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From: Vladimir G. <vla...@du...> - 2010-02-04 15:03:12
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While uploading to 6666 one of the files sent yesterday by Bill (Diatrypaceae BETA.nex) I've got this SQL reject java.sql.BatchUpdateException: Batch entry 0 insert into CHARSET (VERSION, MATRIX_ID, Title, TYPE, CHARSET_ID) values (0, 4157, Gene1, 'U', 2) was aborted. The cause appears to be that some (not all) sequences start with 1, while their tables are far from empty. I'll check all tables and sequences in both treebasedev and treebasestage to fix this, hopefully by noon. --VG |
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From: Vladimir G. <vla...@du...> - 2010-02-04 19:49:02
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I have now updated sequence start values to be larger than max IDs in the corresponding tables. Here a few observations of strange things, if someone wants to get concerned: * Tables where sequences were at 1, but tables had much higher max IDs (in both DB instances): chargroup, charset, charweight. (I generally reinitialized these at the next thousand greater than their max ID) * Table ancestralstate has no data, but the sequence is 4885 (I left it as this). Ditto for usertype, but the sequence is just 4. --Vladimir On Feb 4, 2010, at 10:02 AM, Vladimir Gapeyev wrote: > While uploading to 6666 one of the files sent yesterday by Bill > (Diatrypaceae BETA.nex) I've got this SQL reject > > java.sql.BatchUpdateException: Batch entry 0 insert into CHARSET > (VERSION, MATRIX_ID, Title, TYPE, CHARSET_ID) values (0, 4157, Gene1, > 'U', 2) was aborted. > > The cause appears to be that some (not all) sequences start with 1, > while their tables are far from empty. > > I'll check all tables and sequences in both treebasedev and > treebasestage to fix this, hopefully by noon. > > --VG > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the > business > Choose flexible plans and management services without long-term > contracts > Personal 24x7 support from experience hosting pros just a phone call > away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: William P. <wil...@ya...> - 2010-02-09 14:55:18
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Hi all, 1. Uploading a file with a character and/or tree block results in the message "No matrices or trees uploaded" (so no error stack, just fails to import these objects). I thought we had the Mesquite parser working on dev, just not on stage? At any rate, we cannot effectively test for bugs if we cannot do this basic operation. Can we make this a high priority fix? (or if the port 666 version were returned, I could test for bugs on that one). 2. Youjun has been relying on Rutger to trigger each build on dev. We need to either give Youjun the power to do this or have someone at NESCent available to do this. Bill |
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From: William P. <wil...@ya...> - 2010-02-09 15:30:42
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On Feb 9, 2010, at 9:54 AM, William Piel wrote: > (or if the port 666 version were returned, I could test for bugs on that one). Sorry -- actually, I meant the 6666 version (and indeed, that one is still live). I just tested it on that version but it has the same error: "No matrices or trees uploaded." This is a new bug that has crept in since last week (when uploads worked on dev). It's pretty critical that we be able to test a full basic use cycle of creating a submission, uploading data, publishing it, searching on it, deleting it, so I'm hopeful that this can be fixed right away. bp |
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From: Vladimir G. <vla...@du...> - 2010-02-09 16:50:18
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On Feb 9, 2010, at 9:54 AM, William Piel wrote: > 1. Uploading a file with a character and/or tree block results in > the message "No matrices or trees uploaded" (so no error stack, just > fails to import these objects). I thought we had the Mesquite parser > working on dev, just not on stage? My apologies for this. Jon and I finished the day yesterday happy that we made it work, but apparently something happened since then. I am checking if the problem might be in the WAR and asking Jon to check the servers. > > 2. Youjun has been relying on Rutger to trigger each build on dev. > We need to either give Youjun the power to do this or have someone > at NESCent available to do this. The current arrangement for redeployment is that I build a new treebase-web.war, commit it to a special repository, and send a request to Jon via he...@ne... to redeploy (usually just on treebasedev). Youjun could do the same, I think. The repository for WARs is svn+ssh://USE...@sv.../repos/ treebase (Youjun would need an account for the NESCent file server.) I am not happy with the amount of interaction and manual work in this process, but that's what we'll have to live with till well after the release. Alternatively, if you'd like to have faster turnaround, you cold set up a web front end on a machine over which Youjun has control. We have started a page for sysadmin-oriented installation instructions at http://sourceforge.net/apps/mediawiki/treebase/index.php?title=Deployment_by_a_sysadmin , which would benefit from being tried out. --Vladimir |
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From: Jon A. <jon...@ne...> - 2010-02-09 21:59:58
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Bill, This has been fixed. Mesquite requires that the tomcat startup script export the display # Headless mesquite needs a window server (a virtual one is OK) export DISPLAY=localhost:1.0 -Jon On Feb 9, 2010, at 9:54 AM, William Piel wrote: > Hi all, > > 1. Uploading a file with a character and/or tree block results in the message "No matrices or trees uploaded" (so no error stack, just fails to import these objects). I thought we had the Mesquite parser working on dev, just not on stage? At any rate, we cannot effectively test for bugs if we cannot do this basic operation. Can we make this a high priority fix? (or if the port 666 version were returned, I could test for bugs on that one). > > 2. Youjun has been relying on Rutger to trigger each build on dev. We need to either give Youjun the power to do this or have someone at NESCent available to do this. > > Bill > > > > ------------------------------------------------------------------------------ > The Planet: dedicated and managed hosting, cloud storage, colocation > Stay online with enterprise data centers and the best network in the business > Choose flexible plans and management services without long-term contracts > Personal 24x7 support from experience hosting pros just a phone call away. > http://p.sf.net/sfu/theplanet-com > _______________________________________________ > 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: Rutger V. <rut...@gm...> - 2010-02-12 08:02:17
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This hasn't been fixed yet: mesquite can't be found, the mesquite.folder_dir property is set to "null/foo" at runtime. I assume this is due to the new JNDI configuration system, so the path needs to be set either in web.xml or treebase-web.xml. Vladimir, can you please explain how this is supposed to work and put it on the wiki? On Thu, Feb 11, 2010 at 1:50 PM, William Piel <wil...@ya...> wrote: > > On Feb 9, 2010, at 4:59 PM, Jon Auman wrote: > >> Bill, >> >> This has been fixed. Mesquite requires that the tomcat startup script export the display > > Hi Jon, > > Thanks for whatever you did... but I still can't seem to upload any nexus files... I get a "File upload summary: No matrices or trees uploaded" message. I'm using the dev instance -- tried it with both the port 80 and port 6666 builds. Is there a particular deployment that I should be testing? (attached is a test file, if you need something to try). > > Bill > > > > > ------------------------------------------------------------------------------ > SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, > Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW > http://p.sf.net/sfu/solaris-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- 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. <vla...@du...> - 2010-02-12 14:57:30
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On Feb 12, 2010, at 3:02 AM, Rutger Vos wrote: > This hasn't been fixed yet: mesquite can't be found, the > mesquite.folder_dir property is set to "null/foo" at runtime. I assume > this is due to the new JNDI configuration system, so the path needs to > be set either in web.xml or treebase-web.xml. Vladimir, can you please > explain how this is supposed to work and put it on the wiki? Jon said he fixed the problem, on treebase-dev:80, Thu afternoon; file uploads work for me as of Fri morning. Details are on the wiki at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=Deployment_by_a_sysadmin . If your local or 6666 deployment relies on the WAR-supplied context.xml, you'd need to update it according to the updated treebase-web/src/main/webapp/META-INF/context.xml.example. As you are into the mesquite matters at the moment, I'd like to re- raise the suggestion to drop Mesquite code from SVN (see the forward below). --VG Begin forwarded message: > From: Vladimir Gapeyev <vla...@du...> > Date: February 7, 2010 4:41:35 PM EST > To: TreeBASE Developers <Tre...@li...> > Subject: [Treebase-devel] Get rid of treebase--core/lib ? > > After the re-configuration of server-side access to Mesquite, is there > any remaining need for the Mesquite unpacked under treebase-core/ > lib? My builds appear to be fine both under 'mvn package' and under > Eclipse. > > I'd then suggest removing this Mesquite code from SVN. And, as we are > up for that, would it make sense to clear the whole lib directory? > I.e., is there anything important there? DB2 drivers in lib/ibm are > useless now. What about lib/jars? > > --Vladimir |
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