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From: Rutger V. <rut...@gm...> - 2010-03-15 02:07:51
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Hi all, I've implemented most of the functionality for issue 2960840. Can we have a rebuild and redeployment so we can look at what predicates are now serialized into the rss? After that we should be able (for example) to do the following to get all studies published in nature: http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Nature&format=rss1 (By the way, it looks like there hasn't been a redeployment for a while, such that the fixes for issue 2968150 and 2968156 are also not visible yet. Is the procedure really that we have to ask Vladimir who then has to ask Jon, or is there a quicker way?) 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: William P. <wil...@ya...> - 2010-03-15 03:20:20
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On Mar 14, 2010, at 10:07 PM, Rutger Vos wrote: > (By the way, it looks like there hasn't been a redeployment for a > while, such that the fixes for issue 2968150 and 2968156 are also not > visible yet. Is the procedure really that we have to ask Vladimir who > then has to ask Jon, or is there a quicker way?) Thanks, Rutger, for your huge flurry of recent commits. We definitely need to find an efficient way to rebuild. While it's true that the http://treebase.nescent.org/treebase-web/ deployment is rather old, the http://treebase-stage.nescent.org/treebase-web/ deployment was re-built last Friday at 5PM or so. bp |
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From: youjun g. <you...@ya...> - 2010-03-15 11:41:04
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We may need re-deployment almost every working day until final release. Youjun On Sun, Mar 14, 2010 at 11:20 PM, William Piel <wil...@ya...>wrote: > > On Mar 14, 2010, at 10:07 PM, Rutger Vos wrote: > > > (By the way, it looks like there hasn't been a redeployment for a > > while, such that the fixes for issue 2968150 and 2968156 are also not > > visible yet. Is the procedure really that we have to ask Vladimir who > > then has to ask Jon, or is there a quicker way?) > > Thanks, Rutger, for your huge flurry of recent commits. > > We definitely need to find an efficient way to rebuild. > > While it's true that the http://treebase.nescent.org/treebase-web/deployment is rather old, the > http://treebase-stage.nescent.org/treebase-web/ deployment was re-built > last Friday at 5PM or so. > > 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 > |
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From: Rutger V. <rut...@gm...> - 2010-03-15 12:13:22
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> Thanks, Rutger, for your huge flurry of recent commits. There's still a few more coming, notably: - some interface changes high in the inheritance tree of our domain objects so that there is a uniform way for any object to specify what, if any, its "defining resource" is. By this I mean, say, for a tree node the study within which it is scoped. We can then use this for simple rdf serializations (as produced by the anyObjectAsRdf template) to add rdfs:isDefinedBy predicates, which to me seems to be the last major missing piece to have everything linked up internally such that LinkedData browsers can jump from object to object. - more metadata for other search results, analogous to the study search rss feeds (e.g. for taxon search). - other predicates for ubio and ncbi outlinks. The correct way is probably to use skos:exactMatch and skos:closeMatch, respectively, and to have the values be the canonical URIs (for ubio perhaps lsids?) for the defining resources. Once these are (nearly) done I'll know what to put in my iEvoBio abstract :) -- 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...> - 2010-03-15 14:49:39
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On Mar 14, 2010, at 10:07 PM, Rutger Vos wrote: > Hi all, > > I've implemented most of the functionality for issue 2960840. Can we > have a rebuild and redeployment so we can look at what predicates are > now serialized into the rss? After that we should be able (for > example) to do the following to get all studies published in nature: > > http://purl.org/phylo/treebase/phylows/study/find?query=prism.publicationName=Nature&format=rss1 > > (By the way, it looks like there hasn't been a redeployment for a > while, such that the fixes for issue 2968150 and 2968156 are also not > visible yet. Is the procedure really that we have to ask Vladimir who > then has to ask Jon, or is there a quicker way?) I have trouble starting the new build on my local instance. The relevant lines from catalina.log are appended below. I am investigating what is going on. My current feeling is that geronimo- servlet_2.5_spec-1.2.jar and/or servlet-api-2.4.jar should not be packaged into the WAR. If someone has a good idea what happened and how to fix it, please jump in. --Vladimir Mar 15, 2010 10:22:59 AM org.apache.catalina.loader.WebappClassLoader validateJarFile INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo- servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class Mar 15, 2010 10:22:59 AM org.apache.catalina.loader.WebappClassLoader validateJarFile INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class Mar 15, 2010 10:23:00 AM org.apache.catalina.core.StandardContext start SEVERE: Error listenerStart Mar 15, 2010 10:23:00 AM org.apache.catalina.core.StandardContext start SEVERE: Context [/treebase-web] startup failed due to previous errors Mar 15, 2010 10:23:00 AM org.apache.catalina.core.StandardContext start SEVERE: Error filterStart Mar 15, 2010 10:23:00 AM org.apache.catalina.core.StandardContext start SEVERE: Context [/balancer] startup failed due to previous errors |
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From: Hilmar L. <hl...@ne...> - 2010-03-15 15:02:43
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On Mar 15, 2010, at 10:49 AM, Vladimir Gapeyev wrote: > My current feeling is that geronimo-servlet_2.5_spec-1.2.jar and/or > servlet-api-2.4.jar should not be packaged into the WAR. Right. Why did they end up there? Usually the application server has those already and any attempt to package them into the WAR *at best* has no effect whatsoever. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2010-03-15 16:21:16
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On Mar 15, 2010, at 11:02 AM, Hilmar Lapp wrote: > > On Mar 15, 2010, at 10:49 AM, Vladimir Gapeyev wrote: > >> My current feeling is that geronimo-servlet_2.5_spec-1.2.jar and/or >> servlet-api-2.4.jar should not be packaged into the WAR. > Right. Why did they end up there? Usually the application server has > those already and any attempt to package them into the WAR *at best* > has no effect whatsoever. These jars turned out not to be the culprit, sorry for the alarm. (The culprit was the not-so-clean undeployment procedure on my end, which backfired this time, because there is a new SearchStudiesByKeyword service.) All updates as of this morning should now be visible, both at treebase- dev and treebase-stage. --Vladimir |
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