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From: <vga...@us...> - 2009-12-10 20:28:01
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Revision: 349
http://treebase.svn.sourceforge.net/treebase/?rev=349&view=rev
Author: vgapeyev
Date: 2009-12-10 20:27:55 +0000 (Thu, 10 Dec 2009)
Log Message:
-----------
just esting the commit ability
Added Paths:
-----------
trunk/test-vg.txt
Added: trunk/test-vg.txt
===================================================================
--- trunk/test-vg.txt (rev 0)
+++ trunk/test-vg.txt 2009-12-10 20:27:55 UTC (rev 349)
@@ -0,0 +1 @@
+vg test
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From: SourceForge.net <no...@so...> - 2009-12-10 17:56:52
|
Bugs item #2797430, was opened at 2009-05-27 15:08 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2797430&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: 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. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2797430&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-10 16:26:31
|
Bugs item #2903251, was opened at 2009-11-24 17:34 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2903251&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: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: Rutger Vos (rvos) Summary: Exception when uploading nexus to a new submission Initial Comment: When I log in as a normal user (user: pieltest, password: pieltest) and I try to upload a nexus file to a new submission, I get the following error. bp Uncaught Exception Encountered java.lang.ExceptionInInitializerError at mesquite.Mesquite.main(Mesquite.java:2261) at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232) at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657) at ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-12-10 16:26 Message: ALERT: (Mesquite): Please find the Mesquite manual file named "manual.html", which should be in the "docs/mesquite" directory. java.lang.NullPointerException at mesquite.lib.MesquiteFileDialog.<init>(MesquiteFileDialog.java:31) at mesquite.lib.MesquiteFile.checkFilePath(MesquiteFile.java:2015) at mesquite.Mesquite.findMesquiteDirectory(Mesquite.java:583) at mesquite.Mesquite.processSingleXMLPreference(Mesquite.java:802) at mesquite.lib.MesquiteModule.processPreferencesFromXML(MesquiteModule.java:745) at mesquite.lib.MesquiteModule.loadPreferences(MesquiteModule.java:704) at mesquite.Mesquite.init(Mesquite.java:184) at mesquite.Mesquite.<init>(Mesquite.java:2033) at mesquite.Mesquite.main(Mesquite.java:2088) at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232) at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFilesJDBC(SubmissionServiceImpl.java:581) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.addNexusFilesJDBC(Unknown Source) at org.cipres.treebase.web.controllers.UploadFileController.onSubmit(UploadFileController.java:196) 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) Exception caught in Mesquite: null ALERT: (Mesquite): Mesquite cannot function: no file coordinator available (Following stack trace from object of class: class mesquite.lib.ProjectRead) java.lang.NullPointerException at mesquite.lib.ProjectRead.run(ProjectRead.java:212) at java.lang.Thread.run(Thread.java:636) at mesquite.lib.MesquiteThread.run(MesquiteThread.java:63) at mesquite.lib.ProjectReadThread.run(ProjectReadThread.java:55) ALERT: (Mesquite): File reading could not be completed because an exception or error occurred (i.e. a crash; class java.lang.NullPointerExcepti on). If you save any files, you might best use Save As... in case data were lost or file saving doesn't work properly. To report this as a bug , PLEASE send along the Mesquite_Log file from Mesquite_Support_Files. - ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-10 16:00 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=2903251&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-10 16:00:12
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Bugs item #2903251, was opened at 2009-11-24 17:34 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2903251&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: 9 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: Exception when uploading nexus to a new submission Initial Comment: When I log in as a normal user (user: pieltest, password: pieltest) and I try to upload a nexus file to a new submission, I get the following error. bp Uncaught Exception Encountered java.lang.ExceptionInInitializerError at mesquite.Mesquite.main(Mesquite.java:2261) at org.cipres.treebase.domain.nexus.mesquite.MesquiteConverter.parseOneFile(MesquiteConverter.java:232) at org.cipres.treebase.service.nexus.NexusServiceMesquite.parseNexus(NexusServiceMesquite.java:121) at org.cipres.treebase.service.study.SubmissionServiceImpl.addNexusFile(SubmissionServiceImpl.java:657) at ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-10 16:00 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=2903251&group_id=248804 |
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From: <rv...@us...> - 2009-12-10 13:53:54
|
Revision: 348
http://treebase.svn.sourceforge.net/treebase/?rev=348&view=rev
Author: rvos
Date: 2009-12-10 13:53:41 +0000 (Thu, 10 Dec 2009)
Log Message:
-----------
Working on mesquite issues
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/misc/publish
Modified: trunk/treebase-core/src/main/perl/misc/publish
===================================================================
--- trunk/treebase-core/src/main/perl/misc/publish 2009-12-10 12:13:13 UTC (rev 347)
+++ trunk/treebase-core/src/main/perl/misc/publish 2009-12-10 13:53:41 UTC (rev 348)
@@ -26,10 +26,6 @@
TARGET_DIR="treebase-web"
IP_ADDR=`curl -s checkip.dyndns.org | grep -Eo '[0-9\.]+'`
-# Need to set this for mesquite, in case we're launching
-# on servers that don't have X11 configure
-export DISPLAY=:0.0
-
# Flag to suppress sourre update and rebuilding
update_sources=true
if [ "$1" == "-r" ]; then
@@ -56,7 +52,7 @@
touch ${TREEBASE_HOME}/treebase-web/src/main/webapp/common/footer.jsp
- mvn install -Dmaven.test.skip=true
+ mvn -e install -Dmaven.test.skip=true
fi
# Stop the server, and make sure it's dead before proceeding
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From: <rv...@us...> - 2009-12-10 13:27:58
|
Revision: 347
http://treebase.svn.sourceforge.net/treebase/?rev=347&view=rev
Author: rvos
Date: 2009-12-10 12:13:13 +0000 (Thu, 10 Dec 2009)
Log Message:
-----------
Added a getTitle() override. We always want getTitle() to return something. For ArticleCitations, this field would normally be set with the name of the article. For InBookCitation, this field is populated with the section title, so InBookCitation.getSectionTitle() calls the getTitle() method defined here, from whence we need to go up the inheritance tree to the parent Citation class. For BookCitations, the title field is unset, so we return the BookTitle field instead. This should resolve issue #2903172.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/BookCitation.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/BookCitation.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/BookCitation.java 2009-12-09 17:23:37 UTC (rev 346)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/BookCitation.java 2009-12-10 12:13:13 UTC (rev 347)
@@ -130,6 +130,32 @@
public String getBookTitle() {
return mBookTitle;
}
+
+ /**
+ * Return the BookTitle
+ *
+ * @see org.cipres.treebase.domain.study.Citation#getTitle()
+ * @return String
+ */
+ @Override
+ @Transient
+ public String getTitle () {
+ /*
+ * We always want getTitle() to return something.
+ * For ArticleCitations, this field would normally
+ * be set with the name of the article. For InBookCitation,
+ * this field is populated with the section title, so
+ * InBookCitation.getSectionTitle() calls the getTitle()
+ * method defined here, from whence we need to go up
+ * the inheritance tree to the parent Citation class. For
+ * BookCitations, the title field is unset, so we return
+ * the BookTitle field instead.
+ */
+ if ( this instanceof InBookCitation ) {
+ return super.getTitle();
+ }
+ return getBookTitle();
+ }
/**
* Set the BookTitle field.
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From: SourceForge.net <no...@so...> - 2009-12-10 12:17:39
|
Bugs item #2903172, was opened at 2009-11-24 15:24 Message generated for change (Settings changed) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2903172&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) >Assigned to: Rutger Vos (rvos) Summary: Book citation does not appear in submission Initial Comment: When creating a new submission that has a book as the citation, the "Summary for Current Study" page (e.g.: go here after logging in as a Admin person: http://treebasedb-dev.nescent.org:6666/treebase-web/user/summary.html?id=253) says "Citation information not yet entered. Click the Citation menu item on the right" even though the citation has already been entered. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-12-10 12:17 Message: I added an override for the Citation.getTitle() method, because previously calling this method on the BookCitation child class return null. We always want getTitle() to return something. For ArticleCitations, this field would normally be set with the name of the article. For InBookCitation, this field is populated with the section title, so InBookCitation.getSectionTitle() calls the BookCitation.getTitle() method defined here, from whence we need to go up the inheritance tree to the parent Citation class. For BookCitations, the title field is unset, so we return the BookTitle field instead. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-10 12:17 Message: Your bug has been resolved. Thanks for the report. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2903172&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-09 22:35:47
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Bugs item #2911673, was opened at 2009-12-09 17:35 Message generated for change (Tracker Item Submitted) made by jonauman You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2911673&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Jon Auman (jonauman) Assigned to: Nobody/Anonymous (nobody) Summary: Please repackage war file for Jboss Initial Comment: The current war file explodes into the current directory, which is the webapps folder in tomcat. In Jboss, all wars go in the deploy folder, and Jboss expects them to create a new folder to expand into. So if the app is named treebase-web.war, the war file should expand into a treebase-web/ directory. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2911673&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-09 20:51:43
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Bugs item #2902650, was opened at 2009-11-23 13:31 Message generated for change (Settings changed) made by youjun You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2902650&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: youjun guo (youjun) Summary: Book titles don't appear under study tab Initial Comment: When searching on a study, under the study tab there is a column called "Title" which lists the titles for publications. Journal article titles are fine, but this column ought to also list the title of books, but it does not (that column is blank for books). In the event of book sections, this column should show the title of the chapter in the book. For example, see study_id 253 or tb_study_id S9x6x96c10c10c17 for a book title that does not appear in the column. However, if you look at the study details (e.g. http://treebasedb-dev.nescent.org:6666/treebase-web/search/study/summary.html?id=253) the citation is written properly. The book title is also missing from the BibTeX and RIS output. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2902650&group_id=248804 |
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From: SourceForge.net <no...@so...> - 2009-12-09 17:27:07
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Bugs item #2712095, was opened at 2009-03-25 16:19 Message generated for change (Comment added) made by rvos You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712095&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: piel >Status: Closed Priority: 8 Private: No Submitted By: Mark Dominus (mjdominus) >Assigned to: Rutger Vos (rvos) Summary: Admin summary search has no search by study id Initial Comment: Says BP: > - while the search page lets users search by either study_id or > legacy_study_id, the "Search Submission" Admin access page only lets the > admin person search by legacy_study_id. ---------------------------------------------------------------------- >Comment By: Rutger Vos (rvos) Date: 2009-12-09 17:27 Message: This issue has been resolved: the admin person can now choose the identifier type ("TreeBASE2 Id" or "Legacy accession") by checking a radio button. ---------------------------------------------------------------------- Comment By: Rutger Vos (rvos) Date: 2009-12-09 17:27 Message: Your bug has been resolved. Thanks for the report. ---------------------------------------------------------------------- Comment By: William Piel (sfrgpiel) Date: 2009-11-24 17:25 Message: I just realized that the inability for an admin person to search by study_id (currently they can only search on legacy_study_id) means that no new submissions can be edited by the admin person. This is a fairly critical task, so I'm elevating it to level 9. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2712095&group_id=248804 |
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From: <rv...@us...> - 2009-12-09 17:23:48
|
Revision: 346
http://treebase.svn.sourceforge.net/treebase/?rev=346&view=rev
Author: rvos
Date: 2009-12-09 17:23:37 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Added pre-processing for ID prefixes
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java 2009-12-09 17:18:32 UTC (rev 345)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java 2009-12-09 17:23:37 UTC (rev 346)
@@ -63,11 +63,11 @@
bindExp,
"errors",
"Please provide a study accession number.");
- }
- if ( ! studyAccession.startsWith("S") ) {
- studyAccession = "S" + studyAccession;
- }
+ }
if ( identifierType.equals("TB1") ) {
+ if ( ! studyAccession.startsWith("S") ) {
+ studyAccession = "S" + studyAccession;
+ }
sub = getSubmissionHome().findByStudyAccessionNumber(studyAccession);
}
else {
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From: <rv...@us...> - 2009-12-09 17:18:42
|
Revision: 345
http://treebase.svn.sourceforge.net/treebase/?rev=345&view=rev
Author: rvos
Date: 2009-12-09 17:18:32 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Added default choice for identifierType selection
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 2009-12-09 17:15:16 UTC (rev 344)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp 2009-12-09 17:18:32 UTC (rev 345)
@@ -15,9 +15,9 @@
<tr>
<th><fmt:message key="submission.accession"/>:</th>
- <td>
- <input type="radio" name="identifierType" value="TB1"/>Legacy accession
- <input type="radio" name="identifierType" value="TB2"/>TreeBASE2 Id
+ <td>
+ <input type="radio" name="identifierType" value="TB2" checked="checked"/>TreeBASE2 Id
+ <input type="radio" name="identifierType" value="TB1"/>Legacy accession
<input type="text" name="submissionaccession" maxlength = "25"/>
</td>
</tr>
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From: <rv...@us...> - 2009-12-09 17:15:22
|
Revision: 344
http://treebase.svn.sourceforge.net/treebase/?rev=344&view=rev
Author: rvos
Date: 2009-12-09 17:15:16 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Added pre-processing for ID prefixes
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java 2009-12-09 17:09:04 UTC (rev 343)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java 2009-12-09 17:15:16 UTC (rev 344)
@@ -64,6 +64,9 @@
"errors",
"Please provide a study accession number.");
}
+ if ( ! studyAccession.startsWith("S") ) {
+ studyAccession = "S" + studyAccession;
+ }
if ( identifierType.equals("TB1") ) {
sub = getSubmissionHome().findByStudyAccessionNumber(studyAccession);
}
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From: <rv...@us...> - 2009-12-09 17:09:11
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Revision: 343
http://treebase.svn.sourceforge.net/treebase/?rev=343&view=rev
Author: rvos
Date: 2009-12-09 17:09:04 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Clarified choice between legacy accession number and TreeBASE2 submission Id
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 2009-12-09 17:06:57 UTC (rev 342)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp 2009-12-09 17:09:04 UTC (rev 343)
@@ -16,8 +16,8 @@
<tr>
<th><fmt:message key="submission.accession"/>:</th>
<td>
- <input type="radio" name="identifierType" value="TB1"/>Legacy accession number
- <input type="radio" name="identifierType" value="TB2"/>TreeBASE2 study ID
+ <input type="radio" name="identifierType" value="TB1"/>Legacy accession
+ <input type="radio" name="identifierType" value="TB2"/>TreeBASE2 Id
<input type="text" name="submissionaccession" maxlength = "25"/>
</td>
</tr>
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From: <rv...@us...> - 2009-12-09 17:07:04
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Revision: 342
http://treebase.svn.sourceforge.net/treebase/?rev=342&view=rev
Author: rvos
Date: 2009-12-09 17:06:57 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Added findBySubmissionNumber() logic
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java 2009-12-09 16:56:02 UTC (rev 341)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchBySubmissionIDController.java 2009-12-09 17:06:57 UTC (rev 342)
@@ -53,10 +53,10 @@
BindException bindExp) throws Exception {
String studyAccession = request.getParameter("submissionaccession").trim();
+ String identifierType = request.getParameter("identifierType").trim();
Submission sub;
- if (TreebaseUtil.isEmpty(studyAccession)) {
-
+ if (TreebaseUtil.isEmpty(studyAccession)) {
return setAttributeAndShowForm(
request,
response,
@@ -64,17 +64,13 @@
"errors",
"Please provide a study accession number.");
}
-
-// if (!ControllerUtil.checkForLongNumber(submissionID)) {
-// return setAttributeAndShowForm(
-// request,
-// response,
-// bindExp,
-// "errors",
-// "Submission ID has to be a number.");
-// }
-
- sub = getSubmissionHome().findByStudyAccessionNumber(studyAccession);
+ if ( identifierType.equals("TB1") ) {
+ sub = getSubmissionHome().findByStudyAccessionNumber(studyAccession);
+ }
+ else {
+ sub = getSubmissionHome().findBySubmissionNumber(studyAccession);
+ }
+
if (sub == null) {
return setAttributeAndShowForm(request, response, bindExp, "errors", "Submission accession: '"
+ studyAccession + "' does not exist.");
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From: <rv...@us...> - 2009-12-09 16:56:18
|
Revision: 341
http://treebase.svn.sourceforge.net/treebase/?rev=341&view=rev
Author: rvos
Date: 2009-12-09 16:56:02 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Added prototype and scriptaculous libraries to admin template.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
Modified: trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2009-12-09 16:26:28 UTC (rev 340)
+++ trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2009-12-09 16:56:02 UTC (rev 341)
@@ -14,6 +14,10 @@
<link rel="stylesheet" type="text/css" media="all" href="<c:url value='/styles/treebase.css'/>" />
<link rel="stylesheet" type="text/css" media="all" href="<c:url value='/styles/menuExpandable.css'/>" />
<link rel="stylesheet" type="text/css" media="all" href="<c:url value='/styles/messages.css'/>" />
+<script type="text/javascript" src="/treebase-web/scripts/prototype/prototype.js"></script>
+<script type="text/javascript" src="/treebase-web/scripts/prototype/prototype-1.6.0.3.js"></script>
+<script type="text/javascript" src="/treebase-web/scripts/script.aculo.us/effects.js"></script>
+<script type="text/javascript" src="/treebase-web/scripts/script.aculo.us/controls.js"></script>
<script type="text/javascript" src="<c:url value='/scripts/menuExpandable.js'/>"></script>
<script type="text/javascript" src="<c:url value='/scripts/common.js'/>"></script>
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From: <rv...@us...> - 2009-12-09 16:26:38
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Revision: 340
http://treebase.svn.sourceforge.net/treebase/?rev=340&view=rev
Author: rvos
Date: 2009-12-09 16:26:28 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Updated searchBySubmission view: added help icon, added radio buttons to select identifier type
Modified Paths:
--------------
trunk/treebase-web/src/main/resources/ApplicationResources.properties
trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp
Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties 2009-12-09 16:06:08 UTC (rev 339)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties 2009-12-09 16:26:28 UTC (rev 340)
@@ -170,7 +170,7 @@
submission.list.title = List of Treebase Submissions
submission.mainmenu.title= Treebase Submission Menu
submission.id = Submission Id
-submission.accession = Study Accession Number
+submission.accession = Submission Id
#-- citation section --
citation.page.title = Citation Information
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp 2009-12-09 16:06:08 UTC (rev 339)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchBySubmissionID.jsp 2009-12-09 16:26:28 UTC (rev 340)
@@ -7,13 +7,17 @@
<form method="post" id="dataForm">
<fieldset>
-<legend>Search based on Study Accession Number</legend>
+<legend>Search for submissions by identifiers
+<a href="#" class="openHelp" onclick="openHelp('searchBySubmissionID')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
+</legend>
<table border="0" cellpadding="3" cellspacing="3">
<tr>
<th><fmt:message key="submission.accession"/>:</th>
- <td>
+ <td>
+ <input type="radio" name="identifierType" value="TB1"/>Legacy accession number
+ <input type="radio" name="identifierType" value="TB2"/>TreeBASE2 study ID
<input type="text" name="submissionaccession" maxlength = "25"/>
</td>
</tr>
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From: <rv...@us...> - 2009-12-09 16:07:35
|
Revision: 339
http://treebase.svn.sourceforge.net/treebase/?rev=339&view=rev
Author: rvos
Date: 2009-12-09 16:06:08 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Working on issue 2903251
Modified Paths:
--------------
trunk/treebase-core/src/main/perl/bin/undump
trunk/treebase-core/src/main/perl/misc/publish
Modified: trunk/treebase-core/src/main/perl/bin/undump
===================================================================
--- trunk/treebase-core/src/main/perl/bin/undump 2009-12-09 14:56:56 UTC (rev 338)
+++ trunk/treebase-core/src/main/perl/bin/undump 2009-12-09 16:06:08 UTC (rev 339)
@@ -9,7 +9,7 @@
$commit_batch_size ||= $opt{n};
my $BEGIN = "BEGIN TRANSACTION;\n";
-$BEGIN .= "SET CONSTAINTS ALL DEFERRED;\n" if $opt{d};
+$BEGIN .= "SET CONSTRAINTS ALL DEFERRED;\n" if $opt{d};
my $OK = 1;
Modified: trunk/treebase-core/src/main/perl/misc/publish
===================================================================
--- trunk/treebase-core/src/main/perl/misc/publish 2009-12-09 14:56:56 UTC (rev 338)
+++ trunk/treebase-core/src/main/perl/misc/publish 2009-12-09 16:06:08 UTC (rev 339)
@@ -26,6 +26,10 @@
TARGET_DIR="treebase-web"
IP_ADDR=`curl -s checkip.dyndns.org | grep -Eo '[0-9\.]+'`
+# Need to set this for mesquite, in case we're launching
+# on servers that don't have X11 configure
+export DISPLAY=:0.0
+
# Flag to suppress sourre update and rebuilding
update_sources=true
if [ "$1" == "-r" ]; then
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From: <rv...@us...> - 2009-12-09 14:57:02
|
Revision: 338
http://treebase.svn.sourceforge.net/treebase/?rev=338&view=rev
Author: rvos
Date: 2009-12-09 14:56:56 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Removed mesquite entry from classpath
Modified Paths:
--------------
trunk/treebase-notebook/.classpath
Modified: trunk/treebase-notebook/.classpath
===================================================================
--- trunk/treebase-notebook/.classpath 2009-12-09 14:56:42 UTC (rev 337)
+++ trunk/treebase-notebook/.classpath 2009-12-09 14:56:56 UTC (rev 338)
@@ -6,7 +6,7 @@
<classpathentry kind="src" path="/treebase-core"/>
<classpathentry kind="var" path="M2_REPO/asm/asm/1.5.3/asm-1.5.3.jar"/>
<classpathentry kind="var" path="M2_REPO/org/springframework/spring-remoting/1.2.6/spring-remoting-1.2.6.jar" sourcepath="M2_REPO/org/springframework/spring-remoting/1.2.6/spring-remoting-1.2.6-sources.jar"/>
- <classpathentry kind="var" path="M2_REPO/mesquite/mesquite/1.11/mesquite-1.11.jar"/>
+ <!--classpathentry kind="var" path="M2_REPO/mesquite/mesquite/1.11/mesquite-1.11.jar"/-->
<classpathentry kind="var" path="M2_REPO/org/springframework/spring-core/1.2.6/spring-core-1.2.6.jar" sourcepath="M2_REPO/org/springframework/spring-core/1.2.6/spring-core-1.2.6-sources.jar"/>
<classpathentry kind="var" path="M2_REPO/pal/pal/1.5.1/pal-1.5.1.jar"/>
<classpathentry kind="var" path="M2_REPO/commons-logging/commons-logging/1.0.4/commons-logging-1.0.4.jar" sourcepath="M2_REPO/commons-logging/commons-logging/1.0.4/commons-logging-1.0.4-sources.jar"/>
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From: <rv...@us...> - 2009-12-09 14:56:49
|
Revision: 337
http://treebase.svn.sourceforge.net/treebase/?rev=337&view=rev
Author: rvos
Date: 2009-12-09 14:56:42 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Removed mesquite entry from classpath
Modified Paths:
--------------
trunk/treebase-web/.classpath
Modified: trunk/treebase-web/.classpath
===================================================================
--- trunk/treebase-web/.classpath 2009-12-09 14:56:25 UTC (rev 336)
+++ trunk/treebase-web/.classpath 2009-12-09 14:56:42 UTC (rev 337)
@@ -71,7 +71,7 @@
<classpathentry kind="var" path="M2_REPO/log4j/log4j/1.2.13/log4j-1.2.13.jar"/>
<classpathentry kind="var" path="M2_REPO/logkit/logkit/1.0.1/logkit-1.0.1.jar"/>
<classpathentry kind="var" path="M2_REPO/javax/mail/mail/1.4/mail-1.4.jar"/>
- <classpathentry kind="var" path="M2_REPO/mesquite/mesquite/2.01.tb/mesquite-2.01.tb.jar"/>
+ <!--classpathentry kind="var" path="M2_REPO/mesquite/mesquite/2.01.tb/mesquite-2.01.tb.jar"/-->
<classpathentry kind="var" path="M2_REPO/mrj/MRJToolkitStubs/1.0/MRJToolkitStubs-1.0.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/neethi/neethi/2.0.4/neethi-2.0.4.jar"/>
<classpathentry kind="var" path="M2_REPO/oro/oro/2.0.8/oro-2.0.8.jar"/>
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From: <rv...@us...> - 2009-12-09 14:56:32
|
Revision: 336
http://treebase.svn.sourceforge.net/treebase/?rev=336&view=rev
Author: rvos
Date: 2009-12-09 14:56:25 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Removed mesquite from maven
Modified Paths:
--------------
trunk/treebase-core/pom.xml
Modified: trunk/treebase-core/pom.xml
===================================================================
--- trunk/treebase-core/pom.xml 2009-12-09 14:55:57 UTC (rev 335)
+++ trunk/treebase-core/pom.xml 2009-12-09 14:56:25 UTC (rev 336)
@@ -124,11 +124,11 @@
<version>8.3-603.jdbc3</version>
</dependency>
- <dependency>
+ <!--dependency>
<groupId>mesquite</groupId>
<artifactId>mesquite</artifactId>
<version>2.01.tb</version>
- </dependency>
+ </dependency-->
<dependency>
<groupId>org.cipres</groupId>
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From: <rv...@us...> - 2009-12-09 14:56:04
|
Revision: 335
http://treebase.svn.sourceforge.net/treebase/?rev=335&view=rev
Author: rvos
Date: 2009-12-09 14:55:57 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Removed mesquite entry from classpath
Modified Paths:
--------------
trunk/treebase-core/.classpath
Modified: trunk/treebase-core/.classpath
===================================================================
--- trunk/treebase-core/.classpath 2009-12-09 14:34:39 UTC (rev 334)
+++ trunk/treebase-core/.classpath 2009-12-09 14:55:57 UTC (rev 335)
@@ -58,7 +58,7 @@
<classpathentry kind="var" path="M2_REPO/javax/transaction/jta/1.0.1B/jta-1.0.1B.jar"/>
<classpathentry kind="var" path="M2_REPO/junit/junit/3.8.1/junit-3.8.1.jar"/>
<classpathentry kind="var" path="M2_REPO/log4j/log4j/1.2.13/log4j-1.2.13.jar"/>
- <classpathentry kind="var" path="M2_REPO/mesquite/mesquite/2.01.tb/mesquite-2.01.tb.jar"/>
+ <!--classpathentry kind="var" path="M2_REPO/mesquite/mesquite/2.01.tb/mesquite-2.01.tb.jar"/-->
<classpathentry kind="var" path="M2_REPO/mrj/MRJToolkitStubs/1.0/MRJToolkitStubs-1.0.jar"/>
<classpathentry kind="var" path="M2_REPO/org/apache/neethi/neethi/2.0.4/neethi-2.0.4.jar"/>
<classpathentry kind="var" path="M2_REPO/oro/oro/2.0.8/oro-2.0.8.jar"/>
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From: <rv...@us...> - 2009-12-09 14:34:49
|
Revision: 334
http://treebase.svn.sourceforge.net/treebase/?rev=334&view=rev
Author: rvos
Date: 2009-12-09 14:34:39 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Re-formatted line breaks
Modified Paths:
--------------
trunk/treebase-web/pom.xml
Modified: trunk/treebase-web/pom.xml
===================================================================
--- trunk/treebase-web/pom.xml 2009-12-09 14:34:19 UTC (rev 333)
+++ trunk/treebase-web/pom.xml 2009-12-09 14:34:39 UTC (rev 334)
@@ -95,10 +95,15 @@
<dependencies>
+
<dependency>
+
<groupId>org.nexml.model</groupId>
+
<artifactId>nexml</artifactId>
+
<version>1.5-SNAPSHOT</version>
+
</dependency>
<dependency>
@@ -301,11 +306,15 @@
<version>1.3</version>
<scope>runtime</scope>
</dependency>
-
+
<dependency>
+
<groupId>zing.z3950.org</groupId>
+
<artifactId>cql-java</artifactId>
+
<version>1.0</version>
+
</dependency>
</dependencies>
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From: <rv...@us...> - 2009-12-09 14:34:26
|
Revision: 333
http://treebase.svn.sourceforge.net/treebase/?rev=333&view=rev
Author: rvos
Date: 2009-12-09 14:34:19 +0000 (Wed, 09 Dec 2009)
Log Message:
-----------
Updated SQL creation script
Modified Paths:
--------------
trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
Modified: trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
===================================================================
--- trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2009-12-05 14:17:31 UTC (rev 332)
+++ trunk/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql 2009-12-09 14:34:19 UTC (rev 333)
@@ -2513,4 +2513,22 @@
FOREIGN KEY(COLUMNRANGE_ID)
REFERENCES COLUMNRANGE(COLUMNRANGE_ID)
ON DELETE NO ACTION
- ON UPDATE NO ACTION;
\ No newline at end of file
+ ON UPDATE NO ACTION;
+
+-- INDICES
+CREATE INDEX matrixcolumn_phylochar_id_idx ON matrixcolumn(phylochar_id);
+CREATE INDEX matrixrow_taxonlabel_id_idx ON matrixrow(taxonlabel_id);
+CREATE INDEX matrixrow_matrix_id_idx on matrixrow(matrix_id);
+CREATE INDEX matrixdatatype_phylochar_id_idx ON matrixdatatype(phylochar_id);
+CREATE INDEX rowsegment_matrixrow_id_idx ON rowsegment(matrixrow_id);
+
+CREATE INDEX matrixelement_matrixcolumn_id_idx ON matrixelement(matrixcolumn_id);
+CREATE INDEX matrixelement_matrixrow_id_idx ON matrixelement(matrixrow_id);
+CREATE INDEX matrixelement_discretecharstate_id_idx ON matrixelement(discretecharstate_id);
+
+CREATE INDEX matrixelement_discretecharstate_id_idx ON matrixelement(discretecharstate_id);
+CREATE INDEX discretecharstate_phylochar_id_idx ON discretecharstate(phylochar_id);
+
+CREATE INDEX analysis_study_id_idx ON analysis(study_id);
+CREATE INDEX submission_study_id_idx ON submission(study_id);
+CREATE INDEX study_citation_id_idx ON study(citation_id);
\ No newline at end of file
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From: <rsc...@us...> - 2009-12-05 14:17:38
|
Revision: 332
http://treebase.svn.sourceforge.net/treebase/?rev=332&view=rev
Author: rscherle
Date: 2009-12-05 14:17:31 +0000 (Sat, 05 Dec 2009)
Log Message:
-----------
added the last citation updates from Rosie
Modified Paths:
--------------
trunk/treebase-curation/studyCitations.enl
Modified: trunk/treebase-curation/studyCitations.enl
===================================================================
(Binary files differ)
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