treebase-guts — Commit and tracker messages

[Treebase-guts] [ treebase-Bugs-2782687 ] confusing semantics for book sections vs. articles

[SourceForge.net <no...@so...>]

Bugs item #2782687, was opened at 2009-04-28 08:41
Message generated for change (Tracker Item Submitted) made by rvos
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Category: ui
Group: piel
Status: Open
Priority: 4
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Nobody/Anonymous (nobody)
Summary: confusing semantics for book sections vs. articles

Initial Comment:
> • When entering a book citation, the user is presented with a field for
> "title of citation" and a field for "title of book". What's the difference?
> When entering a book section citation, the user is presented with a field
> for "title of citation", "book section", and "book title" -- again, "title
> of citation" is redundant with "book section title", but at least in this
> case entering in either box seems to fill the same field. My guess is that
> the correct behavior should be the following:
> Journal:
> Citation Title -> title_field
> Journal -> journal_field
> Book:
> Book Title -> title_field
> Book Section:
> Section Title -> title_field
> Book Title -> secondary_title_field
> In other words, we should not have redundant entry points for "title of
> citation" and either ("book title" or "section title").  Also, in each case
> the title_field gets filled, in one case the article title, another the book
> title, and the third the section title.  Do I have this field usage correct,
> or am I mistaken? 

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[Treebase-guts] [ treebase-Bugs-2782685 ] add new email address for existing authors

[SourceForge.net <no...@so...>]

Bugs item #2782685, was opened at 2009-04-28 08:40
Message generated for change (Tracker Item Submitted) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2782685&group_id=248804

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Category: data
Group: piel
Status: Open
Priority: 4
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Mark Dominus (mjdominus)
Summary: add new email address for existing authors

Initial Comment:
BP writes:

> • When selecting an author for a citation, how can a user select an existing
> author yet also be able to update the author's email address? This action
> should edit the email for the new article, but leave the email for old one
> intact. (i.e. the email info should be stored in the author-citation joiner
> table)

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[Treebase-guts] [ treebase-Bugs-2782676 ] few taxa validate for submission 2403

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Bugs item #2782676, was opened at 2009-04-28 08:10
Message generated for change (Tracker Item Submitted) made by rvos
You can respond by visiting: 
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Category: data
Group: piel
Status: Open
Priority: 4
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Mark Dominus (mjdominus)
Summary: few taxa validate for submission 2403

Initial Comment:
BP writes: I've been trying to validate taxa for submission 2403. Few seem to be working, but that may be uBios fault. 

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[Treebase-guts] [ treebase-Bugs-2782675 ] Deleting a tree block throws LockAcquisitionException

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Bugs item #2782675, was opened at 2009-04-28 08:09
Message generated for change (Tracker Item Submitted) made by rvos
You can respond by visiting: 
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Category: data
Group: piel
Status: Open
Priority: 4
Private: No
Submitted By: Rutger Vos (rvos)
Assigned to: Mark Dominus (mjdominus)
Summary: Deleting a tree block throws LockAcquisitionException

Initial Comment:
Deleting a tree block with only two trees started to take forever but then finished with an uncaught exception (attached below).

Uncaught Exception Encountered
org.hibernate.exception.LockAcquisitionException: could not execute native bulk manipulation query at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:82) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.engine.query.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:174) at org.hibernate.impl.SessionImpl.executeNativeUpdate(SessionImpl.java:1163) at org.hibernate.impl.SQLQueryImpl.executeUpdate(SQLQueryImpl.java:334) at org.cipres.treebase.dao.jdbc.PhyloTreeJDBC.deletePhyloTreeNodeSQL(PhyloTreeJDBC.java:70) at org.cipres.treebase.dao.tree.PhyloTreeDAO.realDelete(PhyloTreeDAO.java:176) at org.cipres.treebase.dao.tree.PhyloTreeDAO.deleteTreeBlock(PhyloTreeDAO.java:201) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy65.deleteTreeBlock(Unknown Source) at org.cipres.treebase.web.controllers.DeleteATreeBlockController.onSubmit(DeleteATreeBlockController.java:106) 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:710) at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) 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$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:874) at org.apache.coyote.http11.Http11BaseProtocol$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:595) Caused by: com.ibm.db2.jcc.b.SqlException: DB2 SQL error: SQLCODE: -911, SQLSTATE: 40001, SQLERRMC: 2 at com.ibm.db2.jcc.b.id.e(id.java:1640) at com.ibm.db2.jcc.c.fb.t(fb.java:748) at com.ibm.db2.jcc.c.fb.l(fb.java:398) at com.ibm.db2.jcc.c.fb.a(fb.java:64) at com.ibm.db2.jcc.c.s.a(s.java:48) at com.ibm.db2.jcc.c.xb.c(xb.java:266) at com.ibm.db2.jcc.b.jd.ab(jd.java:1684) at com.ibm.db2.jcc.b.jd.a(jd.java:2253) at com.ibm.db2.jcc.b.jd.W(jd.java:537) at com.ibm.db2.jcc.b.jd.executeUpdate(jd.java:520) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewProxyPreparedStatement.java:105) at org.hibernate.engine.query.NativeSQLQueryPlan.performExecuteUpdate(NativeSQLQueryPlan.java:165) ... 69 more Cookies: itemToHighlight=[http%3A//8ball.sdsc.edu%3A6666/treebase-web/user/treeBlockList.html] JSESSIONID=[4F285F84FEA3650D68B71E616273E85D] __utma=[60813167.1783846415.1214875683.1214875683.1239852153.2] __utmz=[60813167.1239852153.2.1.utmccn]


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[Treebase-guts] First post.

[Rutger V. <rut...@gm...>]

Woohoo.

-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com