From edward.kawas at gmail.com Thu Jul 2 10:37:20 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Jul 2009 07:37:20 -0700 Subject: [MOBY-dev] invoking document literal services Message-ID: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> Hello All, Since Biomoby supports doc/lit services, in theory, I was wondering if anyone had created a doc/lit service and if so, how do you call it? I want to ensure that the Taverna plugin can handle the various flavours of Biomoby services and right now, it is missing doc/lit support. Any pointers on calling these services, pointers to example code or pointers to actual services would be greatly appreciated. Thanks, Eddie From dmitry.repchevski at bsc.es Thu Jul 2 21:17:24 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 02 Jul 2009 18:17:24 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> References: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> Message-ID: <4A4D5C24.7010205@bsc.es> Hello Edward, As far as I know BioMoby doesn't support doc/lit services yet. I've risen this question several times and the answer was always the same "we are working on it".. After BioHackaton Mark contracted a developer (Jason Stewart) to implement it in Perl. Actually, we reach an agreement how such a services would look like. Can't find it on moby list :-( You can read our conversation here: https://www.inab.org/wiki/images/9/96/Dmitry-mail.pdf Actually in INB meeting last November we agreed to support it (and I have implemented it in my library). The main problem is that we still have no information about Perl implementation. Unless it is implemented in Perl I doubt someone will provide such services... Cheers, Dmitry From edward.kawas at gmail.com Thu Jul 2 13:01:27 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Jul 2009 10:01:27 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4D5C24.7010205@bsc.es> References: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> <4A4D5C24.7010205@bsc.es> Message-ID: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> Hi Dmitry, I guess by support, I meant the ability to register doc/lit services with the registry. I wonder if http://soap-wsdl.sourceforge.net/ would be the way to go in implementing doc/lit in perl. Any pointers from you would be appreciated. I also stumbled upon [1] for serving doc/lit services (ugly hack that apparently works). Thanks, Eddie [1] http://www.perlmonks.org/?node_id=645150 -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-02-09 6:17 PM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] invoking document literal services Hello Edward, As far as I know BioMoby doesn't support doc/lit services yet. I've risen this question several times and the answer was always the same "we are working on it".. After BioHackaton Mark contracted a developer (Jason Stewart) to implement it in Perl. Actually, we reach an agreement how such a services would look like. Can't find it on moby list :-( You can read our conversation here: https://www.inab.org/wiki/images/9/96/Dmitry-mail.pdf Actually in INB meeting last November we agreed to support it (and I have implemented it in my library). The main problem is that we still have no information about Perl implementation. Unless it is implemented in Perl I doubt someone will provide such services... Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jul 2 12:49:48 2009 From: markw at illuminae.com (Mark) Date: Thu, 02 Jul 2009 09:49:48 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4D5C24.7010205@bsc.es> References: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> <4A4D5C24.7010205@bsc.es> Message-ID: As far as I know, Jason is still "working on it" :-) the problem is quite deep - the SOAP libraries in Perl don't support doc-lit, and the problem may even go deeper than that... M On Thu, 02 Jul 2009 18:17:24 -0700, Dmitry Repchevsky wrote: > Hello Edward, > > As far as I know BioMoby doesn't support doc/lit services yet. > I've risen this question several times and the answer was always the > same "we are working on it".. > > After BioHackaton Mark contracted a developer (Jason Stewart) to > implement it in Perl. > Actually, we reach an agreement how such a services would look like. > Can't find it on moby list :-( > You can read our conversation here: > https://www.inab.org/wiki/images/9/96/Dmitry-mail.pdf > > Actually in INB meeting last November we agreed to support it (and I > have implemented it in my library). > The main problem is that we still have no information about Perl > implementation. > Unless it is implemented in Perl I doubt someone will provide such > services... > > Cheers, > > Dmitry > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Thu Jul 2 22:27:35 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 02 Jul 2009 19:27:35 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> References: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> Message-ID: <4A4D6C97.9030606@bsc.es> Hello, > I guess by support, I meant the ability to register doc/lit services withthe registry. > Nobody would prevent you from registering "doc-literal" service. The problem is what does it mean... The SOAP-WSDL project looks promising, but they still far away even from [XML schema support ("minimal conformant")]. Anyway I think it's possible to use for the moby. I mean that BioMoby is XML Schema incompatible, so there is no way to use it "right way". My proposal (and Jason agreed with me) was to use Moby message "as is" inside a SOAP BODY. This way only "moby" part of schema is needed (the ontology objects defined as "any"). The implementation is simple and taking into account that all the "moby" artifacts are the same for any service, we do not any schema parser at all... Meanwhile, BioMoby is moving to err... unexplored direction, I'm moving completely to WSDL doc/lit services based on BioMoby ontology. My last breakthrough was asynchrony based on WS-Addressing. Dmitry. P.S. I just realized that you are working with Taverna. I have no any experience with it, and there is almost no documentation... :-( I created a java component (tree) to encode/decode/edit XML messages based on XML Schema and would like to convert it to taverna plugin (wsdl activity). From soiland-reyes at cs.manchester.ac.uk Fri Jul 3 13:54:13 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 3 Jul 2009 18:54:13 +0100 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4D6C97.9030606@bsc.es> References: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> <4A4D6C97.9030606@bsc.es> Message-ID: On Fri, Jul 3, 2009 at 03:27, Dmitry Repchevsky wrote: > My proposal (and Jason agreed with me) was to use Moby message "as is" > inside a SOAP BODY. > This way only "moby" part of schema is needed (the ontology objects defined > as "any"). Excuse me if I sound daft.. but what is the point of making a Document/literal service if you end up having to use xsd:any and a normal Moby message? (Or do we have an XSD schema for Moby messages..?) You might with doc/literal be able to support a more up-to-date clients like Axis2 and CXF for Java, but if it's just a wrapper for the 'real' Moby message inside that needs to be parsed manually or using moby libraries.. what is the big gain? :-) (Not to say I don't recommend using doc/literal instead of rpc/whatever! :-) Just wondering what the benefits would be..) -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From dmitry.repchevski at bsc.es Fri Jul 3 14:15:50 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 03 Jul 2009 11:15:50 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: References: Message-ID: <4A4E4AD6.8090202@bsc.es> > > Excuse me if I sound daft.. but what is the point of making a > Document/literal service if you end up having to use xsd:any and a > normal Moby message? (Or do we have an XSD schema for Moby > messages..?) > I agree with you, it is not my fault that moby is incompatible with schema... Moby message can be divided into two parts, auxiliary one and an ontology one. First part is schema compatible, another one no. > You might with doc/literal be able to support a more up-to-date > clients like Axis2 and CXF for Java, but if it's just a wrapper for > the 'real' Moby message inside that needs to be parsed manually or > using moby libraries.. what is the big gain? :-) > Not exactly. The message like: ************************************************** AGHFJHGDKHGJKADGHJGDJH ************************************************** CAN be parsed using JAX-WS standard methods. I have an alternative BioMoby Java API based on JAX-WS/JAXB and using it I CAN provide STANDARD doc-lit BioMoby services: ************************************************** @WebService() @SOAPBinding(style=SOAPBinding.Style.DOCUMENT, use=SOAPBinding.Use.LITERAL, parameterStyle=SOAPBinding.ParameterStyle.BARE) //@XmlSeeAlso({AminoAcidSequence.class, MobyString.class}) public class MobyDocWebService { @WebResult(name="MOBY", targetNamespace="http://www.biomoby.org/moby") public MobyMessage runMyService(@WebParam(name="MOBY", targetNamespace="http://www.biomoby.org/moby", mode = WebParam.Mode.IN) MobyMessage msg) { return msg; // just to return back the message } } ************************************************** Another project I have done is to automagically generate a JAX-WS proxy application (*.war) for any (including asynchronous) biomoby services. Such a proxy expose biomoby services as WSDL doc-lit ones (+WSA for asynchrony) with preserving all the moby ontology. Cheers, Dmitry From gordonp at ucalgary.ca Fri Jul 3 23:44:20 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 03 Jul 2009 21:44:20 -0600 Subject: [MOBY-dev] Quick Question on Moby Usage in Europe In-Reply-To: <4A4E4AD6.8090202@bsc.es> References: <4A4E4AD6.8090202@bsc.es> Message-ID: <4A4ED014.90204@ucalgary.ca> Hi all, I'm giving a Moby presentation in a few weeks, and I'd like to include a map showing Moby usage in Europe. I know I can get info from the registry, but was hoping that the Europeans among could send me a quick message with: 1) the name of your institution, 2) a one line description of the types of services you offer (from a biologist's perspective), and 3) the target audience for which you created your services, if outside your institution. Any help you can provide is greatly appreciated! Thanks, Paul From dmitry.repchevski at bsc.es Tue Jul 7 22:25:03 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 07 Jul 2009 19:25:03 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral Message-ID: <4A54037F.9070501@bsc.es> Hello, Trying to optimize a little bit my MobyCentral API I found a strange a thing: According the "specification" http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayloads.html#retrieveObjectDefinition There are two ways to get the relationships for an object: first way is to get Relationships directly (through "Relationships" operation): Output: [ OntologyTerm | OntologyTerm ] ... ... This one I used to use... But there is another way using "retrieveObjectDefinition" method: Output: ObjectClassName ExistingObjectType ... your.URI.here owner at their.address.com The problem is that instead of [relationshipType="RelationshipOntologyTerm"] it returns lsid!!! Here is the output: Zip_Encoded inb.bsc.es romina.royo at bsc.es Object String String As far as I understand from the specification it should be: Could someone clarify please... Dmitry From markw at illuminae.com Tue Jul 7 13:44:14 2009 From: markw at illuminae.com (Mark) Date: Tue, 07 Jul 2009 10:44:14 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: <4A54037F.9070501@bsc.es> References: <4A54037F.9070501@bsc.es> Message-ID: Hi Dmitry, It's almost certainly a bug. I wont be able to fix it for a few days, though, as I've got other deadlines to meet this week. If you want to fix it yourself and commit (or send me) the fix that would be fine... but be very very careful because I know that those attributes are often used by other methods, so it may be that other routines are now coded to compensate for this bug! :-P otherwise, give me a week or so and I'll fix it myself. Mark On Tue, 07 Jul 2009 19:25:03 -0700, Dmitry Repchevsky wrote: > Hello, > > Trying to optimize a little bit my MobyCentral API I found a strange a > thing: > > According the "specification" > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayloads.html#retrieveObjectDefinition > > There are two ways to get the relationships for an object: > > first way is to get Relationships directly (through "Relationships" > operation): > > Output: > > > lsid='urn:lsid:authority.uri:namespace:id'> > [ articleName='foo'>OntologyTerm | > OntologyTerm ] > ... > > ... > > > This one I used to use... > > But there is another way using "retrieveObjectDefinition" method: > > Output: > > > lsid='urn:lsid:authority.uri:namespace:id'>ObjectClassName > human readable description > of data type]]> > > lsid='urn:lsid:authority.uri:namespace:id'> > lsid='urn:lsid:authority.uri:namespace:id'>ExistingObjectType > > ... > your.URI.here > > owner at their.address.com > > > > The problem is that instead of > [relationshipType="RelationshipOntologyTerm"] it returns lsid!!! > > Here is the output: > > > lsid='urn:lsid:biomoby.org:objectclass:Zip_Encoded:2007-11-16T11-34-07Z'>Zip_Encoded > > inb.bsc.es > romina.royo at bsc.es > > relationshipType='urn:lsid:biomoby.org:objectrelation:isa'> > lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z'>Object > > relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'> > lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String > lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String > > > > As far as I understand from the specification it should be: > > lsid='urn:lsid:biomoby.org:objectrelation:isa'> > > Could someone clarify please... > > Dmitry > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jul 7 22:56:31 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 07 Jul 2009 19:56:31 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: Message-ID: <4A540ADF.7040900@bsc.es> Hello Mark, I am not that skilled in Perl... :-( But I will ask INB people if they can do this... Anyway it's not critical... Cheers, Dmitry From markw at illuminae.com Tue Jul 7 14:14:38 2009 From: markw at illuminae.com (Mark) Date: Tue, 07 Jul 2009 11:14:38 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: <4A540ADF.7040900@bsc.es> References: <4A540ADF.7040900@bsc.es> Message-ID: On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky wrote: > I am not that skilled in Perl... :-( clearly, neither am I ;-) LOL! Mark From edward.kawas at gmail.com Tue Jul 7 18:31:51 2009 From: edward.kawas at gmail.com (Eddie Kawas) Date: Tue, 7 Jul 2009 15:31:51 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: <4A540ADF.7040900@bsc.es> Message-ID: According to the perldoc, the subroutine does what it says it should do ( http://search.cpan.org/dist/MOBY/lib/MOBY/Central.pm#retrieveObjectDefinition). So I think that the api doc has a misprint in it. Let me know how you devs want to proceed (either update the api doc or update the perldoc for the sub and update the sub). I have a feeling that all software in moby expects it the way that it is and so updating the api doc might be better. Eddie On Tue, Jul 7, 2009 at 11:14 AM, Mark wrote: > On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky < > dmitry.repchevski at bsc.es> wrote: > > > I am not that skilled in Perl... :-( >> > > > clearly, neither am I ;-) > > LOL! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From markw at illuminae.com Tue Jul 7 18:42:08 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Tue, 7 Jul 2009 22:42:08 +0000 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: <4A540ADF.7040900@bsc.es> Message-ID: <149898153-1247006630-cardhu_decombobulator_blackberry.rim.net-348097757-@bxe1266.bisx.prod.on.blackberry> I guess the important thing is, as Dmitry says, to check for *consistancy*. If this is the only routine that returns an LSID as the value of that attribute, then we need to fix the code. If all instances of that attribute contain an LSID, then we need to fix the doc. I simply don't recall which is which... Though my "instincts" tell me that I wrote the code with the intent to return an LSID in all cases... So I think the code is correct and the doc is wrong... I think! M On the Road! -----Original Message----- From: Eddie Kawas Date: Tue, 7 Jul 2009 15:31:51 To: Core developer announcements Subject: Re: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral According to the perldoc, the subroutine does what it says it should do ( http://search.cpan.org/dist/MOBY/lib/MOBY/Central.pm#retrieveObjectDefinition). So I think that the api doc has a misprint in it. Let me know how you devs want to proceed (either update the api doc or update the perldoc for the sub and update the sub). I have a feeling that all software in moby expects it the way that it is and so updating the api doc might be better. Eddie On Tue, Jul 7, 2009 at 11:14 AM, Mark wrote: > On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky < > dmitry.repchevski at bsc.es> wrote: > > > I am not that skilled in Perl... :-( >> > > > clearly, neither am I ;-) > > LOL! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Jul 7 18:43:31 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Tue, 7 Jul 2009 22:43:31 +0000 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: <4A540ADF.7040900@bsc.es> Message-ID: <368069246-1247006713-cardhu_decombobulator_blackberry.rim.net-1534456682-@bxe1266.bisx.prod.on.blackberry> We should also just do a quick test to make sure that those LSID's are still resolvable by the standard LSID resolution stack... With the various moves to new servers we may have missed something... M On the Road! -----Original Message----- From: Eddie Kawas Date: Tue, 7 Jul 2009 15:31:51 To: Core developer announcements Subject: Re: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral According to the perldoc, the subroutine does what it says it should do ( http://search.cpan.org/dist/MOBY/lib/MOBY/Central.pm#retrieveObjectDefinition). So I think that the api doc has a misprint in it. Let me know how you devs want to proceed (either update the api doc or update the perldoc for the sub and update the sub). I have a feeling that all software in moby expects it the way that it is and so updating the api doc might be better. Eddie On Tue, Jul 7, 2009 at 11:14 AM, Mark wrote: > On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky < > dmitry.repchevski at bsc.es> wrote: > > > I am not that skilled in Perl... :-( >> > > > clearly, neither am I ;-) > > LOL! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Wed Jul 8 03:15:21 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 08 Jul 2009 09:15:21 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? Message-ID: <4A544789.1050804@toulouse.inra.fr> Bonjour a tous, Does Moby public server down ? I cannot access hit from Toulouse (France): no answer to "ping moby.ucalgary.ca" I think it's down for approximatively 4hours ... Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Jul 8 10:35:31 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 08 Jul 2009 08:35:31 -0600 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A544789.1050804@toulouse.inra.fr> References: <4A544789.1050804@toulouse.inra.fr> Message-ID: <4A54AEB3.2060205@ucalgary.ca> ?a marche pour moi...and the university's outside connection seems okay. Sebastien Carrere wrote: > Bonjour a tous, > > Does Moby public server down ? > > I cannot access hit from Toulouse (France): no answer to "ping > moby.ucalgary.ca" > I think it's down for approximatively 4hours ... > > Sebastien > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Sebastien.Carrere at toulouse.inra.fr Wed Jul 8 11:17:52 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 08 Jul 2009 17:17:52 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A54AEB3.2060205@ucalgary.ca> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> Message-ID: <4A54B8A0.4090202@toulouse.inra.fr> Now it's back ! ... don't know what happened Sebastien Paul Gordon wrote: > ?a marche pour moi...and the university's outside connection seems okay. > > Sebastien Carrere wrote: >> Bonjour a tous, >> >> Does Moby public server down ? >> >> I cannot access hit from Toulouse (France): no answer to "ping >> moby.ucalgary.ca" >> I think it's down for approximatively 4hours ... >> >> Sebastien >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Jul 8 11:38:23 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 08 Jul 2009 09:38:23 -0600 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A54B8A0.4090202@toulouse.inra.fr> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> Message-ID: <4A54BD6F.5080109@ucalgary.ca> A bit of trivia: Moby Central has been up for 398 days straight! > uptime 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 Sebastien Carrere wrote: > Now it's back ! > ... don't know what happened > > Sebastien > > > Paul Gordon wrote: >> ?a marche pour moi...and the university's outside connection seems okay. >> >> Sebastien Carrere wrote: >>> Bonjour a tous, >>> >>> Does Moby public server down ? >>> >>> I cannot access hit from Toulouse (France): no answer to "ping >>> moby.ucalgary.ca" >>> I think it's down for approximatively 4hours ... >>> >>> Sebastien >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From mgerlich at ipb-halle.de Thu Jul 9 07:50:59 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 09 Jul 2009 13:50:59 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A54BD6F.5080109@ucalgary.ca> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> <4A54BD6F.5080109@ucalgary.ca> Message-ID: <4A55D9A3.8060905@ipb-halle.de> Hi, like yesterday, I can't start Biomoby services from Dashboard if the service invocation is set to "ask registry where service is and call it". "Calling the service" is displayed, but the service seems not to answer this way. If I switch to "use service's usual endpoint", the invocation works fine and the service returns proper results (service is MassBank_unique_DBLinks). In addition, Taverna (T2.1 b1) is currently not able to provide the default Biomoby registry as available service. This causes my workflows that contain Biomoby services not to load at all inside Taverna. It worked for a short time this morning (both Biomoby and Taverna), but it is now the same odd thing as yesterday. Does anyone encounter this too? Regards, Michael Paul Gordon wrote: > A bit of trivia: Moby Central has been up for 398 days straight! > > > uptime > 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 > > > Sebastien Carrere wrote: >> Now it's back ! >> ... don't know what happened >> >> Sebastien >> >> >> Paul Gordon wrote: >>> ?a marche pour moi...and the university's outside connection seems >>> okay. >>> >>> Sebastien Carrere wrote: >>>> Bonjour a tous, >>>> >>>> Does Moby public server down ? >>>> >>>> I cannot access hit from Toulouse (France): no answer to "ping >>>> moby.ucalgary.ca" >>>> I think it's down for approximatively 4hours ... >>>> >>>> Sebastien >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From Sebastien.Carrere at toulouse.inra.fr Thu Jul 9 08:39:24 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 09 Jul 2009 14:39:24 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A55D9A3.8060905@ipb-halle.de> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> <4A54BD6F.5080109@ucalgary.ca> <4A55D9A3.8060905@ipb-halle.de> Message-ID: <4A55E4FC.4040608@toulouse.inra.fr> I had again public registry access problem this night (at 4 a.m. (GMT+1)). But now it's ok. Sebastien Michael Gerlich wrote: > Hi, > > like yesterday, I can't start Biomoby services from Dashboard if the > service invocation is set to "ask registry where service is and call > it". "Calling the service" is displayed, but the service seems not to > answer this way. > > If I switch to "use service's usual endpoint", the invocation works > fine and the service returns proper results (service is > MassBank_unique_DBLinks). > > In addition, Taverna (T2.1 b1) is currently not able to provide the > default Biomoby registry as available service. This causes my > workflows that contain Biomoby services not to load at all inside > Taverna. > > It worked for a short time this morning (both Biomoby and Taverna), > but it is now the same odd thing as yesterday. > > Does anyone encounter this too? > > Regards, > Michael > > > Paul Gordon wrote: >> A bit of trivia: Moby Central has been up for 398 days straight! >> >> > uptime >> 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 >> >> >> Sebastien Carrere wrote: >>> Now it's back ! >>> ... don't know what happened >>> >>> Sebastien >>> >>> >>> Paul Gordon wrote: >>>> ?a marche pour moi...and the university's outside connection seems >>>> okay. >>>> >>>> Sebastien Carrere wrote: >>>>> Bonjour a tous, >>>>> >>>>> Does Moby public server down ? >>>>> >>>>> I cannot access hit from Toulouse (France): no answer to "ping >>>>> moby.ucalgary.ca" >>>>> I think it's down for approximatively 4hours ... >>>>> >>>>> Sebastien >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From mgerlich at ipb-halle.de Thu Jul 9 08:52:33 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 09 Jul 2009 14:52:33 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A55D9A3.8060905@ipb-halle.de> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> <4A54BD6F.5080109@ucalgary.ca> <4A55D9A3.8060905@ipb-halle.de> Message-ID: <4A55E811.6090305@ipb-halle.de> Hmm, its working again (hopefully lasting more than one day...) Michael Michael Gerlich wrote: > Hi, > > like yesterday, I can't start Biomoby services from Dashboard if the > service invocation is set to "ask registry where service is and call > it". "Calling the service" is displayed, but the service seems not to > answer this way. > > If I switch to "use service's usual endpoint", the invocation works > fine and the service returns proper results (service is > MassBank_unique_DBLinks). > > In addition, Taverna (T2.1 b1) is currently not able to provide the > default Biomoby registry as available service. This causes my > workflows that contain Biomoby services not to load at all inside > Taverna. > > It worked for a short time this morning (both Biomoby and Taverna), > but it is now the same odd thing as yesterday. > > Does anyone encounter this too? > > Regards, > Michael > > > Paul Gordon wrote: >> A bit of trivia: Moby Central has been up for 398 days straight! >> >> > uptime >> 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 >> >> >> Sebastien Carrere wrote: >>> Now it's back ! >>> ... don't know what happened >>> >>> Sebastien >>> >>> >>> Paul Gordon wrote: >>>> ?a marche pour moi...and the university's outside connection seems >>>> okay. >>>> >>>> Sebastien Carrere wrote: >>>>> Bonjour a tous, >>>>> >>>>> Does Moby public server down ? >>>>> >>>>> I cannot access hit from Toulouse (France): no answer to "ping >>>>> moby.ucalgary.ca" >>>>> I think it's down for approximatively 4hours ... >>>>> >>>>> Sebastien >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From edward.kawas at gmail.com Fri Jul 10 17:22:35 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 10 Jul 2009 14:22:35 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: <4A54037F.9070501@bsc.es> References: <4A54037F.9070501@bsc.es> Message-ID: <4a57b120.2a528c0a.45d1.ffff9feb@mx.google.com> Hello Moby'ers! I recently ran a patched version of the registry on a virtual machine. The patch basically was to fix this inconsistency and look to see what no longer works. The list of broken things is large, but there is good news too! Only a handful of Classes/Modules needed to be fixed! In CentralImpl, the method createDataTypeFromXML() broke because it is looking for relationshipType.endswith('isa'). In order to be consistent with the XML returned from other registry calls, the relationshipType is now a fully capitalized "ISA". This is easy to fix, but everyone that uses this one function needs to be aware that once the registry goes consistent, a few things will break (Taverna and MoSeS generators, just to name a few). In Perl MoSeS, the fix is similar to that in jMoby. I guess the question is, should we fix this (is being consistent more important than breaking a bunch of Biomoby client software) and if so, how long shall we give people to update their software before deploying the fix on mobycentral? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-07-09 7:25 PM To: Core developer announcements Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral Hello, Trying to optimize a little bit my MobyCentral API I found a strange a thing: According the "specification" http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayload s.html#retrieveObjectDefinition There are two ways to get the relationships for an object: first way is to get Relationships directly (through "Relationships" operation): Output: [ OntologyTerm | OntologyTerm ] ... ... This one I used to use... But there is another way using "retrieveObjectDefinition" method: Output: ObjectClassName ExistingObjectType ... your.URI.here owner at their.address.com The problem is that instead of [relationshipType="RelationshipOntologyTerm"] it returns lsid!!! Here is the output: Zip _Encoded inb.bsc.es romina.royo at bsc.es Object String String As far as I understand from the specification it should be: Could someone clarify please... Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Jul 13 11:02:17 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Jul 2009 08:02:17 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4E4AD6.8090202@bsc.es> References: <4A4E4AD6.8090202@bsc.es> Message-ID: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> Hi Dmitry, Could you send me a wsdl document for any 2 doc/lit services? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-03-09 11:16 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] invoking document literal services > > Excuse me if I sound daft.. but what is the point of making a > Document/literal service if you end up having to use xsd:any and a > normal Moby message? (Or do we have an XSD schema for Moby > messages..?) > I agree with you, it is not my fault that moby is incompatible with schema... Moby message can be divided into two parts, auxiliary one and an ontology one. First part is schema compatible, another one no. > You might with doc/literal be able to support a more up-to-date > clients like Axis2 and CXF for Java, but if it's just a wrapper for > the 'real' Moby message inside that needs to be parsed manually or > using moby libraries.. what is the big gain? :-) > Not exactly. The message like: ************************************************** AGHFJHGDKHGJKADGHJGDJH ************************************************** CAN be parsed using JAX-WS standard methods. I have an alternative BioMoby Java API based on JAX-WS/JAXB and using it I CAN provide STANDARD doc-lit BioMoby services: ************************************************** @WebService() @SOAPBinding(style=SOAPBinding.Style.DOCUMENT, use=SOAPBinding.Use.LITERAL, parameterStyle=SOAPBinding.ParameterStyle.BARE) //@XmlSeeAlso({AminoAcidSequence.class, MobyString.class}) public class MobyDocWebService { @WebResult(name="MOBY", targetNamespace="http://www.biomoby.org/moby") public MobyMessage runMyService(@WebParam(name="MOBY", targetNamespace="http://www.biomoby.org/moby", mode = WebParam.Mode.IN) MobyMessage msg) { return msg; // just to return back the message } } ************************************************** Another project I have done is to automagically generate a JAX-WS proxy application (*.war) for any (including asynchronous) biomoby services. Such a proxy expose biomoby services as WSDL doc-lit ones (+WSA for asynchrony) with preserving all the moby ontology. Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jul 14 00:24:04 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 13 Jul 2009 21:24:04 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> References: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> Message-ID: <4A5C0864.3090909@bsc.es> Hello, Strange thing. I got a main that my message is waiting moderation... Anyway I put WSDLs along with the example application at: http://inb.bsc.es/documents/wsdl/ Cheers, Dmitry From edward.kawas at gmail.com Mon Jul 13 15:42:24 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Jul 2009 12:42:24 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A5C0864.3090909@bsc.es> References: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> <4A5C0864.3090909@bsc.es> Message-ID: <4a5b8e2a.25bb720a.3788.ffffca33@mx.google.com> Thank you. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-13-09 9:24 PM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] invoking document literal services Hello, Strange thing. I got a main that my message is waiting moderation... Anyway I put WSDLs along with the example application at: http://inb.bsc.es/documents/wsdl/ Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jul 14 00:14:58 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 13 Jul 2009 21:14:58 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> References: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> Message-ID: <4A5C0642.5050006@bsc.es> Hello Edward, Actually WSDLs would be very similar. They all have the same "BioMoby" part as a schema. A content of "Simple" is marked as "any". The WSDLs I send generated by JBoss 5.1 from the templates I just invented... (there is no code there). The service receives/returns MobyMessage object that is a part of my MobyCore API. "BioMoby" classes like MobyMessage, MobyContent, MobyData, etc. are JAXB annotated. Ontology generated classes are "JAXB compatible" that means that they are encoded/decoded by JAXB with a minor trick. Also note that because MobySimple contains "ANY" JAX-WS context has no knowledge about "ontology". You must specify classes the service uses using @SeeAlso attribute. There is no need to specify ALL the classes - JAXB will analyze the dependencies - for example if you specify @XmlSeeAlso({AminoAcidSequence.class}) it will infer all "fathers". All the classes that are unrecognized (by JAX-WS context) are converted into a special "AnyMobyObject". You can still work with this class (add/remove properties). Even more this class can be mixed with "ontology generated" ones. So it's possible that ontology generated class "A" contains "AnyMobyObject" that contains ontology generated class "B". I attach the *.war file with the services and the source code (also for the ontology datatypes). Your Sincerely, Dmitry -------------- next part -------------- A non-text attachment was scrubbed... Name: RunNCBIBlastp.wsdl Type: text/xml Size: 8187 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GetAminoAcidSequence.wsdl Type: text/xml Size: 8313 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BioMobyDocLitServices.war Type: application/octet-stream Size: 278332 bytes Desc: not available URL: From mgerlich at ipb-halle.de Tue Jul 14 03:26:27 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Tue, 14 Jul 2009 09:26:27 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? again Message-ID: <4A5C3323.9030609@ipb-halle.de> Hi, I'm encountering the same strange behavior as last week. Ping to ucalgary.ca works, but wget retrieval of http://moby.ucalgary.ca/moby/MOBY-Central.pl doesn't . Services that are invoked via Dashboard only work if they "use service's usual endpoint". According to this, also Taverna workflows relying on Biomoby services won't be loaded into Taverna. Could you check if something goes wrong inside the Biomoby Central registry (or anywhere near to it) ? Regards, Michael -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From edward.kawas at gmail.com Tue Jul 14 09:40:31 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 14 Jul 2009 06:40:31 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <4A5C3323.9030609@ipb-halle.de> References: <4A5C3323.9030609@ipb-halle.de> Message-ID: <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> Hi Michael, I didn't see anything obvious. The next time that this happens, can you try to load the following page (it is a cgi script) http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator and try to ping a group of services? If the page doesn't load let me know what kind of error are you getting (server error, network timeout, etc). Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: July-14-09 12:26 AM To: Core developer announcements Subject: [MOBY-dev] moby.ucalgary.ca down ? again Hi, I'm encountering the same strange behavior as last week. Ping to ucalgary.ca works, but wget retrieval of http://moby.ucalgary.ca/moby/MOBY-Central.pl doesn't . Services that are invoked via Dashboard only work if they "use service's usual endpoint". According to this, also Taverna workflows relying on Biomoby services won't be loaded into Taverna. Could you check if something goes wrong inside the Biomoby Central registry (or anywhere near to it) ? Regards, Michael -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From sneumann at ipb-halle.de Tue Jul 14 10:12:45 2009 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Tue, 14 Jul 2009 16:12:45 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> References: <4A5C3323.9030609@ipb-halle.de> <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> Message-ID: <1247580765.4362.31.camel@paddy> On Tue, 2009-07-14 at 06:40 -0700, Edward Kawas wrote: > group of services? If the page doesn't load let me know what kind of error > are you getting (server error, network timeout, etc). Btw, I remember some discussions on the list about a more fault-tolerant (read: redundant) setup for Moby-central. Is anyone working on this ? Yours, Steffen From edward.kawas at gmail.com Tue Jul 14 10:26:55 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 14 Jul 2009 07:26:55 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <1247580765.4362.31.camel@paddy> References: <4A5C3323.9030609@ipb-halle.de> <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> <1247580765.4362.31.camel@paddy> Message-ID: <4a5c95b8.15bb720a.1338.ffff910f@mx.google.com> I think that we discussed mirroring (I believe Andreas played a big part here) and how we could create redundancy, but never got around to implementing redundancy. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Steffen Neumann Sent: July-14-09 7:13 AM To: Core developer announcements Subject: Re: [MOBY-dev] moby.ucalgary.ca down ? again On Tue, 2009-07-14 at 06:40 -0700, Edward Kawas wrote: > group of services? If the page doesn't load let me know what kind of error > are you getting (server error, network timeout, etc). Btw, I remember some discussions on the list about a more fault-tolerant (read: redundant) setup for Moby-central. Is anyone working on this ? Yours, Steffen _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Jul 14 11:31:31 2009 From: markw at illuminae.com (Mark) Date: Tue, 14 Jul 2009 08:31:31 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> References: <4A5C3323.9030609@ipb-halle.de> <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> Message-ID: > wget retrieval of > http://moby.ucalgary.ca/moby/MOBY-Central.pl doesn't . AFAIK a naked GET on MOBY Central shouldn't succeed even if the server is up... that script requires input, and will return an error (for me it is "unavailable") if you don't send it proper input. So... don't use that as your "acid test" :-) Like Eddie, I haven't noticed MOBY Central being unavailable (and I'm not local! MOBY Central is about 800km away from me!), and I've been hammering it pretty hard in the last week or so as I prepare for a MOBY workshop... I wonder why you're having problems accessing it? I checked with Paul, and we have something like 380 continuous days of up-time on that server!! (yay us!) ...??? I understand your frustration! ...but I can't figure out what the source of the problem is... Mark From edward.kawas at gmail.com Tue Jul 21 16:20:24 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 21 Jul 2009 13:20:24 -0700 Subject: [MOBY-dev] moses and jetty Message-ID: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> Hello All, I am wondering if anyone has ever gotten a moses generated service to work in Jetty? I am trying to get my services running with jetty, but I keep getting the msg: AN ERROR OCCURED DURING THE SERVICE EXECUTION: Class 'org.biomoby.shared.datatypes.MapDataTypes' was not found. It may indicate that you have not generated all Biomoby data types from a Biomoby registry. See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details. If you are a jMoby developer just type: ./build-dev.sh moses-datatypes. Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile. I figure something is missing from the classpath, but not sure why! In my webapp WEB-INF/lib directory I have the biomoby-datatypes.jar and this is the lib with the MapDataTypes class, right? Any ideas? Thanks, Eddie From martin.senger at gmail.com Thu Jul 23 03:36:21 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Jul 2009 15:36:21 +0800 Subject: [MOBY-dev] moses and jetty In-Reply-To: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> References: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> Message-ID: <4d93f07c0907230036s5771cdaan6ed2202c16fe7cb4@mail.gmail.com> > In my > webapp WEB-INF/lib directory I have the biomoby-datatypes.jar and this is > the lib with the MapDataTypes class, right? Yes. > Any ideas? > No :-( M. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Thu Jul 23 09:02:39 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 23 Jul 2009 06:02:39 -0700 Subject: [MOBY-dev] moses and jetty In-Reply-To: <4d93f07c0907230036s5771cdaan6ed2202c16fe7cb4@mail.gmail.com> References: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> <4d93f07c0907230036s5771cdaan6ed2202c16fe7cb4@mail.gmail.com> Message-ID: <4a685f74.21d7720a.312b.3c7a@mx.google.com> Thanks Martin. I got it working on windows, but for some reason it doesn't work on linux. I am still trying to get this working and will update the list once I figure it out. Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: July-23-09 12:36 AM To: Core developer announcements Subject: Re: [MOBY-dev] moses and jetty > In my > webapp WEB-INF/lib directory I have the biomoby-datatypes.jar and this is > the lib with the MapDataTypes class, right? Yes. > Any ideas? > No :-( M. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From pmr at ebi.ac.uk Mon Jul 27 04:55:43 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Jul 2009 09:55:43 +0100 Subject: [MOBY-dev] Open-bio cross-project issues In-Reply-To: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> References: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> Message-ID: <4A6D6B8F.9060108@ebi.ac.uk> Peter C. wrote (to bioperl-l, biopython-l, emboss-dev): > Hi all, > > Peter Rice kindly said he will look into an OBF cross project mailing > list, but in the meantime this has been cross posted to the Biopython, > BioPerl, and EMBOSS development lists. There is a list already for this purpose - open-bio-l I think we will also need a cross-project wiki space on the OBF site. Is there something already used by other projects or should we set something up? I am cross-posting this to other OBF project lists to encourage developers interested in combining efforts to address common problems. This started with FASTQ short read formats, and open-bio-l (a low volume list) has also seen discussion of common test data sets. Please sign up to open-bio-l (if you are not there already) and post suggestions for cross-project issues there. The list subscription page is: http://lists.open-bio.org/mailman/listinfo/open-bio-l Please feel free to forward this to any other projects I may have missed (I picked the obvious addresses from the list.open-bio-org server) regards, Peter Rice From edward.kawas at gmail.com Thu Jul 2 14:37:20 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Jul 2009 07:37:20 -0700 Subject: [MOBY-dev] invoking document literal services Message-ID: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> Hello All, Since Biomoby supports doc/lit services, in theory, I was wondering if anyone had created a doc/lit service and if so, how do you call it? I want to ensure that the Taverna plugin can handle the various flavours of Biomoby services and right now, it is missing doc/lit support. Any pointers on calling these services, pointers to example code or pointers to actual services would be greatly appreciated. Thanks, Eddie From dmitry.repchevski at bsc.es Fri Jul 3 01:17:24 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 02 Jul 2009 18:17:24 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> References: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> Message-ID: <4A4D5C24.7010205@bsc.es> Hello Edward, As far as I know BioMoby doesn't support doc/lit services yet. I've risen this question several times and the answer was always the same "we are working on it".. After BioHackaton Mark contracted a developer (Jason Stewart) to implement it in Perl. Actually, we reach an agreement how such a services would look like. Can't find it on moby list :-( You can read our conversation here: https://www.inab.org/wiki/images/9/96/Dmitry-mail.pdf Actually in INB meeting last November we agreed to support it (and I have implemented it in my library). The main problem is that we still have no information about Perl implementation. Unless it is implemented in Perl I doubt someone will provide such services... Cheers, Dmitry From edward.kawas at gmail.com Thu Jul 2 17:01:27 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 2 Jul 2009 10:01:27 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4D5C24.7010205@bsc.es> References: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> <4A4D5C24.7010205@bsc.es> Message-ID: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> Hi Dmitry, I guess by support, I meant the ability to register doc/lit services with the registry. I wonder if http://soap-wsdl.sourceforge.net/ would be the way to go in implementing doc/lit in perl. Any pointers from you would be appreciated. I also stumbled upon [1] for serving doc/lit services (ugly hack that apparently works). Thanks, Eddie [1] http://www.perlmonks.org/?node_id=645150 -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-02-09 6:17 PM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] invoking document literal services Hello Edward, As far as I know BioMoby doesn't support doc/lit services yet. I've risen this question several times and the answer was always the same "we are working on it".. After BioHackaton Mark contracted a developer (Jason Stewart) to implement it in Perl. Actually, we reach an agreement how such a services would look like. Can't find it on moby list :-( You can read our conversation here: https://www.inab.org/wiki/images/9/96/Dmitry-mail.pdf Actually in INB meeting last November we agreed to support it (and I have implemented it in my library). The main problem is that we still have no information about Perl implementation. Unless it is implemented in Perl I doubt someone will provide such services... Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jul 2 16:49:48 2009 From: markw at illuminae.com (Mark) Date: Thu, 02 Jul 2009 09:49:48 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4D5C24.7010205@bsc.es> References: <4a4cc62a.1ed7720a.4d79.ffffd5df@mx.google.com> <4A4D5C24.7010205@bsc.es> Message-ID: As far as I know, Jason is still "working on it" :-) the problem is quite deep - the SOAP libraries in Perl don't support doc-lit, and the problem may even go deeper than that... M On Thu, 02 Jul 2009 18:17:24 -0700, Dmitry Repchevsky wrote: > Hello Edward, > > As far as I know BioMoby doesn't support doc/lit services yet. > I've risen this question several times and the answer was always the > same "we are working on it".. > > After BioHackaton Mark contracted a developer (Jason Stewart) to > implement it in Perl. > Actually, we reach an agreement how such a services would look like. > Can't find it on moby list :-( > You can read our conversation here: > https://www.inab.org/wiki/images/9/96/Dmitry-mail.pdf > > Actually in INB meeting last November we agreed to support it (and I > have implemented it in my library). > The main problem is that we still have no information about Perl > implementation. > Unless it is implemented in Perl I doubt someone will provide such > services... > > Cheers, > > Dmitry > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Fri Jul 3 02:27:35 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 02 Jul 2009 19:27:35 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> References: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> Message-ID: <4A4D6C97.9030606@bsc.es> Hello, > I guess by support, I meant the ability to register doc/lit services withthe registry. > Nobody would prevent you from registering "doc-literal" service. The problem is what does it mean... The SOAP-WSDL project looks promising, but they still far away even from [XML schema support ("minimal conformant")]. Anyway I think it's possible to use for the moby. I mean that BioMoby is XML Schema incompatible, so there is no way to use it "right way". My proposal (and Jason agreed with me) was to use Moby message "as is" inside a SOAP BODY. This way only "moby" part of schema is needed (the ontology objects defined as "any"). The implementation is simple and taking into account that all the "moby" artifacts are the same for any service, we do not any schema parser at all... Meanwhile, BioMoby is moving to err... unexplored direction, I'm moving completely to WSDL doc/lit services based on BioMoby ontology. My last breakthrough was asynchrony based on WS-Addressing. Dmitry. P.S. I just realized that you are working with Taverna. I have no any experience with it, and there is almost no documentation... :-( I created a java component (tree) to encode/decode/edit XML messages based on XML Schema and would like to convert it to taverna plugin (wsdl activity). From soiland-reyes at cs.manchester.ac.uk Fri Jul 3 17:54:13 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 3 Jul 2009 18:54:13 +0100 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4D6C97.9030606@bsc.es> References: <4a4ce7f2.22ba720a.23f4.ffffe4ce@mx.google.com> <4A4D6C97.9030606@bsc.es> Message-ID: On Fri, Jul 3, 2009 at 03:27, Dmitry Repchevsky wrote: > My proposal (and Jason agreed with me) was to use Moby message "as is" > inside a SOAP BODY. > This way only "moby" part of schema is needed (the ontology objects defined > as "any"). Excuse me if I sound daft.. but what is the point of making a Document/literal service if you end up having to use xsd:any and a normal Moby message? (Or do we have an XSD schema for Moby messages..?) You might with doc/literal be able to support a more up-to-date clients like Axis2 and CXF for Java, but if it's just a wrapper for the 'real' Moby message inside that needs to be parsed manually or using moby libraries.. what is the big gain? :-) (Not to say I don't recommend using doc/literal instead of rpc/whatever! :-) Just wondering what the benefits would be..) -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From dmitry.repchevski at bsc.es Fri Jul 3 18:15:50 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 03 Jul 2009 11:15:50 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: References: Message-ID: <4A4E4AD6.8090202@bsc.es> > > Excuse me if I sound daft.. but what is the point of making a > Document/literal service if you end up having to use xsd:any and a > normal Moby message? (Or do we have an XSD schema for Moby > messages..?) > I agree with you, it is not my fault that moby is incompatible with schema... Moby message can be divided into two parts, auxiliary one and an ontology one. First part is schema compatible, another one no. > You might with doc/literal be able to support a more up-to-date > clients like Axis2 and CXF for Java, but if it's just a wrapper for > the 'real' Moby message inside that needs to be parsed manually or > using moby libraries.. what is the big gain? :-) > Not exactly. The message like: ************************************************** AGHFJHGDKHGJKADGHJGDJH ************************************************** CAN be parsed using JAX-WS standard methods. I have an alternative BioMoby Java API based on JAX-WS/JAXB and using it I CAN provide STANDARD doc-lit BioMoby services: ************************************************** @WebService() @SOAPBinding(style=SOAPBinding.Style.DOCUMENT, use=SOAPBinding.Use.LITERAL, parameterStyle=SOAPBinding.ParameterStyle.BARE) //@XmlSeeAlso({AminoAcidSequence.class, MobyString.class}) public class MobyDocWebService { @WebResult(name="MOBY", targetNamespace="http://www.biomoby.org/moby") public MobyMessage runMyService(@WebParam(name="MOBY", targetNamespace="http://www.biomoby.org/moby", mode = WebParam.Mode.IN) MobyMessage msg) { return msg; // just to return back the message } } ************************************************** Another project I have done is to automagically generate a JAX-WS proxy application (*.war) for any (including asynchronous) biomoby services. Such a proxy expose biomoby services as WSDL doc-lit ones (+WSA for asynchrony) with preserving all the moby ontology. Cheers, Dmitry From gordonp at ucalgary.ca Sat Jul 4 03:44:20 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 03 Jul 2009 21:44:20 -0600 Subject: [MOBY-dev] Quick Question on Moby Usage in Europe In-Reply-To: <4A4E4AD6.8090202@bsc.es> References: <4A4E4AD6.8090202@bsc.es> Message-ID: <4A4ED014.90204@ucalgary.ca> Hi all, I'm giving a Moby presentation in a few weeks, and I'd like to include a map showing Moby usage in Europe. I know I can get info from the registry, but was hoping that the Europeans among could send me a quick message with: 1) the name of your institution, 2) a one line description of the types of services you offer (from a biologist's perspective), and 3) the target audience for which you created your services, if outside your institution. Any help you can provide is greatly appreciated! Thanks, Paul From dmitry.repchevski at bsc.es Wed Jul 8 02:25:03 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 07 Jul 2009 19:25:03 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral Message-ID: <4A54037F.9070501@bsc.es> Hello, Trying to optimize a little bit my MobyCentral API I found a strange a thing: According the "specification" http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayloads.html#retrieveObjectDefinition There are two ways to get the relationships for an object: first way is to get Relationships directly (through "Relationships" operation): Output: [ OntologyTerm | OntologyTerm ] ... ... This one I used to use... But there is another way using "retrieveObjectDefinition" method: Output: ObjectClassName ExistingObjectType ... your.URI.here owner at their.address.com The problem is that instead of [relationshipType="RelationshipOntologyTerm"] it returns lsid!!! Here is the output: Zip_Encoded inb.bsc.es romina.royo at bsc.es Object String String As far as I understand from the specification it should be: Could someone clarify please... Dmitry From markw at illuminae.com Tue Jul 7 17:44:14 2009 From: markw at illuminae.com (Mark) Date: Tue, 07 Jul 2009 10:44:14 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: <4A54037F.9070501@bsc.es> References: <4A54037F.9070501@bsc.es> Message-ID: Hi Dmitry, It's almost certainly a bug. I wont be able to fix it for a few days, though, as I've got other deadlines to meet this week. If you want to fix it yourself and commit (or send me) the fix that would be fine... but be very very careful because I know that those attributes are often used by other methods, so it may be that other routines are now coded to compensate for this bug! :-P otherwise, give me a week or so and I'll fix it myself. Mark On Tue, 07 Jul 2009 19:25:03 -0700, Dmitry Repchevsky wrote: > Hello, > > Trying to optimize a little bit my MobyCentral API I found a strange a > thing: > > According the "specification" > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayloads.html#retrieveObjectDefinition > > There are two ways to get the relationships for an object: > > first way is to get Relationships directly (through "Relationships" > operation): > > Output: > > > lsid='urn:lsid:authority.uri:namespace:id'> > [ articleName='foo'>OntologyTerm | > OntologyTerm ] > ... > > ... > > > This one I used to use... > > But there is another way using "retrieveObjectDefinition" method: > > Output: > > > lsid='urn:lsid:authority.uri:namespace:id'>ObjectClassName > human readable description > of data type]]> > > lsid='urn:lsid:authority.uri:namespace:id'> > lsid='urn:lsid:authority.uri:namespace:id'>ExistingObjectType > > ... > your.URI.here > > owner at their.address.com > > > > The problem is that instead of > [relationshipType="RelationshipOntologyTerm"] it returns lsid!!! > > Here is the output: > > > lsid='urn:lsid:biomoby.org:objectclass:Zip_Encoded:2007-11-16T11-34-07Z'>Zip_Encoded > > inb.bsc.es > romina.royo at bsc.es > > relationshipType='urn:lsid:biomoby.org:objectrelation:isa'> > lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z'>Object > > relationshipType='urn:lsid:biomoby.org:objectrelation:hasa'> > lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String > lsid='urn:lsid:biomoby.org:objectclass:String:2001-09-21T16-00-00Z'>String > > > > As far as I understand from the specification it should be: > > lsid='urn:lsid:biomoby.org:objectrelation:isa'> > > Could someone clarify please... > > Dmitry > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Wed Jul 8 02:56:31 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 07 Jul 2009 19:56:31 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: Message-ID: <4A540ADF.7040900@bsc.es> Hello Mark, I am not that skilled in Perl... :-( But I will ask INB people if they can do this... Anyway it's not critical... Cheers, Dmitry From markw at illuminae.com Tue Jul 7 18:14:38 2009 From: markw at illuminae.com (Mark) Date: Tue, 07 Jul 2009 11:14:38 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: <4A540ADF.7040900@bsc.es> References: <4A540ADF.7040900@bsc.es> Message-ID: On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky wrote: > I am not that skilled in Perl... :-( clearly, neither am I ;-) LOL! Mark From edward.kawas at gmail.com Tue Jul 7 22:31:51 2009 From: edward.kawas at gmail.com (Eddie Kawas) Date: Tue, 7 Jul 2009 15:31:51 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: <4A540ADF.7040900@bsc.es> Message-ID: According to the perldoc, the subroutine does what it says it should do ( http://search.cpan.org/dist/MOBY/lib/MOBY/Central.pm#retrieveObjectDefinition). So I think that the api doc has a misprint in it. Let me know how you devs want to proceed (either update the api doc or update the perldoc for the sub and update the sub). I have a feeling that all software in moby expects it the way that it is and so updating the api doc might be better. Eddie On Tue, Jul 7, 2009 at 11:14 AM, Mark wrote: > On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky < > dmitry.repchevski at bsc.es> wrote: > > > I am not that skilled in Perl... :-( >> > > > clearly, neither am I ;-) > > LOL! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From markw at illuminae.com Tue Jul 7 22:42:08 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Tue, 7 Jul 2009 22:42:08 +0000 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: <4A540ADF.7040900@bsc.es> Message-ID: <149898153-1247006630-cardhu_decombobulator_blackberry.rim.net-348097757-@bxe1266.bisx.prod.on.blackberry> I guess the important thing is, as Dmitry says, to check for *consistancy*. If this is the only routine that returns an LSID as the value of that attribute, then we need to fix the code. If all instances of that attribute contain an LSID, then we need to fix the doc. I simply don't recall which is which... Though my "instincts" tell me that I wrote the code with the intent to return an LSID in all cases... So I think the code is correct and the doc is wrong... I think! M On the Road! -----Original Message----- From: Eddie Kawas Date: Tue, 7 Jul 2009 15:31:51 To: Core developer announcements Subject: Re: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral According to the perldoc, the subroutine does what it says it should do ( http://search.cpan.org/dist/MOBY/lib/MOBY/Central.pm#retrieveObjectDefinition). So I think that the api doc has a misprint in it. Let me know how you devs want to proceed (either update the api doc or update the perldoc for the sub and update the sub). I have a feeling that all software in moby expects it the way that it is and so updating the api doc might be better. Eddie On Tue, Jul 7, 2009 at 11:14 AM, Mark wrote: > On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky < > dmitry.repchevski at bsc.es> wrote: > > > I am not that skilled in Perl... :-( >> > > > clearly, neither am I ;-) > > LOL! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Jul 7 22:43:31 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Tue, 7 Jul 2009 22:43:31 +0000 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: References: <4A540ADF.7040900@bsc.es> Message-ID: <368069246-1247006713-cardhu_decombobulator_blackberry.rim.net-1534456682-@bxe1266.bisx.prod.on.blackberry> We should also just do a quick test to make sure that those LSID's are still resolvable by the standard LSID resolution stack... With the various moves to new servers we may have missed something... M On the Road! -----Original Message----- From: Eddie Kawas Date: Tue, 7 Jul 2009 15:31:51 To: Core developer announcements Subject: Re: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral According to the perldoc, the subroutine does what it says it should do ( http://search.cpan.org/dist/MOBY/lib/MOBY/Central.pm#retrieveObjectDefinition). So I think that the api doc has a misprint in it. Let me know how you devs want to proceed (either update the api doc or update the perldoc for the sub and update the sub). I have a feeling that all software in moby expects it the way that it is and so updating the api doc might be better. Eddie On Tue, Jul 7, 2009 at 11:14 AM, Mark wrote: > On Tue, 07 Jul 2009 19:56:31 -0700, Dmitry Repchevsky < > dmitry.repchevski at bsc.es> wrote: > > > I am not that skilled in Perl... :-( >> > > > clearly, neither am I ;-) > > LOL! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Wed Jul 8 07:15:21 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 08 Jul 2009 09:15:21 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? Message-ID: <4A544789.1050804@toulouse.inra.fr> Bonjour a tous, Does Moby public server down ? I cannot access hit from Toulouse (France): no answer to "ping moby.ucalgary.ca" I think it's down for approximatively 4hours ... Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Jul 8 14:35:31 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 08 Jul 2009 08:35:31 -0600 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A544789.1050804@toulouse.inra.fr> References: <4A544789.1050804@toulouse.inra.fr> Message-ID: <4A54AEB3.2060205@ucalgary.ca> ?a marche pour moi...and the university's outside connection seems okay. Sebastien Carrere wrote: > Bonjour a tous, > > Does Moby public server down ? > > I cannot access hit from Toulouse (France): no answer to "ping > moby.ucalgary.ca" > I think it's down for approximatively 4hours ... > > Sebastien > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Sebastien.Carrere at toulouse.inra.fr Wed Jul 8 15:17:52 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 08 Jul 2009 17:17:52 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A54AEB3.2060205@ucalgary.ca> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> Message-ID: <4A54B8A0.4090202@toulouse.inra.fr> Now it's back ! ... don't know what happened Sebastien Paul Gordon wrote: > ?a marche pour moi...and the university's outside connection seems okay. > > Sebastien Carrere wrote: >> Bonjour a tous, >> >> Does Moby public server down ? >> >> I cannot access hit from Toulouse (France): no answer to "ping >> moby.ucalgary.ca" >> I think it's down for approximatively 4hours ... >> >> Sebastien >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From gordonp at ucalgary.ca Wed Jul 8 15:38:23 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 08 Jul 2009 09:38:23 -0600 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A54B8A0.4090202@toulouse.inra.fr> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> Message-ID: <4A54BD6F.5080109@ucalgary.ca> A bit of trivia: Moby Central has been up for 398 days straight! > uptime 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 Sebastien Carrere wrote: > Now it's back ! > ... don't know what happened > > Sebastien > > > Paul Gordon wrote: >> ?a marche pour moi...and the university's outside connection seems okay. >> >> Sebastien Carrere wrote: >>> Bonjour a tous, >>> >>> Does Moby public server down ? >>> >>> I cannot access hit from Toulouse (France): no answer to "ping >>> moby.ucalgary.ca" >>> I think it's down for approximatively 4hours ... >>> >>> Sebastien >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From mgerlich at ipb-halle.de Thu Jul 9 11:50:59 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 09 Jul 2009 13:50:59 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A54BD6F.5080109@ucalgary.ca> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> <4A54BD6F.5080109@ucalgary.ca> Message-ID: <4A55D9A3.8060905@ipb-halle.de> Hi, like yesterday, I can't start Biomoby services from Dashboard if the service invocation is set to "ask registry where service is and call it". "Calling the service" is displayed, but the service seems not to answer this way. If I switch to "use service's usual endpoint", the invocation works fine and the service returns proper results (service is MassBank_unique_DBLinks). In addition, Taverna (T2.1 b1) is currently not able to provide the default Biomoby registry as available service. This causes my workflows that contain Biomoby services not to load at all inside Taverna. It worked for a short time this morning (both Biomoby and Taverna), but it is now the same odd thing as yesterday. Does anyone encounter this too? Regards, Michael Paul Gordon wrote: > A bit of trivia: Moby Central has been up for 398 days straight! > > > uptime > 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 > > > Sebastien Carrere wrote: >> Now it's back ! >> ... don't know what happened >> >> Sebastien >> >> >> Paul Gordon wrote: >>> ?a marche pour moi...and the university's outside connection seems >>> okay. >>> >>> Sebastien Carrere wrote: >>>> Bonjour a tous, >>>> >>>> Does Moby public server down ? >>>> >>>> I cannot access hit from Toulouse (France): no answer to "ping >>>> moby.ucalgary.ca" >>>> I think it's down for approximatively 4hours ... >>>> >>>> Sebastien >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From Sebastien.Carrere at toulouse.inra.fr Thu Jul 9 12:39:24 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 09 Jul 2009 14:39:24 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A55D9A3.8060905@ipb-halle.de> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> <4A54BD6F.5080109@ucalgary.ca> <4A55D9A3.8060905@ipb-halle.de> Message-ID: <4A55E4FC.4040608@toulouse.inra.fr> I had again public registry access problem this night (at 4 a.m. (GMT+1)). But now it's ok. Sebastien Michael Gerlich wrote: > Hi, > > like yesterday, I can't start Biomoby services from Dashboard if the > service invocation is set to "ask registry where service is and call > it". "Calling the service" is displayed, but the service seems not to > answer this way. > > If I switch to "use service's usual endpoint", the invocation works > fine and the service returns proper results (service is > MassBank_unique_DBLinks). > > In addition, Taverna (T2.1 b1) is currently not able to provide the > default Biomoby registry as available service. This causes my > workflows that contain Biomoby services not to load at all inside > Taverna. > > It worked for a short time this morning (both Biomoby and Taverna), > but it is now the same odd thing as yesterday. > > Does anyone encounter this too? > > Regards, > Michael > > > Paul Gordon wrote: >> A bit of trivia: Moby Central has been up for 398 days straight! >> >> > uptime >> 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 >> >> >> Sebastien Carrere wrote: >>> Now it's back ! >>> ... don't know what happened >>> >>> Sebastien >>> >>> >>> Paul Gordon wrote: >>>> ?a marche pour moi...and the university's outside connection seems >>>> okay. >>>> >>>> Sebastien Carrere wrote: >>>>> Bonjour a tous, >>>>> >>>>> Does Moby public server down ? >>>>> >>>>> I cannot access hit from Toulouse (France): no answer to "ping >>>>> moby.ucalgary.ca" >>>>> I think it's down for approximatively 4hours ... >>>>> >>>>> Sebastien >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From mgerlich at ipb-halle.de Thu Jul 9 12:52:33 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Thu, 09 Jul 2009 14:52:33 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? In-Reply-To: <4A55D9A3.8060905@ipb-halle.de> References: <4A544789.1050804@toulouse.inra.fr> <4A54AEB3.2060205@ucalgary.ca> <4A54B8A0.4090202@toulouse.inra.fr> <4A54BD6F.5080109@ucalgary.ca> <4A55D9A3.8060905@ipb-halle.de> Message-ID: <4A55E811.6090305@ipb-halle.de> Hmm, its working again (hopefully lasting more than one day...) Michael Michael Gerlich wrote: > Hi, > > like yesterday, I can't start Biomoby services from Dashboard if the > service invocation is set to "ask registry where service is and call > it". "Calling the service" is displayed, but the service seems not to > answer this way. > > If I switch to "use service's usual endpoint", the invocation works > fine and the service returns proper results (service is > MassBank_unique_DBLinks). > > In addition, Taverna (T2.1 b1) is currently not able to provide the > default Biomoby registry as available service. This causes my > workflows that contain Biomoby services not to load at all inside > Taverna. > > It worked for a short time this morning (both Biomoby and Taverna), > but it is now the same odd thing as yesterday. > > Does anyone encounter this too? > > Regards, > Michael > > > Paul Gordon wrote: >> A bit of trivia: Moby Central has been up for 398 days straight! >> >> > uptime >> 9:37am up 398 day(s), 22:44, 1 user, load average: 0.01, 0.09, 0.13 >> >> >> Sebastien Carrere wrote: >>> Now it's back ! >>> ... don't know what happened >>> >>> Sebastien >>> >>> >>> Paul Gordon wrote: >>>> ?a marche pour moi...and the university's outside connection seems >>>> okay. >>>> >>>> Sebastien Carrere wrote: >>>>> Bonjour a tous, >>>>> >>>>> Does Moby public server down ? >>>>> >>>>> I cannot access hit from Toulouse (France): no answer to "ping >>>>> moby.ucalgary.ca" >>>>> I think it's down for approximatively 4hours ... >>>>> >>>>> Sebastien >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From edward.kawas at gmail.com Fri Jul 10 21:22:35 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 10 Jul 2009 14:22:35 -0700 Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral In-Reply-To: <4A54037F.9070501@bsc.es> References: <4A54037F.9070501@bsc.es> Message-ID: <4a57b120.2a528c0a.45d1.ffff9feb@mx.google.com> Hello Moby'ers! I recently ran a patched version of the registry on a virtual machine. The patch basically was to fix this inconsistency and look to see what no longer works. The list of broken things is large, but there is good news too! Only a handful of Classes/Modules needed to be fixed! In CentralImpl, the method createDataTypeFromXML() broke because it is looking for relationshipType.endswith('isa'). In order to be consistent with the XML returned from other registry calls, the relationshipType is now a fully capitalized "ISA". This is easy to fix, but everyone that uses this one function needs to be aware that once the registry goes consistent, a few things will break (Taverna and MoSeS generators, just to name a few). In Perl MoSeS, the fix is similar to that in jMoby. I guess the question is, should we fix this (is being consistent more important than breaking a bunch of Biomoby client software) and if so, how long shall we give people to update their software before deploying the fix on mobycentral? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-07-09 7:25 PM To: Core developer announcements Subject: [MOBY-dev] Strange inconsistence (bug?) in MobyCentral Hello, Trying to optimize a little bit my MobyCentral API I found a strange a thing: According the "specification" http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/XMLPayload s.html#retrieveObjectDefinition There are two ways to get the relationships for an object: first way is to get Relationships directly (through "Relationships" operation): Output: [ OntologyTerm | OntologyTerm ] ... ... This one I used to use... But there is another way using "retrieveObjectDefinition" method: Output: ObjectClassName ExistingObjectType ... your.URI.here owner at their.address.com The problem is that instead of [relationshipType="RelationshipOntologyTerm"] it returns lsid!!! Here is the output: Zip _Encoded inb.bsc.es romina.royo at bsc.es Object String String As far as I understand from the specification it should be: Could someone clarify please... Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Jul 13 15:02:17 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Jul 2009 08:02:17 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A4E4AD6.8090202@bsc.es> References: <4A4E4AD6.8090202@bsc.es> Message-ID: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> Hi Dmitry, Could you send me a wsdl document for any 2 doc/lit services? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-03-09 11:16 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] invoking document literal services > > Excuse me if I sound daft.. but what is the point of making a > Document/literal service if you end up having to use xsd:any and a > normal Moby message? (Or do we have an XSD schema for Moby > messages..?) > I agree with you, it is not my fault that moby is incompatible with schema... Moby message can be divided into two parts, auxiliary one and an ontology one. First part is schema compatible, another one no. > You might with doc/literal be able to support a more up-to-date > clients like Axis2 and CXF for Java, but if it's just a wrapper for > the 'real' Moby message inside that needs to be parsed manually or > using moby libraries.. what is the big gain? :-) > Not exactly. The message like: ************************************************** AGHFJHGDKHGJKADGHJGDJH ************************************************** CAN be parsed using JAX-WS standard methods. I have an alternative BioMoby Java API based on JAX-WS/JAXB and using it I CAN provide STANDARD doc-lit BioMoby services: ************************************************** @WebService() @SOAPBinding(style=SOAPBinding.Style.DOCUMENT, use=SOAPBinding.Use.LITERAL, parameterStyle=SOAPBinding.ParameterStyle.BARE) //@XmlSeeAlso({AminoAcidSequence.class, MobyString.class}) public class MobyDocWebService { @WebResult(name="MOBY", targetNamespace="http://www.biomoby.org/moby") public MobyMessage runMyService(@WebParam(name="MOBY", targetNamespace="http://www.biomoby.org/moby", mode = WebParam.Mode.IN) MobyMessage msg) { return msg; // just to return back the message } } ************************************************** Another project I have done is to automagically generate a JAX-WS proxy application (*.war) for any (including asynchronous) biomoby services. Such a proxy expose biomoby services as WSDL doc-lit ones (+WSA for asynchrony) with preserving all the moby ontology. Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jul 14 04:24:04 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 13 Jul 2009 21:24:04 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> References: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> Message-ID: <4A5C0864.3090909@bsc.es> Hello, Strange thing. I got a main that my message is waiting moderation... Anyway I put WSDLs along with the example application at: http://inb.bsc.es/documents/wsdl/ Cheers, Dmitry From edward.kawas at gmail.com Mon Jul 13 19:42:24 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Jul 2009 12:42:24 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4A5C0864.3090909@bsc.es> References: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> <4A5C0864.3090909@bsc.es> Message-ID: <4a5b8e2a.25bb720a.3788.ffffca33@mx.google.com> Thank you. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: July-13-09 9:24 PM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] invoking document literal services Hello, Strange thing. I got a main that my message is waiting moderation... Anyway I put WSDLs along with the example application at: http://inb.bsc.es/documents/wsdl/ Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jul 14 04:14:58 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 13 Jul 2009 21:14:58 -0700 Subject: [MOBY-dev] invoking document literal services In-Reply-To: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> References: <4a5b4c82.1ebc720a.12fb.ffffafca@mx.google.com> Message-ID: <4A5C0642.5050006@bsc.es> Hello Edward, Actually WSDLs would be very similar. They all have the same "BioMoby" part as a schema. A content of "Simple" is marked as "any". The WSDLs I send generated by JBoss 5.1 from the templates I just invented... (there is no code there). The service receives/returns MobyMessage object that is a part of my MobyCore API. "BioMoby" classes like MobyMessage, MobyContent, MobyData, etc. are JAXB annotated. Ontology generated classes are "JAXB compatible" that means that they are encoded/decoded by JAXB with a minor trick. Also note that because MobySimple contains "ANY" JAX-WS context has no knowledge about "ontology". You must specify classes the service uses using @SeeAlso attribute. There is no need to specify ALL the classes - JAXB will analyze the dependencies - for example if you specify @XmlSeeAlso({AminoAcidSequence.class}) it will infer all "fathers". All the classes that are unrecognized (by JAX-WS context) are converted into a special "AnyMobyObject". You can still work with this class (add/remove properties). Even more this class can be mixed with "ontology generated" ones. So it's possible that ontology generated class "A" contains "AnyMobyObject" that contains ontology generated class "B". I attach the *.war file with the services and the source code (also for the ontology datatypes). Your Sincerely, Dmitry -------------- next part -------------- A non-text attachment was scrubbed... Name: RunNCBIBlastp.wsdl Type: text/xml Size: 8187 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: GetAminoAcidSequence.wsdl Type: text/xml Size: 8313 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BioMobyDocLitServices.war Type: application/octet-stream Size: 278332 bytes Desc: not available URL: From mgerlich at ipb-halle.de Tue Jul 14 07:26:27 2009 From: mgerlich at ipb-halle.de (Michael Gerlich) Date: Tue, 14 Jul 2009 09:26:27 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? again Message-ID: <4A5C3323.9030609@ipb-halle.de> Hi, I'm encountering the same strange behavior as last week. Ping to ucalgary.ca works, but wget retrieval of http://moby.ucalgary.ca/moby/MOBY-Central.pl doesn't . Services that are invoked via Dashboard only work if they "use service's usual endpoint". According to this, also Taverna workflows relying on Biomoby services won't be loaded into Taverna. Could you check if something goes wrong inside the Biomoby Central registry (or anywhere near to it) ? Regards, Michael -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany From edward.kawas at gmail.com Tue Jul 14 13:40:31 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 14 Jul 2009 06:40:31 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <4A5C3323.9030609@ipb-halle.de> References: <4A5C3323.9030609@ipb-halle.de> Message-ID: <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> Hi Michael, I didn't see anything obvious. The next time that this happens, can you try to load the following page (it is a cgi script) http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator and try to ping a group of services? If the page doesn't load let me know what kind of error are you getting (server error, network timeout, etc). Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich Sent: July-14-09 12:26 AM To: Core developer announcements Subject: [MOBY-dev] moby.ucalgary.ca down ? again Hi, I'm encountering the same strange behavior as last week. Ping to ucalgary.ca works, but wget retrieval of http://moby.ucalgary.ca/moby/MOBY-Central.pl doesn't . Services that are invoked via Dashboard only work if they "use service's usual endpoint". According to this, also Taverna workflows relying on Biomoby services won't be loaded into Taverna. Could you check if something goes wrong inside the Biomoby Central registry (or anywhere near to it) ? Regards, Michael -- Michael Gerlich Group Bioinformatics & Mass Spectrometry Leibniz Institute of Plant Biochemistry 06120 Halle, Germany _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From sneumann at ipb-halle.de Tue Jul 14 14:12:45 2009 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Tue, 14 Jul 2009 16:12:45 +0200 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> References: <4A5C3323.9030609@ipb-halle.de> <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> Message-ID: <1247580765.4362.31.camel@paddy> On Tue, 2009-07-14 at 06:40 -0700, Edward Kawas wrote: > group of services? If the page doesn't load let me know what kind of error > are you getting (server error, network timeout, etc). Btw, I remember some discussions on the list about a more fault-tolerant (read: redundant) setup for Moby-central. Is anyone working on this ? Yours, Steffen From edward.kawas at gmail.com Tue Jul 14 14:26:55 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 14 Jul 2009 07:26:55 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <1247580765.4362.31.camel@paddy> References: <4A5C3323.9030609@ipb-halle.de> <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> <1247580765.4362.31.camel@paddy> Message-ID: <4a5c95b8.15bb720a.1338.ffff910f@mx.google.com> I think that we discussed mirroring (I believe Andreas played a big part here) and how we could create redundancy, but never got around to implementing redundancy. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Steffen Neumann Sent: July-14-09 7:13 AM To: Core developer announcements Subject: Re: [MOBY-dev] moby.ucalgary.ca down ? again On Tue, 2009-07-14 at 06:40 -0700, Edward Kawas wrote: > group of services? If the page doesn't load let me know what kind of error > are you getting (server error, network timeout, etc). Btw, I remember some discussions on the list about a more fault-tolerant (read: redundant) setup for Moby-central. Is anyone working on this ? Yours, Steffen _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Jul 14 15:31:31 2009 From: markw at illuminae.com (Mark) Date: Tue, 14 Jul 2009 08:31:31 -0700 Subject: [MOBY-dev] moby.ucalgary.ca down ? again In-Reply-To: <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> References: <4A5C3323.9030609@ipb-halle.de> <4a5c8ad8.06d6720a.47b6.ffff8bde@mx.google.com> Message-ID: > wget retrieval of > http://moby.ucalgary.ca/moby/MOBY-Central.pl doesn't . AFAIK a naked GET on MOBY Central shouldn't succeed even if the server is up... that script requires input, and will return an error (for me it is "unavailable") if you don't send it proper input. So... don't use that as your "acid test" :-) Like Eddie, I haven't noticed MOBY Central being unavailable (and I'm not local! MOBY Central is about 800km away from me!), and I've been hammering it pretty hard in the last week or so as I prepare for a MOBY workshop... I wonder why you're having problems accessing it? I checked with Paul, and we have something like 380 continuous days of up-time on that server!! (yay us!) ...??? I understand your frustration! ...but I can't figure out what the source of the problem is... Mark From edward.kawas at gmail.com Tue Jul 21 20:20:24 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 21 Jul 2009 13:20:24 -0700 Subject: [MOBY-dev] moses and jetty Message-ID: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> Hello All, I am wondering if anyone has ever gotten a moses generated service to work in Jetty? I am trying to get my services running with jetty, but I keep getting the msg: AN ERROR OCCURED DURING THE SERVICE EXECUTION: Class 'org.biomoby.shared.datatypes.MapDataTypes' was not found. It may indicate that you have not generated all Biomoby data types from a Biomoby registry. See http://www.biomoby.org/moby-live/Java/docs/Moses.html for details. If you are a jMoby developer just type: ./build-dev.sh moses-datatypes. Or perhaps, they just need to be compiled: ./build-dev.sh moses-compile. I figure something is missing from the classpath, but not sure why! In my webapp WEB-INF/lib directory I have the biomoby-datatypes.jar and this is the lib with the MapDataTypes class, right? Any ideas? Thanks, Eddie From martin.senger at gmail.com Thu Jul 23 07:36:21 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Jul 2009 15:36:21 +0800 Subject: [MOBY-dev] moses and jetty In-Reply-To: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> References: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> Message-ID: <4d93f07c0907230036s5771cdaan6ed2202c16fe7cb4@mail.gmail.com> > In my > webapp WEB-INF/lib directory I have the biomoby-datatypes.jar and this is > the lib with the MapDataTypes class, right? Yes. > Any ideas? > No :-( M. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Thu Jul 23 13:02:39 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 23 Jul 2009 06:02:39 -0700 Subject: [MOBY-dev] moses and jetty In-Reply-To: <4d93f07c0907230036s5771cdaan6ed2202c16fe7cb4@mail.gmail.com> References: <4a66230a.23bb720a.2d7c.28c4@mx.google.com> <4d93f07c0907230036s5771cdaan6ed2202c16fe7cb4@mail.gmail.com> Message-ID: <4a685f74.21d7720a.312b.3c7a@mx.google.com> Thanks Martin. I got it working on windows, but for some reason it doesn't work on linux. I am still trying to get this working and will update the list once I figure it out. Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: July-23-09 12:36 AM To: Core developer announcements Subject: Re: [MOBY-dev] moses and jetty > In my > webapp WEB-INF/lib directory I have the biomoby-datatypes.jar and this is > the lib with the MapDataTypes class, right? Yes. > Any ideas? > No :-( M. -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From pmr at ebi.ac.uk Mon Jul 27 08:55:43 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Jul 2009 09:55:43 +0100 Subject: [MOBY-dev] Open-bio cross-project issues In-Reply-To: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> References: <320fb6e00907240632h53600e73s63590a8deb4e8ffe@mail.gmail.com> Message-ID: <4A6D6B8F.9060108@ebi.ac.uk> Peter C. wrote (to bioperl-l, biopython-l, emboss-dev): > Hi all, > > Peter Rice kindly said he will look into an OBF cross project mailing > list, but in the meantime this has been cross posted to the Biopython, > BioPerl, and EMBOSS development lists. There is a list already for this purpose - open-bio-l I think we will also need a cross-project wiki space on the OBF site. Is there something already used by other projects or should we set something up? I am cross-posting this to other OBF project lists to encourage developers interested in combining efforts to address common problems. This started with FASTQ short read formats, and open-bio-l (a low volume list) has also seen discussion of common test data sets. Please sign up to open-bio-l (if you are not there already) and post suggestions for cross-project issues there. The list subscription page is: http://lists.open-bio.org/mailman/listinfo/open-bio-l Please feel free to forward this to any other projects I may have missed (I picked the obvious addresses from the list.open-bio-org server) regards, Peter Rice