instead, it was expecting
prism=http://prismstandard.org/namespaces/basic/2.0/

Moreover, it appears (at least on demo.dryad.org) that dryadpub.xml is not
yet fully implemented: 
  - <dc:creator> is duplicated in my submissions
  - <bibo:volume/> is empty, even though I have supplied one
  - none of these fields from the submission page propagated into XML:
DOI, journal number and year, keywords. 

As of SVN 761, I have fixed the immediate problem at hand (propagation of
the Journal name), as well as guessed (from the bibo spec and current usage
in dryadpub.xml) how the missing fields would be implemented and added code
to read them (untested). 


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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-18 15:28

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


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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:17

Message:
See
https://www.nescent.org/wg_dryad/TreeBASE_Submission_Integration#Progress_with_Handshaking_.28as_of_7-22-10.29
for how bagit submission works

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[Treebase-guts] SF.net SVN: treebase:[762] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/util

From: <vga...@us...> - 2010-11-18 19:55:52

Revision: 762
          http://treebase.svn.sourceforge.net/treebase/?rev=762&view=rev
Author:   vgapeyev
Date:     2010-11-18 19:55:46 +0000 (Thu, 18 Nov 2010)

Log Message:
-----------
Putative fix: accept "*.nex" as well as "*.nexus" files in Dryad submissions

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java	2010-11-18 19:20:00 UTC (rev 761)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java	2010-11-18 19:55:46 UTC (rev 762)
@@ -101,8 +101,6 @@
 			citation.setPages(pageStart.getText() + "-" + pageEnd.getText()); 
 //end VG 2010-11-18		
 		
-		
-		
 		List<Node> kl = getNodes(pkgRoot,"subject",dcterms);
 		String keywords="";
 		for(int i = 0; i<kl.size(); i++) {

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java	2010-11-18 19:20:00 UTC (rev 761)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/DryadUtil.java	2010-11-18 19:55:46 UTC (rev 762)
@@ -29,7 +29,8 @@
 			 
 			 File[] nexus = files[i].listFiles(new FilenameFilter() {
 		            public boolean accept(File file, String name) {
-		            boolean ret = (name.endsWith("nexus")); 
+		            boolean ret = name.endsWith("nexus")
+		            		   || name.endsWith("nex"); 
 		            return ret;
 		     }});
 			 


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[Treebase-guts] SF.net SVN: treebase:[761] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/util/CitationParser.java

From: <vga...@us...> - 2010-11-18 19:20:07

Revision: 761
          http://treebase.svn.sourceforge.net/treebase/?rev=761&view=rev
Author:   vgapeyev
Date:     2010-11-18 19:20:00 +0000 (Thu, 18 Nov 2010)

Log Message:
-----------
putative fix for SF:3089438 - extracting journal name from bagit metadata (need trebase-dev to test)

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java	2010-11-18 15:46:06 UTC (rev 760)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/CitationParser.java	2010-11-18 19:20:00 UTC (rev 761)
@@ -19,7 +19,10 @@
 	private static final Namespace xs = new Namespace("xs","http://www.w3.org/2001/XMLSchema");
 	private static final Namespace dwc= new Namespace("dwc", "http://rs.tdwg.org/dwc/terms/");
 	private static final Namespace dcterms= new Namespace("dcterms", "http://purl.org/dc/terms/");
-	private static final Namespace prism= new Namespace("prism", "http://prismstandard.org/namespaces/basic/2.0/");
+	
+	//VG 2010-11-18 fixing SF:3089438 - extracting journal name from bagit metadata
+	//-- private static final Namespace prism= new Namespace("prism", "http://prismstandard.org/namespaces/basic/2.0/");
+	private static final Namespace bibo = new Namespace("bibo", "http://purl.org/ontology/bibo/"); 
 
 	private Element pubRoot;
 	private Element pkgRoot;
@@ -66,7 +69,9 @@
 	    Node title = getNode(pubRoot,"title",dcterms);		
 	    if(title!=null)citation.setTitle(title.getText());
 		
-		Node issueIdentifier = getNode(pubRoot,"issueIdentifier",prism);		
+//VG 2010-11-18 fixing SF:3089438 - extracting journal name from bagit metadata
+/*--
+	    Node issueIdentifier = getNode(pubRoot,"issueIdentifier",prism);		
 		if(issueIdentifier!=null)citation.setIssue(issueIdentifier.getText());
 		
 		Node publicationName = getNode(pubRoot,"publicationName",prism);		
@@ -77,7 +82,27 @@
 		
 		Node pageRange = getNode(pubRoot,"pageRange",prism);		
 		if(pageRange!=null)citation.setPages(pageRange.getText());						
-	
+*/		
+		Node journal = getNode(pubRoot,"Journal",bibo);	
+		if (journal!=null) citation.setJournal(journal.getText());
+		
+		Node volume = getNode(pubRoot,"volume",bibo);		
+		if (volume!=null) citation.setVolume(volume.getText());		
+		
+		Node issue = getNode(pubRoot,"Issue",bibo);		
+		if (issue!=null) citation.setIssue(issue.getText());
+		
+		Node pages = getNode(pubRoot,"pages",bibo);		
+		Node pageStart = getNode(pubRoot,"pageStart",bibo);		
+		Node pageEnd = getNode(pubRoot,"pageEnd",bibo);	
+		if (pages != null) 
+			citation.setPages(pages.getText()); 
+		else if (pageStart != null && pageEnd != null) 
+			citation.setPages(pageStart.getText() + "-" + pageEnd.getText()); 
+//end VG 2010-11-18		
+		
+		
+		
 		List<Node> kl = getNodes(pkgRoot,"subject",dcterms);
 		String keywords="";
 		for(int i = 0; i<kl.size(); i++) {
@@ -103,8 +128,8 @@
 		}		
 		
 		try{
-		    int issue = Integer.parseInt(getNode(pubRoot,"issued",dcterms).getText());
-		    citation.setPublishYear(issue);			
+		    int issued = Integer.parseInt(getNode(pubRoot,"issued",dcterms).getText());
+		    citation.setPublishYear(issued);			
 		}catch(Exception e){
 			
 		}


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[Treebase-guts] [ treebase-Bugs-3079602 ] OAI records contain all subjects in a single field

From: SourceForge.net <no...@so...> - 2010-11-18 16:20:21

Bugs item #3079602, was opened at 2010-10-01 15:13
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&group_id=248804

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including the initial issue submission, for this request,
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Category: APIs
Group: None
>Status: Closed
Priority: 7
Private: No
Submitted By: Ryan Scherle (rscherle)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: OAI records contain all subjects in a single field

Initial Comment:
In the OAI records, each <dc:subject> field contains many keywords, separated by commas, like this:

<dc:subject>
Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution, lichens, multigene phylogeny, phylogenomics, plant pathogens, saprobes, Tree of Life
</dc:subject>

It is best practice to put each keyword into a separate <dc:subject> field. This allows harvesting systems (like Dryad) to accurately separate the keywords, and not worry about keywords that may contain commas.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-18 11:20

Message:
Fixed in SVN 760:  Treebase citation.keyword field is now split on both ','
and ';', with the results going into separate <dc:subject> elements.  

'in press' values will show up as <dc:subject>in press</dc:subject> --
this is awaiting Bill's data cleaning on production. 

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-18 11:20

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


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

Comment By: Kevin S. Clarke (ksclarke)
Date: 2010-11-03 15:13

Message:
This was my concern as well with my workaround Dryad code -- that there may
be repositories for whom the comma is significant and not a delimiter.  It
seems that if TreeBASE wants to store all these in one field it might be
good to prescribe that users use a semicolon as a delimiter (perhaps doing
a db cleanup on records that are currently using a comma).  Then the OAI
code could rely on the semicolon as the split to break the string into
separate metadata elements for output via OAI-PMH.

My code was very minimal for this just using a StringTokenizer(value,
";,")  cf. line 785 in
http://code.google.com/p/dryad/source/browse/trunk/dryad/dspace/modules/api/src/main/java/org/dspace/harvest/OAIHarvester.java

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:49

Message:
This is a request for clarification.  

Treebase UI offers a single field to enter keywords, text from which is
stored in a single field in the database.  From the data in treebase-dev I
see that users used ',' or ';' to separate multiple keywords. 

Here is what I can do: Get Kevin's keyword-splitting code and place it on
Treebase side, modifying if necessary to work with both ';' and ','.  This
would not work nicely if the user has a fancy to use comma-containing
keywords separated by semicolons, or the other way around. 

Please confirm that this is what is needed.  

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:49

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


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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:31

Message:
A few URLs that return records exhibiting the problem:
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1908
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s10013
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1122
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s994
Note  that some separate keywords with ',' while others with ';'

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:33

Message:
See https://www.nescent.org/wg_dryad/TreeBASE_OAI_Provider for examples of
URLs that return these OAI records. 

The record schema is at 
http://datadryad.org/profile/v3/dryad.xsd
Both data formats mentioned above formally conform to the schema, but the
best practice is to have several <dc:subject>  elements, one per term. 


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[Treebase-guts] SF.net SVN: treebase:[760] trunk/treebase-web/src/main

From: <vga...@us...> - 2010-11-18 15:46:13

Revision: 760
          http://treebase.svn.sourceforge.net/treebase/?rev=760&view=rev
Author:   vgapeyev
Date:     2010-11-18 15:46:06 +0000 (Thu, 18 Nov 2010)

Log Message:
-----------
Fixing SF:3079602 (multiple keywords into multiple <dc:subject> elements)

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
    trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java	2010-11-15 15:38:56 UTC (rev 759)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/OAIPMHController.java	2010-11-18 15:46:06 UTC (rev 760)
@@ -6,6 +6,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.StringTokenizer;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
@@ -233,8 +234,10 @@
 			 
 		
 			map.put("title", IdentifyUtil.escape4XML(study.getId(),citation.getTitle()));
-			map.put("creator", authors);			
-			map.put("subject", IdentifyUtil.escape4XML(study.getId(),citation.getKeywords()));
+			map.put("creator", authors);	
+			//VG 2010-11-17  fixing SF:3079602 (multiple keywords into multiple <dc:subject> elements)
+			//--map.put("subject", IdentifyUtil.escape4XML(study.getId(),citation.getKeywords()));
+			map.put("subject", splitKeywords(study.getId(),citation.getKeywords())); 
 		    if(study.getName()!=null&study.getNotes()!=null)			
 		    	map.put("description", IdentifyUtil.escape4XML(study.getId(),study.getName()+" "+study.getNotes()));
 		    else if(study.getNotes()==null)
@@ -263,6 +266,21 @@
 			return map;
 		}  
 		
+		//VG 2010-11-17  fixing SF:3079602 (multiple keywords into multiple <dc:subject> elements)
+		private List<String> splitKeywords(long study_id, String kwstring) {
+			List<String> kwlist = new java.util.ArrayList<String>(); 
+			if (null == kwstring) return kwlist; 
+			StringTokenizer tokenizer = new StringTokenizer(kwstring, ",;");
+			while (tokenizer.hasMoreTokens()) {
+				String token = tokenizer.nextToken().trim();               
+				if (!token.equals("")) {
+					kwlist.add(IdentifyUtil.escape4XML(study_id, token));
+				}
+			}	
+			return kwlist; 
+		}
+
+		
 		private List getRecordList(List<Submission> sList)
 		{
 			List recordList=new ArrayList<Map>();

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm	2010-11-15 15:38:56 UTC (rev 759)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/vmFiles/oai_dc_record.vm	2010-11-18 15:46:06 UTC (rev 760)
@@ -18,9 +18,18 @@
 <dc:creator>${person.lastName}, ${person.firstName}</dc:creator>
 #end 
 #end     
+## VG 2010-11-17  fixing SF:3079602 (multiple keywords into multiple <dc:subject> elements)
+#*--
 #if($record.subject)
 <dc:subject>${record.subject}</dc:subject> 
 #end 
+*#
+#if($record.subject)
+#foreach ($keyword in $record.subject)
+<dc:subject>${keyword}</dc:subject> 
+#end
+#end 
+## end VG 2010-11-17 
 #if($record.description)
 <dc:description>${record.description}</dc:description>
 #end 


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[Treebase-guts] [ treebase-Bugs-3089436 ] URL that is returned to Dryad should be treebase.org/...

From: SourceForge.net <no...@so...> - 2010-11-17 15:42:41

Bugs item #3089436, was opened at 2010-10-17 21:00
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3089436&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: APIs
Group: None
>Status: Closed
Priority: 7
Private: No
Submitted By: Kevin S. Clarke (ksclarke)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: URL that is returned to Dryad should be treebase.org/...

Initial Comment:
In the submission integration process between Dryad and TreeBASE, Dryad connects to TreeBASE at:

http://treebase.org/treebase-web

When a successful connection is made, TreeBASE returns a URL that is then passed to the Dryad user so s/he can complete the submission process at TreeBASE.  The URL that is being returned is currently:

http://treebase.nescent.org/treebase-web/login.jsp?importKey=KEY_GOES_HERE

We've heard from Bill Piel that this URL should be to treebase.org not treebase.nescent.org

Would you change the TreeBASE code (or server setup?) to return this URL?  Thanks.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-17 10:42

Message:
I hope this has been resolved after Jon adjusted JNDI config in PROD to
refer to www.treebase.org instead of treebase.nescent.org.  

This still better be tested by submitting through dryad-prod, but I'd
rather not mess with that myself. 

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-17 10:42

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


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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:19

Message:
See 
https://www.nescent.org/wg_dryad/TreeBASE_Submission_Integration#Progress_with_Handshaking_.28as_of_7-22-10.29
for the connection URL

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[Treebase-guts] SF.net SVN: treebase:[759] trunk/treebase-core/src/main/perl/lib

From: <rv...@us...> - 2010-11-15 15:39:05

Revision: 759
          http://treebase.svn.sourceforge.net/treebase/?rev=759&view=rev
Author:   rvos
Date:     2010-11-15 15:38:56 +0000 (Mon, 15 Nov 2010)

Log Message:
-----------
Adding DBIx::Class/Bio::Phylo adaptor classes

Added Paths:
-----------
    trunk/treebase-core/src/main/perl/lib/Bio/
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Algorithm.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysis.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysisstep.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analyzeddata.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancestralstate.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancstateset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Chargroup.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/ChargroupColrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charpartition.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharsetColrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweight.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharweightColrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweightset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citation.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationAuthor.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationEditor.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citationstatus.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CoderecordColrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Codonchar1Colrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Codonchar2Colrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Codonchar3Colrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CodonnoncodingColrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Codonpositionset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Columnrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CompoundElement.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/ContancstateValue.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Cstreenode.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Discretecharstate.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Distancematrixelement.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Gapmode.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Geneticcode.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Geneticcoderecord.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Geneticcodeset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Help.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Itemdefinition.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Itemvalue.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/LeftchangesetCharstate.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Matrix.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/MatrixItemdefinition.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Matrixcolumn.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/MatrixcolumnItemdefinition.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Matrixdatatype.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Matrixelement.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Matrixkind.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Matrixrow.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Nodeattribute.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Person.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Phylochar.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Phylotree.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Phylotreenode.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Polytcount.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/RightchangesetCharstate.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Rowsegment.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Software.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Statechangeset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Stateformat.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Statemodifier.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Stateset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Stepmatrixelement.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Study.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/StudyNexusfile.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Studystatus.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/SubMatrix.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/SubTaxonlabel.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/SubTreeblock.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Submission.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxon.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonauthority.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonlabel.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonlabelgroup.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/TaxonlabelgroupTaxonlabel.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonlabelpartition.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonlabelset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/TaxonlabelsetTaxonlabel.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonlink.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/TaxonsetTaxon.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Taxonvariant.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treeattribute.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treeblock.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treegroup.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/TreegroupPhylotree.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treekind.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treenodeedge.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treepartition.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treequality.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treeset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/TreesetPhylotree.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Treetype.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Typeset.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/User.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Userrole.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Usertype.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Usertyperecord.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/UsertyperrdColrange.pm
    trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE.pm

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Algorithm.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Algorithm.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Algorithm.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,188 @@
+package Bio::Phylo::TreeBASE::Result::Algorithm;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Algorithm
+
+=cut
+
+__PACKAGE__->table("algorithm");
+
+=head1 ACCESSORS
+
+=head2 type
+
+  data_type: 'char'
+  is_nullable: 0
+  size: 1
+
+=head2 algorithm_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'algorithm_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 description
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 2000
+
+=head2 propertyname
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 propertyvalue
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 usertype_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 gapmode_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 polytcount_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "type",
+  { data_type => "char", is_nullable => 0, size => 1 },
+  "algorithm_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "algorithm_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "description",
+  { data_type => "varchar", is_nullable => 1, size => 2000 },
+  "propertyname",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "propertyvalue",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "usertype_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "gapmode_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "polytcount_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("algorithm_id");
+
+=head1 RELATIONS
+
+=head2 gapmode
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Gapmode>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "gapmode",
+  "Bio::Phylo::TreeBASE::Result::Gapmode",
+  { gapmode_id => "gapmode_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 polytcount
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Polytcount>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "polytcount",
+  "Bio::Phylo::TreeBASE::Result::Polytcount",
+  { polytcount_id => "polytcount_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 usertype
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Usertype>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "usertype",
+  "Bio::Phylo::TreeBASE::Result::Usertype",
+  { usertype_id => "usertype_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 analysissteps
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Analysisstep>
+
+=cut
+
+__PACKAGE__->has_many(
+  "analysissteps",
+  "Bio::Phylo::TreeBASE::Result::Analysisstep",
+  { "foreign.algorithm_id" => "self.algorithm_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:wxKvAVkFQHMlQu7n/NcF/A
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysis.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysis.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysis.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,130 @@
+package Bio::Phylo::TreeBASE::Result::Analysis;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Analysis
+
+=cut
+
+__PACKAGE__->table("analysis");
+
+=head1 ACCESSORS
+
+=head2 analysis_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'analysis_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 name
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 notes
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 2000
+
+=head2 validated
+
+  data_type: 'boolean'
+  is_nullable: 1
+
+=head2 study_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 analysis_order
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "analysis_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "analysis_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "name",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "notes",
+  { data_type => "varchar", is_nullable => 1, size => 2000 },
+  "validated",
+  { data_type => "boolean", is_nullable => 1 },
+  "study_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "analysis_order",
+  { data_type => "integer", is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("analysis_id");
+
+=head1 RELATIONS
+
+=head2 study
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Study>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "study",
+  "Bio::Phylo::TreeBASE::Result::Study",
+  { study_id => "study_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 analysissteps
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Analysisstep>
+
+=cut
+
+__PACKAGE__->has_many(
+  "analysissteps",
+  "Bio::Phylo::TreeBASE::Result::Analysisstep",
+  { "foreign.analysis_id" => "self.analysis_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:tZ7CJ1RYuZPag7ntKKRKuA
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysisstep.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysisstep.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analysisstep.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,187 @@
+package Bio::Phylo::TreeBASE::Result::Analysisstep;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Analysisstep
+
+=cut
+
+__PACKAGE__->table("analysisstep");
+
+=head1 ACCESSORS
+
+=head2 analysisstep_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'analysisstep_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 commands
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 2000
+
+=head2 name
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 notes
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 2000
+
+=head2 algorithm_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 analysis_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 software_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 step_order
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "analysisstep_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "analysisstep_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "commands",
+  { data_type => "varchar", is_nullable => 1, size => 2000 },
+  "name",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "notes",
+  { data_type => "varchar", is_nullable => 1, size => 2000 },
+  "algorithm_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "analysis_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "software_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "step_order",
+  { data_type => "integer", is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("analysisstep_id");
+
+=head1 RELATIONS
+
+=head2 algorithm
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Algorithm>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "algorithm",
+  "Bio::Phylo::TreeBASE::Result::Algorithm",
+  { algorithm_id => "algorithm_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 analysis
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Analysis>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "analysis",
+  "Bio::Phylo::TreeBASE::Result::Analysis",
+  { analysis_id => "analysis_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 software
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Software>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "software",
+  "Bio::Phylo::TreeBASE::Result::Software",
+  { software_id => "software_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 analyzeddatas
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Analyzeddata>
+
+=cut
+
+__PACKAGE__->has_many(
+  "analyzeddatas",
+  "Bio::Phylo::TreeBASE::Result::Analyzeddata",
+  { "foreign.analysisstep_id" => "self.analysisstep_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:5AheD5cN0TdR+3kkdXGNzA
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analyzeddata.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analyzeddata.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Analyzeddata.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,166 @@
+package Bio::Phylo::TreeBASE::Result::Analyzeddata;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Analyzeddata
+
+=cut
+
+__PACKAGE__->table("analyzeddata");
+
+=head1 ACCESSORS
+
+=head2 type
+
+  data_type: 'char'
+  is_nullable: 0
+  size: 1
+
+=head2 analyzeddata_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'analyzeddata_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 input
+
+  data_type: 'boolean'
+  is_nullable: 1
+
+=head2 notes
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 2000
+
+=head2 treelength
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 analysisstep_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 matrix_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 phylotree_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "type",
+  { data_type => "char", is_nullable => 0, size => 1 },
+  "analyzeddata_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "analyzeddata_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "input",
+  { data_type => "boolean", is_nullable => 1 },
+  "notes",
+  { data_type => "varchar", is_nullable => 1, size => 2000 },
+  "treelength",
+  { data_type => "integer", is_nullable => 1 },
+  "analysisstep_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "matrix_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "phylotree_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("analyzeddata_id");
+
+=head1 RELATIONS
+
+=head2 matrix
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "matrix",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { matrix_id => "matrix_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 phylotree
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Phylotree>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "phylotree",
+  "Bio::Phylo::TreeBASE::Result::Phylotree",
+  { phylotree_id => "phylotree_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 analysisstep
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Analysisstep>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "analysisstep",
+  "Bio::Phylo::TreeBASE::Result::Analysisstep",
+  { analysisstep_id => "analysisstep_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:2JF1Q0rUjUer1dnLfetDRQ
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancestralstate.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancestralstate.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancestralstate.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,167 @@
+package Bio::Phylo::TreeBASE::Result::Ancestralstate;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Ancestralstate
+
+=cut
+
+__PACKAGE__->table("ancestralstate");
+
+=head1 ACCESSORS
+
+=head2 type
+
+  data_type: 'char'
+  is_nullable: 0
+  size: 1
+
+=head2 ancestralstate_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'ancestralstate_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 ancvalue
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 discretecharstate_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=head2 ancstateset_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "type",
+  { data_type => "char", is_nullable => 0, size => 1 },
+  "ancestralstate_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "ancestralstate_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "ancvalue",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "discretecharstate_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+  "ancstateset_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("ancestralstate_id");
+
+=head1 RELATIONS
+
+=head2 discretecharstate
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Discretecharstate>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "discretecharstate",
+  "Bio::Phylo::TreeBASE::Result::Discretecharstate",
+  { discretecharstate_id => "discretecharstate_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 ancstateset
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Ancstateset>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "ancstateset",
+  "Bio::Phylo::TreeBASE::Result::Ancstateset",
+  { ancstateset_id => "ancstateset_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 contancstate_values
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::ContancstateValue>
+
+=cut
+
+__PACKAGE__->has_many(
+  "contancstate_values",
+  "Bio::Phylo::TreeBASE::Result::ContancstateValue",
+  { "foreign.ancstate_id" => "self.ancestralstate_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 discretecharstates
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Discretecharstate>
+
+=cut
+
+__PACKAGE__->has_many(
+  "discretecharstates",
+  "Bio::Phylo::TreeBASE::Result::Discretecharstate",
+  { "foreign.ancestralstate_id" => "self.ancestralstate_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:0O8yGH1q0Ln7F26g24sJnA
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancstateset.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancstateset.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Ancstateset.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,123 @@
+package Bio::Phylo::TreeBASE::Result::Ancstateset;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Ancstateset
+
+=cut
+
+__PACKAGE__->table("ancstateset");
+
+=head1 ACCESSORS
+
+=head2 ancstateset_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'ancstateset_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 matrix_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "ancstateset_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "ancstateset_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "matrix_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("ancstateset_id");
+
+=head1 RELATIONS
+
+=head2 ancestralstates
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Ancestralstate>
+
+=cut
+
+__PACKAGE__->has_many(
+  "ancestralstates",
+  "Bio::Phylo::TreeBASE::Result::Ancestralstate",
+  { "foreign.ancstateset_id" => "self.ancstateset_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 matrix
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "matrix",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { matrix_id => "matrix_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 matrixes
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->has_many(
+  "matrixes",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { "foreign.ancstateset_id" => "self.ancstateset_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:rsUxLRGfJtShCHIB8eBgeg
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Chargroup.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Chargroup.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Chargroup.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,108 @@
+package Bio::Phylo::TreeBASE::Result::Chargroup;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Chargroup
+
+=cut
+
+__PACKAGE__->table("chargroup");
+
+=head1 ACCESSORS
+
+=head2 chargroup_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'chargroup_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 charpartition_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "chargroup_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "chargroup_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "charpartition_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("chargroup_id");
+
+=head1 RELATIONS
+
+=head2 charpartition
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Charpartition>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "charpartition",
+  "Bio::Phylo::TreeBASE::Result::Charpartition",
+  { charpartition_id => "charpartition_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 chargroup_colranges
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::ChargroupColrange>
+
+=cut
+
+__PACKAGE__->has_many(
+  "chargroup_colranges",
+  "Bio::Phylo::TreeBASE::Result::ChargroupColrange",
+  { "foreign.chargroup_id" => "self.chargroup_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:K4U0nWHRs+OHlRRhkls9Hg
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/ChargroupColrange.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/ChargroupColrange.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/ChargroupColrange.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,82 @@
+package Bio::Phylo::TreeBASE::Result::ChargroupColrange;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::ChargroupColrange
+
+=cut
+
+__PACKAGE__->table("chargroup_colrange");
+
+=head1 ACCESSORS
+
+=head2 chargroup_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 columnrange_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=cut
+
+__PACKAGE__->add_columns(
+  "chargroup_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "columnrange_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+);
+__PACKAGE__->add_unique_constraint("chargroup_colrange_columnrange_id_key", ["columnrange_id"]);
+
+=head1 RELATIONS
+
+=head2 columnrange
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Columnrange>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "columnrange",
+  "Bio::Phylo::TreeBASE::Result::Columnrange",
+  { columnrange_id => "columnrange_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+=head2 chargroup
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Chargroup>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "chargroup",
+  "Bio::Phylo::TreeBASE::Result::Chargroup",
+  { chargroup_id => "chargroup_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WiSPNuUGqOjPptjMQdNfiQ
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charpartition.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charpartition.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charpartition.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,108 @@
+package Bio::Phylo::TreeBASE::Result::Charpartition;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Charpartition
+
+=cut
+
+__PACKAGE__->table("charpartition");
+
+=head1 ACCESSORS
+
+=head2 charpartition_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'charpartition_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 matrix_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "charpartition_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "charpartition_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "matrix_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("charpartition_id");
+
+=head1 RELATIONS
+
+=head2 chargroups
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Chargroup>
+
+=cut
+
+__PACKAGE__->has_many(
+  "chargroups",
+  "Bio::Phylo::TreeBASE::Result::Chargroup",
+  { "foreign.charpartition_id" => "self.charpartition_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 matrix
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "matrix",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { matrix_id => "matrix_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:jbtbS33AWrZksTMRUJ11QQ
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charset.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charset.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charset.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,131 @@
+package Bio::Phylo::TreeBASE::Result::Charset;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Charset
+
+=cut
+
+__PACKAGE__->table("charset");
+
+=head1 ACCESSORS
+
+=head2 type
+
+  data_type: 'char'
+  is_nullable: 0
+  size: 1
+
+=head2 charset_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'charset_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 matrix_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "type",
+  { data_type => "char", is_nullable => 0, size => 1 },
+  "charset_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "charset_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "matrix_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("charset_id");
+
+=head1 RELATIONS
+
+=head2 matrix
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "matrix",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { matrix_id => "matrix_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 charset_colranges
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::CharsetColrange>
+
+=cut
+
+__PACKAGE__->has_many(
+  "charset_colranges",
+  "Bio::Phylo::TreeBASE::Result::CharsetColrange",
+  { "foreign.charset_id" => "self.charset_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 matrixes
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->has_many(
+  "matrixes",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { "foreign.charset_id" => "self.charset_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:U+TzYIJrXwUMX1B+DljwAQ
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharsetColrange.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharsetColrange.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharsetColrange.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,82 @@
+package Bio::Phylo::TreeBASE::Result::CharsetColrange;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::CharsetColrange
+
+=cut
+
+__PACKAGE__->table("charset_colrange");
+
+=head1 ACCESSORS
+
+=head2 charset_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 columnrange_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=cut
+
+__PACKAGE__->add_columns(
+  "charset_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "columnrange_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+);
+__PACKAGE__->add_unique_constraint("charset_colrange_columnrange_id_key", ["columnrange_id"]);
+
+=head1 RELATIONS
+
+=head2 columnrange
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Columnrange>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "columnrange",
+  "Bio::Phylo::TreeBASE::Result::Columnrange",
+  { columnrange_id => "columnrange_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+=head2 charset
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Charset>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "charset",
+  "Bio::Phylo::TreeBASE::Result::Charset",
+  { charset_id => "charset_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WqXcFABK83Yw6t8mWN5rig
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweight.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweight.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweight.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,122 @@
+package Bio::Phylo::TreeBASE::Result::Charweight;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Charweight
+
+=cut
+
+__PACKAGE__->table("charweight");
+
+=head1 ACCESSORS
+
+=head2 type
+
+  data_type: 'char'
+  is_nullable: 0
+  size: 1
+
+=head2 charweight_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'charweight_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 weight
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 realweight
+
+  data_type: 'double precision'
+  is_nullable: 1
+
+=head2 charweightset_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "type",
+  { data_type => "char", is_nullable => 0, size => 1 },
+  "charweight_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "charweight_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "weight",
+  { data_type => "integer", is_nullable => 1 },
+  "realweight",
+  { data_type => "double precision", is_nullable => 1 },
+  "charweightset_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("charweight_id");
+
+=head1 RELATIONS
+
+=head2 charweightset
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Charweightset>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "charweightset",
+  "Bio::Phylo::TreeBASE::Result::Charweightset",
+  { charweightset_id => "charweightset_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 charweight_colranges
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::CharweightColrange>
+
+=cut
+
+__PACKAGE__->has_many(
+  "charweight_colranges",
+  "Bio::Phylo::TreeBASE::Result::CharweightColrange",
+  { "foreign.charweight_id" => "self.charweight_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:zz3CjIbj/VAUeAqM9EKSQA
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharweightColrange.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharweightColrange.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CharweightColrange.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,82 @@
+package Bio::Phylo::TreeBASE::Result::CharweightColrange;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::CharweightColrange
+
+=cut
+
+__PACKAGE__->table("charweight_colrange");
+
+=head1 ACCESSORS
+
+=head2 charweight_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 columnrange_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=cut
+
+__PACKAGE__->add_columns(
+  "charweight_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "columnrange_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+);
+__PACKAGE__->add_unique_constraint("charweight_colrange_columnrange_id_key", ["columnrange_id"]);
+
+=head1 RELATIONS
+
+=head2 columnrange
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Columnrange>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "columnrange",
+  "Bio::Phylo::TreeBASE::Result::Columnrange",
+  { columnrange_id => "columnrange_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+=head2 charweight
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Charweight>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "charweight",
+  "Bio::Phylo::TreeBASE::Result::Charweight",
+  { charweight_id => "charweight_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:r6rX8xb3XGDWbPe4JjCiYw
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweightset.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweightset.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Charweightset.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,123 @@
+package Bio::Phylo::TreeBASE::Result::Charweightset;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Charweightset
+
+=cut
+
+__PACKAGE__->table("charweightset");
+
+=head1 ACCESSORS
+
+=head2 charweightset_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'charweightset_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 matrix_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "charweightset_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "charweightset_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "matrix_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("charweightset_id");
+
+=head1 RELATIONS
+
+=head2 charweights
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Charweight>
+
+=cut
+
+__PACKAGE__->has_many(
+  "charweights",
+  "Bio::Phylo::TreeBASE::Result::Charweight",
+  { "foreign.charweightset_id" => "self.charweightset_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 matrix
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "matrix",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { matrix_id => "matrix_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 matrixes
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Matrix>
+
+=cut
+
+__PACKAGE__->has_many(
+  "matrixes",
+  "Bio::Phylo::TreeBASE::Result::Matrix",
+  { "foreign.charweightset_id" => "self.charweightset_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:c7KqMIx7Y0mt/82fXyZv2Q
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citation.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citation.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citation.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,264 @@
+package Bio::Phylo::TreeBASE::Result::Citation;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::Citation
+
+=cut
+
+__PACKAGE__->table("citation");
+
+=head1 ACCESSORS
+
+=head2 type
+
+  data_type: 'char'
+  is_nullable: 0
+  size: 1
+
+=head2 citation_id
+
+  data_type: 'bigint'
+  is_auto_increment: 1
+  is_nullable: 0
+  sequence: 'citation_id_sequence'
+
+=head2 version
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 pmid
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 url
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 abstract
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 10000
+
+=head2 doi
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 keywords
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 pages
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 publishyear
+
+  data_type: 'integer'
+  is_nullable: 1
+
+=head2 published
+
+  data_type: 'boolean'
+  is_nullable: 1
+
+=head2 title
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 500
+
+=head2 issue
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 journal
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 volume
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 isbn
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 booktitle
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 city
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 publisher
+
+  data_type: 'varchar'
+  is_nullable: 1
+  size: 255
+
+=head2 citationstatus_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 1
+
+=cut
+
+__PACKAGE__->add_columns(
+  "type",
+  { data_type => "char", is_nullable => 0, size => 1 },
+  "citation_id",
+  {
+    data_type         => "bigint",
+    is_auto_increment => 1,
+    is_nullable       => 0,
+    sequence          => "citation_id_sequence",
+  },
+  "version",
+  { data_type => "integer", is_nullable => 1 },
+  "pmid",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "url",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "abstract",
+  { data_type => "varchar", is_nullable => 1, size => 10000 },
+  "doi",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "keywords",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "pages",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "publishyear",
+  { data_type => "integer", is_nullable => 1 },
+  "published",
+  { data_type => "boolean", is_nullable => 1 },
+  "title",
+  { data_type => "varchar", is_nullable => 1, size => 500 },
+  "issue",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "journal",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "volume",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "isbn",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "booktitle",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "city",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "publisher",
+  { data_type => "varchar", is_nullable => 1, size => 255 },
+  "citationstatus_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 1 },
+);
+__PACKAGE__->set_primary_key("citation_id");
+
+=head1 RELATIONS
+
+=head2 citationstatus
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Citationstatus>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "citationstatus",
+  "Bio::Phylo::TreeBASE::Result::Citationstatus",
+  { citationstatus_id => "citationstatus_id" },
+  {
+    is_deferrable => 1,
+    join_type     => "LEFT",
+    on_delete     => "CASCADE",
+    on_update     => "CASCADE",
+  },
+);
+
+=head2 citation_authors
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::CitationAuthor>
+
+=cut
+
+__PACKAGE__->has_many(
+  "citation_authors",
+  "Bio::Phylo::TreeBASE::Result::CitationAuthor",
+  { "foreign.citation_id" => "self.citation_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 citation_editors
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::CitationEditor>
+
+=cut
+
+__PACKAGE__->has_many(
+  "citation_editors",
+  "Bio::Phylo::TreeBASE::Result::CitationEditor",
+  { "foreign.citation_id" => "self.citation_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+=head2 studies
+
+Type: has_many
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Study>
+
+=cut
+
+__PACKAGE__->has_many(
+  "studies",
+  "Bio::Phylo::TreeBASE::Result::Study",
+  { "foreign.citation_id" => "self.citation_id" },
+  { cascade_copy => 0, cascade_delete => 0 },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:qDcoG/xxDv4e0sgMznZgWw
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationAuthor.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationAuthor.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationAuthor.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,89 @@
+package Bio::Phylo::TreeBASE::Result::CitationAuthor;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::CitationAuthor
+
+=cut
+
+__PACKAGE__->table("citation_author");
+
+=head1 ACCESSORS
+
+=head2 citation_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 authors_person_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 author_order
+
+  data_type: 'integer'
+  is_nullable: 0
+
+=cut
+
+__PACKAGE__->add_columns(
+  "citation_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "authors_person_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "author_order",
+  { data_type => "integer", is_nullable => 0 },
+);
+__PACKAGE__->set_primary_key("citation_id", "author_order");
+
+=head1 RELATIONS
+
+=head2 citation
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Citation>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "citation",
+  "Bio::Phylo::TreeBASE::Result::Citation",
+  { citation_id => "citation_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+=head2 authors_person
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Person>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "authors_person",
+  "Bio::Phylo::TreeBASE::Result::Person",
+  { person_id => "authors_person_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HFPvlcMUJ/i+CXW41Pqwrg
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationEditor.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationEditor.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/CitationEditor.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1,89 @@
+package Bio::Phylo::TreeBASE::Result::CitationEditor;
+
+# Created by DBIx::Class::Schema::Loader
+# DO NOT MODIFY THE FIRST PART OF THIS FILE
+
+use strict;
+use warnings;
+
+use base 'DBIx::Class::Core';
+
+
+=head1 NAME
+
+Bio::Phylo::TreeBASE::Result::CitationEditor
+
+=cut
+
+__PACKAGE__->table("citation_editor");
+
+=head1 ACCESSORS
+
+=head2 citation_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 editors_person_id
+
+  data_type: 'bigint'
+  is_foreign_key: 1
+  is_nullable: 0
+
+=head2 editor_order
+
+  data_type: 'integer'
+  is_nullable: 0
+
+=cut
+
+__PACKAGE__->add_columns(
+  "citation_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "editors_person_id",
+  { data_type => "bigint", is_foreign_key => 1, is_nullable => 0 },
+  "editor_order",
+  { data_type => "integer", is_nullable => 0 },
+);
+__PACKAGE__->set_primary_key("citation_id", "editor_order");
+
+=head1 RELATIONS
+
+=head2 citation
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Citation>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "citation",
+  "Bio::Phylo::TreeBASE::Result::Citation",
+  { citation_id => "citation_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+=head2 editors_person
+
+Type: belongs_to
+
+Related object: L<Bio::Phylo::TreeBASE::Result::Person>
+
+=cut
+
+__PACKAGE__->belongs_to(
+  "editors_person",
+  "Bio::Phylo::TreeBASE::Result::Person",
+  { person_id => "editors_person_id" },
+  { is_deferrable => 1, on_delete => "CASCADE", on_update => "CASCADE" },
+);
+
+
+# Created by DBIx::Class::Schema::Loader v0.07002 @ 2010-11-13 19:19:22
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7Ok5pELGYykNKOX9IgEvJQ
+
+
+# You can replace this text with custom content, and it will be preserved on regeneration
+1;

Added: trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citationstatus.pm
===================================================================
--- trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citationstatus.pm	                        (rev 0)
+++ trunk/treebase-core/src/main/perl/lib/Bio/Phylo/TreeBASE/Result/Citationstatus.pm	2010-11-15 15:38:56 UTC (rev 759)
@@ -0,0 +1...
 
[truncated message content]

[Treebase-guts] [ treebase-Bugs-3079602 ] OAI records contain all subjects in a single field

From: SourceForge.net <no...@so...> - 2010-11-03 19:13:53

Bugs item #3079602, was opened at 2010-10-01 12:13
Message generated for change (Comment added) made by ksclarke
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&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,
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Category: APIs
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Ryan Scherle (rscherle)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: OAI records contain all subjects in a single field

Initial Comment:
In the OAI records, each <dc:subject> field contains many keywords, separated by commas, like this:

<dc:subject>
Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution, lichens, multigene phylogeny, phylogenomics, plant pathogens, saprobes, Tree of Life
</dc:subject>

It is best practice to put each keyword into a separate <dc:subject> field. This allows harvesting systems (like Dryad) to accurately separate the keywords, and not worry about keywords that may contain commas.

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

Comment By: Kevin S. Clarke (ksclarke)
Date: 2010-11-03 12:13

Message:
This was my concern as well with my workaround Dryad code -- that there may
be repositories for whom the comma is significant and not a delimiter.  It
seems that if TreeBASE wants to store all these in one field it might be
good to prescribe that users use a semicolon as a delimiter (perhaps doing
a db cleanup on records that are currently using a comma).  Then the OAI
code could rely on the semicolon as the split to break the string into
separate metadata elements for output via OAI-PMH.

My code was very minimal for this just using a StringTokenizer(value,
";,")  cf. line 785 in
http://code.google.com/p/dryad/source/browse/trunk/dryad/dspace/modules/api/src/main/java/org/dspace/harvest/OAIHarvester.java

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 11:49

Message:
This is a request for clarification.  

Treebase UI offers a single field to enter keywords, text from which is
stored in a single field in the database.  From the data in treebase-dev I
see that users used ',' or ';' to separate multiple keywords. 

Here is what I can do: Get Kevin's keyword-splitting code and place it on
Treebase side, modifying if necessary to work with both ';' and ','.  This
would not work nicely if the user has a fancy to use comma-containing
keywords separated by semicolons, or the other way around. 

Please confirm that this is what is needed.  

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 11:49

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


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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 11:31

Message:
A few URLs that return records exhibiting the problem:
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1908
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s10013
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1122
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s994
Note  that some separate keywords with ',' while others with ';'

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 11:33

Message:
See https://www.nescent.org/wg_dryad/TreeBASE_OAI_Provider for examples of
URLs that return these OAI records. 

The record schema is at 
http://datadryad.org/profile/v3/dryad.xsd
Both data formats mentioned above formally conform to the schema, but the
best practice is to have several <dc:subject>  elements, one per term. 


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&group_id=248804

[Treebase-guts] [ treebase-Bugs-3079602 ] OAI records contain all subjects in a single field

From: SourceForge.net <no...@so...> - 2010-11-03 18:49:37

Bugs item #3079602, was opened at 2010-10-01 15:13
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&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: APIs
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Ryan Scherle (rscherle)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: OAI records contain all subjects in a single field

Initial Comment:
In the OAI records, each <dc:subject> field contains many keywords, separated by commas, like this:

<dc:subject>
Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution, lichens, multigene phylogeny, phylogenomics, plant pathogens, saprobes, Tree of Life
</dc:subject>

It is best practice to put each keyword into a separate <dc:subject> field. This allows harvesting systems (like Dryad) to accurately separate the keywords, and not worry about keywords that may contain commas.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:49

Message:
This is a request for clarification.  

Treebase UI offers a single field to enter keywords, text from which is
stored in a single field in the database.  From the data in treebase-dev I
see that users used ',' or ';' to separate multiple keywords. 

Here is what I can do: Get Kevin's keyword-splitting code and place it on
Treebase side, modifying if necessary to work with both ';' and ','.  This
would not work nicely if the user has a fancy to use comma-containing
keywords separated by semicolons, or the other way around. 

Please confirm that this is what is needed.  

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:49

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


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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:31

Message:
A few URLs that return records exhibiting the problem:
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1908
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s10013
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1122
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s994
Note  that some separate keywords with ',' while others with ';'

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:33

Message:
See https://www.nescent.org/wg_dryad/TreeBASE_OAI_Provider for examples of
URLs that return these OAI records. 

The record schema is at 
http://datadryad.org/profile/v3/dryad.xsd
Both data formats mentioned above formally conform to the schema, but the
best practice is to have several <dc:subject>  elements, one per term. 


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&group_id=248804

[Treebase-guts] [ treebase-Bugs-3079602 ] OAI records contain all subjects in a single field

From: SourceForge.net <no...@so...> - 2010-11-03 18:31:26

Bugs item #3079602, was opened at 2010-10-01 15:13
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&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: APIs
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Ryan Scherle (rscherle)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: OAI records contain all subjects in a single field

Initial Comment:
In the OAI records, each <dc:subject> field contains many keywords, separated by commas, like this:

<dc:subject>
Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution, lichens, multigene phylogeny, phylogenomics, plant pathogens, saprobes, Tree of Life
</dc:subject>

It is best practice to put each keyword into a separate <dc:subject> field. This allows harvesting systems (like Dryad) to accurately separate the keywords, and not worry about keywords that may contain commas.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-11-03 14:31

Message:
A few URLs that return records exhibiting the problem:
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1908
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s10013
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1122
http://127.0.0.1:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s994
Note  that some separate keywords with ',' while others with ';'

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:33

Message:
See https://www.nescent.org/wg_dryad/TreeBASE_OAI_Provider for examples of
URLs that return these OAI records. 

The record schema is at 
http://datadryad.org/profile/v3/dryad.xsd
Both data formats mentioned above formally conform to the schema, but the
best practice is to have several <dc:subject>  elements, one per term. 


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&group_id=248804

[Treebase-guts] [ treebase-Bugs-3101147 ] Phylows uses wrong version of Phylowidget

From: SourceForge.net <no...@so...> - 2010-11-02 00:34:13

Bugs item #3101147, was opened at 2010-11-01 20:34
Message generated for change (Tracker Item Submitted) made by sfrgpiel
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3101147&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Phylows uses wrong version of Phylowidget

Initial Comment:
When a tree is viewed from the search/browse web page, the link causes the latest build of Phylowidget to launch from the phylowidget.org website, e.g.:

http://www.phylowidget.org/full/?tree='http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr1000'

This results in an instance of a fully-feathured Phylowidget, and usually performs well. By contrast, when a tree is viewed from /phylows/, it causes a special (but older) copy of Phylowidget to launch, (a) which has fewer features, but (b) also has features for saving modified trees back to the database. For example:

http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1000?format=html

This is not ideal because this older version of Phylowidget is buggy, and the added "Save to database" might be a security hole. Better to have it behave like the other link, or alternatively, use some other viewer altogether (e.g. jsPhyloSVG). 




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

You can respond by visiting: 
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[Treebase-guts] [ treebase-Bugs-3079602 ] OAI records contain all subjects in a single field

From: SourceForge.net <no...@so...> - 2010-10-20 18:33:15

Bugs item #3079602, was opened at 2010-10-01 15:13
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&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: APIs
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Ryan Scherle (rscherle)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: OAI records contain all subjects in a single field

Initial Comment:
In the OAI records, each <dc:subject> field contains many keywords, separated by commas, like this:

<dc:subject>
Ascomycota, Pezizomycotina, Dothideomyceta, fungal evolution, lichens, multigene phylogeny, phylogenomics, plant pathogens, saprobes, Tree of Life
</dc:subject>

It is best practice to put each keyword into a separate <dc:subject> field. This allows harvesting systems (like Dryad) to accurately separate the keywords, and not worry about keywords that may contain commas.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:33

Message:
See https://www.nescent.org/wg_dryad/TreeBASE_OAI_Provider for examples of
URLs that return these OAI records. 

The record schema is at 
http://datadryad.org/profile/v3/dryad.xsd
Both data formats mentioned above formally conform to the schema, but the
best practice is to have several <dc:subject>  elements, one per term. 


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3079602&group_id=248804

[Treebase-guts] [ treebase-Bugs-3089436 ] URL that is returned to Dryad should be treebase.org/...

From: SourceForge.net <no...@so...> - 2010-10-20 18:19:49

Bugs item #3089436, was opened at 2010-10-17 21:00
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3089436&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: APIs
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Kevin S. Clarke (ksclarke)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: URL that is returned to Dryad should be treebase.org/...

Initial Comment:
In the submission integration process between Dryad and TreeBASE, Dryad connects to TreeBASE at:

http://treebase.org/treebase-web

When a successful connection is made, TreeBASE returns a URL that is then passed to the Dryad user so s/he can complete the submission process at TreeBASE.  The URL that is being returned is currently:

http://treebase.nescent.org/treebase-web/login.jsp?importKey=KEY_GOES_HERE

We've heard from Bill Piel that this URL should be to treebase.org not treebase.nescent.org

Would you change the TreeBASE code (or server setup?) to return this URL?  Thanks.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:19

Message:
See 
https://www.nescent.org/wg_dryad/TreeBASE_Submission_Integration#Progress_with_Handshaking_.28as_of_7-22-10.29
for the connection URL

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3089436&group_id=248804

[Treebase-guts] [ treebase-Bugs-3089438 ] Find journal name in Dryad bagit metadata

From: SourceForge.net <no...@so...> - 2010-10-20 18:17:59

Bugs item #3089438, was opened at 2010-10-17 21:04
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3089438&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: APIs
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Kevin S. Clarke (ksclarke)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: Find journal name in Dryad bagit metadata

Initial Comment:
Dryad returns to TreeBASE information about a submission in the bagit format.  This format contains a data/dryadpub.xml record that contains a metadata element with journal information.  The element is <bibo:Journal>  Bill Piel has mentioned that the TreeBASE side is not finding the journal information.  TreeBASE code needs to be updated to look in the data/dryadpub.xml record (after unpacking the bagit format) for this information.

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

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-10-20 14:17

Message:
See
https://www.nescent.org/wg_dryad/TreeBASE_Submission_Integration#Progress_with_Handshaking_.28as_of_7-22-10.29
for how bagit submission works

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

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