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From: SourceForge.net <no...@so...> - 2011-09-19 15:03:33
|
Bugs item #3303076, was opened at 2011-05-16 21:09 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303076&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Search on ISO 8601 date styles Initial Comment: Currently, the API allows the user to search by date, e.g.: http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May 5, 2011"&format=rss1 http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May 5, 2011"&format=rss1 http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May 5, 2011"&format=rss1 However, CQL usually expects the date format to conform to ISO 8601: http://www.loc.gov/standards/sru/resources/cql-context-set-v1-2.html This date style already works for our OAI-PMH service, e.g.: http://treebase.org/treebase-web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&from=2011-05-05T00:00:00Z Let's expand the date format in the API -- if anything it avoids needing to put the date in quotes. The issue is to configure the DateFormat object correctly which is done in the StudySearchController, at lines 311, 332 and 350. You can probably pass date formatting templates to the factory that returns a date parser through the getInstance() call. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303076&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2011-09-19 15:03:00
|
Bugs item #3381449, was opened at 2011-07-28 19:19 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3381449&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Allow submitter to modify published citation Initial Comment: Currently, we have it set so that once a study is published, the submitter has to contact he...@tr... to update the citation information. This model should be relaxed because it puts excessive burden on the editor. Instead, let's allow the submitter (if logged in) to make updates to his or her citation information even after the submission status is set to "published". The relevant page is just the following: http://www.treebase.org/treebase-web/user/citationForm.html And it should be designed so that only the submitter and the administrator is can see the "Update" button, even if published. i.e. other users who, may be logged in, should not be able to save edits to this page. Note that this privilege does not extend to any other part of the submission -- e.g. the authors, matrices, trees, etc. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3381449&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2011-09-19 15:02:11
|
Bugs item #3303002, was opened at 2011-05-16 15:46 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303002&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: NeXML not working for matrix or tree Initial Comment: Downloading NeXML works for the whole study, e.g.: http://purl.org/phylo/treebase/phylows/study/TB2:S586?format=nexml But does not seem to work for matrices in this study, e.g.: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2225?format=nexml Or trees in this study: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr3535?format=nexml ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2011-09-19 11:02 Message: This appears to be working now. Also, while the matrix download was missing the sequences (see http://purl.org/phylo/treebase/phylows/matrix/TB2:M2225?format=nexml) it now seems to contain them (see http://purl.org/phylo/treebase/dev/phylows/matrix/TB2:M2225?format=nexml), thanks, I think, to some recent changes made by Laurel Yohe. ---------------------------------------------------------------------- Comment By: William Piel (sfrgpiel) Date: 2011-07-19 14:47 Message: Actually, the NeXML download for the whole study doesn't work either. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303002&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-09-16 18:07:37
|
Bugs item #3410646, was opened at 2011-09-16 14:07 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3410646&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Uncaught Exception when uploading row segment file Initial Comment: There is some instability when uploading row segment files. This may have to do with return keys (unix vs mac vs win), missing values, and limits on the length of a column value. At any rate, it needs to be made more robust. Here is an example of a problem. First create a submission and upload the attached nexus file. Then try uploading the columns Row Taxon Label, Start Index, End Index, Inst. Acronym, Catalog Number, Genbank Accession, Other Accession, Collector, Country, State, Locality, Notes -- from the attached row segment file. The result is the uncaught exception. bp Uncaught Exception Encountered java.lang.IndexOutOfBoundsException: Index: 15, Size: 15 at java.util.ArrayList.rangeCheck(ArrayList.java:571) at java.util.ArrayList.get(ArrayList.java:349) at org.cipres.treebase.domain.matrix.RowSegment.update(RowSegment.java:379) at org.cipres.treebase.service.matrix.RowSegmentServiceImpl.mapToSegments(RowSegmentServiceImpl.java:380) at org.cipres.treebase.service.matrix.RowSegmentServiceImpl.createSegments(RowSegmentServiceImpl.java:287) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy75.createSegments(Unknown Source) at org.cipres.treebase.web.controllers.RowSegmentDataTableController.onSubmit(RowSegmentDataTableController.java:112) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:70) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: __utmz=[5099126.1305666484.1.1.utmcsr] __utmc=[5099126] __utmb=[5099126.43.9.1316195477908] __utma=[5099126.226138284.1305666484.1316186851.1316194155.50] itemToHighlight=[http%3A//treebase-dev.nescent.org/treebase-web/user/matrixList.html] JSESSIONID=[4660E6A549004EB9B896A6CDBB35A18D] __utmz=[53240375.1315795401.152.31.utmccn] __utma=[53240375.1924499357.1236724314.1315764093.1315795401.152] ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3410646&group_id=248804 |
|
From: <hs...@us...> - 2011-09-15 19:37:34
|
Revision: 961
http://treebase.svn.sourceforge.net/treebase/?rev=961&view=rev
Author: hshyket
Date: 2011-09-15 19:37:28 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Updating RSS feed date so that it goes 6 months back and changing the RSS icon to add transparency
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
trunk/treebase-web/src/main/webapp/images/icons/rss.gif
Modified: trunk/treebase-web/src/main/webapp/common/search-nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 18:31:04 UTC (rev 960)
+++ trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 19:37:28 UTC (rev 961)
@@ -1,7 +1,17 @@
<%@ include file="/common/taglibs.jsp"%>
<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<%@page import="java.util.Date" %>
+<%@page import="java.util.Calendar" %>
+<%@page import="java.text.SimpleDateFormat;" %>
+
<% String purlBase = TreebaseUtil.getPurlBase(); %>
+<%
+ Calendar cal = Calendar.getInstance();
+ cal.add(Calendar.MONTH, -6);
+ SimpleDateFormat isoFormat = new SimpleDateFormat("yyyy-MM-dd");
+%>
+
<ul id="s-nav">
<li id="s-navlabel">Search</li>
<li id="st-study">
@@ -52,7 +62,7 @@
</a>
</li>
<li style="background-color:transparent">
- <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1" style="background-color:transparent; border:none">
+ <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%22<%=isoFormat.format(cal.getTime())%>T05:00:00Z%22&format=rss1" style="background-color:transparent; border:none" target="_blank">
<img
class="iconButton"
src="<fmt:message key="icons.rss"/>"
Modified: trunk/treebase-web/src/main/webapp/images/icons/rss.gif
===================================================================
(Binary files differ)
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|
|
From: <sfr...@us...> - 2011-09-15 18:31:10
|
Revision: 960
http://treebase.svn.sourceforge.net/treebase/?rev=960&view=rev
Author: sfrgpiel
Date: 2011-09-15 18:31:04 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Updating the info people see when they click "ready" so that they know that they can later return to update the citation
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp 2011-09-15 18:18:30 UTC (rev 959)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/readyState.jsp 2011-09-15 18:31:04 UTC (rev 960)
@@ -34,9 +34,10 @@
</p>
<p>
- Changing the status of your study to 'Ready State' means that you are ready for the review process. If yes press Submit,
- else choose the Cancel button. Note that after you press the Submit button you will no longer be able to make any further changes to this study.
- The study will be available in 'READ ONLY' mode.
+ Changing the status of your study to 'Ready State' means that you are ready for the review process. If yes, please press Submit,
+ otherwise choose the Cancel button. Note that after you press the Submit button you will no longer be able to make any further
+ changes to your study, <b>except</b> for updating your citation information. We strongly encourage you to return to your
+ submission to update citation metadata, such as volume, issue, page numbers, or DOI, as needed.
</p>
<p>
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|
|
From: <sfr...@us...> - 2011-09-15 18:18:37
|
Revision: 959
http://treebase.svn.sourceforge.net/treebase/?rev=959&view=rev
Author: sfrgpiel
Date: 2011-09-15 18:18:30 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Missing value for icon.information
Modified Paths:
--------------
trunk/treebase-web/src/main/resources/ApplicationResources.properties
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2011-09-15 17:46:38 UTC (rev 958)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2011-09-15 18:18:30 UTC (rev 959)
@@ -69,7 +69,8 @@
link.action = Action
#-- general values --
-icon.warning=Warning
+icon.warning= Warning
+icon.information= About
#-- left side navigation menu --
nav.admin= Administration
@@ -314,7 +315,7 @@
download.nexml = Download NeXML File
download.json = Download JSON File
download.rdf = Download RDF file
-download.rss = Download RSS
+download.rss = Follow the last 6 months of TreeBASE activity with an RSS feed
#-- matrix row section --
matrix.row.id = Matrix Row ID
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|
|
From: <sfr...@us...> - 2011-09-15 17:46:46
|
Revision: 958
http://treebase.svn.sourceforge.net/treebase/?rev=958&view=rev
Author: sfrgpiel
Date: 2011-09-15 17:46:38 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Moving the RSS button to a more logical location
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/common/search-nav.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 17:30:52 UTC (rev 957)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 17:46:38 UTC (rev 958)
@@ -12,8 +12,6 @@
pageContext.setAttribute("searchOptions", searchOptions);
%>
-<%@page import="org.cipres.treebase.TreebaseUtil"%>
-<% String purlBase = TreebaseUtil.getPurlBase(); %>
<form id="searchSimple" method="post">
<fieldset>
For study IDs with values less than 3000, please search using the "Legacy Study ID" button.<br>
@@ -30,13 +28,6 @@
<a href="#" class="openHelp" onclick="openHelp('studyKeywordSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
- <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1">
- <img
- class="iconButton"
- src="<fmt:message key="icons.rss"/>"
- title="<fmt:message key="download.rss"/>"
- alt="<fmt:message key="download.rss"/>"/>
- </a>
</fieldset>
<jsp:include page="querySearchBox.jsp"/>
</form>
Modified: trunk/treebase-web/src/main/webapp/common/search-nav.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 17:30:52 UTC (rev 957)
+++ trunk/treebase-web/src/main/webapp/common/search-nav.jsp 2011-09-15 17:46:38 UTC (rev 958)
@@ -1,4 +1,6 @@
<%@ include file="/common/taglibs.jsp"%>
+<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<% String purlBase = TreebaseUtil.getPurlBase(); %>
<ul id="s-nav">
<li id="s-navlabel">Search</li>
@@ -49,6 +51,15 @@
src="<fmt:message key="icons.help"/>" alt="?"/>
</a>
</li>
+ <li style="background-color:transparent">
+ <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1" style="background-color:transparent; border:none">
+ <img
+ class="iconButton"
+ src="<fmt:message key="icons.rss"/>"
+ title="<fmt:message key="download.rss"/>"
+ alt="<fmt:message key="download.rss"/>"/>
+ </a>
+ </li>
<!--
<li id="st-taxonView"><a href="<c:url value="/search/taxonView.html"/>"><fmt:message key="search.nav.taxonViewTab"/></a></li>
-->
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|
|
From: <hs...@us...> - 2011-09-15 17:30:58
|
Revision: 957
http://treebase.svn.sourceforge.net/treebase/?rev=957&view=rev
Author: hshyket
Date: 2011-09-15 17:30:52 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Updating it so that any data provided in RSS format is not saved in the memory search results.
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2011-09-15 15:50:53 UTC (rev 956)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2011-09-15 17:30:52 UTC (rev 957)
@@ -395,7 +395,9 @@
root = normalizeParseTree(root);
Set<Study> queryResults = doCQLQuery(root, new HashSet<Study>(),request, response, errors);
StudySearchResults tsr = new StudySearchResults(queryResults);
- saveSearchResults(request, tsr);
+ if (! request.getParameter("format").equals("rss1")) {
+ saveSearchResults(request, tsr);
+ }
if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
return new ModelAndView("search/studySearch", Constants.RESULT_SET, tsr);
}
@@ -414,7 +416,9 @@
res = tsr.convertToTaxa();
}
}
- this.saveSearchResults(request, res);
+ if (! request.getParameter("format").equals("rss1")) {
+ this.saveSearchResults(request, res);
+ }
return this.searchResultsAsRDF(res, request, root, schema, "study");
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2011-09-15 15:51:02
|
Revision: 956
http://treebase.svn.sourceforge.net/treebase/?rev=956&view=rev
Author: sfrgpiel
Date: 2011-09-15 15:50:53 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
fixing the purl base value
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 15:46:00 UTC (rev 955)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 15:50:53 UTC (rev 956)
@@ -12,6 +12,8 @@
pageContext.setAttribute("searchOptions", searchOptions);
%>
+<%@page import="org.cipres.treebase.TreebaseUtil"%>
+<% String purlBase = TreebaseUtil.getPurlBase(); %>
<form id="searchSimple" method="post">
<fieldset>
For study IDs with values less than 3000, please search using the "Legacy Study ID" button.<br>
@@ -23,13 +25,12 @@
${options.value}
</option>
</c:forEach>
- </select>
- <c:set var="basePurl" scope="request" value='${treebase.purl.domain}'/>
+ </select>
<button type="submit" name="submit" >Search</button>
<a href="#" class="openHelp" onclick="openHelp('studyKeywordSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
- <a href="${basePurl}study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1">
+ <a href="<%=purlBase%>study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1">
<img
class="iconButton"
src="<fmt:message key="icons.rss"/>"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2011-09-15 15:46:11
|
Revision: 955
http://treebase.svn.sourceforge.net/treebase/?rev=955&view=rev
Author: sfrgpiel
Date: 2011-09-15 15:46:00 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
updating journal links
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/journal_files/amnat.gif
trunk/treebase-web/src/main/webapp/images/journal_files/ejpp.gif
trunk/treebase-web/src/main/webapp/images/journal_files/fd_algo.gif
trunk/treebase-web/src/main/webapp/images/journal_files/fd_bryo.gif
trunk/treebase-web/src/main/webapp/images/journal_files/fd_myco.gif
trunk/treebase-web/src/main/webapp/images/journal_files/jh.gif
trunk/treebase-web/src/main/webapp/images/journal_files/mer.gif
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-09-15 14:28:32 UTC (rev 954)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/journal.jsp 2011-09-15 15:46:00 UTC (rev 955)
@@ -26,6 +26,7 @@
it in your favorite RSS reader)</p>
</td>
</tr>
+<!-- aliso -->
<tr>
<td>
<p><a href="http://www.rsabg.org/research-department/scientific-publications"
@@ -39,10 +40,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22"
title="Find records in TreeBASE for articles published in Aliso">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Aliso%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Aliso"
</a></p>
</td>
</tr>
+<!-- american journal of botany -->
<tr>
<td>
<p><a href="http://www.amjbot.org/"
@@ -56,12 +58,31 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Journal%20of%20Botany%22"
title="Find records in TreeBASE for articles published in the American Journal of Botany">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Journal%20of%20Botany%22
+ <%=purlBase%>study/find?query=prism.publicationName=="American+Journal+of+Botany"
</a></p>
</td>
</tr>
+<!-- american naturalist -->
<tr>
<td>
+ <p><a href="http://www.asnamnat.org/"
+ title="American Naturalist">
+ <img class="journal"
+ src="images/journal_files/amnat.gif" alt="American Naturalist"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22American%20Naturalist%22"
+ title="Find records in TreeBASE for articles published in the American Naturalist">
+ <%=purlBase%>study/find?query=prism.publicationName=="American+Naturalist"
+ </a></p>
+ </td>
+ </tr>
+<!-- the bryologist -->
+ <tr>
+ <td>
<p><a href="http://192.104.39.110/bryologist.html"
title="The Bryologist">
<img class="journal"
@@ -73,12 +94,85 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22"
title="Find records in TreeBASE for articles published in The Bryologist">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22The%20Bryologist%22
+ <%=purlBase%>study/find?query=prism.publicationName=="The+Bryologist"
</a></p>
</td>
</tr>
+<!-- cryptogamie algologie -->
<tr>
<td>
+ <p><a href="http://www.cryptogamie.com/pagint_en/editeur/revues.php"
+ title="Cryptogamie Algologie">
+ <img class="journal"
+ src="images/journal_files/fd_algo.gif" alt="Cryptogamie Algologie"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Cryptogamie%20Algologie%22"
+ title="Find records in TreeBASE for articles published in the Cryptogamie Algologie">
+ <%=purlBase%>study/find?query=prism.publicationName=="Cryptogamie+Algologie"
+ </a></p>
+ </td>
+ </tr>
+<!-- cryptogamie bryologie -->
+ <tr>
+ <td>
+ <p><a href="http://www.cryptogamie.com/pagint_en/editeur/revue_bryo.php"
+ title="Cryptogamie Bryologie">
+ <img class="journal"
+ src="images/journal_files/fd_algo.gif" alt="Cryptogamie Bryologie"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Cryptogamie%20Bryologie%22"
+ title="Find records in TreeBASE for articles published in the Cryptogamie Bryologie">
+ <%=purlBase%>study/find?query=prism.publicationName=="Cryptogamie+Bryologie"
+ </a></p>
+ </td>
+ </tr>
+<!-- cryptogamie mycologie -->
+ <tr>
+ <td>
+ <p><a href="http://www.cryptogamie.com/pagint_en/editeur/revue_bryo.php"
+ title="Cryptogamie Mycologie">
+ <img class="journal"
+ src="images/journal_files/fd_algo.gif" alt="Cryptogamie Mycologie"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Cryptogamie%20Mycologie%22"
+ title="Find records in TreeBASE for articles published in the Cryptogamie Mycologie">
+ <%=purlBase%>study/find?query=prism.publicationName=="Cryptogamie+Mycologie"
+ </a></p>
+ </td>
+ </tr>
+<!-- european journal of plant pathology" -->
+ <tr>
+ <td>
+ <p><a href="http://www.springer.com/life+sciences/plant+sciences/journal/10658"
+ title=""European Journal of Plant Pathology">
+ <img class="journal"
+ src="images/journal_files/ejpp.gif" alt="European Journal of Plant Pathology"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22European%20Journal%20of%20Plant%20Pathology%22"
+ title="Find records in TreeBASE for articles published in the European Journal of Plant Pathology">
+ <%=purlBase%>study/find?query=prism.publicationName=="European+Journal+of+Plant+Pathology"
+ </a></p>
+ </td>
+ </tr>
+<!-- evolution -->
+ <tr>
+ <td>
<p><a href="http://www.wiley.com/bw/journal.asp?ref=0014-3820"
title="Evolution">
<img class="journal"
@@ -90,10 +184,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DEvolution"
title="Find records in TreeBASE for articles published in Evolution">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DEvolution
+ <%=purlBase%>study/find?query=prism.publicationName==Evolution
</a></p>
</td>
</tr>
+<!-- evolutionary applications -->
<tr>
<td>
<p>
@@ -108,10 +203,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22"
title="Find records in TreeBASE for articles published in Evolutionary Applications">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Evolutionary+Applications%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Evolutionary+Applications"
</a></p>
</td>
</tr>
+<!-- fungal biology -->
<tr>
<td>
<p>
@@ -126,10 +222,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22"
title="Find records in TreeBASE for articles published in Fungal Biology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Fungal+Biology%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Fungal+Biology"
</a></p>
</td>
</tr>
+<!-- ima fungus -->
<tr>
<td>
<p>
@@ -144,10 +241,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22"
title="Find records in TreeBASE for articles published in IMA Fungus">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22IMA+Fungus%22
+ <%=purlBase%>study/find?query=prism.publicationName=="IMA+Fungus"
</a></p>
</td>
</tr>
+<!-- invertebrate systmatics -->
<tr>
<td>
<p>
@@ -162,10 +260,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22"
title="Find records in TreeBASE for articles published in Invertebrate Systematics">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Invertebrate+Systematics%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Invertebrate+Systematics"
</a></p>
</td>
</tr>
+<!-- journal of fish and wildlife management -->
<tr>
<td>
<p>
@@ -180,12 +279,31 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22"
title="Find records in TreeBASE for articles published in Journal of Fish and Wildlife Management">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal+of+Fish+and+Wildlife+Management%22
+ <%=purlBase%>study/find?query=prism.publicationName=="Journal+of+Fish+and+Wildlife+Management"
</a></p>
</td>
</tr>
+<!-- journal of heredity -->
<tr>
<td>
+ <p><a href="http://jhered.oxfordjournals.org/"
+ title="Journal of Heredity">
+ <img class="journal"
+ src="images/journal_files/jh.gif" alt="Journal of Heredity"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Journal%20of%20Heredity%22"
+ title="Find records in TreeBASE for articles published in the Journal of Heredity">
+ <%=purlBase%>study/find?query=prism.publicationName=="Journal+of+Heredity"
+ </a></p>
+ </td>
+ </tr>
+<!-- molecular ecology -->
+ <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>
@@ -193,12 +311,31 @@
<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>
+ <%=purlBase%>study/find?query=prism.publicationName=="Molecular+Ecology"</a>
</p>
</td>
</tr>
+<!-- molecular ecology resources -->
<tr>
<td>
+ <p><a href="http://www.wiley.com/bw/journal.asp?ref=1755-098X"
+ title="Molecular Ecology Resources">
+ <img class="journal"
+ src="images/journal_files/mer.gif" alt="Molecular Ecology Resources"/>
+ </a>
+ </p>
+ </td>
+ <td>
+ <p><a
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Molecular%20Ecology%20Resources%22"
+ title="Find records in TreeBASE for articles published in the Molecular Ecology Resources">
+ <%=purlBase%>study/find?query=prism.publicationName==Molecular+"Ecology+Resources"
+ </a></p>
+ </td>
+ </tr>
+<!-- mycologia -->
+ <tr>
+ <td>
<p><a href="http://www.msafungi.org/">
<img class="journal" src="images/journal_files/image005.gif" alt="Mycologia" /></a></p>
</td>
@@ -206,10 +343,11 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMycologia"
title="Find records in TreeBASE for articles published in Mycologia">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycologia</a>
+ <%=purlBase%>study/find?query=prism.publicationName==Mycologia</a>
</p>
</td>
</tr>
+<!-- mycological progress -->
<tr>
<td>
<p><a
@@ -219,12 +357,13 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial%20Progress%22"
title="Find records in TreeBASE for articles published in Mycologial Progress">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Progress%22</a>
+ <%=purlBase%>study/find?query=prism.publicationName=="Mycologial+Progress"</a>
</p>
</td>
</tr>
+<!-- mycological research -->
<tr>
<td>
<p><a
@@ -235,11 +374,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial%20Research%22"
title="Find records in TreeBASE for articles published in Mycologial Research">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycologial+Research%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Mycologial+Research"</a></p>
</td>
</tr>
+<!-- mycology -->
<tr>
<td>
<p><a
@@ -252,9 +392,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22"
title="Find records in TreeBASE for articles published in Mycology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Mycology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Mycology"</a></p>
</td>
</tr>
+<!-- mycoscience -->
<tr>
<td>
<p><a
@@ -266,9 +407,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMycoscience"
title="Find records in TreeBASE for articles published in Mycoscience">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycoscience</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Mycoscience</a></p>
</td>
</tr>
+<!-- mycosphere -->
<tr>
<td>
<p><a href="http://www.mycosphere.org/">
@@ -278,9 +420,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMycosphere"
title="Find records in TreeBASE for articles published in Mycosphere">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMycosphere</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Mycosphere</a></p>
</td>
</tr>
+<!-- north american fauna -->
<tr>
<td>
<p><a
@@ -291,11 +434,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North%20American%20Fauna%22"
title="Find records in TreeBASE for articles published in North American Fauna">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22North+American+Fauna%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="North+American+Fauna"</a></p>
</td>
</tr>
+<!-- organisms, diversity, and evolution -->
<tr>
<td>
<p><a
@@ -306,11 +450,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms%20Diversity%20&%20Evolution%22"
title="Find records in TreeBASE for articles published in Organisms Diversity & Evolution">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Organisms+Diversity+&+Evolution%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Organisms+Diversity+&+Evolution"</a></p>
</td>
</tr>
+<!-- persoonia -->
<tr>
<td>
<p><a href="http://www.persoonia.org/">
@@ -320,9 +465,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DPersoonia"
title="Find records in TreeBASE for articles published in Persoonia">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DPersoonia</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Persoonia</a></p>
</td>
</tr>
+<!-- phytopathology -->
<tr>
<td>
<p>
@@ -330,17 +476,18 @@
<img
class="journal"
src="images/journal_files/image012.jpg"
- alt="Phytopahology"/>
+ alt="Phytopathology"/>
</a>
</p>
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopahology"
- title="Find records in TreeBASE for articles published in Phytopahology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopahology</a></p>
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DPhytopathology"
+ title="Find records in TreeBASE for articles published in Phytopathology">
+ <%=purlBase%>study/find?query=prism.publicationName==Phytopathology</a></p>
</td>
</tr>
+<!-- plant disease -->
<tr>
<td>
<p><a href="http://www.apsnet.org/pd/">
@@ -349,11 +496,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant%20Disease%22"
title="Find records in TreeBASE for articles published in Plant Disease">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Plant+Disease%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Plant+Disease"</a></p>
</td>
</tr>
+<!-- plos currents tol -->
<tr>
<td>
<p><a href="http://currents.plos.org/treeoflife"><img
@@ -362,11 +510,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS+Currents:+Tree+of+Life%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22PLoS%20Currents:%20Tree%20of%20Life%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>
+ <%=purlBase%>study/find?query=prism.publicationName=="PLoS+Currents:+Tree+of+Life"</a></p>
</td>
</tr>
+<!-- rhodora -->
<tr>
<td>
<p><a href="http://www.rhodora.org/Rhodora.html"><img
@@ -377,9 +526,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora"
title="Find records in TreeBASE for articles published in Rhodora">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DRhodora</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Rhodora</a></p>
</td>
</tr>
+<!-- muelleria -->
<tr>
<td>
<p><a
@@ -391,9 +541,10 @@
<p><a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria"
title="Find records in TreeBASE for articles published in Muelleria">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3DMuelleria</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName==Muelleria</a></p>
</td>
</tr>
+<!-- studies in mycology -->
<tr>
<td>
<p><a href="http://www.studiesinmycology.org/">
@@ -402,11 +553,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies%20in%20Mycology%22"
title="Find records in TreeBASE for articles published in Studies in Mycology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Studies+in+Mycology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Studies+in+Mycology"</a></p>
</td>
</tr>
+<!-- systematic biology -->
<tr>
<td>
<p><a href="http://systbiol.org/">
@@ -415,11 +567,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic%20Biology%22"
title="Find records in TreeBASE for articles published in Systematic Biology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Biology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Systematic+Biology"</a></p>
</td>
</tr>
+<!-- systematic botany -->
<tr>
<td>
<p><a href="http://www.sysbot.org/">
@@ -428,11 +581,12 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic%20Botany%22"
title="Find records in TreeBASE for articles published in Systematic Botany">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Systematic+Botany%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Systematic+Botany"</a></p>
</td>
</tr>
+<!-- tropical bryology -->
<tr>
<td>
<p><a href="http://tropical-bryology.org/">
@@ -441,15 +595,15 @@
</td>
<td>
<p><a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Tropical%20Bryology%22"
title="Find records in TreeBASE for articles published in Tropical Bryology">
- <%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Tropical+Bryology%22</a></p>
+ <%=purlBase%>study/find?query=prism.publicationName=="Tropical+Bryology"</a></p>
</td>
</tr>
</table>
<p><b>Other Journals with a Significant Presence in TreeBASE</b>: <a
- href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Annals+of+the+Missouri+Botanical+Garden%22"
+ href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Annals%20of%20the%20Missouri%20Botanical%20Garden%22"
title="Annals of the Missouri Botanical Garden">Annals of the
Missouri Botanical Garden</a>; <a
href="<%=purlBase%>study/find?query=prism.publicationName%3D%3D%22Biological+Journal+of+the+Linnean+Society%22"
Added: trunk/treebase-web/src/main/webapp/images/journal_files/amnat.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/amnat.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/ejpp.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/ejpp.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fd_algo.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fd_algo.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fd_bryo.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fd_bryo.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/fd_myco.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/fd_myco.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/jh.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/jh.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/journal_files/mer.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/journal_files/mer.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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|
|
From: <sfr...@us...> - 2011-09-15 14:28:40
|
Revision: 954
http://treebase.svn.sourceforge.net/treebase/?rev=954&view=rev
Author: sfrgpiel
Date: 2011-09-15 14:28:32 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Adding RSS feed link for getting a list of all TreeBASE studies
Modified Paths:
--------------
trunk/treebase-web/src/main/resources/ApplicationResources.properties
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/images/icons/rss.gif
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2011-09-15 14:20:34 UTC (rev 953)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2011-09-15 14:28:32 UTC (rev 954)
@@ -314,6 +314,7 @@
download.nexml = Download NeXML File
download.json = Download JSON File
download.rdf = Download RDF file
+download.rss = Download RSS
#-- matrix row section --
matrix.row.id = Matrix Row ID
@@ -485,8 +486,8 @@
icons.json=/treebase-web/images/icons/script.png
icons.permalink=/treebase-web/images/icons/link.png
icons.treebase.16px=/treebase-web/images/logo16px.png
+icons.rss=/treebase-web/images/icons/rss.gif
-
#-- help system --
help.title=Help window
help.admin.legend=Modify help message "{0}" here
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 14:20:34 UTC (rev 953)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-09-15 14:28:32 UTC (rev 954)
@@ -24,10 +24,18 @@
</option>
</c:forEach>
</select>
+ <c:set var="basePurl" scope="request" value='${treebase.purl.domain}'/>
<button type="submit" name="submit" >Search</button>
<a href="#" class="openHelp" onclick="openHelp('studyKeywordSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
- </a>
+ </a>
+ <a href="${basePurl}study/find?query=prism.modificationDate%3E%221996-01-01T05:00:00Z%22&format=rss1">
+ <img
+ class="iconButton"
+ src="<fmt:message key="icons.rss"/>"
+ title="<fmt:message key="download.rss"/>"
+ alt="<fmt:message key="download.rss"/>"/>
+ </a>
</fieldset>
<jsp:include page="querySearchBox.jsp"/>
</form>
Added: trunk/treebase-web/src/main/webapp/images/icons/rss.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/icons/rss.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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|
|
From: <hs...@us...> - 2011-09-15 14:20:41
|
Revision: 953
http://treebase.svn.sourceforge.net/treebase/?rev=953&view=rev
Author: hshyket
Date: 2011-09-15 14:20:34 +0000 (Thu, 15 Sep 2011)
Log Message:
-----------
Search using the dc.date parameter (in the URL) will not do a search by last modified date (exactly like prism.modificationDate)
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2011-09-12 07:10:22 UTC (rev 952)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java 2011-09-15 14:20:34 UTC (rev 953)
@@ -215,7 +215,7 @@
} else if ( index.startsWith("prism.publicationName") ) {
results.addAll(doSearch(request, response, SearchType.byJournal, errors, term.getTerm(),exactMatch,relation));
} else if ( index.startsWith("dc.date") ) {
- results.addAll(doSearch(request,response, SearchType.byReleaseDate, errors, term.getTerm(),exactMatch,relation));
+ results.addAll(doSearch(request,response, SearchType.byLastModifiedDate, errors, term.getTerm(),exactMatch,relation));
} else if ( index.startsWith("prism.creationDate") ) {
results.addAll(doSearch(request,response, SearchType.byCreationDate, errors, term.getTerm(),exactMatch,relation));
} else if ( index.startsWith("prism.publicationDate") ) {
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|
|
From: <lol...@us...> - 2011-09-12 07:10:28
|
Revision: 952
http://treebase.svn.sourceforge.net/treebase/?rev=952&view=rev
Author: loloyohe
Date: 2011-09-12 07:10:22 +0000 (Mon, 12 Sep 2011)
Log Message:
-----------
Added code starting at line 388 that fixes bug #3303002, in which some studies were not printing the matrix in NeXML. I have commented out the original code with the bug in case the new code does not work for some reason.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-09-01 18:31:45 UTC (rev 951)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-09-12 07:10:22 UTC (rev 952)
@@ -384,6 +384,17 @@
OTU xmlOTU = getOTUById(xmlOTUs, tbRow.getTaxonLabel().getId());
int charIndex = 0;
if ( characterList.size() <= MAX_GRANULAR_NCHAR && xmlOTUs.getAllOTUs().size() <= MAX_GRANULAR_NTAX ) {
+ for ( MatrixColumn tbColumn : ((CharacterMatrix)tbMatrix).getColumns() ) {
+ String seq = tbRow.buildElementAsString();
+ xmlMatrix.setSeq(seq, xmlOTU);
+ org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
+ MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
+
+ attachTreeBaseID ((Annotatable) xmlCell, tbColumn , DiscreteMatrixElement.class);
+
+ //The following is commented out as tbRow.getElements() does not work directly and crashes the loop.
+ //The above for loop fixes this issue.
+ /*
for ( MatrixElement tbCell : tbRow.getElements() ) {
org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
@@ -392,6 +403,8 @@
CharacterState xmlState = xmlCharacter.getCharacterStateSet().lookupCharacterStateBySymbol(tbSymbolString);
xmlCell.setValue(xmlState);
attachTreeBaseID((Annotatable)xmlCell,tbCell,DiscreteMatrixElement.class);
+ */
+
for ( RowSegment tbSegment : tbSegments ) {
if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
//declare variables for row-segment annotations
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|
|
From: <sfr...@us...> - 2011-09-01 18:31:52
|
Revision: 951
http://treebase.svn.sourceforge.net/treebase/?rev=951&view=rev
Author: sfrgpiel
Date: 2011-09-01 18:31:45 +0000 (Thu, 01 Sep 2011)
Log Message:
-----------
Allow admin person to save changes to the tree metadata even if submission is in ready state
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeList.jsp 2011-09-01 17:15:05 UTC (rev 950)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/treeList.jsp 2011-09-01 18:31:45 UTC (rev 951)
@@ -163,17 +163,19 @@
</c:if>
<display:footer>
- <c:if test="${publicationState eq 'NotReady'}">
+ <%if(request.isUserInRole("Admin") || request.isUserInRole("Associate Editor")){%>
+ <% request.setAttribute("isEditable","yes");%>
+ <% } %>
+
+ <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
<tr>
<td colspan="10" align="center">
<input type="submit" class="button" name="Update" value="<fmt:message key="button.update"/>" />
<input type="submit" class="button" name="_cancel" value="<fmt:message key="button.cancel"/>" />
</td>
-
</tr>
</c:if>
</display:footer>
-
<display:setProperty name="export.pdf" value="true" />
<display:setProperty name="basic.empty.showtable" value="true"/>
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|
|
From: <sfr...@us...> - 2011-09-01 17:15:11
|
Revision: 950
http://treebase.svn.sourceforge.net/treebase/?rev=950&view=rev
Author: sfrgpiel
Date: 2011-09-01 17:15:05 +0000 (Thu, 01 Sep 2011)
Log Message:
-----------
Adding some hard-coded instructions to address FAQs.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp 2011-08-29 19:34:58 UTC (rev 949)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/nexusFiles.jsp 2011-09-01 17:15:05 UTC (rev 950)
@@ -5,7 +5,12 @@
<body id="submissions"/>
<c:url var="nexusdownloadURL" value="/user/downloadANexusFile.html" />
<c:url var="nexusrctdownloadURL" value="/user/downloadANexusRCTFile.html" />
-<p>The table below shows a list of all the nexus files for the current study.</p>
+<p>The table below shows a list of all the NEXUS files uploaded to the submission.
+These files cannot be deleted unless the entire submission is deleted, however
+they are not visible to the public unless trees or matrices brought in by them
+are published. Consequently, if all trees and matrices are deleted, the original
+file is only visible to the submitter and to the editors of TreeBASE. Retaining
+these files is useful for TreeBASE staff as a record of prior submission activity.</p>
<form method="post">
<fieldset>
<legend>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-08-29 19:34:58 UTC (rev 949)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/studyForm.jsp 2011-09-01 17:15:05 UTC (rev 950)
@@ -5,7 +5,7 @@
<c:choose>
<c:when test="${empty study.submission.id}">
<content tag="heading">Create New Submission</content>
- <p>Please provide a brief title for your study. Usually this is the same title as the title of your pubication.</p>
+ <p>Please provide a brief title for your study. Usually this is the same title as the title of your publication.</p>
<p>The notes for your study are not for the public, but are there for your own benefit and for communicating with TreeBASE staff once your submission status is ready to be made public. </p>
<p>If your submission is part of a sponsored research data management plan, please indicate this in the Notes so that TreeBASE staff know to provide added attention and to assist in making your submission fully compliant with the expectations of the sponsor. For more information, see the <a href="/treebase-web/dataMan.html" target="_blank">NSF Data Management Plan instructions</a>. </p>
</c:when>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp 2011-08-29 19:34:58 UTC (rev 949)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/submissionList.jsp 2011-09-01 17:15:05 UTC (rev 950)
@@ -12,7 +12,7 @@
<legend>Submissions
<a href="#" class="openHelp" onclick="openHelp('submissionList')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
</legend>
-The table below shows a list of your Treebase submissions.
+The table below shows a list of your Treebase submissions. Submissions can only be deleted after all trees and matrices are deleted first.
<display:table
name="${submissionList}"
requestURI=""
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|
|
From: <hs...@us...> - 2011-08-29 19:35:04
|
Revision: 949
http://treebase.svn.sourceforge.net/treebase/?rev=949&view=rev
Author: hshyket
Date: 2011-08-29 19:34:58 +0000 (Mon, 29 Aug 2011)
Log Message:
-----------
Allow the editing of the citation after a study has been published
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp 2011-08-25 15:00:11 UTC (rev 948)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/citationForm.jsp 2011-08-29 19:34:58 UTC (rev 949)
@@ -80,7 +80,7 @@
<% request.setAttribute("isEditable","yes");%>
<% } %>
- <c:if test="${publicationState eq 'NotReady'||isEditable eq 'yes'}">
+ <c:if test="${publicationState eq 'NotReady'|| publicationState eq 'Published' || isEditable eq 'yes'}">
<th></th>
<td colspan="5" align="center">
<c:choose>
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|
|
From: <rv...@us...> - 2011-08-25 15:00:17
|
Revision: 948
http://treebase.svn.sourceforge.net/treebase/?rev=948&view=rev
Author: rvos
Date: 2011-08-25 15:00:11 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Actually, the skos:historyNote should probably be attached to the tree block, not the study
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2011-08-25 14:40:19 UTC (rev 947)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2011-08-25 15:00:11 UTC (rev 948)
@@ -101,7 +101,7 @@
org.nexml.model.TreeBlock xmlTreeBlock = getDocument().createTreeBlock(xmlOTUs);
// attach base uri and skos:historyNote
- getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlTreeBlockConverter $Rev$");
+ xmlTreeBlock.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlTreeBlockConverter $Rev$");
xmlTreeBlock.setBaseURI(mTreeBaseURI);
if ( null != treeBlock.getTitle() ) {
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|
|
From: <rv...@us...> - 2011-08-25 14:40:25
|
Revision: 947
http://treebase.svn.sourceforge.net/treebase/?rev=947&view=rev
Author: rvos
Date: 2011-08-25 14:40:19 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Actually, the skos:historyNote should probably be attached to the taxa, not the study
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2011-08-25 14:39:44 UTC (rev 946)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2011-08-25 14:40:19 UTC (rev 947)
@@ -50,7 +50,7 @@
// attach base uri and skos:historyNote
xmlOTUs.setBaseURI(mTaxonBaseURI);
- getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlOTUConverter $Rev$");
+ xmlOTUs.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlOTUConverter $Rev$");
xmlOTUs.setLabel(taxonLabelSet.getTitle());
attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);
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|
|
From: <rv...@us...> - 2011-08-25 14:39:50
|
Revision: 946
http://treebase.svn.sourceforge.net/treebase/?rev=946&view=rev
Author: rvos
Date: 2011-08-25 14:39:44 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Actually, the skos:historyNote should probably be attached to the characters, not the study
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-08-25 14:35:13 UTC (rev 945)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-08-25 14:39:44 UTC (rev 946)
@@ -179,7 +179,7 @@
CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
// attach base uri and history note
- getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
+ xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
xmlMatrix.setBaseURI(mMatrixBaseURI);
List<List<DiscreteCharState>> tbStateLabels = tbMatrix.getStateLabels();
@@ -232,7 +232,7 @@
// attach base uri and history note
xmlMatrix.setBaseURI(mMatrixBaseURI);
- getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
+ xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
// lookup the equivalent state in tb and attach identifiers
for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
@@ -267,7 +267,7 @@
// attach base uri and history note
xmlMatrix.setBaseURI(mMatrixBaseURI);
- getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
+ xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
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From: <rv...@us...> - 2011-08-25 14:35:19
|
Revision: 945
http://treebase.svn.sourceforge.net/treebase/?rev=945&view=rev
Author: rvos
Date: 2011-08-25 14:35:13 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Added skos:historyNote to keep track of which version of the converter we're using
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Property Changed:
----------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2011-08-25 14:31:28 UTC (rev 944)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2011-08-25 14:35:13 UTC (rev 945)
@@ -3,6 +3,7 @@
import java.util.Iterator;
import java.util.Set;
+import org.cipres.treebase.Constants;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -98,7 +99,11 @@
TaxonLabelSet taxonLabelSet = treeBlock.getTaxonLabelSet();
OTUs xmlOTUs = getOTUsById(taxonLabelSet.getId());
org.nexml.model.TreeBlock xmlTreeBlock = getDocument().createTreeBlock(xmlOTUs);
+
+ // attach base uri and skos:historyNote
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlTreeBlockConverter $Rev$");
xmlTreeBlock.setBaseURI(mTreeBaseURI);
+
if ( null != treeBlock.getTitle() ) {
xmlTreeBlock.setLabel(treeBlock.getTitle());
}
Property changes on: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
___________________________________________________________________
Added: svn:keywords
+ Rev
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From: <rv...@us...> - 2011-08-25 14:31:34
|
Revision: 944
http://treebase.svn.sourceforge.net/treebase/?rev=944&view=rev
Author: rvos
Date: 2011-08-25 14:31:28 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Added skos:historyNote to keep track of which version of the converter we're using
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
Property Changed:
----------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2011-08-25 14:29:19 UTC (rev 943)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java 2011-08-25 14:31:28 UTC (rev 944)
@@ -1,5 +1,6 @@
package org.cipres.treebase.domain.nexus.nexml;
+import org.cipres.treebase.Constants;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -46,7 +47,11 @@
*/
public OTUs fromTreeBaseToXml(TaxonLabelSet taxonLabelSet) {
OTUs xmlOTUs = getDocument().createOTUs();
+
+ // attach base uri and skos:historyNote
xmlOTUs.setBaseURI(mTaxonBaseURI);
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlOTUConverter $Rev$");
+
xmlOTUs.setLabel(taxonLabelSet.getTitle());
attachTreeBaseID(xmlOTUs,taxonLabelSet,TaxonLabelSet.class);
for ( TaxonLabel taxonLabel : taxonLabelSet.getTaxonLabelsReadOnly() ) {
Property changes on: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlOTUConverter.java
___________________________________________________________________
Added: svn:keywords
+ Rev
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From: <rv...@us...> - 2011-08-25 14:29:25
|
Revision: 943
http://treebase.svn.sourceforge.net/treebase/?rev=943&view=rev
Author: rvos
Date: 2011-08-25 14:29:19 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Added skos:historyNote to keep track of which version of the converter we're using
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Property Changed:
----------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-08-25 14:24:16 UTC (rev 942)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-08-25 14:29:19 UTC (rev 943)
@@ -177,7 +177,11 @@
public CategoricalMatrix fromTreeBaseToXml(StandardMatrix tbMatrix) {
OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
+
+ // attach base uri and history note
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
xmlMatrix.setBaseURI(mMatrixBaseURI);
+
List<List<DiscreteCharState>> tbStateLabels = tbMatrix.getStateLabels();
List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
for ( int i = 0; i < tbColumns.size(); i++ ) {
@@ -226,8 +230,9 @@
xmlStateSet = ((MolecularMatrix)xmlMatrix).getProteinCharacterStateSet();
}
- // attach base uri
+ // attach base uri and history note
xmlMatrix.setBaseURI(mMatrixBaseURI);
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
// lookup the equivalent state in tb and attach identifiers
for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
@@ -259,7 +264,11 @@
public org.nexml.model.ContinuousMatrix fromTreeBaseToXml(ContinuousMatrix tbMatrix) {
OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
org.nexml.model.ContinuousMatrix xmlMatrix = getDocument().createContinuousMatrix(xmlOTUs);
+
+ // attach base uri and history note
xmlMatrix.setBaseURI(mMatrixBaseURI);
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlMatrixConverter $Rev$");
+
for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
PhyloChar tbCharacter = tbColumn.getCharacter();
Property changes on: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
___________________________________________________________________
Added: svn:keywords
+ Rev
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From: <rv...@us...> - 2011-08-25 14:24:26
|
Revision: 942
http://treebase.svn.sourceforge.net/treebase/?rev=942&view=rev
Author: rvos
Date: 2011-08-25 14:24:16 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Added skos:historyNote to keep track of which version of the converter we're using
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
Property Changed:
----------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2011-08-25 13:59:02 UTC (rev 941)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java 2011-08-25 14:24:16 UTC (rev 942)
@@ -2,6 +2,7 @@
//import org.cipres.treebase.Constants;
//import org.cipres.treebase.domain.admin.Person;
+import org.cipres.treebase.Constants;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
import org.cipres.treebase.domain.nexus.NexusDataSet;
//import org.cipres.treebase.domain.study.ArticleCitation;
@@ -97,6 +98,7 @@
*/
public Document fromTreeBaseToXml(Study pStudy) {
attachTreeBaseID(getDocument(), pStudy,Study.class);
+ getDocument().addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using NexmlDocumentConverter $Rev$");
NexmlOTUConverter noc = new NexmlOTUConverter(getStudy(),getTaxonLabelHome(),getDocument());
for ( TaxonLabelSet taxonLabelSet : pStudy.getTaxonLabelSets() ) {
Property changes on: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlDocumentConverter.java
___________________________________________________________________
Added: svn:keywords
+ Rev
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From: <rv...@us...> - 2011-08-25 13:59:08
|
Revision: 941
http://treebase.svn.sourceforge.net/treebase/?rev=941&view=rev
Author: rvos
Date: 2011-08-25 13:59:02 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Actually, in order to be valid xsi:type subclasses, they should spell out all possible states for dna/rna/protein, not just the ones we've seen in the database
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-08-25 13:57:44 UTC (rev 940)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java 2011-08-25 13:59:02 UTC (rev 941)
@@ -229,8 +229,7 @@
// attach base uri
xmlMatrix.setBaseURI(mMatrixBaseURI);
- // lookup the equivalent state in tb and attach identifiers, only keep those in matrix
- Set<CharacterState> seenStates = new HashSet<CharacterState>();
+ // lookup the equivalent state in tb and attach identifiers
for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
for (DiscreteCharState tbState : tbStateSet.getStates() ) {
String tbSymbol = tbState.getSymbol().toString().toUpperCase();
@@ -239,10 +238,8 @@
xmlState = xmlStateSet.createCharacterState(tbSymbol);
}
attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
- seenStates.add(xmlState);
}
}
- xmlStateSet.setCharacterStates(seenStates);
// create columns and attach identifiers
for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
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