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From: SourceForge.net <no...@so...> - 2010-04-27 15:22:00
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Bugs item #2972107, was opened at 2010-03-17 14:21 Message generated for change (Comment added) made by hlapp You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2972107&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: 9 Private: No Submitted By: Hilmar Lapp (hlapp) Assigned to: Hilmar Lapp (hlapp) Summary: Disable download analysis function in UI Initial Comment: This needs to be disabled in order for us to do the release. It can be re-enabled after issue# 2970700 and issue# 2970457 have been resolved, which will likely happen only after release. ---------------------------------------------------------------------- >Comment By: Hilmar Lapp (hlapp) Date: 2010-04-27 11:21 Message: Fixed in svn. BTW this is re--enabled now because the underlying problem has been fixed. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-17 15:36 Message: I think I found the links from the analysis tab. This isn't commenting out the link from the summary page (and it looks like there is one too). I think we should leave that one in, as apparently it works for most analyses, and doesn't scramble the taxon labels? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2972107&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-04-27 13:12:45
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Bugs item #2960840, was opened at 2010-02-28 15:05 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2960840&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: Rutger Vos (rvos) Summary: PhyloWS API Issues Need Fixing Initial Comment: A couple of things should be fixed with PhyloWS, some are higher value than others. I would rank items 1 and 4 at level "9," with the other ones lower (but if they are low-hanging easy fixes, it would be great to fix them before the release). 1. Failure with Safari RSS browser: Originally we thought that this failed because RSS results are not delivered with <?xml version="1.0" encoding="utf-8"?> at the top -- but that's not the case. 2. The initial url (e.g. http://purl.org/phylo/treebase/phylows/taxon/find?query=dcterms.title==%22Homo%20sapiens%22&recordSchema=study&format=rss1) uses purl.org but returns a list where the domains change from purl.org to nescent.org -- I'd rather that we not proliferate synonymous URIs that have different domains. Let's keep all "/phylows/" urls with the purl.org domain. 3. Let's add some verbiage to each RSS 1.0 result so that a minium synopsis of readable info is provided to users of RSS browsers. For studies, provide the citation; for matrices, provide matrix name and data type; for trees, provide tree name, tree title, tree type; for taxa, provide the taxon name. So, for example, while the current implementation looks like this: <item rdf:about="http://treebase-dev.nescent.org:6666/treebase-web/phylows/study/TB2:S1925"> <title>TB2:S1925</title> <link>http://treebase-dev.nescent.org:6666/treebase-web/phylows/study/TB2:S1925</link> <description>TB2:S1925</description> </item> ...We need to be more verbose, not only in the <description> so that the user reading the RSS feed has some idea what it is about, but also in the <prism> and <dc> contents, so that machines reading this feed can do something useful with it. In the case of a study, let's return this: <item rdf:about="http://purl.org/phylo/treebase/phylows/study/TB2:S1925"> <title><![CDATA[[Study] Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences]]></title> <link>http://purl.org/phylo/treebase/phylows/study/TB2:S1925</link> <description><![CDATA[Tanaka, E. and C. Tanaka. 2008. Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences. Mycoscience, 49(20): 115-125.]]></description> <dc:creator><![CDATA[Tanaka, E.; Tanaka, C.]]></dc:creator> <dc:date>2007-01-01</dc:date> <dc:subject><![CDATA[Phylogenies]]></dc:subject> <dc:title><![CDATA[[Study] Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences]]></dc:title> <dc:publisher>Mycoscience</dc:publisher> <prism:publicationName>Mycoscience</prism:publicationName> <prism:contributor>Tanaka, Eiji</prism:contributor> <prism:contributor>Tanaka, Chihiro</prism:contributor> <prism:volume>49</prism:volume> <prism:pageRange>115-125</prism:pageRange> <prism:startingPage>115</prism:startingPage> <prism:endingPage>125</prism:endingPage> <prism:doi>10.1007/s10267-007-0401-5</prism:doi> <dcterms:bibliographicCitation>Tanaka, E. and C. Tanaka. 2008. Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences. Mycoscience, 49(20): 115-125.</dcterms:bibliographicCitation> <prism:publicationDate>2007-01-01</prism:publicationDate> <prism:section>Study</prism:section> </item> 4. PhyloWS requests that search on taxa to return a list of trees are so slow as to be unusable. This problem may be fixed by Youjun, seeing as it is also slow in the web GUI interface and Youjun is tackling the problem there. http://purl.org/phylo/treebase/phylows/taxon/find?query=dcterms.title==%22Homo%20sapiens%22&recordSchema=tree&format=rss1 5. My understanding is that our /phylows/study/find? queries do not support searching on the journal name of an article. It would be great if this were offered because that would let us give journal editors RSS feeds into their own data. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2010-04-27 09:12 Message: For the record, I'm adding the following correspondence with Rutger: Hi Rutger, Regarding the RSS problem, I've been playing around with this validator: http://www.ldodds.com/rss_validator/1.0/validator.html ... with some success, but not 100%. One thing I noticed is that if I download the source with Firefox, the saved file has characters in Latin1 instead of UTF8. Thinking that that might be the problem, I posted both original and converted files for this (http://treebase.nescent.org/treebase-web/phylows/study/find?query=prism.publicationName=Nature&format=rss1) feed here: http://treebase.peabody.yale.edu/~piel/nature_orig.rdf http://treebase.peabody.yale.edu/~piel/nature_utf8.rdf Oddly enough, it doesn't seem to make a difference -- in that Safari happily reads and displays both of these. Also, the validator gives the same result whether using the original URL (http://treebase.nescent.org/treebase-web/phylows/study/find?query=prism.publicationName=Nature&format=rss1) or one of these two (it's not happy about the namespace resolution, but other than that, it's okay). So presumably, Safari's problem must have something to do with the mime type or headers communicating the data if they're coming directly from TreeBASE. Next I wanted to look at the case where Firefox won't display it: http://treebase.nescent.org/treebase-web/phylows/study/find?query=prism.publicationName=%22Systematic+Biology%22&format=rss1 If I put this string into the validator, I get: "An invalid XML character (Unicode: 0x1a) was found in the element content of the document." So I put the files here, both original and utf8 converted: http://treebase.peabody.yale.edu/~piel/sysbio_orig.rdf http://treebase.peabody.yale.edu/~piel/sysbio_utf8.rdf Same error with the validator, and Firefox won't render either of them, but oddly enough, Safari is happy to render both of them. So I opened the file in TextWrangler and ran the "Zap Gremlins" feature, and then saved the file here: http://treebase.peabody.yale.edu/~piel/sysbio_zap.rdf With this file, both Firefox and Safari render it okay. However the validator now has a different error: Using org.apache.xerces.parsers.SAXParser Exception net.sf.saxon.trans.XPathException: org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed. org.xml.sax.SAXParseException: The markup in the document following the root element must be well-formed. So... at any rate, it looks like the following is the case: 1. Character coding needs to be in UTF8, even if Safari and Firefox don't have a problem with this -- others might. 2. Safari's problem is in the delivery of the RDF file -- if Apache delivers a static RDF file, Safari has no problem. So it's not the content of the file at issue. 3. Firefox's problem is with hidden control characters. take care, Bill ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-03-12 18:47 Message: 1. I think this might be due to the extension(!), I created a mapping so that we give these feeds a .rdf extension and with mime-type application/rss+xml. They now render as expected. 2. we now use purls throughout. 3. this is much harder to do than you'd think. I'll try. 4. this has been fixed already, apparently. 5. we can now use prism.publicationName as a search predicate. I've committed this progress so far, but it has not been reloaded on the server yet. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-10 13:25 Message: Downgrading to priority 8 as per conversation with Bill. Itrem #4 has been ifxed already. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-03-01 11:09 Message: Ok, I'll work on this. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2010-03-01 11:09 Message: Thanks for reporting this bug. We'll look into it as soon as possible. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2960840&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-04-27 13:08:16
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Bugs item #2992932, was opened at 2010-04-27 09:08 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992932&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: Exact match "==" does not work in PhyloWS query Initial Comment: This query: http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName==Evolution ...results in many journals that are not just "Evolution" but have the word "Evolution" in them (e.g. "Molecular Phylogenetics and Evolution"). So our PhyloWS is not recognizing "==" as an exact match search. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992932&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-04-27 13:04:31
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Bugs item #2992930, was opened at 2010-04-27 09:04 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992930&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: Nobody/Anonymous (nobody) Summary: Uploading metadata with missing values causes exception Initial Comment: The process for uploading metadata is to first download a row segment template, then fill it in in Excel, then upload it. i.e. from this page: http://www.treebase.org/treebase-web/user/uploadRowSegmentData.html On the following page, designate which columns to be uploaded. The problem is that if any of the designated columns have no data for one or more rows, the parser throws an exception. What it should do is treat empty fields as NULL. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992930&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-04-27 12:53:30
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Bugs item #2896043, was opened at 2009-11-11 11:45 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2896043&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: data Group: None >Status: Closed Priority: 5 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Mark Dominus (mjdominus) Summary: nexus from analysis creates redundant taxon blocks Initial Comment: Reconstructing the nexus of an analysis step, such as this: http://treebasedb-dev.nescent.org:6666/treebase-web/search/downloadAnAnalysisStep.html?analysisid=1953 Results in one taxon block per character block and one taxon block per tree block. These are redundant and cause an error in Mesquite. Since analysis steps do not allow trees to have taxa not found in related matrices, each analysis step nexus should have only one taxon block, with all tree and character blocks linking to it. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2896043&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-04-25 16:04:35
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Bugs item #2992022, was opened at 2010-04-25 12:04 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: Yikes when viewing 2164 Initial Comment: An error is thrown when users try to browse to S2164. This *may* be an issue with UTF8 character set rendering, seeing as this study is from Hungarian authors. http://www.treebase.org/treebase-web/search/study/summary.html?id=2164 Yikes! javax.servlet.jsp.el.ELException: An error occurred while getting property "bibtexReference" from an instance of class org.cipres.treebase.domain.study.ArticleCitation at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspx_meth_c_005fout_005f0(nav_jsp.java:285) at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspService(nav_jsp.java:89) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:584) at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:497) at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:965) at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspService(summary_jsp.java:109) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&group_id=248804 |
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From: <sfr...@us...> - 2010-04-24 15:01:20
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Revision: 694
http://treebase.svn.sourceforge.net/treebase/?rev=694&view=rev
Author: sfrgpiel
Date: 2010-04-24 15:01:14 +0000 (Sat, 24 Apr 2010)
Log Message:
-----------
Renamed the identifiers to search on for improved clarity.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp 2010-04-22 18:29:32 UTC (rev 693)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp 2010-04-24 15:01:14 UTC (rev 694)
@@ -16,8 +16,8 @@
<tr>
<th><fmt:message key="submission.accession"/>:</th>
<td>
- <input type="radio" name="identifierType" value="TB2" checked="checked"/>TreeBASE2 Id
- <input type="radio" name="identifierType" value="TB1"/>Legacy accession
+ <input type="radio" name="identifierType" value="TB2" checked="checked"/>TreeBASE2 Submission ID
+ <input type="radio" name="identifierType" value="TB1"/>TreeBASE1 Legacy Study ID
<input type="radio" name="identifierType" value="TB0"/>TreeBase2 Study ID
<input type="text" name="submissionaccession" maxlength = "25"/>
</td>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: SourceForge.net <no...@so...> - 2010-04-22 18:30:40
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Bugs item #2970700, was opened at 2010-03-15 11:29 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970700&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: youjun guo (youjun) Summary: Analysis download scrambles taxon labels Initial Comment: Analysis download scrambles taxon labels Analysis download creates a taxon block in which the order of the names does not match with the order of the names in the associated character block. This will cause software programs like PAUP and Mesquite to scramble the taxon labels with the characters that they are supposed to map to. For example, see here: http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5539&id=10232 By contrast, if I download the matrix alone, a taxon block with the correct order is used: http://treebase-stage.nescent.org/treebase-web/phylows/matrix/TB2:M4847?format=nexus And if I download the *whole* study as nexus, the correct order is used: http://treebase-stage.nescent.org/treebase-web/phylows/study/TB2:S10232?format=nexus So the problem is in the analysis download. It looks as though the analysis download is re-creating new taxon blocks on the fly, whereas the matrix download is fetching them from the "taxonlabelset" and "taxonlabelset_taxonlabel" tables. A quick fix for the analysis download is the following: create taxon blocks using the information in taxonlabelset and taxonlabelset_taxonlabel tables. If any resulting trees come from a tree block that shares the same taxonlabelset_id as a matrix, then the resulting tree should have a "LINK TAXA" command that points to the *same* taxon block as the matrix. i.e. the number of taxa blocks that are generated at the top of the nexus file are determined by the number of unique taxonlabelset_id values linked to all character blocks and all trees/treeblocks linked to the analysis. The long-term fix is more complicated, namely auto-generate a single taxon block for a particular analysis download, use "LINK TAXA" to have all character blocks and tree blocks refer back to this same taxon block, but within each character block insure that the rows are sorted in exactly the same way as in the taxon block. I'll let you guys decide what to do, but I'm guessing that the quick fix is easier to implement, and while not as ideal as the long-term fix, it solves the row scrambling problem prior to public release. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-17 14:22 Message: Downgrade to 8 as we are disabling this feature in the UI until this is resolved. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970700&group_id=248804 |
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From: <yo...@us...> - 2010-04-22 18:29:39
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Revision: 693
http://treebase.svn.sourceforge.net/treebase/?rev=693&view=rev
Author: youjun
Date: 2010-04-22 18:29:32 +0000 (Thu, 22 Apr 2010)
Log Message:
-----------
fix: Analysis download scrambles taxon labels - ID: 2970700
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/analysis.jsp
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java 2010-04-22 18:28:28 UTC (rev 692)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DownloadAnAnalysisStepController.java 2010-04-22 18:29:32 UTC (rev 693)
@@ -140,7 +140,7 @@
PhyloTree tree = data.getTreeData();
Matrix matrix = data.getMatrixData();
if ( tree != null ) {
- tree.getTreeBlock().setTaxonLabelSet(inputLabelSet);
+ tree.getTreeBlock().setTaxonLabelSet(inputLabelSet);
tree.buildNexusBlock(stepContent);
}
if ( matrix != null ) {
@@ -152,7 +152,7 @@
stepContent.append("[ The following blocks are output data for analysis step " + analysisId + " ]\n");
TaxonLabelSet outputLabelSet = step.getOutputTaxonLabelSet();
- outputLabelSet.buildNexusBlockTaxa(stepContent, true, false);
+ //outputLabelSet.buildNexusBlockTaxa(stepContent, true, false);
for ( AnalyzedData data : step.getDataSetReadOnly() ) {
if ( ! data.isInputData() ) {
PhyloTree tree = data.getTreeData();
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp 2010-04-22 18:28:28 UTC (rev 692)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp 2010-04-22 18:29:32 UTC (rev 693)
@@ -45,7 +45,7 @@
alt="<fmt:message key="analysis.notvalidated"/>"/>
</span>
<!-- VG 2010-03-17 Disabled analysis download as requested in #2972107, to mitigate #2970700 and #2970457 -->
-<!-- <a href="/treebase-web/search/downloadAnAnalysisStep.html?analysisid=${analysisStepCommand.id}&id=${analysisStepCommand.analysis.study.id}"> -->
+ <a href="/treebase-web/search/downloadAnAnalysisStep.html?analysisid=${analysisStepCommand.id}&id=${analysisStepCommand.analysis.study.id}">
<img
class="iconButton"
src="<fmt:message key="icons.download.reconstructed"/>"
@@ -56,7 +56,7 @@
title="<fmt:message key="download.unavailable"/>"
alt="<fmt:message key="download.unavailable"/>"
/>
-<!-- </a> -->
+ </a>
<c:if test="${not empty analysisStepCommand.displayName}">
<c:out value="${analysisStepCommand.displayName}"/>
</c:if>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/analysis.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/analysis.jsp 2010-04-22 18:28:28 UTC (rev 692)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/study/analysis.jsp 2010-04-22 18:29:32 UTC (rev 693)
@@ -48,13 +48,13 @@
border="0"
onClick="CollapseExpand('${AnalysisStepId}')"/>
<!-- commented out due to issue# 2970700 and issue# 2970457 -->
- <!-- <a href="/treebase-web/search/downloadAnAnalysisStep.html?analysisid=${analysisStep.id}"> -->
+ <a href="/treebase-web/search/downloadAnAnalysisStep.html?analysisid=${analysisStep.id}">
<img
class="iconButton"
src="<fmt:message key="icons.download.reconstructed"/>"
title="<fmt:message key="download.reconstructedfile"/>"
alt="<fmt:message key="download.reconstructedfile"/>"/>
- <!-- </a> -->
+ </a>
<strong>Analysis Step ${status_analysisStep.count}:</strong>
<c:out value="${analysisStepCommand.name}" />
</li>
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From: <yo...@us...> - 2010-04-22 18:28:34
|
Revision: 692
http://treebase.svn.sourceforge.net/treebase/?rev=692&view=rev
Author: youjun
Date: 2010-04-22 18:28:28 +0000 (Thu, 22 Apr 2010)
Log Message:
-----------
fix: Analysis download scrambles taxon labels - ID: 2970700
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -528,7 +528,7 @@
}
}
pBuilder
- .append(TreebaseUtil.getLineSeparators(2)).append("Study ID = " + pStudy.getId())
+ .append(TreebaseUtil.getLineSeparators(2)).append("TreeBASE Study URI: " + pStudy.getPhyloWSPath().getPurl())
.append("]").append(TreebaseUtil.getLineSeparators(2));
}
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/CharacterMatrix.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -600,7 +600,8 @@
public void generateMatrixTable(StringBuilder pBuilder) {
// MATRIX section:
- List<MatrixRow> matrixRows = getRows();
+ List<MatrixRow> matrixRows = new ArrayList<MatrixRow>(getRows());
+ sortRowByTaxonLabel(matrixRows);
Iterator<MatrixRow> iterator = matrixRows.iterator();
ArrayList<String> tLabel = new ArrayList<String>();
@@ -851,7 +852,7 @@
if (isDefaultCodonSet(codonSet)) {
pStrBuilder.append('*');
}
- pStrBuilder.append(" ").append(codonSet.getTitle()).append(" = ").append(TreebaseUtil.LINESEP);
+ pStrBuilder.append(" ").append(codonSet.getTitle()).append(" (CHARACTERS = ").append(StringUtil.tokenize(getTitle())).append(") = ").append(TreebaseUtil.LINESEP);
codonSet.generateNexusString(pStrBuilder);
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/Matrix.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -1,6 +1,7 @@
package org.cipres.treebase.domain.matrix;
+import java.util.Comparator;
import java.util.List;
import javax.persistence.AttributeOverride;
@@ -419,7 +420,7 @@
pBuilder.append("BEGIN CHARACTERS;").append(TreebaseUtil.LINESEP);
pBuilder
- .append("[! Matrix ID =").append(getId()).append(" ]").append(TreebaseUtil.LINESEP)
+ .append("[! TreeBASE Matrix URI: ").append(getPhyloWSPath().getPurl()).append("]").append(TreebaseUtil.LINESEP)
.append(TreebaseUtil.LINESEP);
pBuilder.append("\tTITLE ").append(StringUtil.tokenize(getTitle())).append(";").append(
@@ -432,7 +433,7 @@
} else {
taxaTitle = "No taxa found for this matrix. Old data. Need to import this matrix again.";
}
- pBuilder.append("\tLINK TAXA = " + StringUtil.tokenize(taxaTitle) + ";").append(
+ pBuilder.append("\tLINK TAXA = " + StringUtil.tokenize(taxaTitle.replaceAll("Input|Output", "")) + ";").append(
TreebaseUtil.LINESEP);
pBuilder.append(getDimensionsInfo()).append(TreebaseUtil.LINESEP);
@@ -516,4 +517,18 @@
public void setDimensions() {
// By default, do nothing
}
+
+ protected void sortRowByTaxonLabel(List<MatrixRow> rList)
+ {
+ java.util.Collections.sort(rList, new Comparator<MatrixRow>() {
+
+ public int compare(MatrixRow pObject1, MatrixRow pObject2) {
+ String id1 = pObject1.getTaxonLabel().getTaxonLabel();
+ String id2 = pObject2.getTaxonLabel().getTaxonLabel();
+ return id1.compareTo(id2);
+ }
+
+ });
+
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/UserDefinedCharSet.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -11,6 +11,8 @@
import javax.persistence.OneToMany;
import javax.persistence.Transient;
+import mesquite.lib.StringUtil;
+
import org.hibernate.annotations.Cache;
import org.hibernate.annotations.CacheConcurrencyStrategy;
@@ -74,7 +76,7 @@
@Override
public String getNexusString() {
StringBuilder sb = new StringBuilder();
- sb.append(getNexusPrefix()).append(getTitle()).append(" = ");
+ sb.append(getNexusPrefix()).append(getTitle()).append(" (CHARACTERS = ").append(StringUtil.tokenize(getMatrix().getTitle())).append(") = ");
for (ColumnRange colRange : getColumns()) {
sb.append(" ");
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelSet.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -2,6 +2,7 @@
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import javax.persistence.AttributeOverride;
@@ -192,11 +193,12 @@
*/
public void buildNexusBlockTaxa(StringBuilder pBuilder, boolean pOnePerLine, boolean pLineNumber) {
- List<TaxonLabel> txnlbllist = getTaxonLabelsReadOnly();
+ List<TaxonLabel> txnlbllist = new ArrayList<TaxonLabel>(getTaxonLabelList());
+ sortByTaxonLabel(txnlbllist);
int numoftxnlbls = txnlbllist.size();
pBuilder.append("BEGIN TAXA;\n");
- pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle()) + ";\n");
+ pBuilder.append(" TITLE " + StringUtil.tokenize(getTitle().replaceAll("Input|Output", "")) + ";\n");
pBuilder.append(" DIMENSIONS NTAX=" + numoftxnlbls + ";\n");
pBuilder.append(" TAXLABELS\n");
pBuilder.append(" ");
@@ -258,4 +260,17 @@
return getTitle();
}
+ private void sortByTaxonLabel(List<TaxonLabel> tList)
+ {
+ java.util.Collections.sort(tList, new Comparator<TaxonLabel>() {
+
+ public int compare(TaxonLabel pObject1, TaxonLabel pObject2) {
+ String id1 = pObject1.getTaxonLabel();
+ String id2 = pObject2.getTaxonLabel();
+ return id1.compareTo(id2);
+ }
+
+ });
+
+ }
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-04-16 17:33:35 UTC (rev 691)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/tree/PhyloTree.java 2010-04-22 18:28:28 UTC (rev 692)
@@ -557,7 +557,7 @@
pBuilder.append("BEGIN TREES;\n");
pBuilder
.append(" TITLE ").append(StringUtil.tokenize(blockTitle)).append(";\n");
- pBuilder.append(" LINK TAXA = ").append(StringUtil.tokenize(taxaTitle)).append(";\n");
+ pBuilder.append(" LINK TAXA = ").append(StringUtil.tokenize(taxaTitle.replaceAll("Input|Output", ""))).append(";\n");
pBuilder.append(" TREE ").append(StringUtil.tokenize(getLabel())).append(" = ");
if (getRootedTree() != null) {
@@ -569,7 +569,7 @@
}
pBuilder.append(getNewickString()).append("\n");
- pBuilder.append("[! TreeBASE tree Id = ").append(getId()).append(" ]\n");
+ pBuilder.append("[! TreeBASE tree URI: ").append(getPhyloWSPath().getPurl()).append("]\n");
pBuilder.append("\n\nEND;\n");
}
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From: SourceForge.net <no...@so...> - 2010-04-20 19:29:41
|
Bugs item #2970700, was opened at 2010-03-15 11:29 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970700&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: youjun guo (youjun) Summary: Analysis download scrambles taxon labels Initial Comment: Analysis download scrambles taxon labels Analysis download creates a taxon block in which the order of the names does not match with the order of the names in the associated character block. This will cause software programs like PAUP and Mesquite to scramble the taxon labels with the characters that they are supposed to map to. For example, see here: http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5539&id=10232 By contrast, if I download the matrix alone, a taxon block with the correct order is used: http://treebase-stage.nescent.org/treebase-web/phylows/matrix/TB2:M4847?format=nexus And if I download the *whole* study as nexus, the correct order is used: http://treebase-stage.nescent.org/treebase-web/phylows/study/TB2:S10232?format=nexus So the problem is in the analysis download. It looks as though the analysis download is re-creating new taxon blocks on the fly, whereas the matrix download is fetching them from the "taxonlabelset" and "taxonlabelset_taxonlabel" tables. A quick fix for the analysis download is the following: create taxon blocks using the information in taxonlabelset and taxonlabelset_taxonlabel tables. If any resulting trees come from a tree block that shares the same taxonlabelset_id as a matrix, then the resulting tree should have a "LINK TAXA" command that points to the *same* taxon block as the matrix. i.e. the number of taxa blocks that are generated at the top of the nexus file are determined by the number of unique taxonlabelset_id values linked to all character blocks and all trees/treeblocks linked to the analysis. The long-term fix is more complicated, namely auto-generate a single taxon block for a particular analysis download, use "LINK TAXA" to have all character blocks and tree blocks refer back to this same taxon block, but within each character block insure that the rows are sorted in exactly the same way as in the taxon block. I'll let you guys decide what to do, but I'm guessing that the quick fix is easier to implement, and while not as ideal as the long-term fix, it solves the row scrambling problem prior to public release. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-17 14:22 Message: Downgrade to 8 as we are disabling this feature in the UI until this is resolved. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970700&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2010-04-20 18:58:28
|
Bugs item #2974738, was opened at 2010-03-22 14:18 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974738&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: youjun guo (youjun) Summary: listing studies causes exception Initial Comment: When admin person wants to get a list of all "in progress" studies, a "yikes" message is returned. http://www.treebase.org/treebase-web/admin/selectStudies.html ============ Yikes! javax.servlet.jsp.el.ELException: An error occurred while getting property "emailAddressString" from an instance of class org.cipres.treebase.domain.admin.User$$EnhancerByCGLIB$$6ece7264 at org.apache.commons.el.Logger.logError(Logger.java:484) at org.apache.commons.el.Logger.logError(Logger.java:588) at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318) at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263) at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190) at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924) at org.apache.jsp.WEB_002dINF.pages.changeStudyStatus_jsp._jspx_meth_display_005fcolumn_005f1(changeStudyStatus_jsp.java:456) at org.apache.jsp.WEB_002dINF.pages.changeStudyStatus_jsp._jspService(changeStudyStatus_jsp.java:160) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2010-04-20 14:58 Message: Appears to be fixed. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2974738&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-04-20 18:45:32
|
Bugs item #2970457, was opened at 2010-03-14 21:58 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970457&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: performance Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: downloading analysis as nexus hangs Initial Comment: I added and finalized a completely new submission to TreeBASE in order to test the submission process from beginning to end. The result is this new study: http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10315 And everything looks good except that I cannot download one of the analyses (and I can't download the whole study either) as nexus -- the browser spins round and round and finally finishes with a Proxy Error. This is the bad one: http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5758&id=10315 But strangely enough, the other analyses work fine (even though they are all pulling about the same amount of data): http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5759&id=10315 http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5760&id=10315 The individual components of the analysis (1 matrix and 2 trees) can be downloaded without a problem. ---------------------------------------------------------------------- Comment By: Hilmar Lapp (hlapp) Date: 2010-03-17 14:23 Message: Downgrading to 8 as we are disabling this in the UI until this and issue# 2970700 have been resolved. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2970457&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-04-20 18:42:51
|
Bugs item #2808555, was opened at 2009-06-18 14:15 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2808555&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: 4 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Nobody/Anonymous (nobody) Summary: DOI column in study list takes up too much space Initial Comment: When a DOI is available for a study, it forces the table to allocate lots of space for the DOI column, causing the Title column (which is the more important one) to be squashed and multi-line. It would be better if we did not even show the whole DOI in the study summary list, but rather just offered the mini-icon with an active DOI resolver link. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2808555&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2010-04-17 02:18:24
|
Bugs item #2984516, was opened at 2010-04-09 11:00 Message generated for change (Comment added) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2984516&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: youjun guo (youjun) Summary: Analysis step broken in IE8 Initial Comment: When creating a new analysis step, the user should be able to select inputs and outputs. In IE8, the user cannot pick the inputs or outputs (IETester http://www.my-debugbar.com/wiki/IETester/HomePage reports a NULL value for the object ID). ---------------------------------------------------------------------- >Comment By: youjun guo (youjun) Date: 2010-04-16 22:18 Message: ie8 cannot return correct array length, yet the innerhtml in select tag cannot work properly ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2984516&group_id=248804 |
|
From: <yo...@us...> - 2010-04-16 17:33:41
|
Revision: 691
http://treebase.svn.sourceforge.net/treebase/?rev=691&view=rev
Author: youjun
Date: 2010-04-16 17:33:35 +0000 (Fri, 16 Apr 2010)
Log Message:
-----------
solve a issue cause by ie bugs
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/user/analysisEditor.js
Modified: trunk/treebase-web/src/main/webapp/scripts/user/analysisEditor.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/user/analysisEditor.js 2010-04-15 21:00:46 UTC (rev 690)
+++ trunk/treebase-web/src/main/webapp/scripts/user/analysisEditor.js 2010-04-16 17:33:35 UTC (rev 691)
@@ -77,25 +77,35 @@
if ( selector.value == 'Matrices' ) {
var m = TreeBASE.submission.submittedMatrices;
for ( var i = 0; i < m.length; i++ ) {
- innerOptions += '<option value="' + m[i].id + '">' + m[i].title + '</option>';
+ if(typeof(m[i])!= "undefined"){
+ innerOptions += '<option value=\"' + m[i].id + '\">' + m[i].title + '</option>';
+ }
}
}
else if ( selector.value == 'TreeBlocks' ) {
var tb = TreeBASE.submission.submittedTreeBlocks;
for ( var i = 0; i < tb.length; i++ ) {
- innerOptions += '<option value="' + tb[i].id + '">' + tb[i].title + '</option>';
- }
+ if(typeof(tb[i])!= "undefined"){
+ innerOptions += '<option value=\"' + tb[i].id + '\">' + tb[i].title + '</option>';
+ }
+ }
}
else if ( selector.value == 'Trees' ) {
var tb = TreeBASE.submission.submittedTreeBlocks;
for ( var i = 0; i < tb.length; i++ ) {
- var t = tb[i].treeList;
- for ( var j = 0; j < t.length; j++ ) {
- innerOptions += '<option value="' + t[j].id + '">' + t[j].label + '</option>';
- }
+ if(typeof(tb[i])!= "undefined"){
+ var t = tb[i].treeList;
+ for ( var j = 0; j < t.length; j++ ) {
+ if(typeof(t[j])!= "undefined"){
+ innerOptions += '<option value=\"' + t[j].id + '\">' + t[j].label + '</option>';
+ }
+ }
+ }
}
}
- selects[1].innerHTML = innerOptions;
+
+ //selects[1].innerHTML = innerOptions;
+ $(selects[1]).update(innerOptions);
selects[1].name = selector.value;
var inputs = theDiv.getElementsByTagName('input');
inputs[0].style.display = 'block';
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <vga...@us...> - 2010-04-15 21:00:53
|
Revision: 690
http://treebase.svn.sourceforge.net/treebase/?rev=690&view=rev
Author: vgapeyev
Date: 2010-04-15 21:00:46 +0000 (Thu, 15 Apr 2010)
Log Message:
-----------
A better TB URL in the text of the password reminder (before, it would show localhost).
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java 2010-04-15 20:09:08 UTC (rev 689)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java 2010-04-15 21:00:46 UTC (rev 690)
@@ -124,9 +124,11 @@
+ "Thank you for requesting username/password from TreeBASE.\n\nHere is your username: "
+ u.getUsername() + "\nYour password: "
+ u.getPassword()
- + "\n\nTreebase login site: "
- + generateServerURL(request)
- + "/login.jsp");
+ + "\n\nTreebase site: "
+ + TreebaseUtil.getSiteUrl());
+// + "\n\nTreebase login site: "
+// + generateServerURL(request)
+// + "/login.jsp");
// send the message
Transport.send(message);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: SourceForge.net <no...@so...> - 2010-04-15 20:20:43
|
Bugs item #2977860, was opened at 2010-03-27 23:41 Message generated for change (Comment added) made by vgapeyev You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977860&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: internals Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Vladimir Gapeyev (vgapeyev) Summary: Exception when requesting password Initial Comment: When user forgets password and asks to have it emailed, exception barf returns. Uncaught Exception Encountered javax.mail.SendFailedException: Send failure (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. )))) at javax.mail.Transport.send(Transport.java:163) at javax.mail.Transport.send(Transport.java:48) at org.cipres.treebase.web.controllers.PasswordFormController.onSubmit(PasswordFormController.java:132) 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.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. ))) at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1196) at com.sun.mail.smtp.SMTPTransport.sendMessage(SMTPTransport.java:584) at javax.mail.Transport.send(Transport.java:95) ... 54 more Caused by: com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. (javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. )) at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1047) ... 56 more Caused by: javax.mail.SendFailedException: Invalid Addresses (com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. ) at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1196) ... 56 more Caused by: com.sun.mail.smtp.SMTPAddressFailedException: 550 5.7.1 ... Relaying denied. Proper authentication required. at com.sun.mail.smtp.SMTPTransport.rcptTo(SMTPTransport.java:1047) ... 56 more Cookies: JSESSIONID=[887390FE613CEE56D2EEFCCE3D7FF91C] __utma=[216002130.839762607.1263756393.1264687215.1264739521.8] __utmz=[216002130.1263756393.1.1.utmccn] ---------------------------------------------------------------------- >Comment By: Vladimir Gapeyev (vgapeyev) Date: 2010-04-15 16:20 Message: SMTP host name should now be supplied as via JNDI parameter tb2/SmtpHost ---------------------------------------------------------------------- Comment By: Vladimir Gapeyev (vgapeyev) Date: 2010-04-09 11:14 Message: On Apr 9, 2010, at 11:00 AM, youjun guo wrote: The problem is "Relaying denied", the cause is org.cipres.treebase.web.controllers.PasswordFormController.onSubmit(PasswordFormController.java:132). I quote the line below: 'props.put("mail.smtp.host", "smtp.ucsd.edu");' AS you can see we need to replace that ucsd smtp server url with NESCent's smtp. The problem is I cannot test it from my personnel server even I have the correct url. There will be most likely another "Relaying denied". ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2977860&group_id=248804 |
|
From: <vga...@us...> - 2010-04-15 20:09:16
|
Revision: 689
http://treebase.svn.sourceforge.net/treebase/?rev=689&view=rev
Author: vgapeyev
Date: 2010-04-15 20:09:08 +0000 (Thu, 15 Apr 2010)
Log Message:
-----------
Added JNDI parameter tb2/SmtpHost. This fixes SF#2977860
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java
trunk/treebase-web/src/main/webapp/META-INF/context.xml.example
trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-15 19:39:53 UTC (rev 688)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/TreebaseUtil.java 2010-04-15 20:09:08 UTC (rev 689)
@@ -45,6 +45,7 @@
private static final Logger LOGGER = Logger.getLogger(TreebaseUtil.class);
private static String mPurlBase;
private static String mSiteUrl;
+ private static String mSmtpHost;
private TreebaseUtil() {
super();
@@ -431,41 +432,25 @@
return date + " GMT";
}
+
- /**
- * This method returns the domain name (possibly with port number)
- * which can be used to construct URLs by prefixing with "http://"
- * and suffixing with the full path (e.g. "/treebase-web")
+ /** Looks up a JNDI Environment parameter that carries a string value.
*
- * @return domain name
*/
- /*--
- public static String getPurlBase() {
- if ( null == mPurlDomain ) {
- Properties properties = new Properties();
- try {
- properties.load(
- TreebaseUtil.class
- .getClassLoader()
- .getResourceAsStream("treebase.properties"));
- LOGGER.info("properties loaded successfully");
- mPurlDomain = properties.getProperty("treebase.purl.domain");
- LOGGER.info("domain name: "+mPurlDomain);
- } catch (FileNotFoundException e) {
- LOGGER.warn("FileNotFoundException: " + e.getMessage());
- e.printStackTrace();
- } catch (IOException e) {
- LOGGER.warn("IOException: "+e.getMessage());
- e.printStackTrace();
- }
- return mPurlDomain;
+ private static String lookupJndiEnvironmentString(String name, String fallback) {
+ String result = fallback;
+ try {
+ InitialContext ic = new InitialContext();
+ result = (String) ic.lookup("java:comp/env/" + name);
+ } catch (NamingException e) {
+ LOGGER.info("Failure looking up " + name + " via JNDI");
+ e.printStackTrace();
}
- else {
- return mPurlDomain;
- }
+ return result;
}
-*/
+
+
/**
* Returns the base URL of the PURL service associated with this Treebase instance,
* which can be used to construct full PURLs by suffixing with a PhyloWS command, e.g. "/study/TB2:S1925"
@@ -473,21 +458,10 @@
* @return the base URL of the PURL service
*/
public static String getPurlBase() {
- if (null != mPurlBase)
- return mPurlBase;
- else {
- try {
- mPurlBase = "http://DUMMY_PURL_BASE/";
- InitialContext ic = new InitialContext();
- mPurlBase = (String) ic.lookup("java:comp/env/tb2/PurlBase");
- } catch (NamingException e) {
- LOGGER.info("Failure looking up tb2/PurlBase via JNDI");
- e.printStackTrace();
- }
- return mPurlBase;
- }
+ if (null == mPurlBase)
+ mPurlBase = lookupJndiEnvironmentString("tb2/PurlBase", "http://DUMMY_PURL_BASE/");
+ return mPurlBase;
}
-
/**
* Returns the base URL of this Treebase instance, by looking it up in Tomcat via JNDI.
@@ -495,22 +469,23 @@
* @return the base URL of of this Treebase instance
*/
public static String getSiteUrl() {
- if (null != mSiteUrl)
- return mSiteUrl;
- else {
- try {
- mSiteUrl = "http://DUMMY_SITE_URL/";
- InitialContext ic = new InitialContext();
- mSiteUrl = (String) ic.lookup("java:comp/env/tb2/SiteUrl");
- } catch (NamingException e) {
- LOGGER.info("Failure looking up tb2/SiteUrl via JNDI");
- e.printStackTrace();
- }
- return mSiteUrl;
- }
+ if (null == mSiteUrl)
+ mSiteUrl = lookupJndiEnvironmentString("tb2/SiteUrl", "http://DUMMY.SITE.COM/");
+ return mSiteUrl;
}
+
+ /**
+ *
+ * @return the SMTP host to use for automated email
+ */
+ public static String getSmtpHost() {
+ if (null == mSmtpHost)
+ mSmtpHost = lookupJndiEnvironmentString("tb2/SmtpHost", "smtp.DUMMY.HOST");
+ return mSmtpHost;
+ }
+
/**
* This method appends header information upon formatting to the nexus file.
*
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java 2010-04-15 19:39:53 UTC (rev 688)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PasswordFormController.java 2010-04-15 20:09:08 UTC (rev 689)
@@ -107,7 +107,7 @@
// create mail session
Properties props = new Properties();
- props.put("mail.smtp.host", "smtp.ucsd.edu");
+ props.put("mail.smtp.host", TreebaseUtil.getSmtpHost());
Session mailSession = Session.getDefaultInstance(props,null);
// create email message header information
Modified: trunk/treebase-web/src/main/webapp/META-INF/context.xml.example
===================================================================
--- trunk/treebase-web/src/main/webapp/META-INF/context.xml.example 2010-04-15 19:39:53 UTC (rev 688)
+++ trunk/treebase-web/src/main/webapp/META-INF/context.xml.example 2010-04-15 20:09:08 UTC (rev 689)
@@ -37,6 +37,10 @@
type="java.lang.String" override="false"
description="The base URL of a PURL service that redirects to this Treebase instance."/>
+ <Environment name="tb2/SmtpHost" value="smtp.YOUR.SERVER.ORG"
+ type="java.lang.String" override="false"
+ description="Host name of an SMTP server that your instance can use without authentication."/>
+
</Context>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-04-15 19:39:53 UTC (rev 688)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml 2010-04-15 20:09:08 UTC (rev 689)
@@ -73,6 +73,11 @@
<env-entry-type>java.lang.String</env-entry-type>
</env-entry>
+ <env-entry>
+ <description>Host name of an SMTP server that your instance can use without authentication.</description>
+ <env-entry-name>tb2/SmtpHost</env-entry-name>
+ <env-entry-type>java.lang.String</env-entry-type>
+ </env-entry>
<!-- ========================================================== -->
<!-- List of Filters -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <vga...@us...> - 2010-04-15 19:39:59
|
Revision: 688
http://treebase.svn.sourceforge.net/treebase/?rev=688&view=rev
Author: vgapeyev
Date: 2010-04-15 19:39:53 +0000 (Thu, 15 Apr 2010)
Log Message:
-----------
Applied the patch to production
Modified Paths:
--------------
trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt
trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql
Modified: trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt 2010-04-15 06:22:27 UTC (rev 687)
+++ trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt 2010-04-15 19:39:53 UTC (rev 688)
@@ -14,4 +14,13 @@
---------
Apply changes as soon as convenient, because it is not impossible that new submissions
-in the interim will map to taxonvariants that this script wants to delete.
\ No newline at end of file
+in the interim will map to taxonvariants that this script wants to delete.
+
+
+----------------
+
+Jon and Vladimir ran this on production 2010-04-15
+Afterwards, we updated the sequences to:
+ taxon_id_sequence 600100
+ taxonvariant_id_sequence 800100
+
\ No newline at end of file
Modified: trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql 2010-04-15 06:22:27 UTC (rev 687)
+++ trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql 2010-04-15 19:39:53 UTC (rev 688)
@@ -1,5 +1,5 @@
-being work;
+begin work;
-- start by creating new records in taxon
-- I'm assuming that it is safe to start taxon_id at 600001
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2010-04-15 06:22:34
|
Revision: 687
http://treebase.svn.sourceforge.net/treebase/?rev=687&view=rev
Author: sfrgpiel
Date: 2010-04-15 06:22:27 +0000 (Thu, 15 Apr 2010)
Log Message:
-----------
Set of edits to the taxonlabel-taxonvariant-taxon tables.
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/
trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt
trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql
Added: trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt 2010-04-15 06:22:27 UTC (rev 687)
@@ -0,0 +1,17 @@
+To apply, run taxon_fixes_4-15-10.sql
+
+--------
+
+These statements help clean up the mapping between taxonlabel, taxonvariant, and
+taxon records. They include INSERTS in which the primary key is being supplied:
+please verify that this is okay, or will it confuse Hibernate's autoincrement?
+
+New taxon_id starts at 600001
+New taxonvariant_id starts at 800000
+
+Please verify that these numbers are beyond the current highest numbers.
+
+---------
+
+Apply changes as soon as convenient, because it is not impossible that new submissions
+in the interim will map to taxonvariants that this script wants to delete.
\ No newline at end of file
Added: trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/taxon_fixes_4-15-10.sql 2010-04-15 06:22:27 UTC (rev 687)
@@ -0,0 +1,160 @@
+
+being work;
+
+-- start by creating new records in taxon
+-- I'm assuming that it is safe to start taxon_id at 600001
+
+INSERT INTO taxon (taxon_id, ubionamebankid, ncbitaxid, name) VALUES (600001, 3877253, NULL, 'Medicago sativa sativa');
+
+-- next create new records in taxonvariant.
+-- I'm assuming that it is safe to start taxonvariant_ids at 800000
+
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800000, 487876, NULL, 3530048, 'Golenkinia parvula', 'Golenkinia parvula');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800001, 487876, NULL, 1982801, 'Golenkinia parvula Woronchin', 'Golenkinia parvula');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800002, 570355, NULL, 3307644, 'Dictyosphaerium tetrachotomum', 'Dictyosphaerium tetrachotomum');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800003, 570355, NULL, 1471279, 'Dictyosphaerium tetrachotomum Printz', 'Dictyosphaerium tetrachotomum');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800004, 5878, NULL, 10129595, 'Parachlorella kessleri (Fott et Novakova) Krienitz et al.', 'Parachlorella kessleri');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800006, 570269, NULL, 5394354, 'Danthonia chilensis var. chilensis', 'Danthonia chilensis chilensis');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800007, 570269, NULL, NULL, 'Danthonia chilensis chilensis', 'Danthonia chilensis chilensis');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800008, 570268, NULL, 5394356, 'Danthonia chilensis var. aureofulva (E. Desv.) C. Baeza, 1996', 'Danthonia chilensis aureofulva');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800009, 570268, NULL, 8585092, 'Danthonia chilensis E. Desv. var. aureofulva (E. Desv.) C. Baeza', 'Danthonia chilensis aureofulva');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800010, 570268, NULL, 10905520, 'Danthonia chilensis var. aureofulva', 'Danthonia chilensis aureofulva');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800011, 570268, NULL, NULL, 'Danthonia chilensis aureofulva', 'Danthonia chilensis aureofulva');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800012, 428221, NULL, 8583992, 'Cortaderia boliviensis M. Lyle', 'Cortaderia boliviensis');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800013, 428221, NULL, 5393919, 'Cortaderia boliviensis M. Lyle, 1996', 'Cortaderia boliviensis');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800014, 452694, NULL, 10751874, 'Danthonia paschalis', 'Danthonia paschalis');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800016, 452694, NULL, 5409860, 'Rytidosperma paschale (Pilg.) C. Baeza, 1990 [1991]', 'Rytidosperma paschale');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800018, 570088, NULL, 1142512, 'Hebeloma victoriense A. A. Holland & Pegler 1983', 'Hebeloma victoriense');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800019, 570015, NULL, NULL, 'Medicago sativa subsp. x hemicycla', 'Medicago sativa hemicycla');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800020, 62238, NULL, 10139860, 'Medicago sativa subsp. x varia', 'Medicago sativa x varia');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800021, 39943, NULL, NULL, 'Hylarana plancyi', 'Hylarana plancyi');
+INSERT INTO taxonvariant (taxonvariant_id, taxon_id, lexicalqualifier, namebankid, fullname, name) VALUES (800022, 24813, NULL, 10259115, 'Sierrana maculata', 'Sierrana maculata');
+
+-- now remap taxonlabel records
+
+UPDATE taxonlabel SET taxonvariant_id = 599278 WHERE taxonlabel_id = 280817;
+UPDATE taxonlabel SET taxonvariant_id = 113112 WHERE taxonlabel_id = 287452;
+UPDATE taxonlabel SET taxonvariant_id = 457054 WHERE taxonlabel_id = 84843;
+UPDATE taxonlabel SET taxonvariant_id = 790039 WHERE taxonlabel_id = 277319;
+UPDATE taxonlabel SET taxonvariant_id = 790138 WHERE taxonlabel_id = 279223;
+UPDATE taxonlabel SET taxonvariant_id = 457054 WHERE taxonlabel_id = 279257;
+UPDATE taxonlabel SET taxonvariant_id = 564067 WHERE taxonlabel_id = 280963;
+UPDATE taxonlabel SET taxonvariant_id = 800011 WHERE taxonlabel_id = 281078;
+UPDATE taxonlabel SET taxonvariant_id = 800007 WHERE taxonlabel_id = 281099;
+UPDATE taxonlabel SET taxonvariant_id = 27564 WHERE taxonlabel_id = 283820;
+UPDATE taxonlabel SET taxonvariant_id = 790655 WHERE taxonlabel_id = 287465;
+UPDATE taxonlabel SET taxonvariant_id = 646502 WHERE taxonlabel_id = 287472;
+UPDATE taxonlabel SET taxonvariant_id = 646502 WHERE taxonlabel_id = 287478;
+
+-- now remap and/or edit taxonvariant records
+
+UPDATE taxonvariant SET lexicalqualifier = 'synonym', namebankid = 10139861, fullname = 'Medicago sativa x Medicago falcata', name = 'Medicago sativa x Medicago falcata', taxon_id = 50823 WHERE taxonvariant_id = 136320;
+UPDATE taxonvariant SET lexicalqualifier = 'synonym', namebankid = 10197530, fullname = 'Fusarium fujikuroi complex', name = 'Fusarium fujikuroi complex', taxon_id = 11549 WHERE taxonvariant_id = 236540;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 5985800, fullname = 'Gibberella fujikuroi complex', name = 'Gibberella fujikuroi complex', taxon_id = 11549 WHERE taxonvariant_id = 236541;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 10203168, fullname = 'Ditylenchus dipsaci from Cirsium setosum', name = 'Ditylenchus dipsaci', taxon_id = 157494 WHERE taxonvariant_id = 246611;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 10203169, fullname = 'Ditylenchus dipsaci from Fragaria sp.', name = 'Ditylenchus dipsaci from Fragaria sp.', taxon_id = 157494 WHERE taxonvariant_id = 246612;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 10203170, fullname = 'Ditylenchus dipsaci from Medicago sativa', name = 'Ditylenchus dipsaci', taxon_id = 157494 WHERE taxonvariant_id = 246613;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 10203171, fullname = 'Ditylenchus dipsaci from Trifolium pratense', name = 'Ditylenchus dipsaci', taxon_id = 157494 WHERE taxonvariant_id = 246614;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 10203172, fullname = 'Ditylenchus dipsaci from Vicia faba', name = 'Ditylenchus dipsaci', taxon_id = 157494 WHERE taxonvariant_id = 246615;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = 10264573, fullname = 'Ditylenchus dipsaci from Daucus carota', name = 'Ditylenchus dipsaci', taxon_id = 157494 WHERE taxonvariant_id = 327113;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 10231531, fullname = 'Alnicola cf. scolecina GLM 37718', name = 'Alnicola scolecina', taxon_id = 221176 WHERE taxonvariant_id = 457054;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 3877253, fullname = 'Medicago sativa sativa', name = 'Medicago sativa sativa', taxon_id = 600001 WHERE taxonvariant_id = 558258;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 6054839, fullname = 'Phrynosoma Douglassi', name = 'Phrynosoma', taxon_id = 34517 WHERE taxonvariant_id = 564155;
+UPDATE taxonvariant SET lexicalqualifier = 'scientific name', namebankid = NULL, fullname = 'Rytidosperma paschale', name = 'Rytidosperma paschale', taxon_id = 452694 WHERE taxonvariant_id = 599276;
+UPDATE taxonvariant SET lexicalqualifier = 'synonym', namebankid = 8588062, fullname = 'Rytidosperma paschale (Pilger) C.M.Baeza', name = 'Rytidosperma paschale', taxon_id = 452694 WHERE taxonvariant_id = 599277;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 10259114, fullname = 'Lithobates maculata', name = 'Lithobates maculata', taxon_id = 24813 WHERE taxonvariant_id = 785042;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 2648840, fullname = 'lunaria', name = 'lunaria', taxon_id = 148165 WHERE taxonvariant_id = 785047;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 10168536, fullname = 'Pelophylax plancyi', name = 'Pelophylax plancyi', taxon_id = 39943 WHERE taxonvariant_id = 785189;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 10127185, fullname = 'Peudomonas aeruginosa', name = 'Peudomonas aeruginosa', taxon_id = 24053 WHERE taxonvariant_id = 785319;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 3877252, fullname = 'Medicago sativa falcata', name = 'Medicago sativa falcata', taxon_id = 50823 WHERE taxonvariant_id = 790033;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10576538, fullname = 'Commiphora angustata', name = 'Commiphora angustata', taxon_id = 570026 WHERE taxonvariant_id = 790049;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10576579, fullname = 'Commiphora glauca', name = 'Commiphora glauca', taxon_id = 570027 WHERE taxonvariant_id = 790050;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10294310, fullname = 'Mucronella sp DJM1309', name = 'Mucronella sp DJM1309', taxon_id = 314202 WHERE taxonvariant_id = 790059;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 2648378, fullname = 'Polanisia uniglandulosa', name = 'Polanisia uniglandulosa C349', taxon_id = 570071 WHERE taxonvariant_id = 790111;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584783, fullname = 'Cleome uncifera', name = 'Cleome uncifera', taxon_id = 570073 WHERE taxonvariant_id = 790113;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584706, fullname = 'Cleome oxalidea', name = 'Cleome oxalidea', taxon_id = 570074 WHERE taxonvariant_id = 790114;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584531, fullname = 'Cleome africana', name = 'Cleome africana', taxon_id = 570075 WHERE taxonvariant_id = 790122;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584553, fullname = 'Cleome breyeri', name = 'Cleome breyeri', taxon_id = 570076 WHERE taxonvariant_id = 790123;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584683, fullname = 'Cleome microaustralica', name = 'Cleome microaustralica', taxon_id = 570078 WHERE taxonvariant_id = 790126;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584566, fullname = 'Cleome cleomoides', name = 'Cleome cleomoides', taxon_id = 570079 WHERE taxonvariant_id = 790127;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10584670, fullname = 'Cleome luederitziana', name = 'Cleome luederitziana', taxon_id = 570081 WHERE taxonvariant_id = 790129;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 2661891, fullname = 'Oryzopsis asperifolia', name = 'Oryzopsis asperifolia', taxon_id = 570096 WHERE taxonvariant_id = 790164;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10748019, fullname = 'Amelichloa brevipes', name = 'Amelichloa brevipes', taxon_id = 570097 WHERE taxonvariant_id = 790165;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10748017, fullname = 'Amelichloa ambigua', name = 'Amelichloa ambigua', taxon_id = 570098 WHERE taxonvariant_id = 790166;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 10751855, fullname = 'Danthonia filifolia', name = 'Danthonia filifolia', taxon_id = 570265 WHERE taxonvariant_id = 790391;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 9739171, fullname = 'Danthonia chilensis var. aureofulva (E. Desv.) C. Baeza', name = 'Danthonia chilensis aureofulva', taxon_id = 570268 WHERE taxonvariant_id = 790394;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 8886481, fullname = 'Danthonia chilensis E. Desv. var. chilensis', name = 'Danthonia chilensis chilensis', taxon_id = 570269 WHERE taxonvariant_id = 790395;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = 3870064, fullname = 'Dictyosphaerium ehrenbergianum', name = 'Dictyosphaerium ehrenbergianum', taxon_id = 570349 WHERE taxonvariant_id = 790655;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 433256, fullname = 'Dictyosphaerium ehrenbergianum Naegeli, 1849', name = 'Dictyosphaerium ehrenbergianum', taxon_id = 570349 WHERE taxonvariant_id = 790656;
+UPDATE taxonvariant SET lexicalqualifier = 'canonical form', namebankid = NULL, fullname = 'Hindakia tetrachotoma', name = 'Hindakia tetrachotoma', taxon_id = 570355 WHERE taxonvariant_id = 790661;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 10751874, fullname = 'Danthonia paschalis', name = 'Danthonia paschalis', taxon_id = 452694 WHERE taxonvariant_id = 800014;
+UPDATE taxonvariant SET lexicalqualifier = NULL, namebankid = 10139860, fullname = 'Medicago sativa subsp. x varia', name = 'Medicago sativa x varia', taxon_id = 62238 WHERE taxonvariant_id = 800020;
+
+-- now edit taxon records
+
+UPDATE taxon SET ncbitaxid = 245165, ubionamebankid = 10231531, name = 'Alnicola cf. scolecina GLM 37718' WHERE taxon_id = 221176;
+UPDATE taxon SET ncbitaxid = 296618, ubionamebankid = 10257505, name = 'Rytidosperma aff. pumilum CHR562184' WHERE taxon_id = 261258;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10576538, name = 'Commiphora angustata' WHERE taxon_id = 570026;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10576579, name = 'Commiphora glauca' WHERE taxon_id = 570027;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 2648378, name = 'Polanisia uniglandulosa' WHERE taxon_id = 570071;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584783, name = 'Cleome uncifera' WHERE taxon_id = 570073;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584706, name = 'Cleome oxalidea' WHERE taxon_id = 570074;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584531, name = 'Cleome africana' WHERE taxon_id = 570075;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584553, name = 'Cleome breyeri' WHERE taxon_id = 570076;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584683, name = 'Cleome microaustralica' WHERE taxon_id = 570078;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584566, name = 'Cleome cleomoides' WHERE taxon_id = 570079;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10584670, name = 'Cleome luederitziana' WHERE taxon_id = 570081;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 2661891, name = 'Oryzopsis asperifolia' WHERE taxon_id = 570096;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10748019, name = 'Amelichloa brevipes' WHERE taxon_id = 570097;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10748017, name = 'Amelichloa ambigua' WHERE taxon_id = 570098;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = 10751855, name = 'Danthonia filifolia' WHERE taxon_id = 570265;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = NULL, name = 'Danthonia chilensis aureofulva' WHERE taxon_id = 570268;
+UPDATE taxon SET ncbitaxid = NULL, ubionamebankid = NULL, name = 'Danthonia chilensis chilensis' WHERE taxon_id = 570269;
+UPDATE taxon SET ncbitaxid = 745283, ubionamebankid = 3870064, name = 'Dictyosphaerium ehrenbergianum' WHERE taxon_id = 570349;
+UPDATE taxon SET ncbitaxid = 745284, ubionamebankid = 3307644, name = 'Dictyosphaerium tetrachotomum' WHERE taxon_id = 570355;
+
+-- taxonvariant records can now be deleted
+
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790047;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790055;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790136;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790140;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790373;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790390;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790393;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790584;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790633;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790634;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790635;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790658;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790663;
+DELETE FROM taxonvariant WHERE taxonvariant_id = 790664;
+
+-- finally, taxon records can be deleted
+
+DELETE FROM taxon WHERE taxon_id = 161564;
+DELETE FROM taxon WHERE taxon_id = 172733;
+DELETE FROM taxon WHERE taxon_id = 172734;
+DELETE FROM taxon WHERE taxon_id = 172735;
+DELETE FROM taxon WHERE taxon_id = 172736;
+DELETE FROM taxon WHERE taxon_id = 172737;
+DELETE FROM taxon WHERE taxon_id = 271867;
+DELETE FROM taxon WHERE taxon_id = 428261;
+DELETE FROM taxon WHERE taxon_id = 564233;
+DELETE FROM taxon WHERE taxon_id = 564366;
+DELETE FROM taxon WHERE taxon_id = 564472;
+DELETE FROM taxon WHERE taxon_id = 570024;
+DELETE FROM taxon WHERE taxon_id = 570032;
+DELETE FROM taxon WHERE taxon_id = 570036;
+DELETE FROM taxon WHERE taxon_id = 570086;
+DELETE FROM taxon WHERE taxon_id = 570264;
+DELETE FROM taxon WHERE taxon_id = 570267;
+DELETE FROM taxon WHERE taxon_id = 570329;
+DELETE FROM taxon WHERE taxon_id = 570330;
+DELETE FROM taxon WHERE taxon_id = 570331;
+DELETE FROM taxon WHERE taxon_id = 570352;
+DELETE FROM taxon WHERE taxon_id = 570357;
+DELETE FROM taxon WHERE taxon_id = 570358;
+
+commit;
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sfr...@us...> - 2010-04-13 17:23:09
|
Revision: 686
http://treebase.svn.sourceforge.net/treebase/?rev=686&view=rev
Author: sfrgpiel
Date: 2010-04-13 17:23:02 +0000 (Tue, 13 Apr 2010)
Log Message:
-----------
Fixes a missing-semicolon problem with some newickstrings that prevent the tree from being viewed in PhyloWidget
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/
trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/README.txt
trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/newickstring_semi.sql
Added: trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/README.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/README.txt 2010-04-13 17:23:02 UTC (rev 686)
@@ -0,0 +1,7 @@
+To apply, run newickstring_semi.sql
+
+--------
+
+This statement will add semicolons to the ends of newickstrings that, for some reason, lack them
+
+---------
Added: trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/newickstring_semi.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/newickstring_semi.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-13_missing_semi_in_newick/newickstring_semi.sql 2010-04-13 17:23:02 UTC (rev 686)
@@ -0,0 +1,14 @@
+
+
+begin work;
+
+UPDATE phylotree
+SET newickstring = newickstring || ';'
+WHERE newickstring NOT LIKE '%;'
+AND newickstring NOT LIKE '% '
+AND newickstring IS NOT NULL;
+
+-- results in 3 changes
+
+commit;
+
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From: <sfr...@us...> - 2010-04-13 15:43:46
|
Revision: 685
http://treebase.svn.sourceforge.net/treebase/?rev=685&view=rev
Author: sfrgpiel
Date: 2010-04-13 15:43:40 +0000 (Tue, 13 Apr 2010)
Log Message:
-----------
New patch to standardize the journal name "Organisms Diversity & Evolution"
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/
trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/README.txt
trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/standardize_journal_names.sql
Added: trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/README.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/README.txt 2010-04-13 15:43:40 UTC (rev 685)
@@ -0,0 +1,9 @@
+To apply, run standardize_journal_names.sql
+
+--------
+
+This statement will standardize how we name the journal "Organisms Diversity & Evolution"
+
+
+---------
+
Added: trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/standardize_journal_names.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/standardize_journal_names.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-13_standardize_journal_names/standardize_journal_names.sql 2010-04-13 15:43:40 UTC (rev 685)
@@ -0,0 +1,10 @@
+
+begin work;
+
+UPDATE citation SET journal = 'Organisms Diversity & Evolution'
+WHERE journal = 'Organisms, Diversity and Evolution'
+OR journal = 'Organisms Diversity and Evolution';
+
+-- should result in about 11 changes
+
+commit;
\ No newline at end of file
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From: <vga...@us...> - 2010-04-13 14:39:52
|
Revision: 684
http://treebase.svn.sourceforge.net/treebase/?rev=684&view=rev
Author: vgapeyev
Date: 2010-04-13 14:39:33 +0000 (Tue, 13 Apr 2010)
Log Message:
-----------
A data patch from Bill
Added Paths:
-----------
trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/
trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/README.txt
trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/set_study_in_phylotrees.sql
Added: trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/README.txt (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/README.txt 2010-04-13 14:39:33 UTC (rev 684)
@@ -0,0 +1,22 @@
+To apply, run set_study_in_phylotrees.sql
+
+--------
+
+From: wil...@ya...
+ Subject: Re: [help.nescent.org #7817] Access to TreeBASE data
+ Date: April 13, 2010 1:03:36 AM EDT
+ To: he...@ne...
+ Cc: vga...@ne..., hl...@ne...
+
+
+So indeed, the study_id value is missing from the phylotree table. This is quite weird because it's very sporadic -- only 10 trees
+(among 433 trees that are new to TreeBASE since we went live) have this problem. It will be hard to replicate the bug, wherever it is.
+
+Bill ran this on treebase-stage 2010-04-13, and after that he was able to go here:
+http://treebase-stage.nescent.org/treebase-web/phylows/study/TB2:S10349?x-access-code=d5039fb25843a2c8a19d7ec93cbe1541&format=html
+... and view and download tree Tr7238 without a problem.
+
+
+---------
+
+Jon will run this on production 2010-04-13
\ No newline at end of file
Added: trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/set_study_in_phylotrees.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/set_study_in_phylotrees.sql (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-04-13_set_study_in_phylotrees/set_study_in_phylotrees.sql 2010-04-13 14:39:33 UTC (rev 684)
@@ -0,0 +1,21 @@
+begin work;
+
+SELECT phylotree_id, study_id from phylotree where phylotree_id = 7238;
+
+-- should result in a NULL value for study_id
+
+UPDATE phylotree pt
+ SET study_id = sub.study_id
+FROM treeblock tb JOIN sub_treeblock stb USING (treeblock_id)
+JOIN submission sub USING (submission_id)
+WHERE pt.treeblock_id = tb.treeblock_id
+AND pt.study_id IS NULL
+AND sub.study_id > 10000;
+
+-- should result in about 10 records updated
+
+SELECT phylotree_id, study_id from phylotree where phylotree_id = 7238;
+
+-- should result in "10349" for study_id
+
+commit;
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From: <yo...@us...> - 2010-04-13 14:21:29
|
Revision: 683
http://treebase.svn.sourceforge.net/treebase/?rev=683&view=rev
Author: youjun
Date: 2010-04-13 14:21:23 +0000 (Tue, 13 Apr 2010)
Log Message:
-----------
change the taxontabels cascade type, allowing remove
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java 2010-04-11 14:40:20 UTC (rev 682)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/Submission.java 2010-04-13 14:21:23 UTC (rev 683)
@@ -174,8 +174,8 @@
*
* @return Set<Taxon>
*/
- @OneToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
- // @OneToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REMOVE})
+ //@OneToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST})
+ @OneToMany(cascade = {CascadeType.MERGE, CascadeType.PERSIST, CascadeType.REMOVE})
@JoinTable(name = "SUB_TAXONLABEL", joinColumns = {@JoinColumn(name = "SUBMISSION_ID")}, inverseJoinColumns = @JoinColumn(name = "TAXONLABEL_ID"))
// @IndexColumn(name = "TAXONLABEL_ORDER")
@Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "studyCache")
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