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From: Rutger V. <rut...@gm...> - 2010-05-28 17:52:56
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Great! On Fri, May 28, 2010 at 6:02 PM, Jon Auman <jon...@du...> wrote: > I've configured hudson, our continuous integration server, to check the > treebase svn repository every ten minutes for new source files. If new code > has been checked in, it will trigger a new build and deploy to the > treebase-dev instance (http://treebase-dev.nescent.org/treebase-web). If a > developer breaks a build so that it does not compile, he will be sent an > email (in theory). However, I'm not sure how that will work since the svn > repository is not integrated with NESCent ldap. In any regard, Vladimir > will be sent an email after every rebuild. > -Jon > On May 28, 2010, at 12:22 PM, Jon Auman wrote: > > I'm working on autodeployment via hudson, that will automatically check out > new code in subversion and deploy it to dev. I'll send out a message in a > little bit once I've ironed out the deployment script. > -Jon > On May 28, 2010, at 12:18 PM, Hilmar Lapp wrote: > > Although Jon is on this list, could you then please send a ticket to > he...@ne... > . (Vladimir - or is there a different procedure that you, Jon, and > Youjun hashed out?) > > -hilmar > > On May 28, 2010, at 7:54 AM, Rutger Vos wrote: > > Yes. > > On Fri, May 28, 2010 at 2:05 PM, Hilmar Lapp <hl...@ne...> > > wrote: > > I don't think we can redeploy individual classes - are you > > essentially > > asking for a rebuild and redeploy? > > -hilmar > > On May 28, 2010, at 2:19 AM, Rutger Vos wrote: > > AbstractDownloadController > > anyObjectAsRDF.jsp > > searchResultsAsRDF.jsp > > These address a mismatch between the content type in the http header > > (which defaulted to ISO-8859-1) and the xml and rdf bodies (which > > specify UTF-8). > > Thanks, > > Rutger > > > > -- > > 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 > > > ------------------------------------------------------------------------------ > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > > =========================================================== > > > > > > > > -- > > 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 > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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... > ------------------------------------------------------ > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > 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: Jon A. <jon...@du...> - 2010-05-28 17:02:34
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I've configured hudson, our continuous integration server, to check the treebase svn repository every ten minutes for new source files. If new code has been checked in, it will trigger a new build and deploy to the treebase-dev instance (http://treebase-dev.nescent.org/treebase-web). If a developer breaks a build so that it does not compile, he will be sent an email (in theory). However, I'm not sure how that will work since the svn repository is not integrated with NESCent ldap. In any regard, Vladimir will be sent an email after every rebuild. -Jon On May 28, 2010, at 12:22 PM, Jon Auman wrote: > I'm working on autodeployment via hudson, that will automatically check out new code in subversion and deploy it to dev. I'll send out a message in a little bit once I've ironed out the deployment script. > > -Jon > > On May 28, 2010, at 12:18 PM, Hilmar Lapp wrote: > >> Although Jon is on this list, could you then please send a ticket to he...@ne... >> . (Vladimir - or is there a different procedure that you, Jon, and >> Youjun hashed out?) >> >> -hilmar >> >> On May 28, 2010, at 7:54 AM, Rutger Vos wrote: >> >>> Yes. >>> >>> On Fri, May 28, 2010 at 2:05 PM, Hilmar Lapp <hl...@ne...> >>> wrote: >>>> I don't think we can redeploy individual classes - are you >>>> essentially >>>> asking for a rebuild and redeploy? >>>> >>>> -hilmar >>>> >>>> On May 28, 2010, at 2:19 AM, Rutger Vos wrote: >>>> >>>>> AbstractDownloadController >>>>> anyObjectAsRDF.jsp >>>>> searchResultsAsRDF.jsp >>>>> >>>>> These address a mismatch between the content type in the http header >>>>> (which defaulted to ISO-8859-1) and the xml and rdf bodies (which >>>>> specify UTF-8). >>>>> >>>>> Thanks, >>>>> >>>>> Rutger >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>> >>>> -- >>>> =========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>> =========================================================== >>>> >>>> >>>> >>>> >>> >>> >>> >>> -- >>> 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 >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> 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... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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: Jon A. <jon...@du...> - 2010-05-28 16:22:40
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I'm working on autodeployment via hudson, that will automatically check out new code in subversion and deploy it to dev. I'll send out a message in a little bit once I've ironed out the deployment script. -Jon On May 28, 2010, at 12:18 PM, Hilmar Lapp wrote: > Although Jon is on this list, could you then please send a ticket to he...@ne... > . (Vladimir - or is there a different procedure that you, Jon, and > Youjun hashed out?) > > -hilmar > > On May 28, 2010, at 7:54 AM, Rutger Vos wrote: > >> Yes. >> >> On Fri, May 28, 2010 at 2:05 PM, Hilmar Lapp <hl...@ne...> >> wrote: >>> I don't think we can redeploy individual classes - are you >>> essentially >>> asking for a rebuild and redeploy? >>> >>> -hilmar >>> >>> On May 28, 2010, at 2:19 AM, Rutger Vos wrote: >>> >>>> AbstractDownloadController >>>> anyObjectAsRDF.jsp >>>> searchResultsAsRDF.jsp >>>> >>>> These address a mismatch between the content type in the http header >>>> (which defaulted to ISO-8859-1) and the xml and rdf bodies (which >>>> specify UTF-8). >>>> >>>> Thanks, >>>> >>>> Rutger >>>> >>>> >>>> >>>> -- >>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >> >> >> >> -- >> 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 > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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: Hilmar L. <hl...@ne...> - 2010-05-28 16:18:40
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Although Jon is on this list, could you then please send a ticket to he...@ne... . (Vladimir - or is there a different procedure that you, Jon, and Youjun hashed out?) -hilmar On May 28, 2010, at 7:54 AM, Rutger Vos wrote: > Yes. > > On Fri, May 28, 2010 at 2:05 PM, Hilmar Lapp <hl...@ne...> > wrote: >> I don't think we can redeploy individual classes - are you >> essentially >> asking for a rebuild and redeploy? >> >> -hilmar >> >> On May 28, 2010, at 2:19 AM, Rutger Vos wrote: >> >>> AbstractDownloadController >>> anyObjectAsRDF.jsp >>> searchResultsAsRDF.jsp >>> >>> These address a mismatch between the content type in the http header >>> (which defaulted to ISO-8859-1) and the xml and rdf bodies (which >>> specify UTF-8). >>> >>> Thanks, >>> >>> Rutger >>> >>> >>> >>> -- >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> > > > > -- > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-05-28 13:54:29
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Yes. On Fri, May 28, 2010 at 2:05 PM, Hilmar Lapp <hl...@ne...> wrote: > I don't think we can redeploy individual classes - are you essentially > asking for a rebuild and redeploy? > > -hilmar > > On May 28, 2010, at 2:19 AM, Rutger Vos wrote: > >> AbstractDownloadController >> anyObjectAsRDF.jsp >> searchResultsAsRDF.jsp >> >> These address a mismatch between the content type in the http header >> (which defaulted to ISO-8859-1) and the xml and rdf bodies (which >> specify UTF-8). >> >> Thanks, >> >> Rutger >> >> >> >> -- >> 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 >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- 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...> - 2010-05-28 13:05:19
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I don't think we can redeploy individual classes - are you essentially asking for a rebuild and redeploy? -hilmar On May 28, 2010, at 2:19 AM, Rutger Vos wrote: > AbstractDownloadController > anyObjectAsRDF.jsp > searchResultsAsRDF.jsp > > These address a mismatch between the content type in the http header > (which defaulted to ISO-8859-1) and the xml and rdf bodies (which > specify UTF-8). > > Thanks, > > Rutger > > > > -- > 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 > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-05-28 08:19:44
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AbstractDownloadController anyObjectAsRDF.jsp searchResultsAsRDF.jsp These address a mismatch between the content type in the http header (which defaulted to ISO-8859-1) and the xml and rdf bodies (which specify UTF-8). Thanks, Rutger -- 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: Rutger V. <rut...@gm...> - 2010-05-27 13:41:27
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On Thu, May 27, 2010 at 2:15 PM, Hilmar Lapp <hl...@ne...> wrote: > What you describe sounds similar in concept to NCBI's GQuery, so you might > want to look at that: > > http://www.ncbi.nlm.nih.gov/gquery/ It's no coincidence that it sounds similar. The OP was meant to replicate that functionality on a shoestring :-) -- 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: Xianhua L. <xl...@du...> - 2010-05-27 13:26:28
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My 2 cents. Please consider supporting pagination of searching results. Too many hits in the search results will overwhelm the browser and make it hang forever. Xianhua On May 27, 2010, at 9:15 AM, Hilmar Lapp wrote: > What you describe sounds similar in concept to NCBI's GQuery, so you > might want to look at that: > > http://www.ncbi.nlm.nih.gov/gquery/ > > -hilmar > > On May 27, 2010, at 4:06 AM, Rutger Vos wrote: > >> Ok, so, about the searching thing. Here's what I think we could do: >> >> * we create a separate page, something like "meta search", or "simple >> search" or whatever >> >> * on that page is just a single search box, a la google >> >> * you stick in anything you like and press the button >> >> * with javascript, we then compose all phylows queries we currently >> support, i.e. match against taxon names, taxon IDs, study IDs, etc., >> >> * we fire those requests as AJAX calls >> >> * on the server side, we return the results structured as rss (but >> maybe translate them to JSON) >> >> * as the AJAX responses are coming in, we count the number of items >> in >> each result feed >> >> * we can then report how many hits there were on each supported query >> >> * and we can make expandable boxes to actually list those hits, or >> make the hit reports clickable to take you to our normal results >> pages >> >> It seems to me that this would be the easiest way to support this >> functionality. >> >> On Tue, May 25, 2010 at 1:35 PM, Rutger Vos <rut...@gm...> >> wrote: >>> http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html >>> >>> -- >>> 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 >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Hilmar L. <hl...@ne...> - 2010-05-27 13:15:13
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What you describe sounds similar in concept to NCBI's GQuery, so you might want to look at that: http://www.ncbi.nlm.nih.gov/gquery/ -hilmar On May 27, 2010, at 4:06 AM, Rutger Vos wrote: > Ok, so, about the searching thing. Here's what I think we could do: > > * we create a separate page, something like "meta search", or "simple > search" or whatever > > * on that page is just a single search box, a la google > > * you stick in anything you like and press the button > > * with javascript, we then compose all phylows queries we currently > support, i.e. match against taxon names, taxon IDs, study IDs, etc., > > * we fire those requests as AJAX calls > > * on the server side, we return the results structured as rss (but > maybe translate them to JSON) > > * as the AJAX responses are coming in, we count the number of items in > each result feed > > * we can then report how many hits there were on each supported query > > * and we can make expandable boxes to actually list those hits, or > make the hit reports clickable to take you to our normal results pages > > It seems to me that this would be the easiest way to support this > functionality. > > On Tue, May 25, 2010 at 1:35 PM, Rutger Vos <rut...@gm...> > wrote: >> http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html >> >> -- >> 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 > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-05-27 10:06:20
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Ok, so, about the searching thing. Here's what I think we could do: * we create a separate page, something like "meta search", or "simple search" or whatever * on that page is just a single search box, a la google * you stick in anything you like and press the button * with javascript, we then compose all phylows queries we currently support, i.e. match against taxon names, taxon IDs, study IDs, etc., * we fire those requests as AJAX calls * on the server side, we return the results structured as rss (but maybe translate them to JSON) * as the AJAX responses are coming in, we count the number of items in each result feed * we can then report how many hits there were on each supported query * and we can make expandable boxes to actually list those hits, or make the hit reports clickable to take you to our normal results pages It seems to me that this would be the easiest way to support this functionality. On Tue, May 25, 2010 at 1:35 PM, Rutger Vos <rut...@gm...> wrote: > http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html > > -- > 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: Hilmar L. <hl...@ne...> - 2010-05-26 17:32:37
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So it turns out the NCBI URLs aren't even the ones published as a "URL API". And that API contains .php in the path. Sigh. See http://www.phylo.org/treebase/urlapi.php The NCBI LinkOut file won't address the above, obviously. Bill - can you please comment for each of the URL patterns in the old URL API whether they are still supported, and what the (presumably PhyloWS-based) pattern would look like now. Jon - can you check whether the fact that a URL rewrite for this would interfere with the default action handler for .php. I can't think why it would, but better to be sure. I am also assuming that if we place these URL rewrites first, they would take precedence over the proxying rewrites. Can you conform this. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-05-26 04:32:38
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On May 25, 2010, at 6:01 PM, William Piel wrote: > If this letter to him is still relevant, please make comments / edits. I don't think it's still relevant. The instructions are here: http://bit.ly/NCBI_LinkOut We can email him once we have those two files set up and deposited. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-05-26 00:01:26
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On May 25, 2010, at 8:41 AM, Hilmar Lapp wrote: > Instead, we should construct a new LinkOut mapping file for NCBI and submit it to their ftp server at the appropriate location. That would be the clean and Right Way. Ah... I didn't know the outlinks could be submitted that way. I was preparing the send off the (below) message to Scott Federhen. If this letter to him is still relevant, please make comments / edits. I'm thinking that I should remove the bit about returning a list of studies / matrices / trees because those links don't seem to work -- they are returning the taxon tab instead of jumping to the respective study / matrix/ tree tab. Bill ===================================================== On May 1, 2003, at 6:21 AM, Scott Federhen wrote: > Hi Bill: > > The TreeBase links went up in Entrez yesterday - > you can find all of them with: > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy > search for "loprovtreebase[filter]" (no quotes) and hit 'Go' > switch from 'Summary' to 'LinkOut' and hit 'Display' Dear Scott, Thanks very much for posting NCBI's outlinks to TreeBASE over the last seven years. TreeBASE has now been redeveloped from the ground up. Among the new features, the following items are relevant to NCBI's outlinks: - TreeBASE has a new RESTful API based on the PhyloWS standard - Regrettably, TreeBASE has had to reissue new taxon id numbers. The old version was essentially just a distinct list of taxon labels. The new version is the result of a mapping between taxon labels in each study and a taxonomy, in which homonyms receive distinct IDs. Since our concept of what is a "taxon" has changed (from unique string to a vetted list) the ID numbers for these has also changed. - TreeBASE now tries to store the equivalent NCBi taxid for each taxon in TreeBASE. This means that Entrez can outlink to TreeBASE by using NCBI taxids rather than having to store any of TreeBASE's IDs. All that's needed is for NCBI to know which of its taxa are also in TreeBASE. I am attaching a list of all NCBI taxids that current map to data objects in TreeBASE. The PhyloWS format for creating an outlink to Homo sapiens in TreeBASE (using NCBI taxid 9606) is as follows: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi=9606&format=html or if it's safer to use %3D as a substitute for the equals sign: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html If you want to return a list of studies, use the following: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html&recordSchema=study If you want to return a list of matrices (i.e. alignments), use the following: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html&recordSchema=matrix If you want to return a list of trees, use the following: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html&recordSchema=tree I hope you're able to update your outlinks without too much trouble. I'd be happy to provide these data in a difference format, if it's helpful. regards, Bill |
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From: William P. <wil...@ya...> - 2010-05-25 15:42:48
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On May 25, 2010, at 7:53 AM, Jon Auman wrote: > We could : > 1) keep the old site up and running and redirect all '/cgi-bin/foo' requests to the old server (seems backward) > 2) Fix the 404 page to send users to the search page or custom 404 page (we should do this irregardless) > 3) Create a lookup table that maps legacy taxonIDs to new ones. Seems like a one time thing, cause all new studies will not have legacy ID, right? > 4) do #2 and not worry about the rest The legacy APIs are described here: http://treebase.peabody.yale.edu/treebase/urlapi.html -- In the case of uBio, they used the "Link by Taxon Name" -- so that would be an easy rewrite. However, they have already said that they will be rewriting their outlinks to comply with our /phylows/. So it's hardly worth changing for them. -- In the case of NCBI, they used the "Link by Taxon ID Number" method, so the problem there is that we don't have a /phylows/find/taxon/ that uses TB1 legacy ids (which are stored in the tb1legacyid field in the taxonlabel table). So to make us compatible with NCBI, we'd need to write additional API code. Note that NCBI's outlinks are based on a very very old dump to them (e.g. back when TreeBASE had only 15,000 names, instead of the 100,000+ names that it has now). It would be vastly better if we get NCBI to change their outlinks over to /phylows/ and use NCBI taxids instead of legacy TB1 ids. Perhaps we should create a /phylows/ query that asks "give list of all NCBI taxids" (e.g. find all taxa with ncbi taxid > 0 that relate to at least one taxonlabel in TreeBASE), so that NCBI can dynamically update their outlinks rather than relying on periodic dumps. bp |
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From: Hilmar L. <hl...@ne...> - 2010-05-25 15:41:23
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I vote against putting effort into that. It would be perpetuating old URLs for no new ground being gained, and bypasses the proper mechanism, so really is a hack. Instead, we should construct a new LinkOut mapping file for NCBI and submit it to their ftp server at the appropriate location. That would be the clean and Right Way. -hilmar On May 25, 2010, at 8:53 AM, Jon Auman wrote: > We could : > 1) keep the old site up and running and redirect all '/cgi-bin/foo' > requests to the old server (seems backward) > 2) Fix the 404 page to send users to the search page or custom 404 > page (we should do this irregardless) > 3) Create a lookup table that maps legacy taxonIDs to new ones. > Seems like a one time thing, cause all new studies will not have > legacy ID, right? > 4) do #2 and not worry about the rest > > Just me 2 cents worth. > > Jon > > On May 25, 2010, at 10:38 AM, Rutger Vos wrote: > >> On Tue, May 25, 2010 at 3:32 PM, Jon Auman <jon...@du...> >> wrote: >>> If you all tell me what should rewrite to what, I can turn on the >>> mojo and >>> make it happen. We've got apache on the front end, so mod_rewrite is >>> available. >> >> Bill probably still has the documentation for the URL API from >> version >> 1. If he can dig that up we should be able to rewrite a significant >> portion of those URLs to become PhyloWS URLs. This won't address his >> complaint about the old taxon IDs being gone though. >> >> -- >> 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 > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Jon A. <jon...@du...> - 2010-05-25 14:53:30
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We could : 1) keep the old site up and running and redirect all '/cgi-bin/foo' requests to the old server (seems backward) 2) Fix the 404 page to send users to the search page or custom 404 page (we should do this irregardless) 3) Create a lookup table that maps legacy taxonIDs to new ones. Seems like a one time thing, cause all new studies will not have legacy ID, right? 4) do #2 and not worry about the rest Just me 2 cents worth. Jon On May 25, 2010, at 10:38 AM, Rutger Vos wrote: > On Tue, May 25, 2010 at 3:32 PM, Jon Auman <jon...@du...> wrote: >> If you all tell me what should rewrite to what, I can turn on the mojo and >> make it happen. We've got apache on the front end, so mod_rewrite is >> available. > > Bill probably still has the documentation for the URL API from version > 1. If he can dig that up we should be able to rewrite a significant > portion of those URLs to become PhyloWS URLs. This won't address his > complaint about the old taxon IDs being gone though. > > -- > 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 ------------------------------------------------------- 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...> - 2010-05-25 14:38:28
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On Tue, May 25, 2010 at 3:32 PM, Jon Auman <jon...@du...> wrote: > If you all tell me what should rewrite to what, I can turn on the mojo and > make it happen. We've got apache on the front end, so mod_rewrite is > available. Bill probably still has the documentation for the URL API from version 1. If he can dig that up we should be able to rewrite a significant portion of those URLs to become PhyloWS URLs. This won't address his complaint about the old taxon IDs being gone though. -- 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: Jon A. <jon...@du...> - 2010-05-25 14:32:44
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If you all tell me what should rewrite to what, I can turn on the mojo and make it happen. We've got apache on the front end, so mod_rewrite is available. -Jon On May 25, 2010, at 8:35 AM, Rutger Vos wrote: > http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html > > -- > 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 > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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...> - 2010-05-25 12:35:59
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http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html -- 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...> - 2010-05-24 18:26:44
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On May 24, 2010, at 9:58 AM, Hilmar Lapp wrote: > The stack trace means that there is a situation when two taxon labels are being compared that either one of the two TaxonLabel objects, or the taxonLabel property of one, is null. Thanks all. Looking at the user's *original* data files, when I try to open them in Mesquite, not only is there a taxon label mismatch between matrix and trees, but Mesquite kicks out an error saying something about detecting a reticulation in the tree (???). At any rate, I cleaned up the original files so that Mesquite no longer has any issues. After getting Rutger's feedback, I tried deleting all matrices and trees from the problem study (which should delete all associated taxon labels), and then completely re-uploading with fresh, and fixed, datasets. But the error persisted. So in the end I created a new submission, uploaded the files, and that works fine. > Indeed, the TaxonLabel.taxonLabel property property is nullable (why?), so this seems to be a legitimate situation and the fact that the code assumes that it can never be null is a bug. I fixed this and committed it to trunk. I haven't had a chance to rebuild, so I'm hoping it compiles. Thanks for doing that -- unfortunately I went ahead with creating a new submission and deleting the old files before seeing that you made this fix. On May 24, 2010, at 11:01 AM, Jon Auman wrote: > Instead of a tracestack, I now get : > > Access denied > Sorry! your action is not authorized. > > > -jon Yeah, that has to do with me converting the submission back to "in progress" so that I can mess with it. But now it has been deleted, so you should get a "no results" return. bp |
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From: Jon A. <jon...@du...> - 2010-05-24 18:01:40
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I've rebuilt the webapp and deployed it on treebase-stage >> http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10526 Instead of a tracestack, I now get : Access denied Sorry! your action is not authorized. -jon On May 24, 2010, at 12:58 PM, Hilmar Lapp wrote: > The stack trace means that there is a situation when two taxon labels > are being compared that either one of the two TaxonLabel objects, or > the taxonLabel property of one, is null. > > Indeed, the TaxonLabel.taxonLabel property property is nullable > (why?), so this seems to be a legitimate situation and the fact that > the code assumes that it can never be null is a bug. I fixed this and > committed it to trunk. I haven't had a chance to rebuild, so I'm > hoping it compiles. > > -hilmar > > On May 24, 2010, at 12:06 PM, William Piel wrote: > >> >> I've been plodding through tables and records associated with >> study_id 10526, but I have not found a spurious NULL value, yet we >> continue to get an uncaught exception when we try to access the >> summary page for the study. >> >> Is there someone skilled at reading the trace barfs (see below) who >> can point me in the right direction? (or, Jon, do you have a more >> informative error log about what is causing the >> "NullPointerException"?) >> >> thanks, >> >> Bill >> >> >> http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10526 >> http://treebase.nescent.org/treebase-web/search/study/summary.html?id=10526 >> >> Uncaught Exception Encountered >> java.lang.NullPointerException at org.cipres.treebase.web.controllers.SearchSummaryController >> $TaxonLabelByLabelComparator.compare(SearchSummaryController.java: >> 550) at org.cipres.treebase.web.controllers.SearchSummaryController >> $TaxonLabelByLabelComparator.compare(SearchSummaryController.java: >> 548) at java.util.Arrays.mergeSort(Arrays.java:1283) at >> java.util.Arrays.mergeSort(Arrays.java:1294) at >> java.util.Arrays.mergeSort(Arrays.java:1294) at >> java.util.Arrays.mergeSort(Arrays.java:1294) at >> java.util.Arrays.mergeSort(Arrays.java:1294) at >> java.util.Arrays.sort(Arrays.java:1223) at >> java.util.Collections.sort(Collections.java:176) at >> org >> .cipres >> .treebase >> .web >> .controllers >> .SearchSummaryController.showForm(SearchSummaryController.java:415) >> at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm >> (AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal >> (AbstractFormController.java:278) at org.springframework.web.s >> ervlet.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.doGet >> (FrameworkServlet.java:431) at >> javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at >> javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at >> org >> .apache >> .catalina >> .core >> .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: >> 269) at >> org >> .apache >> .catalina >> .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: >> 188) at >> org >> .tuckey >> .web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) >> at org.tuckey.web.filters.urlrewri >> te.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(ApplicationF >> ilterChain.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.aceg >> isecurity.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.a >> pache >> .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) Cookies: >> JSESSIONID=[708FEE6348ECE9CE1D3288CA0EE772E1] >> __utma=[53240375.1924499357.1236724314.127 >> 3464586.1273467037.78] __utmz=[53240375.1271940457.73.13.utmccn] >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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: Hilmar L. <hl...@ne...> - 2010-05-24 16:58:38
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The stack trace means that there is a situation when two taxon labels are being compared that either one of the two TaxonLabel objects, or the taxonLabel property of one, is null. Indeed, the TaxonLabel.taxonLabel property property is nullable (why?), so this seems to be a legitimate situation and the fact that the code assumes that it can never be null is a bug. I fixed this and committed it to trunk. I haven't had a chance to rebuild, so I'm hoping it compiles. -hilmar On May 24, 2010, at 12:06 PM, William Piel wrote: > > I've been plodding through tables and records associated with > study_id 10526, but I have not found a spurious NULL value, yet we > continue to get an uncaught exception when we try to access the > summary page for the study. > > Is there someone skilled at reading the trace barfs (see below) who > can point me in the right direction? (or, Jon, do you have a more > informative error log about what is causing the > "NullPointerException"?) > > thanks, > > Bill > > > http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10526 > http://treebase.nescent.org/treebase-web/search/study/summary.html?id=10526 > > Uncaught Exception Encountered > java.lang.NullPointerException at org.cipres.treebase.web.controllers.SearchSummaryController > $TaxonLabelByLabelComparator.compare(SearchSummaryController.java: > 550) at org.cipres.treebase.web.controllers.SearchSummaryController > $TaxonLabelByLabelComparator.compare(SearchSummaryController.java: > 548) at java.util.Arrays.mergeSort(Arrays.java:1283) at > java.util.Arrays.mergeSort(Arrays.java:1294) at > java.util.Arrays.mergeSort(Arrays.java:1294) at > java.util.Arrays.mergeSort(Arrays.java:1294) at > java.util.Arrays.mergeSort(Arrays.java:1294) at > java.util.Arrays.sort(Arrays.java:1223) at > java.util.Collections.sort(Collections.java:176) at > org > .cipres > .treebase > .web > .controllers > .SearchSummaryController.showForm(SearchSummaryController.java:415) > at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm > (AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal > (AbstractFormController.java:278) at org.springframework.web.s > ervlet.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.doGet > (FrameworkServlet.java:431) at > javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at > javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at > org > .apache > .catalina > .core > .ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java: > 269) at > org > .apache > .catalina > .core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java: > 188) at > org > .tuckey > .web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) > at org.tuckey.web.filters.urlrewri > te.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(ApplicationF > ilterChain.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.aceg > isecurity.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.a > pache > .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) Cookies: > JSESSIONID=[708FEE6348ECE9CE1D3288CA0EE772E1] > __utma=[53240375.1924499357.1236724314.127 > 3464586.1273467037.78] __utmz=[53240375.1271940457.73.13.utmccn] > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-05-24 16:07:06
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I've been plodding through tables and records associated with study_id 10526, but I have not found a spurious NULL value, yet we continue to get an uncaught exception when we try to access the summary page for the study. Is there someone skilled at reading the trace barfs (see below) who can point me in the right direction? (or, Jon, do you have a more informative error log about what is causing the "NullPointerException"?) thanks, Bill http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10526 http://treebase.nescent.org/treebase-web/search/study/summary.html?id=10526 Uncaught Exception Encountered java.lang.NullPointerException at org.cipres.treebase.web.controllers.SearchSummaryController$TaxonLabelByLabelComparator.compare(SearchSummaryController.java:550) at org.cipres.treebase.web.controllers.SearchSummaryController$TaxonLabelByLabelComparator.compare(SearchSummaryController.java:548) at java.util.Arrays.mergeSort(Arrays.java:1283) at java.util.Arrays.mergeSort(Arrays.java:1294) at java.util.Arrays.mergeSort(Arrays.java:1294) at java.util.Arrays.mergeSort(Arrays.java:1294) at java.util.Arrays.mergeSort(Arrays.java:1294) at java.util.Arrays.sort(Arrays.java:1223) at java.util.Collections.sort(Collections.java:176) at org.cipres.treebase.web.controllers.SearchSummaryController.showForm(SearchSummaryController.java:415) at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm(AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:278) 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.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.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) Cookies: JSESSIONID=[708FEE6348ECE9CE1D3288CA0EE772E1] __utma=[53240375.1924499357.1236724314.1273464586.1273467037.78] __utmz=[53240375.1271940457.73.13.utmccn] |
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From: Hilmar L. <hl...@ne...> - 2010-05-22 20:33:30
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FYI. Anyone willing to help with the draft? Rutger, I'm looking at you. -hilmar Begin forwarded message: > From: ad...@is... > Date: May 22, 2010 12:36:46 AM EDT > To: hl...@ne... > Subject: ISMB 2010 Killer App Award > > Dear Hilmar Lapp, > > thanks for you indicating interest in the ISMB Killer App Award. To > complete your application, please go to the following submission form: > > https://www.iscb.org/submissions/edit.php?id=19209&editcode=451dd06f > > and provide a short explanation (500 words max.) of how your tool > benefits biologists. > > To be eligible, you need to provide this explanation on or before > June 12, 2010. > > Three finalists will be announced on 1 July; the finalists will be > invited to give a short presentation about their tool at a Tech > Track session (2pm, Tuesday 13 July, 2010) during ISMB 2010. > > The winner of the Killer App Award will receive a free Apple iPad! > In addition, their work will be featured on Elseiver's platforms. > > Additional information is located here: http://www.iscb.org/ismb2010-submission-details/673-ismb2010-killer-app-award > > Sincerely, > Sean O'Donoghue, EMBL, Germany > Anita de Waard, Elsevier, USA > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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