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From: Hilmar L. <hl...@ne...> - 2010-04-15 15:11:25
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On Apr 15, 2010, at 10:55 AM, Rutger Vos wrote: > I know there's a requirement to have an open source license, I'm not > sure that means I'd have to mention it in the abstract. Yes, you should mention it in the abstract. (The documentation states that.) If you don't, reviewers (or committee members) have to go looking for it. > If I do, would it be OK to just say TreeBASE is released under a > "BSD-style license"? Why not say "BSD license"? Isn't it a BSD license? "BSD-style" sounds more wishy-washy than it is. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-04-15 14:55:17
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On Thu, Apr 15, 2010 at 3:09 PM, William Piel <wil...@ya...> wrote: > Isn't there a requirement to state the license? (does that have to go in the abstract?) I'm a bit unclear about this. I know there's a requirement to have an open source license, I'm not sure that means I'd have to mention it in the abstract. If I do, would it be OK to just say TreeBASE is released under a "BSD-style license"? I mean, isn't that where we stand right now? -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2010-04-15 14:50:27
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On Apr 15, 2010, at 10:26 AM, Vladimir Gapeyev wrote: > As you anticipated, inserting new PKs will > confuse Hibernate, since the PKs the update creates are higher than > the current values in the sequences that generate the PKs under normal > operation. The latter will catch up and clash eventually. Thanks for catching this, Vladimir! All INSERTs or UPDATEs that create new PK values must not specify these as literals. They either need to be left to the database to create, or the script needs to draw them from the correct sequences. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2010-04-15 14:26:28
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On Apr 15, 2010, at 2:22 AM, sfr...@us... wrote: > Revision: 687 > http://treebase.svn.sourceforge.net/treebase/? > rev=687&view=rev > Author: sfrgpiel > Date: 2010-04-15 06:22:27 +0000 (Thu, 15 Apr 2010) > > Log Message: > ----------- > Set of edits to the taxonlabel-taxonvariant-taxon tables. > > Added Paths: > ----------- > trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/ > trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/README.txt > trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/ > taxon_fixes_4-15-10.sql > > Added: trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/ > README.txt > =================================================================== > --- trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/ > README.txt (rev 0) > +++ trunk/treebase-core/db/cleaning/2010-04-15_taxon_fixes/ > README.txt 2010-04-15 06:22:27 UTC (rev 687) > @@ -0,0 +1,17 @@ > +To apply, run taxon_fixes_4-15-10.sql > + > +-------- > + > +These statements help clean up the mapping between taxonlabel, > taxonvariant, and > +taxon records. They include INSERTS in which the primary key is > being supplied: > +please verify that this is okay, or will it confuse Hibernate's > autoincrement? > + > +New taxon_id starts at 600001 > +New taxonvariant_id starts at 800000 > + > +Please verify that these numbers are beyond the current highest > numbers. > + > +--------- > + > +Apply changes as soon as convenient, because it is not impossible > that new submissions > +in the interim will map to taxonvariants that this script wants to > delete. ..... <rest omitted> Bill, I am sad to bring the bad news, but we need to be more careful with updates like this. As you anticipated, inserting new PKs will confuse Hibernate, since the PKs the update creates are higher than the current values in the sequences that generate the PKs under normal operation. The latter will catch up and clash eventually. Can you modify the script that the INSERT statements do not specify the PK values? Then the PKs will be properly generated by postgres from the sequences and Hibernate will be aware of that. We went through some pains a few months ago to make this scenario possible! When later in the script you need to know the generated IDs, I hope you will be able to look them up unambiguously via ubionamebankid and namebankid. Will this work? --Vladimir |
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From: Rutger V. <rut...@gm...> - 2010-04-15 11:32:47
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Hi all, please find attached a first draft of my abstract for iEvoBio. In terms of dividing up the work I think I will spend most time talking about PhyloWS and NeXML (both as relevant for TreeBASE) and not that much time talking about CDAO per se. In a separate mail I have sent all relevant people* I have put a link to a web folder that contains an editable version of this abstract, and the powerpoint slides which I will be adapting for iEvoBio (they're from the CIPRES all-hands meeting so they'll need some work). All comments very welcome! Rutger * that I could think of in the spur of the moment. Please let me know if I accidentally left you out! On Wed, Apr 14, 2010 at 5:11 PM, Rutger Vos <rut...@gm...> wrote: > Am I being too cute if I call my talk "TreeBASE2: Rise of the Machines > (-readable architecture)"? > > On Wed, Apr 14, 2010 at 4:58 PM, Rutger Vos <rut...@gm...> wrote: >>> The only plan I've heard so far was Rutger planning a full talk around >>> TreeBASE's ventures into semweb and linked data compatibility. Is that still >>> on? That would presumably cover NeXML, and at least give basics on PhyloWS? >> >> Yes, yes and yes. >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-04-15 06:29:21
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On Apr 14, 2010, at 5:39 PM, Vladimir Gapeyev wrote: > That's interesting. I do not see the red X marks -- see attached screenshot from the treebase-dev instance. I do see the red frames, so hopefully I am not color-blind! Could it be because I am a regular user, not an admin or an editor? Ah, yes, you have to click on the Matrix item in the Tool Box, not open the Matrix item on the Tool Box with the +/- buttons. Clicking on it takes you to the list of uploaded matrices, which includes the red X mark. bp |
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From: Vladimir G. <vla...@du...> - 2010-04-14 21:39:55
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On Apr 14, 2010, at 4:52 PM, William Piel wrote: > > On Apr 14, 2010, at 4:29 PM, Vladimir Gapeyev wrote: > >> For my edification, how does one delete a tree or a matrix? I really >> thought that a whole-sale study deletion was the only option in the >> UI. > > Enter the submission, click on "Matrices" form the toolbox to see a > list of matrices. Next to each matrix is a red X mark. Clicking that > deletes it. Same idea for the trees (you can either delete a whole > tree block or enter a tree block and delete trees individually -- > when the last tree is deleted, the containing tree block gets > deleted automatically). That's interesting. I do not see the red X marks -- see attached screenshot from the treebase-dev instance. I do see the red frames, so hopefully I am not color-blind! Could it be because I am a regular user, not an admin or an editor? --Vg |
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From: William P. <wil...@ya...> - 2010-04-14 20:52:46
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On Apr 14, 2010, at 4:29 PM, Vladimir Gapeyev wrote: > For my edification, how does one delete a tree or a matrix? I really > thought that a whole-sale study deletion was the only option in the UI. Enter the submission, click on "Matrices" form the toolbox to see a list of matrices. Next to each matrix is a red X mark. Clicking that deletes it. Same idea for the trees (you can either delete a whole tree block or enter a tree block and delete trees individually -- when the last tree is deleted, the containing tree block gets deleted automatically). > Jon has just deployed this vesrion to production thanks! We can now start spring cleaning on various submissions that were abandoned. bp |
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From: Vladimir G. <vla...@du...> - 2010-04-14 20:29:43
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On Apr 14, 2010, at 2:43 PM, William Piel wrote: > > On Apr 14, 2010, at 11:35 AM, Vladimir Gapeyev wrote: > >> The build with this fix (SVN #686) still gives an exception dump at >> an >> attempt to delete a study, at least on my local and treebase-dev >> instances, see appended. This is both for studies I had in my >> account for awhile, and for a study I created in the fresh build. > > Deleting a submission that still contains matrices or trees fails -- > this is a known bug, but a separate one from the inability to delete > trees and matrices. > > I just tested deleting trees and matrices using dev and it works. For my edification, how does one delete a tree or a matrix? I really thought that a whole-sale study deletion was the only option in the UI. >> Continue working on it? So far, Jon has redeployed only to >> treebase- dev. > > Lets deploy on production because providing the ability to delete > trees and matrices is valuable. Jon has just deployed this vesrion to production --VG |
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From: Jon A. <jon...@du...> - 2010-04-14 20:28:56
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The latest version of the app was just deployed on production. -Jon On Apr 14, 2010, at 2:43 PM, William Piel wrote: > > On Apr 14, 2010, at 11:35 AM, Vladimir Gapeyev wrote: > >> The build with this fix (SVN #686) still gives an exception dump at an >> attempt to delete a study, at least on my local and treebase-dev >> instances, see appended. This is both for studies I had in my >> account for awhile, and for a study I created in the fresh build. > > Deleting a submission that still contains matrices or trees fails -- this is a known bug, but a separate one from the inability to delete trees and matrices. > > I just tested deleting trees and matrices using dev and it works. > > >> Continue working on it? So far, Jon has redeployed only to treebase- dev. > > Lets deploy on production because providing the ability to delete trees and matrices is valuable. > > It may take some time before we address the delete-submission bug -- but in the meantime, if someone removes all trees and matrices from their submission, then they can also delete the submission. > > regards, > > Bill > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-04-14 18:45:09
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On Apr 14, 2010, at 11:35 AM, Vladimir Gapeyev wrote: > The build with this fix (SVN #686) still gives an exception dump at an > attempt to delete a study, at least on my local and treebase-dev > instances, see appended. This is both for studies I had in my > account for awhile, and for a study I created in the fresh build. Deleting a submission that still contains matrices or trees fails -- this is a known bug, but a separate one from the inability to delete trees and matrices. I just tested deleting trees and matrices using dev and it works. > Continue working on it? So far, Jon has redeployed only to treebase- dev. Lets deploy on production because providing the ability to delete trees and matrices is valuable. It may take some time before we address the delete-submission bug -- but in the meantime, if someone removes all trees and matrices from their submission, then they can also delete the submission. regards, Bill |
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From: Hilmar L. <hl...@ne...> - 2010-04-14 17:23:31
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On Apr 14, 2010, at 12:11 PM, Rutger Vos wrote: > Am I being too cute if I call my talk "TreeBASE2: Rise of the Machines > (-readable architecture)"? Not if you leave out the stuff in parentheses. Let them guess. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-04-14 16:11:34
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Am I being too cute if I call my talk "TreeBASE2: Rise of the Machines (-readable architecture)"? On Wed, Apr 14, 2010 at 4:58 PM, Rutger Vos <rut...@gm...> wrote: >> The only plan I've heard so far was Rutger planning a full talk around >> TreeBASE's ventures into semweb and linked data compatibility. Is that still >> on? That would presumably cover NeXML, and at least give basics on PhyloWS? > > Yes, yes and yes. > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Vladimir G. <vga...@ne...> - 2010-04-14 15:39:27
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On Apr 13, 2010, at 10:56 AM, William Piel wrote: > Also, it looks like Youjun has licked the bug that prevented > deletion of matrices and trees. A pretty critical fix with only one > line of code modified. > > Can we rebuild on production with his latest change? The build with this fix (SVN #686) still gives an exception dump at an attempt to delete a study, at least on my local and treebase-dev instances, see appended. This is both for studies I had in my account for awhile, and for a study I created in the fresh build. Continue working on it? So far, Jon has redeployed only to treebase- dev. --Vladimir Deleting a study from http://treebase-dev.nescent.org/treebase-web/user/submissionList.html gives page http://treebase-dev.nescent.org/treebase-web/user/deleteStudy.html?submissionid=10331 with Data Access Failure Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1; nested exception is org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1 org .springframework .orm.hibernate3.HibernateOptimisticLockingFailureException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1; nested exception is org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1 Caused by: org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1 at org.hibernate.jdbc.Expectations $BasicExpectation.checkBatched(Expectations.java:61) at org.hibernate.jdbc.Expectations $BasicExpectation.verifyOutcome(Expectations.java:46) at org.hibernate.jdbc.BatchingBatcher.checkRowCounts(BatchingBatcher.java: 68) at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java: 48) at org.hibernate.jdbc.BatchingBatcher.addToBatch(BatchingBatcher.java:34) at org .hibernate .persister .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: 2525) at org .hibernate .persister .entity.AbstractEntityPersister.delete(AbstractEntityPersister.java: 2702) at org .hibernate.action.EntityDeleteAction.execute(EntityDeleteAction.java: 77) at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:279) at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java: 263) at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:172) at org .hibernate .event .def .AbstractFlushingEventListener .performExecutions(AbstractFlushingEventListener.java:298) at org .hibernate .event .def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java: 27) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1000) at org.springframework.orm.hibernate3.HibernateTemplate $27.doInHibernate(HibernateTemplate.java:811) at org .springframework .orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:372) at org .springframework .orm.hibernate3.HibernateTemplate.flush(HibernateTemplate.java:809) at org.cipres.treebase.dao.AbstractDAO.flush(AbstractDAO.java:158) 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.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:198) at $Proxy53.flush(Unknown Source) at org .cipres .treebase .service .study .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: 428) at org .cipres .treebase .service .study .SubmissionServiceImpl.deleteSubmission(SubmissionServiceImpl.java: 900) 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 $Proxy81.deleteSubmission(Unknown Source) at org.cipres.treebase.web.controllers.DeleteStudyController.onSubmit (DeleteStudyController.java:71) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission (SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission (CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal (AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest (AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle (SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch (DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService (DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest (FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost (FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 269) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java: 164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java: 141) at org .tuckey .web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java: 90) at org .tuckey .web .filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java: 406) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .displaytag .filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java: 125) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .springframework .orm .hibernate3 .support .OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java: 198) at org .springframework .web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java: 75) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com .opensymphony .module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com .opensymphony .module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org .acegisecurity .intercept .web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java: 107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter (FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .ui .ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java: 110) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .wrapper .SecurityContextHolderAwareRequestFilter .doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java: 217) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org .acegisecurity .context .HttpSessionContextIntegrationFilter .doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy $VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java: 148) at org .acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java: 90) at org .apache .catalina .core .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: 215) at org .apache .catalina .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org .apache .catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java: 213) at org .apache .catalina.core.StandardContextValve.invoke(StandardContextValve.java: 172) at org .apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java: 127) at org .apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java: 117) at org .apache .catalina.core.StandardEngineValve.invoke(StandardEngineValve.java: 108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java: 174) at org .apache .coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol $Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java: 1286) at java.lang.Thread.run(Thread.java:636) « Back |
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From: William P. <wil...@ya...> - 2010-04-11 17:00:10
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Dear Jon and Vladimir, Turns out that the record deletion build did not fix the problem -- evidently two different methods for establishing the mapping between study and taxonlabels have been used, and the result is a conflict that's difficult to fix. At any rate, Youjun thinks he has it licked now, but we cannot test it at the Peabody because our development build is on Windows, and we lack Mesquite for uploading data files. Don't know if either of you happen to be in today, but it would be great if we could have a build on dev so that I can test this new fix. If this new fix works, then we can build on production. thanks, Bill |
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From: youjun g. <you...@ya...> - 2010-04-09 22:23:38
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> Has a rebuild happened yet? (sorry -- I'm not sure how to tell -- seeing as > the revision number is not being updated) > Bill, It was done. Try these oai-pmh links by replace "http://130.132.27.212:8080<http://130.132.27.212:8080/treebase-web/top/oai?verb=Identify>" with "treebase.org". Youun http://130.132.27.212:8080/treebase-web/top/oai?verb=Identify http://130.132.27.212:8080/<http://130.132.27.212:8080/data_provider_web/top/oai?verb=ListSets> treebase- <http://130.132.27.212:8080/treebase-web/top/oai?verb=Identify> web/top/oai?verb=ListSets<http://130.132.27.212:8080/treebase-web/top/oai?verb=ListSets> http://130.132.27.212:8080/<http://130.132.27.212:8080/data_provider_web/top/oai?verb=ListMetadataFormats> treebase-<http://130.132.27.212:8080/data_provider_web/top/oai?verb=Identify> web/top/oai?verb=ListMetadataFormats<http://130.132.27.212:8080/treebase-web/top/oai?verb=ListMetadataFormats> http://130.132.27.212:8080/<http://130.132.27.212:8080/data_provider_web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&until=1996-11-04T00:00:00Z> treebase-<http://130.132.27.212:8080/data_provider_web/top/oai?verb=Identify> web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&until=1996-11-04T00:00:00Z<http://130.132.27.212:8080/treebase-web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&until=1996-11-04T00:00:00Z> http://130.132.27.212:8080/<http://130.132.27.212:8080/data_provider_web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1234> treebase-<http://130.132.27.212:8080/data_provider_web/top/oai?verb=Identify> web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1234<http://130.132.27.212:8080/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1234> http://130.132.27.212:8080/<http://130.132.27.212:8080/data_provider_web/top/oai?verb=ListIdentifiers&metadataPrefix=oai_dc&until=1996-11-04T00:00:00Z> treebase-<http://130.132.27.212:8080/data_provider_web/top/oai?verb=Identify> web/top/oai?verb=ListIdentifiers&metadataPrefix=oai_dc&until=1996-11-04T00:00:00Z<http://130.132.27.212:8080/treebase-web/top/oai?verb=ListIdentifiers&metadataPrefix=oai_dc&until=1996-11-04T00:00:00Z> |
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From: Jon A. <jon...@du...> - 2010-04-09 21:28:38
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Yes, this morning. I think there is some move towards getting build dates to display on at least one of the jsp pages. -Jon On Apr 9, 2010, at 4:40 PM, William Piel wrote: > > On Apr 8, 2010, at 5:00 PM, Vladimir Gapeyev wrote: > >> If you are confident you do not want to see it on dev first, we'll redeploy to dev and prod at the >> same time. Otherwise, send a stop-order. > > Has a rebuild happened yet? (sorry -- I'm not sure how to tell -- seeing as the revision number is not being updated) > > It's important that rev 680 happen as soon as we can -- because with prior-to-680 versions, any use of delete matrix or delete tree causes a corruption in the whole submission. > > bp > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-04-09 20:40:18
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On Apr 8, 2010, at 5:00 PM, Vladimir Gapeyev wrote: > If you are confident you do not want to see it on dev first, we'll redeploy to dev and prod at the > same time. Otherwise, send a stop-order. Has a rebuild happened yet? (sorry -- I'm not sure how to tell -- seeing as the revision number is not being updated) It's important that rev 680 happen as soon as we can -- because with prior-to-680 versions, any use of delete matrix or delete tree causes a corruption in the whole submission. bp |
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From: William P. <wil...@ya...> - 2010-04-09 15:21:16
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For local (Yale) testing, this should work: mail.yale.edu (which I don't think requires authentication if used within the Yale domain). But, indeed, since this is ultimately for deployment at NESCent, we should solve the problem at NESCent. bp On Apr 9, 2010, at 11:00 AM, youjun guo wrote: > Hi, Vladimir, > > I am working on this bug: http://sourceforge.net/tracker/?func=detail&aid=2977860&group_id=248804&atid=1126676 > > The problem is "Relaying denied", the cause is org.cipres.treebase.web.controllers.PasswordFormContr > oller.onSubmit(PasswordFormController.java:132). I quote the line below: > > 'props.put("mail.smtp.host", "smtp.ucsd.edu");' > > AS you can see we need to replace that ucsd smtp server url with NESCent's smtp. The problem is I cannot test it from my personnel server even I have the correct url. There will be most likely another "Relaying denied". > > Can I re-assign this to you? > > Youjun |
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From: Vladimir G. <vla...@du...> - 2010-04-09 15:12:03
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It looks like you figured it out -- thanks. I and Jon should be able to proceed from here. On Apr 9, 2010, at 11:00 AM, youjun guo wrote: > Hi, Vladimir, > > I am working on this bug: http://sourceforge.net/tracker/?func=detail&aid=2977860&group_id=248804&atid=1126676 > > The problem is "Relaying denied", the cause is org.cipres.treebase.web.controllers.PasswordFormContr > oller.onSubmit(PasswordFormController.java:132). I quote the line > below: > > 'props.put("mail.smtp.host", "smtp.ucsd.edu");' > > AS you can see we need to replace that ucsd smtp server url with > NESCent's smtp. The problem is I cannot test it from my personnel > server even I have the correct url. There will be most likely > another "Relaying denied". > > Can I re-assign this to you? > > Youjun > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: youjun g. <you...@gm...> - 2010-04-09 15:01:05
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Hi, Vladimir, I am working on this bug: http://sourceforge.net/tracker/?func=detail&aid=2977860&group_id=248804&atid=1126676 The problem is "Relaying denied", the cause is org.cipres.treebase.web.controllers.PasswordFormContr oller.onSubmit(PasswordFormController.java:132). I quote the line below: 'props.put("mail.smtp.host", "smtp.ucsd.edu");' AS you can see we need to replace that ucsd smtp server url with NESCent's smtp. The problem is I cannot test it from my personnel server even I have the correct url. There will be most likely another "Relaying denied". Can I re-assign this to you? Youjun |
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From: youjun g. <you...@ya...> - 2010-04-08 22:29:38
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The source code of oai-pmh was seamlessly merged into treebase-web MVC. It has become part of the treebase in sourceforge. Re-build the most uptodate vreson of treebase as usual will do the job. Youjun On Thu, Apr 8, 2010 at 5:00 PM, Vladimir Gapeyev <vla...@du...>wrote: > Did we have OAI-PMH in operation before? If you are confident you do > not want to see it on dev first, we'll redeploy to dev and prod at the > same time. Otherwise, send a stop-order. > > In any case, please let me know if I need to be aware of anything > regarding AOI-PMH in order to maintain the deployments here. So far, > I do not even have its source code configured in my Eclipse. (I just > presume the Maven command 'mvn package -Dmaven.test.skip=true' does > everything that's needed.) > > --Vladimir > > On Apr 8, 2010, at 4:02 PM, William Piel wrote: > > > Hi, > > > > Youjun's latest commit is a valuable addition because it should (for > > now) solve the problem of "ghost data" and being unable to work with > > submissions after deleting one of the matrices. Also, he has made > > improvements to our OAI-PMH service. > > > > Can we do a new build for this today? > > > > thanks, > > > > BIll > > > > > > > > > ------------------------------------------------------------------------------ > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: youjun g. <you...@ya...> - 2010-04-08 22:16:39
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Just take it as a group of new pages(xml) in treebase-web, no extra mainlines need to be done. Youjun On Thu, Apr 8, 2010 at 5:00 PM, Vladimir Gapeyev <vla...@du...>wrote: > Did we have OAI-PMH in operation before? If you are confident you do > not want to see it on dev first, we'll redeploy to dev and prod at the > same time. Otherwise, send a stop-order. > > In any case, please let me know if I need to be aware of anything > regarding AOI-PMH in order to maintain the deployments here. So far, > I do not even have its source code configured in my Eclipse. (I just > presume the Maven command 'mvn package -Dmaven.test.skip=true' does > everything that's needed.) > > --Vladimir > > On Apr 8, 2010, at 4:02 PM, William Piel wrote: > > > Hi, > > > > Youjun's latest commit is a valuable addition because it should (for > > now) solve the problem of "ghost data" and being unable to work with > > submissions after deleting one of the matrices. Also, he has made > > improvements to our OAI-PMH service. > > > > Can we do a new build for this today? > > > > thanks, > > > > BIll > > > > > > > > > ------------------------------------------------------------------------------ > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: Vladimir G. <vla...@du...> - 2010-04-08 21:01:01
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Did we have OAI-PMH in operation before? If you are confident you do not want to see it on dev first, we'll redeploy to dev and prod at the same time. Otherwise, send a stop-order. In any case, please let me know if I need to be aware of anything regarding AOI-PMH in order to maintain the deployments here. So far, I do not even have its source code configured in my Eclipse. (I just presume the Maven command 'mvn package -Dmaven.test.skip=true' does everything that's needed.) --Vladimir On Apr 8, 2010, at 4:02 PM, William Piel wrote: > Hi, > > Youjun's latest commit is a valuable addition because it should (for > now) solve the problem of "ghost data" and being unable to work with > submissions after deleting one of the matrices. Also, he has made > improvements to our OAI-PMH service. > > Can we do a new build for this today? > > thanks, > > BIll > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: William P. <wil...@ya...> - 2010-04-08 20:02:37
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Hi, Youjun's latest commit is a valuable addition because it should (for now) solve the problem of "ghost data" and being unable to work with submissions after deleting one of the matrices. Also, he has made improvements to our OAI-PMH service. Can we do a new build for this today? thanks, BIll |
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