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From: Jon A. <jon...@du...> - 2010-06-15 15:10:41
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Yes, they are the same version. They are exactly the same bytes in size, and I copied from dev instance to production. -Jon On Jun 15, 2010, at 9:36 AM, William Piel wrote: > > On Jun 14, 2010, at 11:22 AM, Vladimir Gapeyev wrote: > >>> Has a new build been triggered yet? It would be nice to see this on >>> production. >> >> According to Jon, deployed to production this morning. > > Thanks Vladimir. > > This is a bit odd because the lat/longs are not showing up in the NeXML of these matrices: > > http://purl.org/phylo/treebase/phylows/matrix/TB2:M5572?format=nexml > http://purl.org/phylo/treebase/phylows/matrix/TB2:M5212?format=nexml > > ... yet they should be there. > > Can we confirm that, indeed, the dev and prod builds are identical versions? > > bp > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > 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: William P. <wil...@ya...> - 2010-06-15 13:55:37
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On Jun 14, 2010, at 11:22 AM, Vladimir Gapeyev wrote: >> Has a new build been triggered yet? It would be nice to see this on >> production. > > According to Jon, deployed to production this morning. Thanks Vladimir. This is a bit odd because the lat/longs are not showing up in the NeXML of these matrices: http://purl.org/phylo/treebase/phylows/matrix/TB2:M5572?format=nexml http://purl.org/phylo/treebase/phylows/matrix/TB2:M5212?format=nexml ... yet they should be there. Can we confirm that, indeed, the dev and prod builds are identical versions? bp |
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From: Hilmar L. <hl...@ne...> - 2010-06-14 17:35:15
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Val - that's great to hear and, yes, now that you remind me I do recall. What are your thoughts on OPM? -hilmar On Jun 14, 2010, at 11:17 AM, Val Tannen wrote: > I am very much involved in the data provenance community. This is > in fact my main research area. On my web page there are some slides > on a recent talk (http://www.cis.upenn.edu/~val/EDBTkeynoteLausanne.pdf > ) > > And on the workflow side of pPOD, yes we have used phylogenetic > examples, as Bertram must have told you. > > I would be keen to work with anybody interested on provenance in > TreeBASE. > > Val > > > > > On Jun 13, 2010, at 9:14 PM, Hilmar Lapp wrote: > >> I don't know whether this has been considered already in the past, >> but >> it certainly seems relevant to TreeBASE, more so than ever with the >> analysis steps annotation that is now required from depositors - it >> looks to me that this might essentially be the standard for exposing >> them. >> >> The Open Provenance Model Core Specification (v1.1) >> http://eprints.ecs.soton.ac.uk/18332/1/opm.pdf >> >> BTW there is a summer student internship project sponsored by DataONE >> on data provenance: >> http://groups.google.com/group/datatol >> >> Bertram Ludäscher wanted a phylogenetics-oriented use-case too, and >> it >> seems to me like the analysis steps that connect input data with >> alignment and output tree could be a great example. >> >> -hilmar >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> >> ------------------------------------------------------------------------------ >> ThinkGeek and WIRED's GeekDad team up for the Ultimate >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the >> lucky parental unit. See the prize list and enter to win: >> http://p.sf.net/sfu/thinkgeek-promo >> _______________________________________________ >> 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: Val T. <va...@ci...> - 2010-06-14 15:36:21
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I am very much involved in the data provenance community. This is in fact my main research area. On my web page there are some slides on a recent talk (http://www.cis.upenn.edu/~val/EDBTkeynoteLausanne.pdf) And on the workflow side of pPOD, yes we have used phylogenetic examples, as Bertram must have told you. I would be keen to work with anybody interested on provenance in TreeBASE. Val On Jun 13, 2010, at 9:14 PM, Hilmar Lapp wrote: > I don't know whether this has been considered already in the past, but > it certainly seems relevant to TreeBASE, more so than ever with the > analysis steps annotation that is now required from depositors - it > looks to me that this might essentially be the standard for exposing > them. > > The Open Provenance Model Core Specification (v1.1) > http://eprints.ecs.soton.ac.uk/18332/1/opm.pdf > > BTW there is a summer student internship project sponsored by DataONE > on data provenance: > http://groups.google.com/group/datatol > > Bertram Ludäscher wanted a phylogenetics-oriented use-case too, and it > seems to me like the analysis steps that connect input data with > alignment and output tree could be a great example. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Vladimir G. <vla...@du...> - 2010-06-14 15:22:11
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On Jun 11, 2010, at 3:27 PM, William Piel wrote: > > On Jun 9, 2010, at 9:17 AM, Rutger Vos wrote: > >> I have made some changes in how coordinates are attached to NeXML and >> how RDF is generated. Could these go to production? > > Has a new build been triggered yet? It would be nice to see this on > production. According to Jon, deployed to production this morning. --VG |
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From: Rutger V. <rut...@gm...> - 2010-06-14 09:51:27
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That does seem very relevant! Here is the link: http://openprovenance.org/ On Mon, Jun 14, 2010 at 2:14 AM, Hilmar Lapp <hl...@ne...> wrote: > I don't know whether this has been considered already in the past, but > it certainly seems relevant to TreeBASE, more so than ever with the > analysis steps annotation that is now required from depositors - it > looks to me that this might essentially be the standard for exposing > them. > > The Open Provenance Model Core Specification (v1.1) > http://eprints.ecs.soton.ac.uk/18332/1/opm.pdf > > BTW there is a summer student internship project sponsored by DataONE > on data provenance: > http://groups.google.com/group/datatol > > Bertram Ludäscher wanted a phylogenetics-oriented use-case too, and it > seems to me like the analysis steps that connect input data with > alignment and output tree could be a great example. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > 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...> - 2010-06-14 01:15:03
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I don't know whether this has been considered already in the past, but it certainly seems relevant to TreeBASE, more so than ever with the analysis steps annotation that is now required from depositors - it looks to me that this might essentially be the standard for exposing them. The Open Provenance Model Core Specification (v1.1) http://eprints.ecs.soton.ac.uk/18332/1/opm.pdf BTW there is a summer student internship project sponsored by DataONE on data provenance: http://groups.google.com/group/datatol Bertram Ludäscher wanted a phylogenetics-oriented use-case too, and it seems to me like the analysis steps that connect input data with alignment and output tree could be a great example. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-06-11 19:27:26
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On Jun 9, 2010, at 9:17 AM, Rutger Vos wrote: > I have made some changes in how coordinates are attached to NeXML and > how RDF is generated. Could these go to production? Has a new build been triggered yet? It would be nice to see this on production. bp |
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From: Hilmar L. <hl...@ne...> - 2010-06-10 18:17:07
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The deadline for this is Saturday. I won't have time today, and not much tomorrow either, so if others could get their thoughts down in the meantime that'd be greatly helpful. -hilmar On May 22, 2010, at 12:42 PM, Hilmar Lapp wrote: > 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: >> >> [URL] >> >> 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: [...] >> >> Sincerely, >> Sean O'Donoghue, EMBL, Germany >> Anita de Waard, Elsevier, USA >> >> > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-06-09 15:02:06
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Hi, the dev instance is not properly configured with respect to the purls, now everything comes out looking like http://dummy_purl_base/study/TB2:S10362?x-access-code=128aaad91df95ba3207f34d7f03f3ad1&format=html, which is due to an incomplete JNDI configuration, I gather. 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...> - 2010-06-09 13:17:46
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Hi, I have made some changes in how coordinates are attached to NeXML and how RDF is generated. Could these go to production? 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: Hilmar L. <hl...@ne...> - 2010-06-04 18:52:49
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On Jun 4, 2010, at 11:44 AM, Rutger Vos wrote: >> >> But why can't the redirection from >> http://purl.org/phylo/treebase/phylows/tree/16354 to >> http://treebase.org/phylows/tree/16354 be a 301 or a 302? They should >> probably also be connected by owl:sameAs. In fact, because they are >> owl:sameAs, shouldn't they be redirected through 301 or 302, >> because 303 >> says "See also". But this is not seeAlso - they are owl:sameAs! > > Eh, ok, where would we make that owl:sameAs statement? Well, in the RDF of course. So if someone dereferences http://purl.org/phylo/treebase/phylows/tree/16354 and wants RDF, they get first redirected (using 301 or 302 in my opinion) to http://treebase.org/phylows/tree/16354, which is resolved via 303 to http://treebase.org/phylows/tree/16354?format=rdf through content negotiation. In the RDF, you can say that http://treebase.org/phylows/tree/16354 owl:sameAs http://purl.org/phylo/treebase/phylows/tree/16354 -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-06-04 18:42:41
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On Jun 4, 2010, at 11:44 AM, Rutger Vos wrote: > http://purl.org/phylo/treebase/phylows/tree/16354 would be > redirected to the PhyloWSController, which could do the conneg and 303 > redirect the client to > http://purl.org/phylo/treebase/phylows/tree/16354?format=rdf, except > the hops from purl to the PhyloWSController wouldn't be 303s. > Ah - now we're getting closer. Why would the PhyloWSController have to redirect to the PURL-based URL? It sits already under a treebase.org URL, why go back out to purl.org? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-06-04 15:44:22
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On Thu, Jun 3, 2010 at 6:54 PM, Hilmar Lapp <hl...@ne...> wrote: > > On Jun 3, 2010, at 1:36 PM, Rutger Vos wrote: > >>> Going from a canonical URI to the implementation URL sounds like a 302 to >>> me, not a 303. >> >> Really? I interpret the examples I've seen as 303, not 302. > > > I think the examples you've seen are for going from the thing URI to the > information about the thing URL. Mmmm... yeah, I guess you're right about that. > So for example, accessing http://treebase.org/phylows/tree/16354 would > return a 303, with either http://treebase.org/phylows/tree/16354?format=rdf > or http://treebase.org/phylows/tree/16354?format=html as the Location > parameter, determined by content negotiation. This one can't be a 301 or > 302. Right. > But why can't the redirection from > http://purl.org/phylo/treebase/phylows/tree/16354 to > http://treebase.org/phylows/tree/16354 be a 301 or a 302? They should > probably also be connected by owl:sameAs. In fact, because they are > owl:sameAs, shouldn't they be redirected through 301 or 302, because 303 > says "See also". But this is not seeAlso - they are owl:sameAs! Eh, ok, where would we make that owl:sameAs statement? > Conversely, going from http://purl.org/phylo/treebase/phylows/tree/16354 to > http://purl.org/phylo/treebase/phylows/tree/16354?format=rdf would have to > be a 303, as would going to > http://treebase.org/phylows/tree/16354?format=rdf have to be - but purl.org > doesn't actually support those redirects. It just goes to another site, not > to another representation, or to a site with information "about" the URI > being redirected. Sure, but http://purl.org/phylo/treebase/phylows/tree/16354 would be redirected to the PhyloWSController, which could do the conneg and 303 redirect the client to http://purl.org/phylo/treebase/phylows/tree/16354?format=rdf, except the hops from purl to the PhyloWSController wouldn't be 303s. -- 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...> - 2010-06-03 17:54:21
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On Jun 3, 2010, at 1:36 PM, Rutger Vos wrote: >> Going from a canonical URI to the implementation URL sounds like a >> 302 to >> me, not a 303. > > Really? I interpret the examples I've seen as 303, not 302. I think the examples you've seen are for going from the thing URI to the information about the thing URL. So for example, accessing http://treebase.org/phylows/tree/16354 would return a 303, with either http://treebase.org/phylows/tree/16354?format=rdf or http://treebase.org/phylows/tree/16354?format=html as the Location parameter, determined by content negotiation. This one can't be a 301 or 302. But why can't the redirection from http://purl.org/phylo/treebase/phylows/tree/16354 to http://treebase.org/phylows/tree/16354 be a 301 or a 302? They should probably also be connected by owl:sameAs. In fact, because they are owl:sameAs, shouldn't they be redirected through 301 or 302, because 303 says "See also". But this is not seeAlso - they are owl:sameAs! Conversely, going from http://purl.org/phylo/treebase/phylows/tree/ 16354 to http://purl.org/phylo/treebase/phylows/tree/16354?format=rdf would have to be a 303, as would going to http://treebase.org/phylows/tree/16354?format=rdf have to be - but purl.org doesn't actually support those redirects. It just goes to another site, not to another representation, or to a site with information "about" the URI being redirected. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-06-03 17:44:44
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On Jun 3, 2010, at 1:36 PM, Rutger Vos wrote: > Linkeddata browsers apparently (according to @rdmpage, mind) expect > 303, but our purls give them 302. They won't know what to do with > that, so until we > reconfigure our purls, we can't use them in a linkeddata context. Where does it say that? So long as our URIs don't either always return RDF, or return RDF based on content negotiation and a 303 response, it won't work in an LD browser. Changing the PURLs to 303 doesn't change that, does it? It's a bit hard to believe that LD browsers will refuse to follow 302 and 301 redirects from one site to another, but if there's a spec somewhere that states that I'll believe it. Until then, the crux of the problem is the LD non-compliant *endpoint*, not the initial PURL redirect. Or are you saying the endpoint is LD compliant? That should be easily testable - just change the PURL base to the endpoint URL base (removing the PURL.org redirect), and point an LD client at it. Test it on dev. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-06-03 17:36:35
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I think the problem we want to solve is that we can give a canonical treebase purl to a linkeddata browser and it can do something with it, whether that's through conneg is almost secondary. Linkeddata browsers apparently (according to @rdmpage, mind) expect 303, but our purls give them 302. They won't know what to do with that, so until we reconfigure our purls, we can't use them in a linkeddata context. On Wed, Jun 2, 2010 at 10:15 PM, Hilmar Lapp <hl...@ne...> wrote: > I don't think the issue is that easy. Without content negotiation, the 303 > makes not much sense to hop from one place to the next, so I'm not sure why > it's being used right now over a 301 or a 302. LD is somewhat being glued together by convention, so I'm as baffled as you - but if the convention is 303 and we wanna play, we'll have to do 303 also. > LD compliance requires more than using 303. You need to have separate URIs > for a thing, and resources about that thing. A tree would be a thing, with > one URI. The HTML page about it can't have the same URI, nor can the RDF > document about it. Right, the canonical thing URI would be the purl, and the different serializations describing it are identified by the phylows "?format=$foo" query string parameter. > Going from a canonical URI to the implementation URL sounds like a 302 to > me, not a 303. Really? I interpret the examples I've seen as 303, not 302. > Maybe I'm wrong here but that's why I think we need to think this through > first. I'll try to come up with some scenarios with visuals, I'll have to for the ievobio talk anyway. > On Jun 2, 2010, at 4:56 PM, Rutger Vos wrote: > >> On Wed, Jun 2, 2010 at 8:27 PM, Hilmar Lapp <hl...@ne...> wrote: >>> >>> I think we need to wrap this issue into discussing how to make PhyloWS >>> LD-compliant. Once we understand the full picture and have a diagram of >>> which URI we want to behave how we can implement it. >> >> Well, maybe - but this isn't about phylows per se, but about how we go >> from purl to treebase, as opposed to from phylows urls to the "ugly" >> urls (for this redirect, as implemented in the PhyloWSController, we >> have always used 303). In this sense, phylows is already linkeddata >> compliant, but the simple purls aren't (for that you need to use the >> "advanced" purls). >> >>> On Jun 2, 2010, at 12:38 PM, Rutger Vos wrote: >>> >>>> Hi, >>>> >>>> it seems our current purl configuration results in 302 redirects. >>>> Hilmar, maybe you can make these 303 redirects? Unless I am >>>> misunderstanding the admin interface I don't have the privilege to do >>>> so. >>>> >>>> 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 : > =========================================================== > > > > -- 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...> - 2010-06-02 21:46:08
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I have fixed the automatic deployment for treebase-dev. Any time you check in code to the sourceforge repo, you should get an automatic rebuild and deploy to treebase-dev. I've tested it and it works now as advertised. -Jon On Jun 2, 2010, at 12:44 PM, Rutger Vos wrote: > Hi Jon, > > this doesn't seem to be working: I've committed a number of bug fixes, > but they aren't being deployed. > > Rutger > > 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 ------------------------------------------------------- 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...> - 2010-06-02 21:16:01
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I don't think the issue is that easy. Without content negotiation, the 303 makes not much sense to hop from one place to the next, so I'm not sure why it's being used right now over a 301 or a 302. LD compliance requires more than using 303. You need to have separate URIs for a thing, and resources about that thing. A tree would be a thing, with one URI. The HTML page about it can't have the same URI, nor can the RDF document about it. Going from a canonical URI to the implementation URL sounds like a 302 to me, not a 303. Maybe I'm wrong here but that's why I think we need to think this through first. -hilmar On Jun 2, 2010, at 4:56 PM, Rutger Vos wrote: > On Wed, Jun 2, 2010 at 8:27 PM, Hilmar Lapp <hl...@ne...> wrote: >> I think we need to wrap this issue into discussing how to make >> PhyloWS >> LD-compliant. Once we understand the full picture and have a >> diagram of >> which URI we want to behave how we can implement it. > > Well, maybe - but this isn't about phylows per se, but about how we go > from purl to treebase, as opposed to from phylows urls to the "ugly" > urls (for this redirect, as implemented in the PhyloWSController, we > have always used 303). In this sense, phylows is already linkeddata > compliant, but the simple purls aren't (for that you need to use the > "advanced" purls). > >> On Jun 2, 2010, at 12:38 PM, Rutger Vos wrote: >> >>> Hi, >>> >>> it seems our current purl configuration results in 302 redirects. >>> Hilmar, maybe you can make these 303 redirects? Unless I am >>> misunderstanding the admin interface I don't have the privilege to >>> do >>> so. >>> >>> 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...> - 2010-06-02 20:56:49
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On Wed, Jun 2, 2010 at 8:27 PM, Hilmar Lapp <hl...@ne...> wrote: > I think we need to wrap this issue into discussing how to make PhyloWS > LD-compliant. Once we understand the full picture and have a diagram of > which URI we want to behave how we can implement it. Well, maybe - but this isn't about phylows per se, but about how we go from purl to treebase, as opposed to from phylows urls to the "ugly" urls (for this redirect, as implemented in the PhyloWSController, we have always used 303). In this sense, phylows is already linkeddata compliant, but the simple purls aren't (for that you need to use the "advanced" purls). > On Jun 2, 2010, at 12:38 PM, Rutger Vos wrote: > >> Hi, >> >> it seems our current purl configuration results in 302 redirects. >> Hilmar, maybe you can make these 303 redirects? Unless I am >> misunderstanding the admin interface I don't have the privilege to do >> so. >> >> 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...> - 2010-06-02 19:27:57
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I think we need to wrap this issue into discussing how to make PhyloWS LD-compliant. Once we understand the full picture and have a diagram of which URI we want to behave how we can implement it. -hilmar On Jun 2, 2010, at 12:38 PM, Rutger Vos wrote: > Hi, > > it seems our current purl configuration results in 302 redirects. > Hilmar, maybe you can make these 303 redirects? Unless I am > misunderstanding the admin interface I don't have the privilege to do > so. > > 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...> - 2010-06-02 16:44:25
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Hi Jon, this doesn't seem to be working: I've committed a number of bug fixes, but they aren't being deployed. Rutger 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: Rutger V. <rut...@gm...> - 2010-06-02 16:38:22
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Hi, it seems our current purl configuration results in 302 redirects. Hilmar, maybe you can make these 303 redirects? Unless I am misunderstanding the admin interface I don't have the privilege to do so. 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...> - 2010-06-02 12:45:35
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On Jun 1, 2010, at 1:31 PM, Rutger Vos wrote: > * here's my suggested fix Thanks Rutger. I've committed your fix to "treebase-core/db/cleaning/2010-06-02_fix_S2164" Jon -- feel free to run this whenever is convenient. bp |
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From: Rutger V. <rut...@gm...> - 2010-06-01 17:31:56
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Hi all, I'm trying to fix issue 2992022, which was hypothesised to be a character encoding problem. This is not the case, it has nothing to do with UTF-8 handling. It's a database inconsistency: * in the person table, there's both an entry for "Balázs Tímea", person_id=3971 and for "Tímea Balázs", person_id=5609 * in the latter record, first and last name are in the correct order, but the author's email address is missing, and the author order index is 5, on a three-author paper. In the former record, the first and last name are switched around, but everything else is in the correct order. It looks like the nullpointer exception is thrown because there is no author 4 (see: http://www.mycologia.org/cgi/content/abstract/101/2/247). * here's my suggested fix: correct the name order in record 3971, purge record 5609 from person and from citation_author, i.e.: update person set firstname='Tímea', lastname='Balázs' where person_id=3971; delete from citation_author where authors_person_id=5609; delete from person where person_id=5609; On the test instance this fixes the exception, the citation is serialised correctly. Can someone fix this on the production instance? I re-assigned this bug to Bill, but whoever has access to the prod server can run those SQL snippets and everything should be OK. Cheers, 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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