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From: William P. <wil...@ya...> - 2010-03-16 19:54:59
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On Mar 16, 2010, at 3:44 PM, Vladimir Gapeyev wrote: > There were 1002 trees with the null treetype, now there are only 33 (below). For the remaining 33, can you give them "single" trees (which is kind of our default) thanks, Bill |
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From: Vladimir G. <vla...@du...> - 2010-03-16 19:44:35
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On Mar 16, 2010, at 2:48 PM, William Piel wrote: >> >>> A artifact of the March migration was that trees did not get their >>> proper "Tree Type" designation (i.e. consensus vs single). I have >>> created an easy look-up table containing legacy tree IDs and their >>> tree type designation. These designations need to be converted to >>> integers before updating based on a matching the legacy ID values. >>> >>> http://www.treebase.org/treebase/migration/Mar-10/tree_types.txt >> > > > Whoops. Can you map the "Simple Tree" to "Single" and the NULL tree > to "Single". I have applied the treetype to the DB, as corrected. There were 1002 trees with the null treetype, now there are only 33 (below). --Vladimir treebasestage=> -- The trees with the null treetype treebasestage=> select phylotree_id, tb1_treeid, treetype_id treebasestage-> from phylotree treebasestage-> where treetype_id is null; phylotree_id | tb1_treeid | treetype_id --------------+------------+------------- 2556 | Tree4532 | 2557 | Tree4533 | 2727 | Tree4962 | 2726 | Tree4963 | 5921 | | 5962 | | 5961 | | 5981 | | 6959 | | 6964 | | 6963 | | 6961 | | 6972 | | 6971 | | 6973 | | 6962 | | 6970 | | 6969 | | 6968 | | 6967 | | 6966 | | 6965 | | 6960 | | 6074 | | 5941 | | 5963 | | 6874 | | 6521 | | 6075 | | 6750 | | 6176 | | 6358 | | 6433 | | (33 rows) |
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From: William P. <wil...@ya...> - 2010-03-16 18:48:31
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On Mar 16, 2010, at 2:17 PM, Vladimir Gapeyev wrote: > > On Mar 13, 2010, at 1:44 PM, William Piel wrote: >> A artifact of the March migration was that trees did not get their proper "Tree Type" designation (i.e. consensus vs single). I have created an easy look-up table containing legacy tree IDs and their tree type designation. These designations need to be converted to integers before updating based on a matching the legacy ID values. >> >> http://www.treebase.org/treebase/migration/Mar-10/tree_types.txt > > > Bill, > > Here are the treetype entries in the DB: > > tb2migrplay=> select * from treetype; > treetype_id | version | description > -------------+---------+------------- > 1 | 1 | Single > 2 | 1 | Consensus > 3 | 1 | SuperTree > > > Here are the counts of distinct treetype names in your file: > > tb2migrplay=> select treetypename, count(*) from phtrtype group by treetypename; > treetypename | count > --------------+------- > consensus | 2279 > | 1 > single | 4274 > Simple Tree | 15 > > > Questions: > > (1) Are SuperTree (in the dictionary) and Simple Tree (in your file) the same thing? If so, which one should remain in the DB? > > (2) The tree with the missing treetype is T391c2x7x96c15c45c54 -- what's up with it? > > Thanks, > > --Vladimir Whoops. Can you map the "Simple Tree" to "Single" and the NULL tree to "Single". Although TB1 has got Supertrees in it, they were not annotated as such -- we will have to edit that manually later. bp |
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From: Vladimir G. <vla...@du...> - 2010-03-16 18:17:56
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On Mar 13, 2010, at 1:44 PM, William Piel wrote: > A artifact of the March migration was that trees did not get their > proper "Tree Type" designation (i.e. consensus vs single). I have > created an easy look-up table containing legacy tree IDs and their > tree type designation. These designations need to be converted to > integers before updating based on a matching the legacy ID values. > > http://www.treebase.org/treebase/migration/Mar-10/tree_types.txt Bill, Here are the treetype entries in the DB: tb2migrplay=> select * from treetype; treetype_id | version | description -------------+---------+------------- 1 | 1 | Single 2 | 1 | Consensus 3 | 1 | SuperTree Here are the counts of distinct treetype names in your file: tb2migrplay=> select treetypename, count(*) from phtrtype group by treetypename; treetypename | count --------------+------- consensus | 2279 | 1 single | 4274 Simple Tree | 15 Questions: (1) Are SuperTree (in the dictionary) and Simple Tree (in your file) the same thing? If so, which one should remain in the DB? (2) The tree with the missing treetype is T391c2x7x96c15c45c54 -- what's up with it? Thanks, --Vladimir |
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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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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 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: 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: 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: 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: 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 01:58:40
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I'll add this as a bug, but I wanted to also post it here -- given that we're in the final sprint. I added and finalized a completely new submission to TreeBASE in order to test the submission process from beginning to end. The result is this new study: http://treebase-stage.nescent.org/treebase-web/search/study/summary.html?id=10315 And everything looks good except that I cannot download one of the analyses (and I can't download the whole study either) as nexus -- the browser spins round and round and finally finishes with a Proxy Error. This is the bad one: http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5758&id=10315 But strangely enough, the other analyses work fine (even though they are all pulling about the same amount of data): http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5759&id=10315 http://treebase-stage.nescent.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=5760&id=10315 The individual components of the analysis (1 matrix and 2 trees) can be downloaded without a problem. bp |
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From: William P. <wil...@ya...> - 2010-03-13 22:19:08
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This is mainly for Vladimir: I think I've found the problem with the migration data -- as mentioned before, the migrated data fail to display taxon mapping and fail to download trees. To investigate this, I selected two taxonlabel_ids, 4013 and 271332. I selected these because they both correspond to the taxon label string 'Agaricus bisporus', and in both cases they are correctly mapped to the TI (both have a taxonvariant_id of 1420). The only difference is that one is found in study_id 1959 (from an older migration) while the other is found in study_id 10294 (migrated in the last batch). We have a table called taxonlabelset and a many-to-many joiner table called taxonlabelset_taxonlabel. The taxonlabelset table roughly represents the "BEGIN TAXA" block in the NEXUS format: an ordered list of taxonlabels that is referred to by subsequent "BEGIN TREE" blocks, "BEGIN DATA" blocks, or "BEGIN CHARACTERS" blocks. When I run this query: SELECT study_id, taxonlabelset_id, taxonlabel_id, taxonlabel_order FROM taxonlabelset_taxonlabel JOIN taxonlabelset USING (taxonlabelset_id) WHERE taxonlabel_id IN (271332, 4013) I get the output below, indicating that these two taxonlabel_ids are found in many taxonlabelsets. Unfortunately, most of them are bogus, orphaned taxonlabelset records that seem to be created in great abundance -- these are the ones with study_id 22 and study_id 10215. I gather that study_id 22 and 10215 serve as temporary parking spots for migrated data, but unfortunately not all records get deleted after the data are moved to their proper study_ids. You'll notice, that taxonlabel_id 4013 belongs to taxonlabelset_id 13428. This taxonlabelset_id is referenced by a matrix record and a treeblock record. Which is good: it shows that taxonlabel_id 4013 belongs to a taxonlabelset that is referenced by a treeblock and a matrix, which presumably are both linked in the same analysis step. i.e., the taxonlabels in the trees match with the taxonlabels in the matrices that these trees are derived from. With respect to taxonlabel_id 271332, we have a different story. On the one hand, taxonlabel_id 271332 is found in a bunch of orphaned records linked to the bogus study_id 10215. Unfortunately, unlike taxonlabel_id 4013, taxonlabel_id 271332 does not belong to a single taxonlabelset that references study_id 10294. Now, study_id 10294 does have a matrix that lists taxonlabelset_id 15812, but in the taxonlabelset table, taxonlabelset_id 15812 references the bogus study_id. So one correction is the following: FOR ALL taxonlabelset RECORDS THAT REFERENCE study_id 10215, CHANGE THEIR study_id TO MATCH THE study_id REFERENCED IN THE matrix RECORDS THAT USE THE SAME taxonlabelset_id. But unfortunately we're not done. When I examined the treeblock table, I noticed that the treeblock record that is related to taxonlabel_id 271332 has NULL for taxonlabelset_id. This surely explains why trees can't be downloaded. To fix this, we need to update the treeblock table with the same taxonlabelset_id as the matrix (or one of the matrices) that this treeblock is related to by way of an analysis step linkage. This is because we need to pick a set of taxon labels that is compatible with the block of trees, and trees can only belong to the same analysis step as a matrix if their taxon labels are compatible. So... I think that this query provides a list of each treeblock_id and a taxonlabelset_id from a corresponding matrix that is joined to this treeblock by way of an analysisstep: SELECT DISTINCT ON (tb.treeblock_id) tb.treeblock_id, mx.taxonlabelset_id FROM matrix mx JOIN analyzeddata am ON (mx.matrix_id = am.matrix_id) JOIN analyzeddata at ON (am.analysisstep_id = at.analysisstep_id) JOIN phylotree pt ON (at.phylotree_id = pt.phylotree_id) JOIN treeblock tb ON (pt.treeblock_id = tb.treeblock_id) WHERE tb.taxonlabelset_id IS NULL We should take this list and use the first column to update the treeblock table with the taxonlabelset_id values in the second column. regards, Bill study_id, taxonlabelset_id, taxonlabel_id, taxonlabel_order ------------------------------- 22 181 4013 68 22 226 4013 35 22 403 4013 4 22 404 4013 24 22 413 4013 20 22 544 4013 20 22 586 4013 20 22 787 4013 20 22 872 4013 122 22 874 4013 65 22 875 4013 0 22 1003 4013 52 22 1692 4013 26 22 2300 4013 2 22 2357 4013 8 22 2358 4013 82 22 2401 4013 25 22 2463 4013 51 22 2510 4013 71 22 2590 4013 208 22 2663 4013 20 22 2720 4013 22 22 2904 4013 175 22 2927 4013 20 22 2942 4013 20 22 3654 4013 20 22 3898 4013 13 22 4013 4013 20 22 4748 4013 44 22 4830 4013 20 22 5498 4013 35 22 5499 4013 35 22 5500 4013 35 22 5647 4013 59 22 5921 4013 54 22 5963 4013 181 22 6606 4013 30 22 6920 4013 16 22 7549 4013 35 22 7652 4013 8 22 7654 4013 107 22 7655 4013 107 22 7691 4013 107 22 7700 4013 73 22 7701 4013 73 22 7702 4013 73 22 7703 4013 73 22 7829 4013 51 22 7830 4013 29 22 7831 4013 29 22 7840 4013 23 22 8126 4013 24 22 8413 4013 44 22 9045 4013 53 22 9046 4013 53 22 9058 4013 143 22 9089 4013 19 22 9112 4013 107 22 9113 4013 136 22 9114 4013 11 22 9115 4013 11 10215 15687 271332 20 10215 15812 271332 54 10215 15854 271332 20 10215 15927 271332 80 1959 13428 4013 20 |
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From: Rutger V. <rut...@gm...> - 2010-03-13 19:58:03
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Absolutely, it seems to me this needs to go in a location from where the webapp can serve it up statically from behind a pretty purl. I just hadn't gotten around to it. On Saturday, March 13, 2010, Hilmar Lapp <hl...@ne...> wrote: > Also, shouldn't that be committed to svn? > > -hilmar > > On Mar 12, 2010, at 1:36 PM, Rutger Vos wrote: > > > I've had the attached owl kicking around for ages but never actually > published it. Perhaps it needs to go somewhere such that > http://purl.org/phylo/treebase/terms/ (or something like it) points to > it and we use that as the namespace? > > On Wed, Mar 10, 2010 at 4:26 PM, Hilmar Lapp <hl...@ne...> wrote: > > The API documentation right now states for example that > "tb:identifier.ubio inherits from dcterms:identifier and so any of the > latter's semantics apply to the former." > > Where is this formalized? The namespace URI given in the spreadsheet > [1] yields a 404. Has the vocabulary been published as RDF or OWL? > > If not, we need to revise the above statement. > > -hilmar > > [1] TreeBASE terms and predicates <http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw&single=true&gid=0&output=html> > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > 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 > > > > > > -- > 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.owl> > > > -- > =========================================================== > : 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: William P. <wil...@ya...> - 2010-03-13 18:44:24
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Vladimir: A artifact of the March migration was that trees did not get their proper "Tree Type" designation (i.e. consensus vs single). I have created an easy look-up table containing legacy tree IDs and their tree type designation. These designations need to be converted to integers before updating based on a matching the legacy ID values. http://www.treebase.org/treebase/migration/Mar-10/tree_types.txt bp |
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From: William P. <wil...@ya...> - 2010-03-13 18:16:15
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On Mar 12, 2010, at 4:30 PM, Vladimir Gapeyev wrote: > > On Mar 12, 2010, at 2:37 PM, William Piel wrote: > >> >> The final taxon intel tables are now available. >> >> http://www.treebase.org/treebase/migration/Mar-10/ >> TI_for_Mar10_utf8.zip > > They are now in the treebasestage instance. > --VG Thanks. This last mapping effort worked for older data, but not the March migration data -- perhaps taxon label records are missing in this migration? For example, one newly-migrated dataset has the following tb2 IDs: study id = S10294 matrix id = M4906 tree id = Tr6769 Yet, click the taxon tab from any of these objects and you get zero records. i.e., there's no mapping between taxon labels and taxa and/or all the taxon labels are missing. The actual files have, for example, the taxon label "Agaricus bisporus" which perfectly maps to a taxon record of the exactly the same string. My guess is that this data-bug with the March migration is related to the fact that we're unable to download trees (you and I discussed this problem earlier this week). bp |
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From: Hilmar L. <hl...@ne...> - 2010-03-13 17:43:15
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Also, shouldn't that be committed to svn? -hilmar On Mar 12, 2010, at 1:36 PM, Rutger Vos wrote: > I've had the attached owl kicking around for ages but never actually > published it. Perhaps it needs to go somewhere such that > http://purl.org/phylo/treebase/terms/ (or something like it) points to > it and we use that as the namespace? > > On Wed, Mar 10, 2010 at 4:26 PM, Hilmar Lapp <hl...@ne...> > wrote: >> The API documentation right now states for example that >> "tb:identifier.ubio inherits from dcterms:identifier and so any of >> the >> latter's semantics apply to the former." >> >> Where is this formalized? The namespace URI given in the spreadsheet >> [1] yields a 404. Has the vocabulary been published as RDF or OWL? >> >> If not, we need to revise the above statement. >> >> -hilmar >> >> [1] http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw&single=true&gid=0&output=html >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> > > > > -- > 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.owl> -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2010-03-12 22:22:12
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On Mar 5, 2010, at 10:22 AM, youjun guo wrote: > Dear All, > > There is a new treebase unit test failure appeared recently. It due > to "submissions do not have a related submitter". > > Following query result from the treebase-db may give you a better > idea: > > select count(*) from submission where user_id is null : 2044 > There should be no submission.user_id nulls in treebasedev, as of today. --vg |
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From: Vladimir G. <vla...@du...> - 2010-03-12 21:30:12
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On Mar 12, 2010, at 2:37 PM, William Piel wrote: > > The final taxon intel tables are now available. > > http://www.treebase.org/treebase/migration/Mar-10/ > TI_for_Mar10_utf8.zip They are now in the treebasestage instance. --VG |
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From: Vladimir G. <vla...@du...> - 2010-03-12 19:56:00
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On Mar 12, 2010, at 2:37 PM, William Piel wrote: > > The final taxon intel tables are now available. > > http://www.treebase.org/treebase/migration/Mar-10/ > TI_for_Mar10_utf8.zip Bill, please confirm that, as before, this is a wholesale replacement for the prior TI data. That is, I should drop all existing taxa and taxonvariants and put these ones instead. --VG |
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From: William P. <wil...@ya...> - 2010-03-12 19:37:29
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The final taxon intel tables are now available. http://www.treebase.org/treebase/migration/Mar-10/TI_for_Mar10_utf8.zip bp |
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From: Rutger V. <rut...@gm...> - 2010-03-12 18:40:58
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Hi Hilmar, we use RSS1.0 (i.e. RDF) in two contexts: 1. when we try to dereference a resource without serialization format specifier we use it to list the locations where different serializations are available. So this is at most a list of four items right now, each having the resource URL itself plus ?format=(rdf|xml|html|nexus) 2. when we list the results from a CQL query and we give a format=rss1 specifier we list all the hits in an RSS feed. Rutger On Wed, Mar 10, 2010 at 3:32 PM, Hilmar Lapp <hl...@ne...> wrote: > Rutger - > > can you elaborate on how we are using RSS technically? You say in your > comments to the website text draft that it is being used for search results > that are lists. > > Is this the native response format of the web-application then and an XSLT > is used to convert to HTML? I think not, right? So I'm still pretty > confused. > > -hilmar > -- > =========================================================== > : 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: Rutger V. <rut...@gm...> - 2010-03-12 18:36:39
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I've had the attached owl kicking around for ages but never actually published it. Perhaps it needs to go somewhere such that http://purl.org/phylo/treebase/terms/ (or something like it) points to it and we use that as the namespace? On Wed, Mar 10, 2010 at 4:26 PM, Hilmar Lapp <hl...@ne...> wrote: > The API documentation right now states for example that > "tb:identifier.ubio inherits from dcterms:identifier and so any of the > latter's semantics apply to the former." > > Where is this formalized? The namespace URI given in the spreadsheet > [1] yields a 404. Has the vocabulary been published as RDF or OWL? > > If not, we need to revise the above statement. > > -hilmar > > [1] http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw&single=true&gid=0&output=html > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > 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 > -- 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...> - 2010-03-12 15:42:01
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You can make it that way, but I'm not sure I agree that this should be the canonical URI for TreeBASE. Why shouldn't that be http://treebase.org , and TreeBASE as a resource and concept exists without the existence of phyloWS, so I don't see why to tether those two together. If you want the base phyloWS URL to resolve to something useful, have it resolve to the TreeBASE PhyloWS API documentation. You could even add conneg or client name interpretation to return a WSDL2.0 description if it's a machine that's accessing that URL. -hilmar On Mar 12, 2010, at 7:41 AM, Rutger Vos wrote: > Hi all, > > I'm working on issue 2960840, and a conceptual issue has come up. What > should http://purl.org/phylo/treebase/phylows/ itself, without path > fragments, point to? I am of the opinion that, in a semweb world, this > should be the canonical resource that identifies treebase and so this > should be the One, True homepage of treebase - or even an RDF > description of what treebase is. What do you think? > > 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 > > ------------------------------------------------------------------------------ > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-03-12 12:41:12
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Hi all, I'm working on issue 2960840, and a conceptual issue has come up. What should http://purl.org/phylo/treebase/phylows/ itself, without path fragments, point to? I am of the opinion that, in a semweb world, this should be the canonical resource that identifies treebase and so this should be the One, True homepage of treebase - or even an RDF description of what treebase is. What do you think? 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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