treebase-guts — Commit and tracker messages

[Treebase-guts] SF.net SVN: treebase:[696] trunk/treebase-web/src/main/webapp/WEB-INF/pages /algorithm.jsp

[<sfr...@us...>]

Revision: 696
          http://treebase.svn.sourceforge.net/treebase/?rev=696&view=rev
Author:   sfrgpiel
Date:     2010-05-01 15:13:17 +0000 (Sat, 01 May 2010)

Log Message:
-----------
Changed the download message from "download unavailable" to "download reconstructed"

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

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp	2010-04-29 19:03:07 UTC (rev 695)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/algorithm.jsp	2010-05-01 15:13:17 UTC (rev 696)
@@ -49,12 +49,14 @@
 			<img 
 				class="iconButton" 
 				src="<fmt:message key="icons.download.reconstructed"/>" 
-<%--
+
 				title="<fmt:message key="download.reconstructedfile"/>" 
 				alt="<fmt:message key="download.reconstructedfile"/>"
---%>
+
+<%-- 
 				title="<fmt:message key="download.unavailable"/>" 
 				alt="<fmt:message key="download.unavailable"/>"	
+--%>
 				/>	
 		</a>	  	
 		<c:if test="${not empty analysisStepCommand.displayName}">


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[Treebase-guts] SF.net SVN: treebase:[695] trunk/treebase-core/src/main/resources

[<vga...@us...>]

Revision: 695
          http://treebase.svn.sourceforge.net/treebase/?rev=695&view=rev
Author:   vgapeyev
Date:     2010-04-29 19:03:07 +0000 (Thu, 29 Apr 2010)

Log Message:
-----------
Making sure that jdbc.properties is not referenced by the web application. 
(We do not have jdbc.properties in svn anymore, but there still was one reference to it, 
which prevented a clean (svn co; mvn package) build)

Modified Paths:
--------------
    trunk/treebase-core/src/main/resources/applicationContext-dao.xml
    trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
    trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
    trunk/treebase-core/src/main/resources/jdbc.properties.example
    trunk/treebase-core/src/main/resources/treebase.properties

Modified: trunk/treebase-core/src/main/resources/applicationContext-dao.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-dao.xml	2010-04-24 15:01:14 UTC (rev 694)
+++ trunk/treebase-core/src/main/resources/applicationContext-dao.xml	2010-04-29 19:03:07 UTC (rev 695)
@@ -11,6 +11,8 @@
 
 	
 
+<!-- VG 2010-01-11, 1010-04-29  instead, see applicationContext-db-webapp.xml and applicationContext-db-standalone.xml
+
 	<bean id="propertyConfigurer"
 		class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
 		<property name="ignoreUnresolvablePlaceholders" value="true" />
@@ -22,8 +24,6 @@
 		</property>
 	</bean>
 
-
-<!-- VG 2010-01-11  instead, see applicationContext-db-webapp.xml and applicationContext-db-standalone.xml
 	<bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close">
 		<property name="driverClass" value="${jdbc.driverClassName}" />
 		<property name="jdbcUrl" value="${jdbc.url}" />

Modified: trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml	2010-04-24 15:01:14 UTC (rev 694)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-standalone.xml	2010-04-29 19:03:07 UTC (rev 695)
@@ -9,6 +9,18 @@
     http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd" 
     default-autowire="no">
 
+
+	<bean id="propertyConfigurer"
+		class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
+		<property name="ignoreUnresolvablePlaceholders" value="true" />
+		<property name="locations">
+		<list>
+		 	<value>classpath:jdbc.properties</value>
+			<value>classpath:treebase.properties</value>
+		</list>
+		</property>
+	</bean>
+
 	<bean id="dataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource" destroy-method="close">
 		<property name="driverClass" value="${jdbc.driverClassName}" />
 		<property name="jdbcUrl" value="${jdbc.url}" />

Modified: trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml
===================================================================
--- trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml	2010-04-24 15:01:14 UTC (rev 694)
+++ trunk/treebase-core/src/main/resources/applicationContext-db-webapp.xml	2010-04-29 19:03:07 UTC (rev 695)
@@ -9,6 +9,17 @@
     http://www.directwebremoting.org/schema/spring-dwr-2.0.xsd" 
     default-autowire="no">
 
+
+	<bean id="propertyConfigurer"
+		class="org.springframework.beans.factory.config.PropertyPlaceholderConfigurer">
+		<property name="ignoreUnresolvablePlaceholders" value="true" />
+		<property name="locations">
+		<list>
+			<value>classpath:treebase.properties</value>
+		</list>
+		</property>
+	</bean>
+
 	<bean id="dataSource" class="org.springframework.jndi.JndiObjectFactoryBean">
 		<property name="jndiName" value="java:comp/env/jdbc/TreebaseDB"/>
 	</bean>

Modified: trunk/treebase-core/src/main/resources/jdbc.properties.example
===================================================================
--- trunk/treebase-core/src/main/resources/jdbc.properties.example	2010-04-24 15:01:14 UTC (rev 694)
+++ trunk/treebase-core/src/main/resources/jdbc.properties.example	2010-04-29 19:03:07 UTC (rev 695)
@@ -1,21 +1,10 @@
-# This tells our object-relational mapping libraries
-# to use postgres-specific SQL dialect
-hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
+# If needed, copy this to jdbc.properties and supply appropriate values. 
 
-# for development only:
-hibernate.show_sql=false
-hibernate.format_sql=true
-hibernate.generate_statistics=false
+# As of 2010-04-29, jdbc.properties should only contain counterparts of JNDI parameters
+# specified in /treebase-web/src/main/webapp/META-INF/context.xml or in the Tomcat installation. 
+# jdbc.properties is not read by the web application; it is only used by locally-run tools 
+# such as unit tests, data importers (in cipres.teebase.util) and data checkers. 
 
-# options are: validate | update | create | create-drop
-hibernate.hbm2ddl.auto=
-
-
-#### VG 2010-02-07 Properties below are not read by the webapp anymore. 
-#### Instead, equivalent resources are looked up through JNDI -- see /treebase-web/src/main/webapp/META-INF/context.xml
-#### These properties are only read by tests and, possibly, by data importing classes in cipres.teebase.util
-#### (see treebase-core/src/main/java/org/cipres/treebase/core/CoreServiceLauncher.java)
-
 jdbc.driverClassName=org.postgresql.Driver
 
 # Login credentials, obtain the actual values from

Modified: trunk/treebase-core/src/main/resources/treebase.properties
===================================================================
--- trunk/treebase-core/src/main/resources/treebase.properties	2010-04-24 15:01:14 UTC (rev 694)
+++ trunk/treebase-core/src/main/resources/treebase.properties	2010-04-29 19:03:07 UTC (rev 695)
@@ -1,2 +1,26 @@
 #options are: NexusServiceMesquite | NexusServiceNCL
 nexus.parser.impl=NexusServiceMesquite
+
+########################################################################
+###  Prior to 2010-04-29, these were in jdbc.properties, 
+###  which now contains only properties not used by the web app
+###  and is not read by the web app. 
+###  In case the below properties are not used by the web app either 
+###  (I don't know --VG), they should be moved back to jdbc.properties. 
+########################################################################
+
+# This tells our object-relational mapping libraries
+# to use postgres-specific SQL dialect
+hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
+
+# for development only:
+hibernate.show_sql=false
+hibernate.format_sql=true
+hibernate.generate_statistics=false
+
+# options are: validate | update | create | create-drop
+hibernate.hbm2ddl.auto=
+
+########################################################################
+###  end old jdbc.properties
+########################################################################


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[Treebase-guts] [ treebase-Bugs-2993081 ] Better document on the UI which NEXUS flavors are supported

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Bugs item #2993081, was opened at 2010-04-27 12:29
Message generated for change (Tracker Item Submitted) made by hlapp
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2993081&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: Hilmar Lapp (hlapp)
Assigned to: Nobody/Anonymous (nobody)
Summary: Better document on the UI which NEXUS flavors are supported

Initial Comment:
Some people have submitted NEXUS files that we know we do not support, such as certain ones created by MrBayes. We need to document more clearly on the submission UI which NEXUS creators and flavors we support and what to do if a submitter's file was created by a different program. 

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

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[Treebase-guts] [ treebase-Feature Requests-2810819 ] Clearly distinguish refined tree search and new tree search

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Feature Requests item #2810819, was opened at 2009-06-23 06:32
Message generated for change (Comment added) made by hlapp
You can respond by visiting: 
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Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Nobody/Anonymous (nobody)
Summary: Clearly distinguish refined tree search and new tree search

Initial Comment:
I'm not sure this is a bug or a feature request:
When I search trees here: http://8ball.sdsc.edu:6666/treebase-web/search/treeSearch.html I have to discard all results before doing a new research, otherwise it seems that the research is done among the trees found by the previous research. This default behaviour is a bit surprising. For example, I searched the trees with 6 taxa, then the trees with 7 taxa, and the second research yielded no result.

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:28

Message:
The behavior you observed was (and still is) actually the advertised
behavior. At the time you tested the help documentation may not have been
very good about explaining this. If you still find this equally confusing
on the current TreeBASE site (at http://www.treebase.org) could you please
submit this as a bug requesting better documentation on the user interface.
 

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

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[Treebase-guts] [ treebase-Bugs-2992022 ] Yikes when viewing 2164: UTF8 handling problem?

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Bugs item #2992022, was opened at 2010-04-25 16:04
Message generated for change (Comment added) made by rvos
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2992022&group_id=248804

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including the initial issue submission, for this request,
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Category: ui
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Rutger Vos (rvos)
Summary: Yikes when viewing 2164: UTF8 handling problem?

Initial Comment:

An error is thrown when users try to browse to S2164. This *may* be an issue with UTF8 character set rendering, seeing as this study is from Hungarian authors. 

http://www.treebase.org/treebase-web/search/study/summary.html?id=2164

Yikes!

javax.servlet.jsp.el.ELException: An error occurred while getting property "bibtexReference" from an instance of class org.cipres.treebase.domain.study.ArticleCitation
	at org.apache.commons.el.Logger.logError(Logger.java:484)
	at org.apache.commons.el.Logger.logError(Logger.java:588)
	at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318)
	at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190)
	at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924)
	at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspx_meth_c_005fout_005f0(nav_jsp.java:285)
	at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspService(nav_jsp.java:89)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:584)
	at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:497)
	at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:965)
	at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspService(summary_jsp.java:109)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
	at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
	at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239)
	at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879)
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
	at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
	at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
	at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
	at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
	at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
	at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
	at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873)
	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
	at java.lang.Thread.run(Thread.java:636)
	

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

Comment By: Rutger Vos (rvos)
Date: 2010-04-27 16:27

Message:
Also test this with issue 2669366

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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 15:36

Message:
This may indicate a larger problem with UTF8 handling.

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

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[Treebase-guts] [ treebase-Bugs-2715233 ] Missing TB1 objects

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Bugs item #2715233, was opened at 2009-03-26 15:34
Message generated for change (Settings changed) made by hlapp
You can respond by visiting: 
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Category: data
Group: None
Status: Open
Priority: 6
Private: No
Submitted By: Mark Dominus (mjdominus)
>Assigned to: William Piel (sfrgpiel)
Summary: Missing TB1 objects

Initial Comment:
A number of TB1 objects are still missing from the TB2 database.

The program org.cipres.treebase.util.WhatsMissing can be used to make a list of what should be there but isn't.

Its current output is attached.

Summary:
25 studies are missing
24 matrices are missing
97 trees are missing

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

Comment By: Mark Dominus (mjdominus)
Date: 2009-03-27 16:27

Message:
Summary:  
11 studies are missing
14 matrices are missing
0 trees are missing


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[Treebase-guts] [ treebase-Bugs-2776454 ] Four unimported citations

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Bugs item #2776454, was opened at 2009-04-20 12:35
Message generated for change (Settings changed) made by hlapp
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Category: data
Group: None
Status: Open
>Priority: 5
Private: No
Submitted By: Mark Dominus (mjdominus)
>Assigned to: William Piel (sfrgpiel)
Summary: Four unimported citations

Initial Comment:
MJD -> BP:

There are four studies whose citations have not yet been imported.

These are the citations for studies
S9x6x96c10c10c17
S451
S801
S914

The reason is that the citation dump file you sent specifies citation types "Thesis", "Thesis", "Electronic Source", and "Conference Proceedings", respectively.  But our data model has (at present) only citations of types "Journal Article", "Book", and "Book Section". Rutger quite properly had the citation data importer ignore citations of unknown types.


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

Comment By: Mark Dominus (mjdominus)
Date: 2009-04-20 14:36

Message:
BP says:

My sense is that "Thesis" and "Electronic Source" can be squeezed into
"Book"; and "Conference Proceedings" can be squeezed into "Book Section" --
we can do that for now just to accommodate these cases. But a future "new
feature" might be to expand the repertoire of our publication categories --
but definitely only for down the road. 

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[Treebase-guts] [ treebase-Bugs-2809146 ] Taxon validation fails with trinomials plus suffix

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Bugs item #2809146, was opened at 2009-06-19 12:59
Message generated for change (Comment added) made by hlapp
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Category: data
Group: None
Status: Open
>Priority: 5
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Taxon validation fails with trinomials plus suffix

Initial Comment:
In submission S2440, you will notice that all binomial taxon labels with suffix codes (e.g. "Arianta schmidtii EG71B") validate automatically, but trinomial taxon labels with suffix codes (e.g. "Arianta arbustorum styriaca EG468") fail to validate (except where I have entered uBio IDs manually, such as with "Arianta arbustorum styriaca AT EG454"). I'm not sure where the problem lies (and, in fact, most if not all of these trinomials are already in TreeBASE, so the problem happens "in house" prior to using uBio's web services), but I would suggest that the solution is run a series of regular expressions on each taxon label. e.g. (1) first make sure that there is a space between species or subspecies names and suffix codes, assuming that a lower case followed by an upper case or a number probably indicates the presence of a suffix code stuck to the end of a species or subspecies name -- i.e. s/([a-z]{3,})([A-Z\d+]+)/\1 \2/  Then (2), test to see if there is a trinomial followed by a possible suffix, realizing that hyphens are allowed in species and subspecies names: m/^([A-Z][a-z]+) ([a-z\-]+) ([a-z\-]+)(.*)$/ -- if you get a hit, search the taxon_variants table for "$1 $2 $3" and if nothing there, throw "$1 $2 $3" against uBio's web services. If no hit, then (3) test to see if there is a binomial followed by a possible suffix: m/^([A-Z][a-z]+) ([a-z\-]+)(.*)$/ and if you get a hit, search the taxon_variants table for "$1 $2" and if nothing there, throw "$1 $2" at uBio's web services. 

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:18

Message:
People can work around this by hand. Downgrading the priority.

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

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[Treebase-guts] [ treebase-Bugs-2809146 ] Taxon validation fails with trinomials plus suffix

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Bugs item #2809146, was opened at 2009-06-19 12:59
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Category: data
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Nobody/Anonymous (nobody)
Summary: Taxon validation fails with trinomials plus suffix

Initial Comment:
In submission S2440, you will notice that all binomial taxon labels with suffix codes (e.g. "Arianta schmidtii EG71B") validate automatically, but trinomial taxon labels with suffix codes (e.g. "Arianta arbustorum styriaca EG468") fail to validate (except where I have entered uBio IDs manually, such as with "Arianta arbustorum styriaca AT EG454"). I'm not sure where the problem lies (and, in fact, most if not all of these trinomials are already in TreeBASE, so the problem happens "in house" prior to using uBio's web services), but I would suggest that the solution is run a series of regular expressions on each taxon label. e.g. (1) first make sure that there is a space between species or subspecies names and suffix codes, assuming that a lower case followed by an upper case or a number probably indicates the presence of a suffix code stuck to the end of a species or subspecies name -- i.e. s/([a-z]{3,})([A-Z\d+]+)/\1 \2/  Then (2), test to see if there is a trinomial followed by a possible suffix, realizing that hyphens are allowed in species and subspecies names: m/^([A-Z][a-z]+) ([a-z\-]+) ([a-z\-]+)(.*)$/ -- if you get a hit, search the taxon_variants table for "$1 $2 $3" and if nothing there, throw "$1 $2 $3" against uBio's web services. If no hit, then (3) test to see if there is a binomial followed by a possible suffix: m/^([A-Z][a-z]+) ([a-z\-]+)(.*)$/ and if you get a hit, search the taxon_variants table for "$1 $2" and if nothing there, throw "$1 $2" at uBio's web services. 

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

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[Treebase-guts] [ treebase-Bugs-2962228 ] Orphaned records and failure to delete related records

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Bugs item #2962228, was opened at 2010-03-02 17:26
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Category: data
Group: None
Status: Open
Priority: 6
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: William Piel (sfrgpiel)
Summary: Orphaned records and failure to delete related records

Initial Comment:
The database contains many orphaned objects. For example, under the Taxa tab, search on NCBI taxid 114498, then click either the Trees or Matrices tabs. This results in records even though none of them belong to an existing study. The problem is in part because trees and matrices don't actually get deleted properly: create a submission, upload trees or matrices, then delete the trees or matrices -- the only thing that is deleted is the linking record in the sub_matrix table. None of the column records, row records, or element records (etc) seem to get deleted. Youjun explained that the design of the matrix object does not allow the code to access the matrix rows (etc) for easy deletion. One possible solution is to include cascade-delete constraints on the tables so that deleting a matrix record automatically delete all related records without leaving behind any orphans.  At any rate, it behooves us to prevent the accumulation of orphans and to write data cleansers to get rid of the existing ones.

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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 11:59

Message:
Needs to be verified first that the bug still replicates.

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

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[Treebase-guts] [ treebase-Bugs-2809146 ] Taxon validation fails with trinomials plus suffix

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Bugs item #2809146, was opened at 2009-06-19 12:59
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Category: data
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: William Piel (sfrgpiel)
Summary: Taxon validation fails with trinomials plus suffix

Initial Comment:
In submission S2440, you will notice that all binomial taxon labels with suffix codes (e.g. "Arianta schmidtii EG71B") validate automatically, but trinomial taxon labels with suffix codes (e.g. "Arianta arbustorum styriaca EG468") fail to validate (except where I have entered uBio IDs manually, such as with "Arianta arbustorum styriaca AT EG454"). I'm not sure where the problem lies (and, in fact, most if not all of these trinomials are already in TreeBASE, so the problem happens "in house" prior to using uBio's web services), but I would suggest that the solution is run a series of regular expressions on each taxon label. e.g. (1) first make sure that there is a space between species or subspecies names and suffix codes, assuming that a lower case followed by an upper case or a number probably indicates the presence of a suffix code stuck to the end of a species or subspecies name -- i.e. s/([a-z]{3,})([A-Z\d+]+)/\1 \2/  Then (2), test to see if there is a trinomial followed by a possible suffix, realizing that hyphens are allowed in species and subspecies names: m/^([A-Z][a-z]+) ([a-z\-]+) ([a-z\-]+)(.*)$/ -- if you get a hit, search the taxon_variants table for "$1 $2 $3" and if nothing there, throw "$1 $2 $3" against uBio's web services. If no hit, then (3) test to see if there is a binomial followed by a possible suffix: m/^([A-Z][a-z]+) ([a-z\-]+)(.*)$/ and if you get a hit, search the taxon_variants table for "$1 $2" and if nothing there, throw "$1 $2" at uBio's web services. 

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

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[Treebase-guts] [ treebase-Bugs-2798604 ] no block of taxa could be created from a MrBayes .con tree

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Bugs item #2798604, was opened at 2009-05-29 17:21
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Category: data
Group: None
Status: Open
>Priority: 2
Private: No
Submitted By: Blaise Li (blaiseli)
Assigned to: Rutger Vos (rvos)
Summary: no block of taxa could be created from a MrBayes .con tree

Initial Comment:
The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:13

Message:
We won't fix this directly because we can't support all variants of NEXUS.
However, we should better document which NEXUS versions we do support, and
at some point we may also switch out Mesquite as the NEXUS parser to
another one, e.g., NCL. (Though no NEXUS parser can be expected to support
all flavors.)

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

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 07:11

Message:
I think this needs to be closed: there is simply no way we will ever
support all nexus variants. It is a feature of treebase that we support
mesquite-compatible files. We state this very clearly. If people decide to
upload files that are not compatible with mesquite there's not much we can
do.

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

Comment By: Rutger Vos (rvos)
Date: 2009-11-18 13:23

Message:
This has been downgraded. We can't fix this unless mesquite gets fixed. If
people want to upload mrbayes files they will have to run them through
mesquite first on their own machines.

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

Comment By: Rutger Vos (rvos)
Date: 2009-06-27 03:31

Message:
The issue is because, although mesquite *can* create a taxa block on the
fly while reading a tree block without a translation table, it doesn't want
to. It prods the user for feedback, which makes the import hang in headless
mode. Bill has emailed the Maddisons about this, and it looks like the
issue could certainly be fixed in their code (even if that would make it
some sort of treebase special). But - then we have to fold that change into
our previous treebase special version of mesquite, which was a snapshot
roughly at version 2.1, and we're now at 2.6. I did some testing and some
methods have changed or have been removed, so we would need to adapt our
code base to that new api.

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

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 10:29

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


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

Comment By: William Piel (sfrgpiel)
Date: 2009-06-23 10:29

Message:
This looks like a difficult bug to fix because the problem stems from
Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from
a tree block that does not use a translation table. I've tried opening
trees like this in Mesquite v. 2 with no success... 

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

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[Treebase-guts] [ treebase-Bugs-2992932 ] Exact match "==" does not work in PhyloWS query

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Bugs item #2992932, was opened at 2010-04-27 13:08
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Category: ui
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
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.


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[Treebase-guts] [ treebase-Bugs-2797430 ] Password hashing

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Bugs item #2797430, was opened at 2009-05-27 11:08
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Category: data
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: Mark Dominus (mjdominus)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: Password hashing

Initial Comment:
Passwords are stored in the USER table of the database in plain text.

They should be hashed instead.


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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:08

Message:
According to Bill, several fixes need to go with this, e.g., fixing the
email notification, and a script that converts existing accounts.

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[Treebase-guts] [ treebase-Bugs-2977283 ] crossdomain.xml

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Bugs item #2977283, was opened at 2010-03-26 21:18
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Category: None
Group: easy
Status: Open
Priority: 5
Private: No
Submitted By: Mike Keesey (tmkeesey)
>Assigned to: Rutger Vos (rvos)
Summary: crossdomain.xml

Initial Comment:
In order for Adobe Flash-based web applications to be able to use the PhyloWS API, there needs to be a permissions file at <http://treebase.org/crossdomain.xml>. See, for example, <http://static.flickr.com/crossdomain.xml>.

More information on cross-domain policy files can be found here: <http://www.adobe.com/devnet/articles/crossdomain_policy_file_spec.html>.

Attahced is an example crossdomain.xml which would allow the fewest retrictions.

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[Treebase-guts] [ treebase-Bugs-2960840 ] PhyloWS API Issues Need Fixing

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Bugs item #2960840, was opened at 2010-02-28 15:05
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Category: ui
Group: None
Status: Open
>Priority: 7
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: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:05

Message:
Needs fixing but not threatening TB2 operation. Downgraded to priority 7.

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

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.


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

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[Treebase-guts] [ treebase-Bugs-2960905 ] Taxon mapping error despite all mapped

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Bugs item #2960905, was opened at 2010-02-28 18:12
Message generated for change (Comment added) made by hlapp
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Category: ui
Group: None
Status: Open
>Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Nobody/Anonymous (nobody)
Summary: Taxon mapping error despite all mapped

Initial Comment:
As a normal user, I went to the submission list:

http://treebasedb-dev.nescent.org/treebase-web/user/submissionList.html

Clicked "Change to Ready State" for a submission. (i.e. http://treebasedb-dev.nescent.org/treebase-web/user/readyState.html?submissionid=10053). 

This returned the statement "We notice that some of your taxon labels have failed to be validated against an external taxonomy. Unless it is impossible to validate these labels, TreeBASE may refuse or delay the acceptance of your data." -- however, in reality I had mapped all names fully (though I had do do some of it manually). So it seems that the software did not notice that all labels had, in fact, been mapped. 

bp


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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 12:02

Message:
Downgrading to priority 7. Annoying but not a threat to operating TB2.

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[Treebase-guts] [ treebase-Bugs-2973502 ] Numbers of studies in TB2 and TB1 are different

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Bugs item #2973502, was opened at 2010-03-19 22:08
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Category: data
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: Vladimir Gapeyev (vgapeyev)
>Assigned to: William Piel (sfrgpiel)
Summary: Numbers of studies in TB2 and TB1 are different

Initial Comment:
[This is based on Bill's email of 2010-03-19: https://sourceforge.net/mailarchive/forum.php?thread_name=F1EC532F-64D4-4F51-9397-2F7F7C6644F8%40yale.edu&forum_name=treebase-devel ]

We have a total of 2417 studies in TreeBASE2. That includes two new ones that were never in TreeBASE1. TreeBASE1, however, has 2427 studies -- so that means we have 12 missing studies. Not a show-stopper. After release, we will identify these and re-enter them manually. 

Note: The 2417 number for TB2 is after duplicates of Study 84 are removed: 
http://purl.org/phylo/treebase/phylows/study/find?query=tb.identifier.study=66+or+tb.identifier.study=67+or+tb.identifier.study=68+or+tb.identifier.study=69+or+tb.identifier.study=70+or+tb.identifier.study=71+or+tb.identifier.study=72+or+tb.identifier.study=73&recordSchema=study

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[Treebase-guts] [ treebase-Bugs-2962228 ] Orphaned records and failure to delete related records

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Bugs item #2962228, was opened at 2010-03-02 17:26
Message generated for change (Comment added) made by hlapp
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Category: data
Group: None
Status: Open
>Priority: 6
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Mark Dominus (mjdominus)
Summary: Orphaned records and failure to delete related records

Initial Comment:
The database contains many orphaned objects. For example, under the Taxa tab, search on NCBI taxid 114498, then click either the Trees or Matrices tabs. This results in records even though none of them belong to an existing study. The problem is in part because trees and matrices don't actually get deleted properly: create a submission, upload trees or matrices, then delete the trees or matrices -- the only thing that is deleted is the linking record in the sub_matrix table. None of the column records, row records, or element records (etc) seem to get deleted. Youjun explained that the design of the matrix object does not allow the code to access the matrix rows (etc) for easy deletion. One possible solution is to include cascade-delete constraints on the tables so that deleting a matrix record automatically delete all related records without leaving behind any orphans.  At any rate, it behooves us to prevent the accumulation of orphans and to write data cleansers to get rid of the existing ones.

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 11:59

Message:
Needs to be verified first that the bug still replicates.

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

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[Treebase-guts] [ treebase-Bugs-2972133 ] Add to connotea, del.icio.us etc broken due to absolute URL

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Bugs item #2972133, was opened at 2010-03-17 14:52
Message generated for change (Settings changed) made by hlapp
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Category: ui
Group: None
Status: Open
>Priority: 7
Private: No
Submitted By: Hilmar Lapp (hlapp)
Assigned to: Rutger Vos (rvos)
Summary: Add to connotea, del.icio.us etc broken due to absolute URL

Initial Comment:
The code uses an absolute path, which results in things like http://localhost.localdomain:8280/treebase-web/search/study/summary.html?id=1021, which obviously won't work.

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

Comment By: Rutger Vos (rvos)
Date: 2010-03-26 07:07

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


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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-03-17 15:02

Message:
Turns out I do have a CiteULike account. The code adds an entry to the
library but w/o a link back to the TreeBASE URL (or the article URL). Is
that intended?

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

Comment By: Hilmar Lapp (hlapp)
Date: 2010-03-17 14:57

Message:
This may only affect Connotea actually. The add to Del.icio.us code works,
can't test CiteULike as a I don't have an account. 

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[Treebase-guts] [ treebase-Bugs-2973502 ] Numbers of studies in TB2 and TB1 are different

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Bugs item #2973502, was opened at 2010-03-19 18:08
Message generated for change (Settings changed) made by hlapp
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Category: data
Group: None
Status: Open
>Priority: 7
Private: No
Submitted By: Vladimir Gapeyev (vgapeyev)
Assigned to: Mark Dominus (mjdominus)
Summary: Numbers of studies in TB2 and TB1 are different

Initial Comment:
[This is based on Bill's email of 2010-03-19: https://sourceforge.net/mailarchive/forum.php?thread_name=F1EC532F-64D4-4F51-9397-2F7F7C6644F8%40yale.edu&forum_name=treebase-devel ]

We have a total of 2417 studies in TreeBASE2. That includes two new ones that were never in TreeBASE1. TreeBASE1, however, has 2427 studies -- so that means we have 12 missing studies. Not a show-stopper. After release, we will identify these and re-enter them manually. 

Note: The 2417 number for TB2 is after duplicates of Study 84 are removed: 
http://purl.org/phylo/treebase/phylows/study/find?query=tb.identifier.study=66+or+tb.identifier.study=67+or+tb.identifier.study=68+or+tb.identifier.study=69+or+tb.identifier.study=70+or+tb.identifier.study=71+or+tb.identifier.study=72+or+tb.identifier.study=73&recordSchema=study

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[Treebase-guts] [ treebase-Bugs-2978845 ] Timestamps on builds

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Bugs item #2978845, was opened at 2010-03-29 17:35
Message generated for change (Settings changed) made by sfrgpiel
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Category: internals
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: Vladimir Gapeyev (vgapeyev)
>Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: Timestamps on builds

Initial Comment:
(Some?) pages of the treebase-dev site should contain a timestamp of the build (ex. Version: 2.2.1   Built: 03/26/2010 12:43 PM ), as an indication what version is being run on a given instance.  Ideally, this should include source code version from SVN. 

To make the timestamp invisible on production, there are a couple options: 
  - Put it inside an <!-- --> HTML comment. 
  - Make it's JSP rendering conditional depending on the value of the parameter like amIProduction that comes from Tomcat via JNDI.
 

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

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-03-30 09:26

Message:
From: 	rut...@gm...
	Subject: 	Re: [Treebase-devel] Is TreeBASE down?
	Date: 	March 29, 2010 6:00:48 PM EDT
	To: 	vla...@du...
	Cc: 	tre...@li...

If you look in the html source of any page and you scroll all the way
down to 'p class="footerLogo"' it will show the SVN revision of that
deployment. At least, this used to work back when MJD and I were using
the 'publish' script, which used
${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java
as a little servlet to embed the SVN revision in  the footer.jsp (this
is done by deleting and then updating this version file). Perhaps this
can be re-instated?


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[Treebase-guts] [ treebase-Bugs-2992022 ] Yikes when viewing 2164: UTF8 handling problem?

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Bugs item #2992022, was opened at 2010-04-25 12:04
Message generated for change (Settings changed) made by hlapp
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Category: ui
Group: None
Status: Open
Priority: 8
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
>Summary: Yikes when viewing 2164: UTF8 handling problem?

Initial Comment:

An error is thrown when users try to browse to S2164. This *may* be an issue with UTF8 character set rendering, seeing as this study is from Hungarian authors. 

http://www.treebase.org/treebase-web/search/study/summary.html?id=2164

Yikes!

javax.servlet.jsp.el.ELException: An error occurred while getting property "bibtexReference" from an instance of class org.cipres.treebase.domain.study.ArticleCitation
	at org.apache.commons.el.Logger.logError(Logger.java:484)
	at org.apache.commons.el.Logger.logError(Logger.java:588)
	at org.apache.commons.el.ArraySuffix.evaluate(ArraySuffix.java:318)
	at org.apache.commons.el.ComplexValue.evaluate(ComplexValue.java:145)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:263)
	at org.apache.commons.el.ExpressionEvaluatorImpl.evaluate(ExpressionEvaluatorImpl.java:190)
	at org.apache.jasper.runtime.PageContextImpl.proprietaryEvaluate(PageContextImpl.java:924)
	at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspx_meth_c_005fout_005f0(nav_jsp.java:285)
	at org.apache.jsp.WEB_002dINF.pages.search.study.nav_jsp._jspService(nav_jsp.java:89)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.doInclude(ApplicationDispatcher.java:584)
	at org.apache.catalina.core.ApplicationDispatcher.include(ApplicationDispatcher.java:497)
	at org.apache.jasper.runtime.JspRuntimeLibrary.include(JspRuntimeLibrary.java:965)
	at org.apache.jsp.WEB_002dINF.pages.search.study.summary_jsp._jspService(summary_jsp.java:109)
	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:331)
	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:329)
	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:39)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
	at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
	at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142)
	at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:239)
	at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1142)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:879)
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
	at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:627)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
	at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
	at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
	at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
	at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
	at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191)
	at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
	at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
	at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873)
	at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
	at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
	at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
	at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
	at java.lang.Thread.run(Thread.java:636)
	

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 11:36

Message:
This may indicate a larger problem with UTF8 handling.

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[Treebase-guts] [ treebase-Bugs-2992930 ] Uploading metadata with missing values causes exception

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Bugs item #2992930, was opened at 2010-04-27 09:04
Message generated for change (Comment added) made by hlapp
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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. 

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 11:33

Message:
There is no good workaround, and this is bad enough that it could cause
people to give up on submitting data.

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[Treebase-guts] [ treebase-Bugs-2899240 ] Data consistency checking

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Bugs item #2899240, was opened at 2009-11-17 12:17
Message generated for change (Comment added) made by hlapp
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Category: data
Group: None
Status: Open
>Priority: 6
Private: No
Submitted By: Rutger Vos (rvos)
>Assigned to: Nobody/Anonymous (nobody)
Summary: Data consistency checking

Initial Comment:
Goal: to develop, implement and execute a strategy for ascertaining that all old data has been imported and is consistent.

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

>Comment By: Hilmar Lapp (hlapp)
Date: 2010-04-27 11:30

Message:
The most critical consistency reports were implemented and run before
release, but they are far from automated and require extensive manual
inspection and understanding of the data. So this remains on the table, but
with a new priority. 

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

Comment By: Rutger Vos (rvos)
Date: 2009-11-24 12:32

Message:
This issue subsumes issue #2717395 which refers to old consistency checker
logs. New logs have been produced that need to be resolved. These new logs
were created using the perl API that has been ported to postgres.

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