Menu
▾
▴
treebase-devel
|
From: Carl B. <cbo...@gm...> - 2011-05-12 00:04:01
|
Hi list, I'm trying to get a better idea of what's available in terms of OAI-PMH verbs described on the wiki: http://sourceforge.net/apps/mediawiki/treebase/index.php?title=OAI-PMH (I promise to help update the wiki once I get this right ;-) For instance, it will ListRecord will take "after" as well as "until"? It seems that the date used by ListRecord corresponds to the datestamp in the header, which isn't the year of the publication? I thought it might be the date added to TreeBASE, but some go back to 1980? Is this spelled out a bit more anywhere? It would be great to be able to query by publication date, but mostly just curious about what's possible here. Thanks much, -Carl On Wed, May 11, 2011 at 4:35 PM, Carl Boettiger <cbo...@gm...> wrote: > Working for me now too. > > On Wed, May 11, 2011 at 4:21 PM, William Piel <wil...@ya...> wrote: >> It works for me (?) >> >> bp >> >> >> On May 11, 2011, at 5:25 PM, Jon Auman wrote: >> >>> Bill, >>> >>> I updated the application around 5 PM today. Should I rollback to the previous version? >>> >>> -Jon >>> >>> On May 11, 2011, at 5:10 PM, Carl Boettiger wrote: >>> >>>> Hi Treebase, >>>> >>>> >>>> This worked a moment ago: >>>> http://treebase.org/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s1234 >>>> >>>> >>>> Now I get an error: >>>> Uncaught Exception Encountered >>>> java.lang.reflect.InvocationTargetException at >>>> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at >>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) >>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >>>> at java.lang.reflect.Method.invoke(Method.java:616) at >>>> org.cipres.treebase.web.controllers.OAIPMHController.handle(OAIPMHController.java:117) >>>> at org.springframework.web.servlet.mvc.AbstractCommandController.handleRequestInternal(AbstractCommandController.java:84) >>>> at >>>> [...] >>>> >>>> >>>> basic queries are still there: >>>> http://treebase.org/treebase-web/top/oai?verb=Identify >>>> but not and GetRecord queries. >>>> >>>> Just curious if this is a problem at my end or just a temporary interruption. >>>> >>>> Thanks, >>>> Carl >>>> -- >>>> Carl Boettiger >>>> UC Davis >>>> http://www.carlboettiger.info/ >>>> >>>> - >> > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
|
From: William P. <wil...@ya...> - 2011-05-12 00:17:00
|
On May 11, 2011, at 8:03 PM, Carl Boettiger wrote: > For instance, it will ListRecord will take "after" as well as "until"? it should... > It seems that the date used by ListRecord corresponds to the datestamp > in the header, which isn't the year of the publication? that's right... so the main motivation for creating this service was to allow Dryad to mirror TreeBASE -- any modifications to old records get an updated time-stamp, which allows Dryad to not just suck down new records, but also update existing records that have changed. > I thought it might be the date added to TreeBASE, but some go back to 1980? Oh... whoops. Maybe I'm wrong about this. The earliest date should be 1995-11-04. I'll have to check this. > Is this spelled out a bit more anywhere? It ought to be... bp |
|
From: Carl B. <cbo...@gm...> - 2011-05-12 00:24:21
|
On Wed, May 11, 2011 at 5:16 PM, William Piel <wil...@ya...> wrote: > > On May 11, 2011, at 8:03 PM, Carl Boettiger wrote: > >> For instance, it will ListRecord will take "after" as well as "until"? > > it should... hmm, I don't think I have the right adjective, seems that "after" gives me the whole of treebase independent of the date. Same with "since" Can I look up the vocabulary somewhere? I was extracting dates from <dc:dates> but pulling with ListRecord=until, which was using the <datestamp> date instead, which is why I got 1980s dates. Sorry about that. So I guess the only way to query by author date is to pull the metadata for all studies and filter from there? Fine for treebase at it's current size I suppose... -Carl > >> It seems that the date used by ListRecord corresponds to the datestamp >> in the header, which isn't the year of the publication? > > that's right... so the main motivation for creating this service was to allow Dryad to mirror TreeBASE -- any modifications to old records get an updated time-stamp, which allows Dryad to not just suck down new records, but also update existing records that have changed. > >> I thought it might be the date added to TreeBASE, but some go back to 1980? > > Oh... whoops. Maybe I'm wrong about this. The earliest date should be 1995-11-04. I'll have to check this. > >> Is this spelled out a bit more anywhere? > > It ought to be... > > bp > > > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
|
From: William P. <wil...@ya...> - 2011-05-12 01:11:07
|
On May 11, 2011, at 8:24 PM, Carl Boettiger wrote: > hmm, I don't think I have the right adjective, seems that "after" > gives me the whole of treebase independent of the date. Same with > "since" Can I look up the vocabulary somewhere? the mot juste in OAI lingo is "from". I just added this example to the wiki: http://treebase.org/treebase-web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&from=2011-04-30T00:00:00Z > So I guess the only way to query by author date is to pull the > metadata for all studies and filter from there? Fine for treebase at > it's current size I suppose... I also wish the phylows API had the ability to search by publication year. Alas, not yet. bp |
|
From: Rutger V. <R....@re...> - 2011-05-12 13:40:16
|
http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May 5, 2011"&format=rss1 http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May 5, 2011"&format=rss1 http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May 5, 2011"&format=rss1 still ironing out the bugs with prism.publicationDate, but prism.modificationDate seems to work. On Thu, May 12, 2011 at 2:10 AM, William Piel <wil...@ya...> wrote: > > On May 11, 2011, at 8:24 PM, Carl Boettiger wrote: > >> hmm, I don't think I have the right adjective, seems that "after" >> gives me the whole of treebase independent of the date. Same with >> "since" Can I look up the vocabulary somewhere? > > the mot juste in OAI lingo is "from". I just added this example to the wiki: > > http://treebase.org/treebase-web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&from=2011-04-30T00:00:00Z > >> So I guess the only way to query by author date is to pull the >> metadata for all studies and filter from there? Fine for treebase at >> it's current size I suppose... > > I also wish the phylows API had the ability to search by publication year. Alas, not yet. > > bp > > > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > 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://rutgervos.blogspot.com |
|
From: William P. <wil...@ya...> - 2011-05-16 19:02:12
|
Hi Rutger: I notice that all the examples given for date searches in CQL use ISO 8601 date styles: http://www.loc.gov/standards/sru/resources/cql-context-set-v1-2.html But both of these queries throw exceptions: http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"2011-05-05" http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>2011-05-05 => java.text.ParseException: Unparseable date: "2011-05-05" at com.ibm.icu.text.DateFormat.parse(DateFormat.java:390) at... ... but conforming to ISO 8601 has various advantages, including the ability to include the time zone. Our OAI-PMH service seems to understand ISO 8601, e.g.: ?verb=ListRecords&metadataPrefix=oai_dc&from=2011-05-05T00:00:00Z Can the date parser for phylows be made more intelligent? bp On May 12, 2011, at 9:40 AM, Rutger Vos wrote: > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May 5, 2011"&format=rss1 > > still ironing out the bugs with prism.publicationDate, but > prism.modificationDate seems to work. |
|
From: William P. <wil...@ya...> - 2011-05-12 14:11:31
|
On May 12, 2011, at 9:40 AM, Rutger Vos wrote: > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May > 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May > 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May > 5, 2011"&format=rss1 > > still ironing out the bugs with prism.publicationDate, but > prism.modificationDate seems to work. Hey -- this is excellent. Presently I have an RSS feed in my Apple Mail client program that lists all (new) submissions to TreeBASE, but the PhyloWS query is a silly kluge, like finding all articles with the letter "e" in the title. Once your changes are rebuilt on production, I'll change this to find all after modification date x. bp |
|
From: Rutger V. <R....@re...> - 2011-05-12 14:48:41
|
I think I got publicationDate to work as well, should be available on the dev shortly. On Thu, May 12, 2011 at 3:11 PM, William Piel <wil...@ya...> wrote: > > On May 12, 2011, at 9:40 AM, Rutger Vos wrote: > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May > 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May > 5, 2011"&format=rss1 > > http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May > 5, 2011"&format=rss1 > > still ironing out the bugs with prism.publicationDate, but > prism.modificationDate seems to work. > > Hey -- this is excellent. Presently I have an RSS feed in my Apple Mail > client program that lists all (new) submissions to TreeBASE, but the PhyloWS > query is a silly kluge, like finding all articles with the letter "e" in the > title. Once your changes are rebuilt on production, I'll change this to find > all after modification date x. > bp > > > ------------------------------------------------------------------------------ > Achieve unprecedented app performance and reliability > What every C/C++ and Fortran developer should know. > Learn how Intel has extended the reach of its next-generation tools > to help boost performance applications - inlcuding clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > 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://rutgervos.blogspot.com |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X