From heese at mpiz-koeln.mpg.de Tue Apr 4 06:34:58 2006 From: heese at mpiz-koeln.mpg.de (heese at mpiz-koeln.mpg.de) Date: Tue, 4 Apr 2006 12:34:58 +0200 (CEST) Subject: [MOBY-dev] RDF file generation for test registry Message-ID: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi, these are 3 questions for Eddie, but the answers might be interesting for others, that's why I post it to the whole list. I'm quite new in the BioMoby business, so I hope my questions havn't been asked before (at least I didn't find anything). 1. Is there a page available equivalent to http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm to create/update an rdf document for services registered in the TestCentral at (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? 2. I registered a couple of services at the TestCentral the old way without giving a RDF signature URL. Now I wanted to deregister them the old way but it failed since you generated an rdf last week that included my services. Can you please deregister them, so I can regain control over them? I will use an RDF file for registration next time, I promise :) ... 3. Is it correct that the "getSignatureForm"-script is only meant to help people updating their already working Services, i.e. generating an RDF file for those? And that in future one should generate an RDF file by hand and then use only the agent to register it? Or will it always be possible to first register the old way, then use "getSignatureForm" to update the RDF? Thanks, maren From dgpisano at cnb.uam.es Tue Apr 4 07:04:18 2006 From: dgpisano at cnb.uam.es (David Gonzalez Pisano) Date: Tue, 4 Apr 2006 13:04:18 +0200 Subject: [MOBY-dev] Object naming inconsistencies Message-ID: Hi, Gonzalo Claros from INB at Malaga and some other members have found some inconsistencies in the moby ontology datatypes names. Looking at an BioMOBY ontology release from 05/10/04, we deduced that it was recommended to use compound names with the underscore "_" to separate words. However, right now, we can find strange cases like: text_plain text-plain PMUT-Text PMUT_Text PDB-Text text-formatted text_formatted text-html text_html and so on When differences are in final datatypes (PMUT_Text, PDB-Text, etc) it is not so disturbing,, but when the alternate names correspond to key nodes like text_formatted, plain_text or text_html, the name difference can affect implementations (INB implementations and your own services, that's why we ask here). At INB, we are considering using the underscore "_" in any case, but we would like to maintain compatibility with BioMOBY Central in Canada. So, which will be considered the main root object, the one with "-" or the one with "-"? What are you using? Cheers, David From gordonp at ucalgary.ca Tue Apr 4 09:49:13 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 04 Apr 2006 07:49:13 -0600 Subject: [MOBY-dev] Object naming inconsistencies In-Reply-To: References: Message-ID: <44327959.7030801@ucalgary.ca> May I humbly suggest that we use the hyphen ('-'), as this at the very least feigns the desire to use the existing standards in HTTP content-type headers/MIME/etc... > Hi, > > Gonzalo Claros from INB at Malaga and some other members have found > some inconsistencies in the moby ontology datatypes names. Looking at > an BioMOBY ontology release from 05/10/04, we deduced that it was > recommended to use compound names with the underscore "_" to separate > words. However, right now, we can find strange cases like: > > text_plain > text-plain > PMUT-Text > PMUT_Text > PDB-Text > text-formatted > text_formatted > text-html > text_html > > and so on > > When differences are in final datatypes (PMUT_Text, PDB-Text, etc) it > is not so disturbing,, but when the alternate names correspond to key > nodes like text_formatted, plain_text or text_html, the name > difference can affect implementations (INB implementations and your > own services, that's why we ask here). > > At INB, we are considering using the underscore "_" in any case, but > we would like to maintain compatibility with BioMOBY Central in > Canada. So, which will be considered the main root object, the one > with "-" or the one with "-"? What are you using? > > Cheers, > > David > > _______________________________________________ > 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 Apr 4 11:56:50 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 04 Apr 2006 08:56:50 -0700 Subject: [MOBY-dev] [moby] RDF file generation for test registry In-Reply-To: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <1144166210.5952.14.camel@bioinfo.icapture.ubc.ca> On Tue, 2006-04-04 at 12:34 +0200, heese at mpiz-koeln.mpg.de wrote: > my services. Can you please deregister them, so I can regain control over > them? I will use an RDF file for registration next time, I promise :) ... The RDF signature migration has been a painfully slow process for a number of reasons - partly the desire to coordinate with other efforts who are on a different schedule, and in part because the desire to create an RDF document that is both extensible *and* computable ("reason-able") is very strong. On the other hand, removing the ability of a script kiddie to delete the entire registry was also a high priority, so we currently find ourselves "in limbo". The latest hiccup was my discovery last week that the Dublin Core RDF is ~OWL Full, and we use Dublin Core in our RDF signature. This means that we could not use a reasoner to do request/service mapping... which is one of the useful features of moving to an RDF-based service description (a la S-MOBY). Matthew H at Manchester has just given me a heads-up of a "patched" version of the Dublin Core that we can use instead of the native one, and this should allow us to use a DL reasoner. I'm trying to find time to test this in reality using a few signature RDF's, but my own time is quite limited these days as we approach the end of the school term. It's just a lack of hands for what it turning out to be a more difficult task than we had first imagined! Eddie can answer the other comments. M From edward.kawas at gmail.com Tue Apr 4 10:02:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 4 Apr 2006 07:02:57 -0700 Subject: [MOBY-dev] RDF file generation for test registry In-Reply-To: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <001501c657f0$7b294e70$6500a8c0@notebook> > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > heese at mpiz-koeln.mpg.de > Sent: Tuesday, April 04, 2006 3:35 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] RDF file generation for test registry > > Hi, > > these are 3 questions for Eddie, but the answers might be > interesting for others, that's why I post it to the whole list. > > I'm quite new in the BioMoby business, so I hope my questions > havn't been asked before (at least I didn't find anything). > > 1. Is there a page available equivalent to > http://mobycentral.icapture.ubc.ca/servlets/forms/getSignature > Form to create/update an rdf document for services registered > in the TestCentral at > (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? There is no such page for the test registry. I can make one if you wish though. > > 2. I registered a couple of services at the TestCentral the > old way without giving a RDF signature URL. Now I wanted to > deregister them the old way but it failed since you generated > an rdf last week that included my services. Can you please > deregister them, so I can regain control over them? I will > use an RDF file for registration next time, I promise :) ... > Sure I can, let me know the service name/authority and I will remove them. > 3. Is it correct that the "getSignatureForm"-script is only > meant to help people updating their already working Services, > i.e. generating an RDF file for those? And that in future one > should generate an RDF file by hand and then use only the > agent to register it? Or will it always be possible to first > register the old way, then use "getSignatureForm" to update the RDF? > Correct, the script is only for people updating their already working services. In the future, the RDF will be returned to you so long as you provide a signature url. If no signatureURL is provided, then I guess that you could use the getSignatureForm. I wouldn't be generating this stuff by hand ;-) Eddie > Thanks, > maren > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From senger at ebi.ac.uk Wed Apr 5 13:25:12 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 5 Apr 2006 18:25:12 +0100 (BST) Subject: [MOBY-dev] RDF file generation for test registry In-Reply-To: <001501c657f0$7b294e70$6500a8c0@notebook> Message-ID: > > in the TestCentral at > > (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? > > There is no such page for the test registry. I can make one if you > wish though. > If such page is useful (and obviously it is), its code should be well documented and provided within the moby central distribution. Each moby central provider should be instructed how to set her/his registry in order to provide this information. (Ideally, the URL of such page should be return by a call in the Moby API - as it is for RESOURCE). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Wed Apr 5 11:59:08 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 5 Apr 2006 16:59:08 +0100 (BST) Subject: [MOBY-dev] jMoby seems not to compile In-Reply-To: <4433D329.1060109@mmb.pcb.ub.es> Message-ID: > Perhaps I'm committing some mistake but I think I've updated my local > copy from the last version in the CVS and when I try to compile jMoby by > doing "build-dev.sh all" I get the following error: > Thanks for spotting it. Somebody (Paul?) changed MobyRequest but did not make './build-dev clean compile'. For now, I have removed HelloMOBY2.java. Please (whoever) put it back when you fix it. Thanks. Eddie, could you please fix these warnings? [javac] Issued 2 semantic warnings compiling "/home/senger/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RDFConfigure.java": [javac] 190. Model model = ModelFactory.createDefaultModel(); [javac] ^---^ [javac] *** Semantic Warning: Local "model" shadows a field of the same name in "org.biomoby.client.rdf.builder.RDFConfigure". [javac] 359. Model model = ModelFactory.createDefaultModel(); [javac] ^---^ [javac] *** Semantic Warning: Local "model" shadows a field of the same name in "org.biomoby.client.rdf.builder.RDFConfigure". [javac] Compiling 19 source files to /home/senger/moby-live/Java/build/Clients Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Thu Apr 6 09:43:31 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 06 Apr 2006 07:43:31 -0600 Subject: [MOBY-dev] jMoby seems not to compile In-Reply-To: References: Message-ID: <44351B03.6050106@ucalgary.ca> Oops, sorry! My first bad CVS commit. I've fixed this now. >> Perhaps I'm committing some mistake but I think I've updated my local >> copy from the last version in the CVS and when I try to compile jMoby by >> doing "build-dev.sh all" I get the following error: >> >> > Thanks for spotting it. Somebody (Paul?) changed MobyRequest but did > not make './build-dev clean compile'. For now, I have removed > HelloMOBY2.java. Please (whoever) put it back when you fix it. Thanks. > > Eddie, could you please fix these warnings? > > [javac] Issued 2 semantic warnings compiling > "/home/senger/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RDFConfigure.java": > > [javac] 190. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > > > [javac] 359. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > [javac] Compiling 19 source files to > /home/senger/moby-live/Java/build/Clients > > > Thanks, > Martin > > From gordonp at ucalgary.ca Thu Apr 6 09:43:31 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 06 Apr 2006 07:43:31 -0600 Subject: [MOBY-dev] jMoby seems not to compile In-Reply-To: References: Message-ID: <44351B03.6050106@ucalgary.ca> Oops, sorry! My first bad CVS commit. I've fixed this now. >> Perhaps I'm committing some mistake but I think I've updated my local >> copy from the last version in the CVS and when I try to compile jMoby by >> doing "build-dev.sh all" I get the following error: >> >> > Thanks for spotting it. Somebody (Paul?) changed MobyRequest but did > not make './build-dev clean compile'. For now, I have removed > HelloMOBY2.java. Please (whoever) put it back when you fix it. Thanks. > > Eddie, could you please fix these warnings? > > [javac] Issued 2 semantic warnings compiling > "/home/senger/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RDFConfigure.java": > > [javac] 190. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > > > [javac] 359. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > [javac] Compiling 19 source files to > /home/senger/moby-live/Java/build/Clients > > > Thanks, > Martin > > From edward.kawas at gmail.com Thu Apr 6 19:28:40 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 6 Apr 2006 16:28:40 -0700 Subject: [MOBY-dev] Quick poll Message-ID: <004c01c659d1$d716f240$6500a8c0@notebook> Hi, Just out of curiosity, who is using the RDFs that mobycentral is currently generating. If you are using them, what tasks are you using them for. I ask, because the RDF that is generated by mobycentral is different than the one that is generated by the test machine. The difference lies on the fact that mobycentral identifies resources based on URIs, while the test registry uses LSIDs. There are some other changes, but mainly additions (for instance, object ontology rdf now has more information in it, like the authority of the creator, the creators email address, etc). We are hoping to deploy the new RDF onto mobycentral very soon, and I just want to get a head count of who it is that will yell (beat up, etc) at me ;-) Thanks, Eddie From akerhornou at imim.es Fri Apr 7 05:04:00 2006 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Fri, 07 Apr 2006 11:04:00 +0200 Subject: [MOBY-dev] Quick poll In-Reply-To: <004c01c659d1$d716f240$6500a8c0@notebook> References: <004c01c659d1$d716f240$6500a8c0@notebook> Message-ID: <44362B00.7020301@imim.es> Hi Eddie, I have updated my services, and they all have a signature URL. I have a RDF document that includes in it all my services in there, http://genome.imim.es/webservices/RDFs/services.rdf i don't use the RDF, i guess in future i could use it for parameters and input objects validation - this way validatino could be done on the fly generically. Also, quick question, is the agent on ? Is it going to check the RDF document on a regular basis, and being able to update the central registry if i modify the specs of my services? regards, Arnaud Edward Kawas wrote: > Hi, > > Just out of curiosity, who is using the RDFs that mobycentral is currently > generating. If you are using them, what tasks are you using them for. > > I ask, because the RDF that is generated by mobycentral is different than the > one that is generated by the test machine. The difference lies on the fact that > mobycentral identifies resources based on URIs, while the test registry uses > LSIDs. There are some other changes, but mainly additions (for instance, object > ontology rdf now has more information in it, like the authority of the creator, > the creators email address, etc). > > We are hoping to deploy the new RDF onto mobycentral very soon, and I just want > to get a head count of who it is that will yell (beat up, etc) at me ;-) > > Thanks, > > Eddie > > > From heese at mpiz-koeln.mpg.de Fri Apr 7 08:59:45 2006 From: heese at mpiz-koeln.mpg.de (heese at mpiz-koeln.mpg.de) Date: Fri, 7 Apr 2006 14:59:45 +0200 (CEST) Subject: [MOBY-dev] RDF file generation for test registry Message-ID: <1062.80.135.69.229.1144414785.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Eddi, thanks for the answers, I just found them in the archives, since I somehow kicked myself out of the mailing list trying to switch from digest to normal mode - but now I'm back in ... > > 1. Is there a page available equivalent to > http://mobycentral.icapture.ubc.ca/servlets/forms/getSignature > Form to create/update an rdf document for services registered > in the TestCentral at > (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? > There is no such page for the test registry. I can make one if you wish >though. I think it would be a nice feature, since I havn't found another way to get an RDF for several services in one go (so far I used the dashboard to register my services & get the RDF). In fact, I havn't been able to get a valid RDF document for the TestRegistry at all. When I used the dasboard, the RDF I recieved was empty (just the RDF-tags). Then I tried to take the detour over the MobyCentral registry (i.e. I registered the same service there (via dashboard), got an RDF with content, and tried to use this RDF for the TestRestigry as well. But since the RDFs for MobyCentralRegistry and TestRegistry aren't alike (I wasn't aware of that), it obviously didn't work either. So, what would be the correct way to generate a valid RDF-document for the Test registry at the moment? > > 2. I registered a couple of services at the TestCentral the > old way without giving a RDF signature URL. Now I wanted to > deregister them the old way but it failed since you generated > an rdf last week that included my services. Can you please > deregister them, so I can regain control over them? I will > use an RDF file for registration next time, I promise :) ... > > Sure I can, let me know the service name/authority and I will remove them. Please remove all services with the authority mpiz-koeln.mpg.de starting with MH_ from the TestRegistry and if there is another one with the authority mpiz-koeln.mpg.de that has your RDF signature URL, please remove that one as well (I'm not at work right now, so I cannot look up the name, sorry). Thanks, maren From edward.kawas at gmail.com Fri Apr 7 10:03:37 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 7 Apr 2006 07:03:37 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <44362B00.7020301@imim.es> Message-ID: <000501c65a4c$12691a10$6500a8c0@notebook> Hi, The agent isnt on yet (on mobycentral that is, it is running on the test registry). We want to make sure that the RDF is 100% correct before the agent is deployed. 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 > Arnaud Kerhornou > Sent: Friday, April 07, 2006 2:04 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > Hi Eddie, > > I have updated my services, and they all have a signature > URL. I have a RDF document that includes in it all my > services in there, http://genome.imim.es/webservices/RDFs/services.rdf > > i don't use the RDF, i guess in future i could use it for > parameters and input objects validation - this way validatino > could be done on the fly generically. > > Also, quick question, is the agent on ? Is it going to check > the RDF document on a regular basis, and being able to update > the central registry if i modify the specs of my services? > > regards, > Arnaud > > Edward Kawas wrote: > > Hi, > > > > Just out of curiosity, who is using the RDFs that mobycentral is > > currently generating. If you are using them, what tasks are > you using them for. > > > > I ask, because the RDF that is generated by mobycentral is > different > > than the one that is generated by the test machine. The difference > > lies on the fact that mobycentral identifies resources > based on URIs, > > while the test registry uses LSIDs. There are some other > changes, but > > mainly additions (for instance, object ontology rdf now has more > > information in it, like the authority of the creator, the > creators email address, etc). > > > > We are hoping to deploy the new RDF onto mobycentral very > soon, and I > > just want to get a head count of who it is that will yell (beat up, > > etc) at me ;-) > > > > Thanks, > > > > Eddie > > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From joecker at mpiz-koeln.mpg.de Fri Apr 7 10:03:32 2006 From: joecker at mpiz-koeln.mpg.de (Anika Joecker) Date: Fri, 7 Apr 2006 16:03:32 +0200 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: References: Message-ID: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Hello, I implemented a JMOBY webservice, which returns a BioMoby BLAST-Text object. Content, namespace and ID are added by JMOBY API like this: BLAST_Text text = new BLAST_Text(); text.setId("output"); text.setNamespace("BLAST"); text.set_content(result); By executing my BioMoby service I found, that some tags (XML namespaces) in the output XML file were prefixed with "moby:" and all JMoby primitives were not. For example: <-- here Because of that I've got some problems by parsing the XML output with Java JDOM. So my questions are: Why have the primitives no "moby" XML namespace? Is it possible to change the JMoby api so that all primitives get a "moby" XML namespace too? Thanks, Anika From gordonp at ucalgary.ca Fri Apr 7 11:16:35 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 09:16:35 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: <44368253.5020705@ucalgary.ca> Him They do. In the top level tag, http://www.biomoby.org/moby is defined as the default namespace. If the tags don't have that namespace in your DOM, you might want to make sure that you've set the parser's namespace awareness option to "on". Cheers, Paul > Hello, > > I implemented a JMOBY webservice, which returns a BioMoby BLAST-Text object. > Content, namespace and ID are added by JMOBY API like this: > > BLAST_Text text = new BLAST_Text(); > text.setId("output"); > text.setNamespace("BLAST"); > text.set_content(result); > > By executing my BioMoby service I found, that some tags (XML namespaces) in > the output XML file were prefixed with "moby:" and all JMoby primitives were > not. > For example: > > > xmlns='http://www.biomoby.org/moby'> > > > > > <-- here > > > Because of that I've got some problems by parsing the XML output with Java > JDOM. > So my questions are: > > Why have the primitives no "moby" XML namespace? > Is it possible to change the JMoby api so that all primitives get a "moby" XML > namespace too? > > Thanks, > Anika > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Fri Apr 7 11:22:20 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 09:22:20 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: <443683AC.8050704@ucalgary.ca> Hi all, Not directly related to the question below, I would like to *strongly* encourage people using formatted output such as GFF, BLAST, etc. to explicitly add a xml:space="preserve" attribute to their string objects. Otherwise an XML parser (or XSLT stylesheet as I use) can irreversibly collapse all those nice formatting whitespace characters into a single space to produce very ugly results. I've added this to org.biomoby.shared.MobyDataString, but haven't commited yet since I'm waiting for Ediie's RDF stuff to go live... Cheers, Paul > Hello, > > I implemented a JMOBY webservice, which returns a BioMoby BLAST-Text object. > Content, namespace and ID are added by JMOBY API like this: > > BLAST_Text text = new BLAST_Text(); > text.setId("output"); > text.setNamespace("BLAST"); > text.set_content(result); > > By executing my BioMoby service I found, that some tags (XML namespaces) in > the output XML file were prefixed with "moby:" and all JMoby primitives were > not. > For example: > > > xmlns='http://www.biomoby.org/moby'> > > > > > <-- here > > > Because of that I've got some problems by parsing the XML output with Java > JDOM. > So my questions are: > > Why have the primitives no "moby" XML namespace? > Is it possible to change the JMoby api so that all primitives get a "moby" XML > namespace too? > > Thanks, > Anika > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Fri Apr 7 11:24:51 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 09:24:51 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <443683AC.8050704@ucalgary.ca> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> <443683AC.8050704@ucalgary.ca> Message-ID: <44368443.6060802@ucalgary.ca> Oops. I meant org.biomoby.shared.data.MobyDataString. > org.biomoby.shared.MobyDataString, but haven't commited yet since I'm > From martin.senger at gmail.com Fri Apr 7 11:02:01 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 07 Apr 2006 16:02:01 +0100 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: <44367EE9.10008@gmail.com> Hi, > By executing my BioMoby service I found, that some tags (XML namespaces) in > the output XML file were prefixed with "moby:" and all JMoby primitives were > not. > > Because of that I've got some problems by parsing the XML output with Java > JDOM. > So my questions are: > > Why have the primitives no "moby" XML namespace? > Is it possible to change the JMoby api so that all primitives get a "moby" XML > namespace too? > I had similar problems. When I was using JDOM I was always asked two questions: first using a local name, second with the moby namespace. I have even added two methods in (jMoby) org.biomoby.shared.Utils: * Get a child by 'name' from 'parent'. It tries first a child * without any namespace, then with {@link #MOBY_NS}.

* public static Element getChild (Element parent, String name); * Get text of a child 'name' from 'parent'. It tries first a * child without any namespace, then with {@link #MOBY_NS}.

* public static String getChildText (Element parent, String name); But I wonder if this is a correct way to do it. Anybody (perhaps Paul?) knows more about how to treat namespaces? Also, (Mark, Eddie?) what is in the Moby API about namepaces? Are they mandatory or not? I can surely add namespaces to primitive types as well... But I would rather first wait for the answers... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Apr 7 12:42:43 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 10:42:43 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <44367EE9.10008@gmail.com> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> <44367EE9.10008@gmail.com> Message-ID: <44369683.2040904@ucalgary.ca> This must be a bug in JDOM, because the namespaces in the actual document are correct. Attributes is another story though, as by default, these do not have namespaces. > I had similar problems. When I was using JDOM I was always asked > two questions: first using a local name, second with the moby namespace. > I have even added two methods in (jMoby) org.biomoby.shared.Utils: > > > * Get a child by 'name' from 'parent'. It tries first a child > * without any namespace, then with {@link #MOBY_NS}.

> * > public static Element getChild (Element parent, String name); > > * Get text of a child 'name' from 'parent'. It tries first a > * child without any namespace, then with {@link #MOBY_NS}.

> * > public static String getChildText (Element parent, String name); > > But I wonder if this is a correct way to do it. Anybody (perhaps > Paul?) knows more about how to treat namespaces? > Also, (Mark, Eddie?) what is in the Moby API about namepaces? Are > they mandatory or not? > I can surely add namespaces to primitive types as well... But I > would rather first wait for the answers... > > Cheers, > Martin > > From senger at ebi.ac.uk Mon Apr 10 05:12:04 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 10 Apr 2006 10:12:04 +0100 (BST) Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: > Because of that I've got some problems by parsing the XML output with Java > JDOM. > Just from curiosity: why would you need to parse XML at all? From your example, I understand, that you are using jMoby generated classes (Moses) - and for them you could use jMoby's XML parser (class MobyParser). Please let me know if you have any questions regarding how to use Moses and its parser. With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Mon Apr 10 06:30:53 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 10 Apr 2006 11:30:53 +0100 (BST) Subject: [MOBY-dev] namespaces in Moby (and generally) Message-ID: Hi all (and perhaps especially Paul), I am unsure if I am doing namespace things properly in jMoby. Perhaps somebody can enlighten me on the topic. Thanks in advance. When I am parsing a moby XML I assume that the elements and attributes either do not have any namespace attached, or that they have the namespace exactly like this: http://www.biomoby.org/moby. But I have this namespace hard-coded (actually taken from one of Paul's classes in jMoby). Is this correct, or should I rather read the parsed XML, and find there the namespace definition (in this case in the MOBY element: ... and to use the string that is defined there? For example, recently I was in a discussion with Ivan from INB, his message started as: ... Thanks and with regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Mon Apr 10 12:13:05 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Apr 2006 10:13:05 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: References: Message-ID: <443A8411.1030509@ucalgary.ca> Ditto for me, if you are using org.biomoby.shared.data.MobyDataUtils. You should never have to touch the XML directly... With two different implementations of data parsing in jMOBY, you shouldn't need to create a third :-) >> Because of that I've got some problems by parsing the XML output with Java >> JDOM. >> >> > Just from curiosity: why would you need to parse XML at all? From your > example, I understand, that you are using jMoby generated classes > (Moses) - and for them you could use jMoby's XML parser (class > MobyParser). Please let me know if you have any questions regarding how to > use Moses and its parser. > > With regards, > Martin > > From gordonp at ucalgary.ca Mon Apr 10 12:48:58 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Apr 2006 10:48:58 -0600 Subject: [MOBY-dev] namespaces in Moby (and generally) In-Reply-To: References: Message-ID: <443A8C7A.6060605@ucalgary.ca> The moby namespace is defined here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InputMessage.html So Ivan's is incorrect as far as I can see...no disrespect to the Spanish. I've noticed they have the most inconsistencies with the API, but that's because they are also producing most of the services that actually work! :-) It'd be great if we could all get together again some time, now that we have a lot of clients and servers, and work out these interoperability kinks more efficiently... Martin Senger wrote: > Hi all (and perhaps especially Paul), > I am unsure if I am doing namespace things properly in jMoby. Perhaps > somebody can enlighten me on the topic. Thanks in advance. > When I am parsing a moby XML I assume that the elements and attributes > either do not have any namespace attached, or that they have the namespace > exactly like this: http://www.biomoby.org/moby. > But I have this namespace hard-coded (actually taken from one of Paul's > classes in jMoby). Is this correct, or should I rather read the parsed > XML, and find there the namespace definition (in this case in the MOBY > element: > > ... > > and to use the string that is defined there? For example, recently I was > in a discussion with Ivan from INB, his message started as: > > ... > > Thanks and with regards, > Martin > > From gordonp at ucalgary.ca Mon Apr 10 19:20:36 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Apr 2006 17:20:36 -0600 Subject: [MOBY-dev] Quick poll In-Reply-To: <000501c65a4c$12691a10$6500a8c0@notebook> References: <000501c65a4c$12691a10$6500a8c0@notebook> Message-ID: <443AE844.5040301@ucalgary.ca> Umm.. the test server has reverted to http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID based. Is this intentional? It breaks all my code :-( > Hi, > > The agent isnt on yet (on mobycentral that is, it is running on the test > registry). We want to make sure that the RDF is 100% correct before the agent is > deployed. > > 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 >> Arnaud Kerhornou >> Sent: Friday, April 07, 2006 2:04 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Quick poll >> >> Hi Eddie, >> >> I have updated my services, and they all have a signature >> URL. I have a RDF document that includes in it all my >> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >> >> i don't use the RDF, i guess in future i could use it for >> parameters and input objects validation - this way validatino >> could be done on the fly generically. >> >> Also, quick question, is the agent on ? Is it going to check >> the RDF document on a regular basis, and being able to update >> the central registry if i modify the specs of my services? >> >> regards, >> Arnaud >> >> Edward Kawas wrote: >> >>> Hi, >>> >>> Just out of curiosity, who is using the RDFs that mobycentral is >>> currently generating. If you are using them, what tasks are >>> >> you using them for. >> >>> I ask, because the RDF that is generated by mobycentral is >>> >> different >> >>> than the one that is generated by the test machine. The difference >>> lies on the fact that mobycentral identifies resources >>> >> based on URIs, >> >>> while the test registry uses LSIDs. There are some other >>> >> changes, but >> >>> mainly additions (for instance, object ontology rdf now has more >>> information in it, like the authority of the creator, the >>> >> creators email address, etc). >> >>> We are hoping to deploy the new RDF onto mobycentral very >>> >> soon, and I >> >>> just want to get a head count of who it is that will yell (beat up, >>> etc) at me ;-) >>> >>> Thanks, >>> >>> Eddie >>> >>> >>> >>> >> _______________________________________________ >> 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 Mon Apr 10 19:39:05 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 10 Apr 2006 16:39:05 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443AE844.5040301@ucalgary.ca> References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> Message-ID: More specifics please. which ontology are you looking at? On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon wrote: > Umm.. the test server has reverted to > http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID > based. Is this intentional? It breaks all my code :-( >> Hi, >> >> The agent isnt on yet (on mobycentral that is, it is running on the test >> registry). We want to make sure that the RDF is 100% correct before the >> agent is >> deployed. >> >> 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 >>> Arnaud Kerhornou >>> Sent: Friday, April 07, 2006 2:04 AM >>> To: Core developer announcements >>> Subject: Re: [MOBY-dev] Quick poll >>> >>> Hi Eddie, >>> >>> I have updated my services, and they all have a signature >>> URL. I have a RDF document that includes in it all my >>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>> >>> i don't use the RDF, i guess in future i could use it for >>> parameters and input objects validation - this way validatino >>> could be done on the fly generically. >>> >>> Also, quick question, is the agent on ? Is it going to check >>> the RDF document on a regular basis, and being able to update >>> the central registry if i modify the specs of my services? >>> >>> regards, >>> Arnaud >>> >>> Edward Kawas wrote: >>> >>>> Hi, >>>> >>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>> currently generating. If you are using them, what tasks are >>>> >>> you using them for. >>> >>>> I ask, because the RDF that is generated by mobycentral is >>>> >>> different >>> >>>> than the one that is generated by the test machine. The difference >>>> lies on the fact that mobycentral identifies resources >>>> >>> based on URIs, >>> >>>> while the test registry uses LSIDs. There are some other >>>> >>> changes, but >>> >>>> mainly additions (for instance, object ontology rdf now has more >>>> information in it, like the authority of the creator, the >>>> >>> creators email address, etc). >>> >>>> We are hoping to deploy the new RDF onto mobycentral very >>>> >>> soon, and I >>> >>>> just want to get a head count of who it is that will yell (beat up, >>>> etc) at me ;-) >>>> >>>> Thanks, >>>> >>>> Eddie >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From markw at illuminae.com Mon Apr 10 19:44:07 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 10 Apr 2006 16:44:07 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443AE844.5040301@ucalgary.ca> References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> Message-ID: Hi Paul, Can you send us a copy of what you are seeing, and the URL that you retrieved it from? From our perspective, it is still LSID-based... ?? M On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon wrote: > Umm.. the test server has reverted to > http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID > based. Is this intentional? It breaks all my code :-( >> Hi, >> >> The agent isnt on yet (on mobycentral that is, it is running on the test >> registry). We want to make sure that the RDF is 100% correct before the >> agent is >> deployed. >> >> 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 >>> Arnaud Kerhornou >>> Sent: Friday, April 07, 2006 2:04 AM >>> To: Core developer announcements >>> Subject: Re: [MOBY-dev] Quick poll >>> >>> Hi Eddie, >>> >>> I have updated my services, and they all have a signature >>> URL. I have a RDF document that includes in it all my >>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>> >>> i don't use the RDF, i guess in future i could use it for >>> parameters and input objects validation - this way validatino >>> could be done on the fly generically. >>> >>> Also, quick question, is the agent on ? Is it going to check >>> the RDF document on a regular basis, and being able to update >>> the central registry if i modify the specs of my services? >>> >>> regards, >>> Arnaud >>> >>> Edward Kawas wrote: >>> >>>> Hi, >>>> >>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>> currently generating. If you are using them, what tasks are >>>> >>> you using them for. >>> >>>> I ask, because the RDF that is generated by mobycentral is >>>> >>> different >>> >>>> than the one that is generated by the test machine. The difference >>>> lies on the fact that mobycentral identifies resources >>>> >>> based on URIs, >>> >>>> while the test registry uses LSIDs. There are some other >>>> >>> changes, but >>> >>>> mainly additions (for instance, object ontology rdf now has more >>>> information in it, like the authority of the creator, the >>>> >>> creators email address, etc). >>> >>>> We are hoping to deploy the new RDF onto mobycentral very >>>> >>> soon, and I >>> >>>> just want to get a head count of who it is that will yell (beat up, >>>> etc) at me ;-) >>>> >>>> Thanks, >>>> >>>> Eddie >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From edward.kawas at gmail.com Mon Apr 10 19:28:22 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 10 Apr 2006 16:28:22 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443AE844.5040301@ucalgary.ca> Message-ID: <000a01c65cf6$763a24b0$636fa8c0@notebook> Hi Paul, I am seeing LSIDs, what ontology are you talking about? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Monday, April 10, 2006 4:21 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > Umm.. the test server has reverted to > http://www.w3.org/2000/01/rdf-schema#label type RDF instead > of LSID based. Is this intentional? It breaks all my code :-( > > Hi, > > > > The agent isnt on yet (on mobycentral that is, it is running on the > > test registry). We want to make sure that the RDF is 100% correct > > before the agent is deployed. > > > > 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 Arnaud > >> Kerhornou > >> Sent: Friday, April 07, 2006 2:04 AM > >> To: Core developer announcements > >> Subject: Re: [MOBY-dev] Quick poll > >> > >> Hi Eddie, > >> > >> I have updated my services, and they all have a signature > URL. I have > >> a RDF document that includes in it all my services in there, > >> http://genome.imim.es/webservices/RDFs/services.rdf > >> > >> i don't use the RDF, i guess in future i could use it for > parameters > >> and input objects validation - this way validatino could > be done on > >> the fly generically. > >> > >> Also, quick question, is the agent on ? Is it going to > check the RDF > >> document on a regular basis, and being able to update the central > >> registry if i modify the specs of my services? > >> > >> regards, > >> Arnaud > >> > >> Edward Kawas wrote: > >> > >>> Hi, > >>> > >>> Just out of curiosity, who is using the RDFs that mobycentral is > >>> currently generating. If you are using them, what tasks are > >>> > >> you using them for. > >> > >>> I ask, because the RDF that is generated by mobycentral is > >>> > >> different > >> > >>> than the one that is generated by the test machine. The > difference > >>> lies on the fact that mobycentral identifies resources > >>> > >> based on URIs, > >> > >>> while the test registry uses LSIDs. There are some other > >>> > >> changes, but > >> > >>> mainly additions (for instance, object ontology rdf now has more > >>> information in it, like the authority of the creator, the > >>> > >> creators email address, etc). > >> > >>> We are hoping to deploy the new RDF onto mobycentral very > >>> > >> soon, and I > >> > >>> just want to get a head count of who it is that will yell > (beat up, > >>> etc) at me ;-) > >>> > >>> Thanks, > >>> > >>> Eddie > >>> > >>> > >>> > >>> > >> _______________________________________________ > >> 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 gordonp at ucalgary.ca Tue Apr 11 10:09:36 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 11 Apr 2006 08:09:36 -0600 Subject: [MOBY-dev] Quick poll In-Reply-To: References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> Message-ID: <443BB8A0.60303@ucalgary.ca> It is in the Object ontology, but only the last two lines I guess, which look like: In the file http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects Which causes the following error (so the problem might actually be that org.biomoby.shared.extended.DataTypeParser should ignore this field but doesn't?): Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeParser.java:173) > Hi Paul, > > Can you send us a copy of what you are seeing, and the URL that you > retrieved it from? From our perspective, it is still LSID-based... > > ?? > > M > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > wrote: > > >> Umm.. the test server has reverted to >> http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID >> based. Is this intentional? It breaks all my code :-( >> >>> Hi, >>> >>> The agent isnt on yet (on mobycentral that is, it is running on the test >>> registry). We want to make sure that the RDF is 100% correct before the >>> agent is >>> deployed. >>> >>> 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 >>>> Arnaud Kerhornou >>>> Sent: Friday, April 07, 2006 2:04 AM >>>> To: Core developer announcements >>>> Subject: Re: [MOBY-dev] Quick poll >>>> >>>> Hi Eddie, >>>> >>>> I have updated my services, and they all have a signature >>>> URL. I have a RDF document that includes in it all my >>>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>>> >>>> i don't use the RDF, i guess in future i could use it for >>>> parameters and input objects validation - this way validatino >>>> could be done on the fly generically. >>>> >>>> Also, quick question, is the agent on ? Is it going to check >>>> the RDF document on a regular basis, and being able to update >>>> the central registry if i modify the specs of my services? >>>> >>>> regards, >>>> Arnaud >>>> >>>> Edward Kawas wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>>> currently generating. If you are using them, what tasks are >>>>> >>>>> >>>> you using them for. >>>> >>>> >>>>> I ask, because the RDF that is generated by mobycentral is >>>>> >>>>> >>>> different >>>> >>>> >>>>> than the one that is generated by the test machine. The difference >>>>> lies on the fact that mobycentral identifies resources >>>>> >>>>> >>>> based on URIs, >>>> >>>> >>>>> while the test registry uses LSIDs. There are some other >>>>> >>>>> >>>> changes, but >>>> >>>> >>>>> mainly additions (for instance, object ontology rdf now has more >>>>> information in it, like the authority of the creator, the >>>>> >>>>> >>>> creators email address, etc). >>>> >>>> >>>>> We are hoping to deploy the new RDF onto mobycentral very >>>>> >>>>> >>>> soon, and I >>>> >>>> >>>>> just want to get a head count of who it is that will yell (beat up, >>>>> etc) at me ;-) >>>>> >>>>> Thanks, >>>>> >>>>> Eddie >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 edward.kawas at gmail.com Tue Apr 11 10:11:59 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 11 Apr 2006 07:11:59 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443BB8A0.60303@ucalgary.ca> Message-ID: <000f01c65d71$e6f3c1e0$6600a8c0@notebook> Hi Paul, I will update the parsers in a moment and let you know. We made some changes yesterday to the RDF to make our ontologies owl-dl (actually Mark is trying to make owl-dl and I just code the changes ;-). Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Tuesday, April 11, 2006 7:10 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > It is in the Object ontology, but only the last two lines I > guess, which look like: > > rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"> > > In the file > http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects > > Which causes the following error (so the problem might > actually be that org.biomoby.shared.extended.DataTypeParser > should ignore this field but > doesn't?): > > Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: > Expected an LSID as a URI, instead got > http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > org.biomoby.shared.MobyException: Expected an LSID as a URI, > instead got http://www.w3.org/2000/01/rdf-schema#comment 200 > : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > at > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFro > mRDF(DataTypeParser.java:173) > > > Hi Paul, > > > > Can you send us a copy of what you are seeing, and the URL that you > > retrieved it from? From our perspective, it is still LSID-based... > > > > ?? > > > > M > > > > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > > > wrote: > > > > > >> Umm.. the test server has reverted to > >> http://www.w3.org/2000/01/rdf-schema#label type RDF > instead of LSID > >> based. Is this intentional? It breaks all my code :-( > >> > >>> Hi, > >>> > >>> The agent isnt on yet (on mobycentral that is, it is > running on the > >>> test registry). We want to make sure that the RDF is 100% correct > >>> before the agent is deployed. > >>> > >>> 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 Arnaud > >>>> Kerhornou > >>>> Sent: Friday, April 07, 2006 2:04 AM > >>>> To: Core developer announcements > >>>> Subject: Re: [MOBY-dev] Quick poll > >>>> > >>>> Hi Eddie, > >>>> > >>>> I have updated my services, and they all have a signature URL. I > >>>> have a RDF document that includes in it all my services > in there, > >>>> http://genome.imim.es/webservices/RDFs/services.rdf > >>>> > >>>> i don't use the RDF, i guess in future i could use it for > >>>> parameters and input objects validation - this way > validatino could > >>>> be done on the fly generically. > >>>> > >>>> Also, quick question, is the agent on ? Is it going to check the > >>>> RDF document on a regular basis, and being able to update the > >>>> central registry if i modify the specs of my services? > >>>> > >>>> regards, > >>>> Arnaud > >>>> > >>>> Edward Kawas wrote: > >>>> > >>>> > >>>>> Hi, > >>>>> > >>>>> Just out of curiosity, who is using the RDFs that > mobycentral is > >>>>> currently generating. If you are using them, what tasks are > >>>>> > >>>>> > >>>> you using them for. > >>>> > >>>> > >>>>> I ask, because the RDF that is generated by mobycentral is > >>>>> > >>>>> > >>>> different > >>>> > >>>> > >>>>> than the one that is generated by the test machine. The > difference > >>>>> lies on the fact that mobycentral identifies resources > >>>>> > >>>>> > >>>> based on URIs, > >>>> > >>>> > >>>>> while the test registry uses LSIDs. There are some other > >>>>> > >>>>> > >>>> changes, but > >>>> > >>>> > >>>>> mainly additions (for instance, object ontology rdf now > has more > >>>>> information in it, like the authority of the creator, the > >>>>> > >>>>> > >>>> creators email address, etc). > >>>> > >>>> > >>>>> We are hoping to deploy the new RDF onto mobycentral very > >>>>> > >>>>> > >>>> soon, and I > >>>> > >>>> > >>>>> just want to get a head count of who it is that will yell (beat > >>>>> up, > >>>>> etc) at me ;-) > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Eddie > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>> _______________________________________________ > >>>> 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 From edward.kawas at gmail.com Tue Apr 11 10:57:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 11 Apr 2006 07:57:57 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443BB8A0.60303@ucalgary.ca> Message-ID: <001401c65d78$528f2790$6600a8c0@notebook> Hi Paul, The RDF parsers have been updated. Let me know if you run into any problems. 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 Paul Gordon > Sent: Tuesday, April 11, 2006 7:10 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > It is in the Object ontology, but only the last two lines I > guess, which look like: > > rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"> > > In the file > http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects > > Which causes the following error (so the problem might > actually be that org.biomoby.shared.extended.DataTypeParser > should ignore this field but > doesn't?): > > Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: > Expected an LSID as a URI, instead got > http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > org.biomoby.shared.MobyException: Expected an LSID as a URI, > instead got http://www.w3.org/2000/01/rdf-schema#comment 200 > : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > at > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFro > mRDF(DataTypeParser.java:173) > > > Hi Paul, > > > > Can you send us a copy of what you are seeing, and the URL that you > > retrieved it from? From our perspective, it is still LSID-based... > > > > ?? > > > > M > > > > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > > > wrote: > > > > > >> Umm.. the test server has reverted to > >> http://www.w3.org/2000/01/rdf-schema#label type RDF > instead of LSID > >> based. Is this intentional? It breaks all my code :-( > >> > >>> Hi, > >>> > >>> The agent isnt on yet (on mobycentral that is, it is > running on the > >>> test registry). We want to make sure that the RDF is 100% correct > >>> before the agent is deployed. > >>> > >>> 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 Arnaud > >>>> Kerhornou > >>>> Sent: Friday, April 07, 2006 2:04 AM > >>>> To: Core developer announcements > >>>> Subject: Re: [MOBY-dev] Quick poll > >>>> > >>>> Hi Eddie, > >>>> > >>>> I have updated my services, and they all have a signature URL. I > >>>> have a RDF document that includes in it all my services > in there, > >>>> http://genome.imim.es/webservices/RDFs/services.rdf > >>>> > >>>> i don't use the RDF, i guess in future i could use it for > >>>> parameters and input objects validation - this way > validatino could > >>>> be done on the fly generically. > >>>> > >>>> Also, quick question, is the agent on ? Is it going to check the > >>>> RDF document on a regular basis, and being able to update the > >>>> central registry if i modify the specs of my services? > >>>> > >>>> regards, > >>>> Arnaud > >>>> > >>>> Edward Kawas wrote: > >>>> > >>>> > >>>>> Hi, > >>>>> > >>>>> Just out of curiosity, who is using the RDFs that > mobycentral is > >>>>> currently generating. If you are using them, what tasks are > >>>>> > >>>>> > >>>> you using them for. > >>>> > >>>> > >>>>> I ask, because the RDF that is generated by mobycentral is > >>>>> > >>>>> > >>>> different > >>>> > >>>> > >>>>> than the one that is generated by the test machine. The > difference > >>>>> lies on the fact that mobycentral identifies resources > >>>>> > >>>>> > >>>> based on URIs, > >>>> > >>>> > >>>>> while the test registry uses LSIDs. There are some other > >>>>> > >>>>> > >>>> changes, but > >>>> > >>>> > >>>>> mainly additions (for instance, object ontology rdf now > has more > >>>>> information in it, like the authority of the creator, the > >>>>> > >>>>> > >>>> creators email address, etc). > >>>> > >>>> > >>>>> We are hoping to deploy the new RDF onto mobycentral very > >>>>> > >>>>> > >>>> soon, and I > >>>> > >>>> > >>>>> just want to get a head count of who it is that will yell (beat > >>>>> up, > >>>>> etc) at me ;-) > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Eddie > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>> _______________________________________________ > >>>> 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 From markw at illuminae.com Tue Apr 11 11:25:27 2006 From: markw at illuminae.com (mark wilkinson) Date: Tue, 11 Apr 2006 15:25:27 +0000 GMT Subject: [MOBY-dev] Quick poll In-Reply-To: <443BB8A0.60303@ucalgary.ca> References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> <443BB8A0.60303@ucalgary.ca> Message-ID: <565197944-1144769236-cardhu_blackberry.rim.net-31034-@engine18-cell01> Yeah that's necessary. Your code needs to be clever and detect different types of uri's M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Tue, 11 Apr 2006 08:09:36 To:Core developer announcements Subject: Re: [MOBY-dev] Quick poll It is in the Object ontology, but only the last two lines I guess, which look like: In the file http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects Which causes the following error (so the problem might actually be that org.biomoby.shared.extended.DataTypeParser should ignore this field but doesn't?): Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeParser.java:173) > Hi Paul, > > Can you send us a copy of what you are seeing, and the URL that you > retrieved it from? From our perspective, it is still LSID-based... > > ?? > > M > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > wrote: > > >> Umm.. the test server has reverted to >> http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID >> based. Is this intentional? It breaks all my code :-( >> >>> Hi, >>> >>> The agent isnt on yet (on mobycentral that is, it is running on the test >>> registry). We want to make sure that the RDF is 100% correct before the >>> agent is >>> deployed. >>> >>> 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 >>>> Arnaud Kerhornou >>>> Sent: Friday, April 07, 2006 2:04 AM >>>> To: Core developer announcements >>>> Subject: Re: [MOBY-dev] Quick poll >>>> >>>> Hi Eddie, >>>> >>>> I have updated my services, and they all have a signature >>>> URL. I have a RDF document that includes in it all my >>>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>>> >>>> i don't use the RDF, i guess in future i could use it for >>>> parameters and input objects validation - this way validatino >>>> could be done on the fly generically. >>>> >>>> Also, quick question, is the agent on ? Is it going to check >>>> the RDF document on a regular basis, and being able to update >>>> the central registry if i modify the specs of my services? >>>> >>>> regards, >>>> Arnaud >>>> >>>> Edward Kawas wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>>> currently generating. If you are using them, what tasks are >>>>> >>>>> >>>> you using them for. >>>> >>>> >>>>> I ask, because the RDF that is generated by mobycentral is >>>>> >>>>> >>>> different >>>> >>>> >>>>> than the one that is generated by the test machine. The difference >>>>> lies on the fact that mobycentral identifies resources >>>>> >>>>> >>>> based on URIs, >>>> >>>> >>>>> while the test registry uses LSIDs. There are some other >>>>> >>>>> >>>> changes, but >>>> >>>> >>>>> mainly additions (for instance, object ontology rdf now has more >>>>> information in it, like the authority of the creator, the >>>>> >>>>> >>>> creators email address, etc). >>>> >>>> >>>>> We are hoping to deploy the new RDF onto mobycentral very >>>>> >>>>> >>>> soon, and I >>>> >>>> >>>>> just want to get a head count of who it is that will yell (beat up, >>>>> etc) at me ;-) >>>>> >>>>> Thanks, >>>>> >>>>> Eddie >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 From d.haase at gsf.de Thu Apr 13 03:58:19 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 13 Apr 2006 09:58:19 +0200 Subject: [MOBY-dev] Moby Collections in Taverna Message-ID: <200604130958.20054.d.haase@gsf.de> Hi all, I noticed that the handling of Moby collection outputs has changed in Taverna. Formerly (until version 1.2), a collection of n objects was processed with n invocations of the following step in the workflow. Now (version 1.3.1) this is done with only one invocation with n distinct queries (mobyData blocks). That's nice, because it reduces overhead. The downside is that for large collections this will inescapably lead to timeout problems. For our blast services for example I observed a limit of about 20 queries per invocation. I also found that the old multi-invocation behavior is still accessible by using the non-moby 'output' port. However I'm not sure if this is really the intended way... I think the optimal solution would be to have a 'max-number-of-queries-per-invocation' parameter to be set in the workflow definition. Is that feasible? Regards, dirk -- ---------------------------------------------------------- Dirk Haase phone +49 89 3187 3583 http://mips.gsf.de/~haase email d.haase at gsf.de From edward.kawas at gmail.com Thu Apr 13 09:56:30 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 13 Apr 2006 06:56:30 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604130958.20054.d.haase@gsf.de> Message-ID: <000b01c65f02$164e95a0$6700a8c0@notebook> Hi Dirk, The output port behaviour has been cloned for collections with a new port, Collection 'As Simples'. So that port now takes the n items in a collection and produces n simples that Taverna can iterate over. However, if that port isn't used and a collection is passed to a service that expects a simple, I transparently break apart the collection with n items into n invocations containing a simple and then invoke the service n times, rather than one time with a n invocation message. This was done, because I noticed that there were time out issues with very large collections. I haven't committed my changes in the Taverna cvs yet, so the only way to try these changes is to download an updated taverna-1.3.1.jar file from http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. I also have some example workflows at http://bioinfo.icapture.ubc.ca/ekawas/workflows/. Once I am ready, I will commit my changes and hopefully in the next release of Taverna (very soon I hear) the plugin will be updated. 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 Dirk Haase > Sent: Thursday, April 13, 2006 12:58 AM > To: Moby Developers > Subject: [MOBY-dev] Moby Collections in Taverna > > Hi all, > > I noticed that the handling of Moby collection outputs has > changed in Taverna. > Formerly (until version 1.2), a collection of n objects was > processed with n invocations of the following step in the workflow. > > Now (version 1.3.1) this is done with only one invocation > with n distinct queries (mobyData blocks). That's nice, > because it reduces overhead. The downside is that for large > collections this will inescapably lead to timeout problems. > For our blast services for example I observed a limit of > about 20 queries per invocation. > > I also found that the old multi-invocation behavior is still > accessible by using the non-moby 'output' port. However I'm > not sure if this is really the intended way... > > I think the optimal solution would be to have a > 'max-number-of-queries-per-invocation' parameter to be set in > the workflow definition. Is that feasible? > > Regards, > dirk > > -- > > ---------------------------------------------------------- > Dirk Haase phone +49 89 3187 3583 > http://mips.gsf.de/~haase email d.haase at gsf.de > _______________________________________________ > 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 Thu Apr 13 09:56:30 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 13 Apr 2006 06:56:30 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604130958.20054.d.haase@gsf.de> Message-ID: <000b01c65f02$164e95a0$6700a8c0@notebook> Hi Dirk, The output port behaviour has been cloned for collections with a new port, Collection 'As Simples'. So that port now takes the n items in a collection and produces n simples that Taverna can iterate over. However, if that port isn't used and a collection is passed to a service that expects a simple, I transparently break apart the collection with n items into n invocations containing a simple and then invoke the service n times, rather than one time with a n invocation message. This was done, because I noticed that there were time out issues with very large collections. I haven't committed my changes in the Taverna cvs yet, so the only way to try these changes is to download an updated taverna-1.3.1.jar file from http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. I also have some example workflows at http://bioinfo.icapture.ubc.ca/ekawas/workflows/. Once I am ready, I will commit my changes and hopefully in the next release of Taverna (very soon I hear) the plugin will be updated. 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 Dirk Haase > Sent: Thursday, April 13, 2006 12:58 AM > To: Moby Developers > Subject: [MOBY-dev] Moby Collections in Taverna > > Hi all, > > I noticed that the handling of Moby collection outputs has > changed in Taverna. > Formerly (until version 1.2), a collection of n objects was > processed with n invocations of the following step in the workflow. > > Now (version 1.3.1) this is done with only one invocation > with n distinct queries (mobyData blocks). That's nice, > because it reduces overhead. The downside is that for large > collections this will inescapably lead to timeout problems. > For our blast services for example I observed a limit of > about 20 queries per invocation. > > I also found that the old multi-invocation behavior is still > accessible by using the non-moby 'output' port. However I'm > not sure if this is really the intended way... > > I think the optimal solution would be to have a > 'max-number-of-queries-per-invocation' parameter to be set in > the workflow definition. Is that feasible? > > Regards, > dirk > > -- > > ---------------------------------------------------------- > Dirk Haase phone +49 89 3187 3583 > http://mips.gsf.de/~haase email d.haase at gsf.de > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Apr 19 09:45:40 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 19 Apr 2006 15:45:40 +0200 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <000b01c65f02$164e95a0$6700a8c0@notebook> References: <000b01c65f02$164e95a0$6700a8c0@notebook> Message-ID: <200604191545.41064.d.haase@gsf.de> Hi Eddie, On Thursday 13 April 2006 15:56, Edward Kawas wrote: > Hi Dirk, > > The output port behaviour has been cloned for collections with a new port, > Collection 'As Simples'. So that port now takes the n items in a collection > and produces n simples that Taverna can iterate over. Wow, that's what I call a prompt fix! > However, if that port isn't used and a collection is passed to a service > that expects a simple, I transparently break apart the collection with n > items into n invocations containing a simple and then invoke the service n > times, rather than one time with a n invocation message. This was done, > because I noticed that there were time out issues with very large > collections. OK, I see this behavior when I use the 'output' port. For the old collection-type port 'Object(Collection - )' things are strange: it seems that only the first element in the collection is piped to the next service. However, I think this solution is very convenient. The drawback is that we now have three distinct types of output ports for moby services, this will confuse people. What I want to say is that good documentation is desperately needed ;-) Thanks, dirk From edward.kawas at gmail.com Wed Apr 19 10:52:47 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Apr 2006 07:52:47 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604191545.41064.d.haase@gsf.de> Message-ID: <000401c663c0$ed443a20$6500a8c0@notebook> One last thing, When creating new workflows, stay away from the ports labelled 'input' and 'output'. They are there only for legacy reasons. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, April 19, 2006 6:46 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > Hi Eddie, > > On Thursday 13 April 2006 15:56, Edward Kawas wrote: > > Hi Dirk, > > > > The output port behaviour has been cloned for collections > with a new > > port, Collection 'As Simples'. So that port now takes the n > items in a > > collection and produces n simples that Taverna can iterate over. > > Wow, that's what I call a prompt fix! > > > However, if that port isn't used and a collection is passed to a > > service that expects a simple, I transparently break apart the > > collection with n items into n invocations containing a simple and > > then invoke the service n times, rather than one time with a n > > invocation message. This was done, because I noticed that > there were > > time out issues with very large collections. > > OK, I see this behavior when I use the 'output' port. For the > old collection-type port 'Object(Collection - > )' things are > strange: it seems that only the first element in the > collection is piped to the next service. > > However, I think this solution is very convenient. The > drawback is that we now have three distinct types of output > ports for moby services, this will confuse people. What I > want to say is that good documentation is desperately needed ;-) > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Apr 19 11:28:02 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 19 Apr 2006 17:28:02 +0200 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <000401c663c0$ed443a20$6500a8c0@notebook> References: <000401c663c0$ed443a20$6500a8c0@notebook> Message-ID: <200604191728.03047.d.haase@gsf.de> On Wednesday 19 April 2006 16:52, Edward Kawas wrote: > One last thing, > > When creating new workflows, stay away from the ports labelled 'input' and > 'output'. They are there only for legacy reasons. But currently I still need the 'output' for linking non-moby services/widgets, right? For example to use the 'Flatten' processor to merge lists of lists. From edward.kawas at gmail.com Wed Apr 19 11:30:25 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Apr 2006 08:30:25 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604191728.03047.d.haase@gsf.de> Message-ID: <000501c663c6$2f4eb6c0$6500a8c0@notebook> For the moby widgets, the output port isnt necessary. They should work with the other ports as well. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, April 19, 2006 8:28 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > On Wednesday 19 April 2006 16:52, Edward Kawas wrote: > > One last thing, > > > > When creating new workflows, stay away from the ports > labelled 'input' > > and 'output'. They are there only for legacy reasons. > > But currently I still need the 'output' for linking non-moby > services/widgets, right? For example to use the 'Flatten' > processor to merge lists of lists. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Apr 19 10:50:52 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Apr 2006 07:50:52 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604191545.41064.d.haase@gsf.de> Message-ID: <000301c663c0$a8d54e60$6500a8c0@notebook> Hi Dirk, You are right about the documentation and I plan on updating it today, but I want to outline what the behaviour is now: Service Output ----Connects to ---> Service Input 1 Simple Simple 2 Simple Collection 3 Collection Simple 4 Collection Collection 5 CollAsSimples Simples 6 CollAsSimples Collection Note that CollAsSimples transforms a collection into a list of simples. Case 1, 4 are straight forward - the output is passed to the input as is. Case 2, 6 - the simple (or a 'taverna list' of simples) are placed in a collection and passed to the service. Case 3 - the collection is broken down and each simple in the collection is passed to the downstream service one at a time (in a single invocation message). i.e. 1 2 3 4 Becomes 1 2 3 4 Case 5 - The collection became a list of simples and this case becomes similar to case 1. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, April 19, 2006 6:46 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > Hi Eddie, > > On Thursday 13 April 2006 15:56, Edward Kawas wrote: > > Hi Dirk, > > > > The output port behaviour has been cloned for collections > with a new > > port, Collection 'As Simples'. So that port now takes the n > items in a > > collection and produces n simples that Taverna can iterate over. > > Wow, that's what I call a prompt fix! > > > However, if that port isn't used and a collection is passed to a > > service that expects a simple, I transparently break apart the > > collection with n items into n invocations containing a simple and > > then invoke the service n times, rather than one time with a n > > invocation message. This was done, because I noticed that > there were > > time out issues with very large collections. > > OK, I see this behavior when I use the 'output' port. For the > old collection-type port 'Object(Collection - > )' things are > strange: it seems that only the first element in the > collection is piped to the next service. > > However, I think this solution is very convenient. The > drawback is that we now have three distinct types of output > ports for moby services, this will confuse people. What I > want to say is that good documentation is desperately needed ;-) > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Thu Apr 20 03:42:54 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 20 Apr 2006 09:42:54 +0200 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <000301c663c0$a8d54e60$6500a8c0@notebook> References: <000301c663c0$a8d54e60$6500a8c0@notebook> Message-ID: <200604200942.55192.d.haase@gsf.de> Eddie, thanks for clarification, but if in case 3 (Collection -> Simple) a _single_ invocation message is sent wouldn't the XML rather look like: 1 2 3 4 On Wednesday 19 April 2006 16:50, Edward Kawas wrote: > Service Output ----Connects to ---> Service Input > 3 ?Collection???????????????????????????Simple > Case 3 - the collection is broken down and each simple in the collection is > passed to the downstream service one at a time (in a single invocation > message). i.e. > > > ? > ???????? > ????????????????1 > ???????? > ? > > > > ? > ???????? > ????????????????2 > ???????? > ? > > > > ? > ???????? > ????????????????3 > ???????? > ? > > > > ? > ???????? > ????????????????4 > ???????? > ? > From edward.kawas at gmail.com Thu Apr 20 09:42:53 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 20 Apr 2006 06:42:53 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604200942.55192.d.haase@gsf.de> Message-ID: <000701c66480$53c48f60$6500a8c0@notebook> Hi, The message could look like that if I sent it all at once. But I don?t because conceivably, there could be hundreds of invocations and would most likely timeout. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, April 20, 2006 12:43 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > Eddie, > > thanks for clarification, but if in case 3 (Collection -> > Simple) a _single_ invocation message is sent wouldn't the > XML rather look like: > > > > > 1 > > > 2 > > > 3 > > > 4 > > > > > On Wednesday 19 April 2006 16:50, Edward Kawas wrote: > > Service Output ----Connects to ---> Service Input > > 3 ?Collection???????????????????????????Simple > > > Case 3 - the collection is broken down and each simple in the > > collection is passed to the downstream service one at a time (in a > > single invocation message). i.e. > > > > > > ? > > ???????? > > ????????????????1 > > ???????? > > ? > > > > > > > > ? > > ???????? > > ????????????????2 > > ???????? > > ? > > > > > > > > ? > > ???????? > > ????????????????3 > > ???????? > > ? > > > > > > > > ? > > ???????? > > ????????????????4 > > ???????? > > ? > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From senger at ebi.ac.uk Sun Apr 23 14:22:17 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 23 Apr 2006 19:22:17 +0100 (BST) Subject: [MOBY-dev] jMoby does not compile Message-ID: Eddie! Quo usque tandem abutere, Catilina, patientia nostra? (We are *not*, at least not yet, using Java 1.5...) Martin PS: [javac] Found 4 semantic errors compiling "/home/senger/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceInstanceEditorWindow.java": [javac] 172. this.setMaximumSize(new java.awt.Dimension(600, 550)); [javac] ^---------------------------------------------------^ [javac] *** Semantic Error: No accessible method with signature "setMaximumSize(java.awt.Dimension)" was found in type "org.biomoby.client.ui.graphical.applets.serviceInstanceCreationTool.ServiceInstanceEditorWindow". [javac] 173. this.setMinimumSize(new java.awt.Dimension(600, 550)); [javac] ^---------------------------------------------------^ [javac] *** Semantic Error: No accessible method with signature "setMinimumSize(java.awt.Dimension)" was found in type "org.biomoby.client.ui.graphical.applets.serviceInstanceCreationTool.ServiceInstanceEditorWindow". ...etc... -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Mon Apr 24 10:06:44 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Apr 2006 15:06:44 +0100 (BST) Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <444CDAD9.9020308@ucalgary.ca> Message-ID: > Should we require Java 1.5, or at least set some date, say August 2006, > at which we will require 1.5? > Fine with me (I have just decided to make a similar suggestion when your email came :-)). Perhaps middle of the year, June 30? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Mon Apr 24 10:06:44 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Apr 2006 15:06:44 +0100 (BST) Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <444CDAD9.9020308@ucalgary.ca> Message-ID: > Should we require Java 1.5, or at least set some date, say August 2006, > at which we will require 1.5? > Fine with me (I have just decided to make a similar suggestion when your email came :-)). Perhaps middle of the year, June 30? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Mon Apr 24 10:16:41 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:16:41 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDDC9.1080805@ucalgary.ca> June 30th sounds good to me! Perhaps we should create a Java 1.4 branch in CVS after that date for fixes, but no code improvements. That way any 1.4 users can still have the basic functionality until they can upgrade, and we can start changing the code on the CVS trunk as much as we want right away... >> Should we require Java 1.5, or at least set some date, say August 2006, >> at which we will require 1.5? >> >> > Fine with me (I have just decided to make a similar suggestion when > your email came :-)). Perhaps middle of the year, June 30? > > Martin > > From gordonp at ucalgary.ca Mon Apr 24 10:16:41 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:16:41 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDDC9.1080805@ucalgary.ca> June 30th sounds good to me! Perhaps we should create a Java 1.4 branch in CVS after that date for fixes, but no code improvements. That way any 1.4 users can still have the basic functionality until they can upgrade, and we can start changing the code on the CVS trunk as much as we want right away... >> Should we require Java 1.5, or at least set some date, say August 2006, >> at which we will require 1.5? >> >> > Fine with me (I have just decided to make a similar suggestion when > your email came :-)). Perhaps middle of the year, June 30? > > Martin > > From gordonp at ucalgary.ca Mon Apr 24 10:04:09 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:04:09 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDAD9.9020308@ucalgary.ca> Maybe we should we open up the question: Should we require Java 1.5, or at least set some date, say August 2006, at which we will require 1.5? If we don't set something in stone, it will never happen. It's been out for 2 years now...Java 1.6 is going to be out soon! On the developer side there is virtually no reason not to use 1.5. Changing your 'enum' variables isn't hard. The only client side issue I've run in to is Mac OS X 10.3 or lower users (who aren't upgrading because they require legacy Mac OS 9 binary compatibility for old programs they still need). > Eddie! > Quo usque tandem abutere, Catilina, patientia nostra? > > (We are *not*, at least not yet, using Java 1.5...) > > From gordonp at ucalgary.ca Mon Apr 24 10:04:09 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:04:09 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDAD9.9020308@ucalgary.ca> Maybe we should we open up the question: Should we require Java 1.5, or at least set some date, say August 2006, at which we will require 1.5? If we don't set something in stone, it will never happen. It's been out for 2 years now...Java 1.6 is going to be out soon! On the developer side there is virtually no reason not to use 1.5. Changing your 'enum' variables isn't hard. The only client side issue I've run in to is Mac OS X 10.3 or lower users (who aren't upgrading because they require legacy Mac OS 9 binary compatibility for old programs they still need). > Eddie! > Quo usque tandem abutere, Catilina, patientia nostra? > > (We are *not*, at least not yet, using Java 1.5...) > > From markw at illuminae.com Tue Apr 25 10:53:45 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 25 Apr 2006 07:53:45 -0700 Subject: [MOBY-dev] updating MOBY Central with input/output articleNames Message-ID: Hi all, A few months ago the spec for service registration was tightened such that all inputs and outputs require an articleName. This is now required also in Taverna workflows, and as such, many "illegitimate" services currently in the registry will not function with Taverna even though they are perfectly functional in reality. Given that these services are not looking for an articleName, it will do no harm to them if one were added. Thus the fastest way to bring all service registrations back into compliance with the API would be for me to manipulate the MOBY Central database directly and add "dummy" articleNames ("input", "output") to all inputs and outputs that are currently un-named. Would this bother anyone? Please let me know ASAP. Mark From senger at ebi.ac.uk Tue Apr 25 17:25:58 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Apr 2006 22:25:58 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <444CDDC9.1080805@ucalgary.ca> Message-ID: If you disagree please say so. Your silence will be (in due time) considered as a yes vote. Thanks and regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Tue Apr 25 19:21:22 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 25 Apr 2006 16:21:22 -0700 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: Message-ID: <003001c668be$f8392f50$6700a8c0@notebook> If it means that my commits wont break things, I am in ;-) Ed > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Martin Senger > Sent: Tuesday, April 25, 2006 2:26 PM > To: Moby Developers > Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. > from June 30, 2006 > > If you disagree please say so. Your silence will be (in due > time) considered as a yes vote. > > Thanks and regards, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Apr 25 19:21:22 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 25 Apr 2006 16:21:22 -0700 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: Message-ID: <003001c668be$f8392f50$6700a8c0@notebook> If it means that my commits wont break things, I am in ;-) Ed > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Martin Senger > Sent: Tuesday, April 25, 2006 2:26 PM > To: Moby Developers > Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. > from June 30, 2006 > > If you disagree please say so. Your silence will be (in due > time) considered as a yes vote. > > Thanks and regards, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From senger at ebi.ac.uk Tue Apr 25 21:08:08 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 02:08:08 +0100 (BST) Subject: [MOBY-dev] BioMoby/BioCASE integration Message-ID: Dear all, Me and Milko (from IPGRI) have finished the first version of integrating BioCASE and BioMoby. The project is documented here (the same link is also available from the main jMoby page): http://moby.generationcp.org/bb_services/docs/index.html. There is only one service of this kind running, so much more testing is needed - but one has to start somewhere, right? Any comments welcome, With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Wed Apr 26 12:07:05 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 26 Apr 2006 10:07:05 -0600 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <003001c668be$f8392f50$6700a8c0@notebook> References: <003001c668be$f8392f50$6700a8c0@notebook> Message-ID: <444F9AA9.3020801@ucalgary.ca> Would anyone be opposed to creating a 'java15' branch right away? On June 30th, we can merge it back into the trunk. I suggest this for two reasons: 1) It allows me to commit a bunch of changes right away without affecting trunk users 2) We won't have to do as much work on the transition date if we know in advance that the java15 branch works nicely > If it means that my commits wont break things, I am in ;-) > > Ed > > >> -----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: Tuesday, April 25, 2006 2:26 PM >> To: Moby Developers >> Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. >> from June 30, 2006 >> >> If you disagree please say so. Your silence will be (in due >> time) considered as a yes vote. >> >> Thanks and regards, >> Martin >> >> -- >> Martin Senger >> email: martin.senger at gmail.com >> skype: martinsenger >> >> >> _______________________________________________ >> 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 senger at ebi.ac.uk Wed Apr 26 12:15:06 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 17:15:06 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <444F9AA9.3020801@ucalgary.ca> Message-ID: > Would anyone be opposed to creating a 'java15' branch right away? > I would like to continue to work on the HEAD (or is it called TRUNK?). Otherwise, I do not mind. But isn't it easier just to move to java 1.5. sooner? Is there anyone around still in need of pure 1.4? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Wed Apr 26 12:27:37 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 26 Apr 2006 10:27:37 -0600 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: References: Message-ID: <444F9F79.7030009@ucalgary.ca> True. Perhaps we are flattering ourselves by assuming there are so many jMOBY developers to appease :-) I think Martin, Eddie and myself account for 99% of the commits to jMOBY... In terms of jMOBY library *users*, if they need Java 1.4, we can put a 'preJava15' tag on the trunk right now, and they'll have to upgrade their Java before they can check out any newer code. The sooner we switch, the better! > I would like to continue to work on the HEAD (or is it called > TRUNK?). Otherwise, I do not mind. But isn't it easier just to move to > java 1.5. sooner? Is there anyone around still in need of pure 1.4? > > Martin > > From senger at ebi.ac.uk Wed Apr 26 12:51:57 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 17:51:57 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <444F9F79.7030009@ucalgary.ca> Message-ID: I agree. Let's wait for at least one confirming reply from Spain and from Germany. Anybody there to give us green light for Java 1.5. now? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Wed Apr 26 13:03:57 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 18:03:57 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: Message-ID: Also we need a green light from Eddie because he needs to check whether jmoby.jar, created with java 1.5., will be allowed to put in taverna - I am not sure if they still use 1.4 or already switched to 1.5. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From d.haase at gsf.de Thu Apr 27 10:54:04 2006 From: d.haase at gsf.de (Haase, Dirk) Date: Thu, 27 Apr 2006 16:54:04 +0200 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 References: Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A0882@sw-rz010.gsf.de> Hmm, I don't know if you refer to us (Heiko, MIPS, me) when you say Germany... As we are not actively developing (we are only always complaining ;-) we give the greenest light possible. Regards, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Wed 4/26/2006 6:51 PM To: Paul Gordon Cc: Core developer announcements Subject: Re: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 I agree. Let's wait for at least one confirming reply from Spain and from Germany. Anybody there to give us green light for Java 1.5. now? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ 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: not available Type: application/ms-tnef Size: 3128 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20060427/01fbd989/attachment.bin From senger at ebi.ac.uk Thu Apr 27 20:24:11 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 01:24:11 +0100 (BST) Subject: [MOBY-dev] jMoby/Dashboard update Message-ID: Hi, Recently, I have made few fixes in Dashboard (and some in jMoby itself) so it is worth to cvs update. The main fixes were made thanks to Dirk who very nicely and accurately described some found bugs. Thanks. What has been changed: * the local cache default directory includes now a user name (on Windows that was true before, but on Unix/Mac the default was just /tmp) - this makes it easier to use Dashboard during workshops where people share the same machine * I tried to improve visibility of the progress bars when a local cache is loaded. I hope I have improved it - but still there are some situations when it still continues to load the cache behind the scene (e.g. if you add new panel during loading). Please let me know if you spot strange behaviour. Synchronizing entity trees showed to be, so far, the most challenging part of Dashboard (from the developer's point of view), so I will be glad to make it better any time. * The editing of various tables (e.g. editing article names in the registering service panel) is properly finished just by loosing focus, hitting ENTER is not needed any more. [ A side comment for Java developers: this was amazingly easy to fix once I found the solution on google. There is a single property to be set in a JTable constructor, and that's it!: putClientProperty ("terminateEditOnFocusLost", Boolean.TRUE); ] * The ant configuration file build.xml: - was splitted into more files to be easier maintained. - I have commented out some dependency rules in build.xml - search there for 'dependset' to see details - jmoby.jar now splitted (jmoby.jar and jmoby-dashboard.jar): I would like to separate into more jar files in the future (see my next email about) * small improvement in the deployment sub-panel in the pattern field (see {Service} at the end of the panel help page about it) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Thu Apr 27 20:32:50 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 01:32:50 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar Message-ID: Eddie (and others), I think about making more (splitted) jar files, not only jmoby.jar. I would like to have a lightweight version of jmoby.jar that can be used for biomoby service providers (for those implementing a moby service in a different directory etc.). For normal jMoby users this would not be any change. Could you perhaps identify what which from your packages do not need to be for those who are writting service implementation? I will then update the build.xml. (Look there and you will see I have in mind: search for jmoby-dashboard.) Think also about how many of these new jar files (and which ones) you will need to move to taverna (together with the lightweight jmoby.jar, of course). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Thu Apr 27 23:59:32 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 27 Apr 2006 20:59:32 -0700 Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: Message-ID: <000101c66a78$28e5b3c0$6500a8c0@notebook> Hi Martin, Most likely all of the classes in the package org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry are not needed by clients writing services. Classes in the package org.biomoby.shared.extended are used for parsing RDF and are probably no use to clients. Eddie > -----Original Message----- > From: Martin Senger [mailto:senger at ebi.ac.uk] > Sent: Thursday, April 27, 2006 5:33 PM > To: Edward Kawas > Cc: Moby Developers > Subject: splitting jmoby.jar > > Eddie (and others), > I think about making more (splitted) jar files, not only > jmoby.jar. I would like to have a lightweight version of > jmoby.jar that can be used for biomoby service providers (for > those implementing a moby service in a different directory > etc.). For normal jMoby users this would not be any change. > Could you perhaps identify what which from your packages > do not need to be for those who are writting service > implementation? I will then update the build.xml. (Look there > and you will see I have in mind: search for > jmoby-dashboard.) > Think also about how many of these new jar files (and > which ones) you will need to move to taverna (together with > the lightweight jmoby.jar, of course). > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > > From ivanp at mmb.pcb.ub.es Fri Apr 28 04:51:09 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 28 Apr 2006 10:51:09 +0200 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: References: Message-ID: <4451D77D.10200@mmb.pcb.ub.es> Hi, Sorry for my delay in answering. I've been ill (and offline) the last days. Java 1.5 is welcome from Spain, in fact, we've working with 1.5 since it was launched. Regards, Iv?n P?rraga Garc?a Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es http://mmb.pcb.ub.es Martin Senger escribi?: > I agree. > Let's wait for at least one confirming reply from Spain and from > Germany. Anybody there to give us green light for Java 1.5. now? > > Martin > > From senger at ebi.ac.uk Fri Apr 28 06:35:30 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 11:35:30 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <4451D77D.10200@mmb.pcb.ub.es> Message-ID: Eddie, how is going your Taverna 1.5.enquiries? It seems that we may make a tag 1.4, and start to use 1.5 when you give us a green light. Don't worry, however, it does not need to be *now*. Cheers, Martin > Sorry for my delay in answering. I've been ill (and offline) the last > days. Java 1.5 is welcome from Spain, in fact, we've working with 1.5 > since it was launched. > > Regards, > > Iv?n P?rraga Garc?a > Molecular Modelling & Bioinformatics Unit > INB - Instituto Nacional de Bioinform?tica > Josep Samitier 1-5 > 08028 Barcelona > Spain > tel.: +34 93 403 71 55 > fax.: +34 93 403 71 57 > e-mail: ivanp at mmb.pcb.ub.es > http://mmb.pcb.ub.es > > > > Martin Senger escribi?: > > I agree. > > Let's wait for at least one confirming reply from Spain and from > > Germany. Anybody there to give us green light for Java 1.5. now? > > > > Martin > > > > > -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Apr 28 10:01:44 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 08:01:44 -0600 Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <000101c66a78$28e5b3c0$6500a8c0@notebook> References: <000101c66a78$28e5b3c0$6500a8c0@notebook> Message-ID: <44522048.3010503@ucalgary.ca> Hi Ediie, Actually, I write clients, and use org.biomoby.shared.extended to type-check data, so yes a client may need these. In my Seahawk application (which uses Java 1.5), these are the MOBY directories I imported from src/main/org/biomoby: ./client ./client/rdf ./client/rdf/vocabulary ./registry ./registry/definitions ./registry/definitions/types ./registry/properties ./service ./service/generated ./shared ./shared/data ./shared/dom ./shared/dom/wrappers ./shared/parser ./shared/extended ./shared/schema If we are really interested in making truly lightweight JARs available, I may be able to help, should go to Java 1.5 sooner rather than later. I've made uncommitted changes to several classes so that MOBY doesn't absoluely require having the tulsoft, JDOM and ebi JARs around. Seahawk packs everything it needs to call MOBY Central and remote services into a 2.5 MB JAR file (including the relevant classes from Axis, Xerces, Xalan, Commons Logging, etc., etc.)... Regards, Paul > Hi Martin, > > Most likely all of the classes in the package > org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry are > not needed by clients writing services. > > Classes in the package org.biomoby.shared.extended are used for parsing RDF and > are probably no use to clients. > > Eddie > > >> -----Original Message----- >> From: Martin Senger [mailto:senger at ebi.ac.uk] >> Sent: Thursday, April 27, 2006 5:33 PM >> To: Edward Kawas >> Cc: Moby Developers >> Subject: splitting jmoby.jar >> >> Eddie (and others), >> I think about making more (splitted) jar files, not only >> jmoby.jar. I would like to have a lightweight version of >> jmoby.jar that can be used for biomoby service providers (for >> those implementing a moby service in a different directory >> etc.). For normal jMoby users this would not be any change. >> Could you perhaps identify what which from your packages >> do not need to be for those who are writting service >> implementation? I will then update the build.xml. (Look there >> and you will see I have in mind: search for >> jmoby-dashboard.) >> Think also about how many of these new jar files (and >> which ones) you will need to move to taverna (together with >> the lightweight jmoby.jar, of course). >> >> Cheers, >> Martin >> >> -- >> Martin Senger >> email: martin.senger at gmail.com >> skype: martinsenger >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From senger at ebi.ac.uk Fri Apr 28 10:08:38 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 15:08:38 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <44522048.3010503@ucalgary.ca> Message-ID: > Actually, I write clients > I am not talking about clients. My motivation for splitting is to make a lightweight jmoby.jar for service providers. That's all. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Apr 28 10:30:20 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 08:30:20 -0600 Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: References: Message-ID: <445226FC.7090203@ucalgary.ca> Right, I realize that. I was replying to Eddie's post: "Classes in the package org.biomoby.shared.extended are used for parsing RDF and are probably no use to clients." Perhaps he meant service providers, not clients? In any case, if we are interested in having more people use jMOBY in their current work, we should keep it in the back of our minds that they may not be using the jMOBY CVS checkout as their primary development directory. I, for example am in that boat, since my main program (Bluejay) has its own CVS directory. Self-contained JARs would make using jMOBY a lot easier for such situations. This is what I have done, and I am willing to provide these to others. The current option is for such developers to adopt the 50MB of JAR files in jMOBY's lib directory in their application deployments... Don't get me wrong, the current setup is great for people developing jMOBY code, but it's not ideal for people who just want to use jMOBY code in another application... My CAN$0.02, Paul Martin Senger wrote: >> Actually, I write clients >> >> > I am not talking about clients. My motivation for splitting is to make > a lightweight jmoby.jar for service providers. That's all. > > Martin > > From senger at ebi.ac.uk Fri Apr 28 11:43:03 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 16:43:03 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <000101c66a78$28e5b3c0$6500a8c0@notebook> Message-ID: > Most likely all of the classes in the package > org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry are > Okay, I splitted jmoby.jar into 3: jmoby-dashboard.jar has org.biomoby.service.dashboard, jmoby-others has org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry, and jmoby.jar has the rest. Which means that if anybody wants to develop a service in a different directory (if it does directly in jMoby directiry, nothing changed), she needs to copy there only jmoby.jar (and few others third-party libraries - I have also created a short document "How to develop a BioMoby service" (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopment.html) to summarize what har files are needed. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Fri Apr 28 11:45:35 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 16:45:35 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <445226FC.7090203@ucalgary.ca> Message-ID: > Perhaps he meant service providers, not clients? > That was also my interpretation. > In any case, if we are interested in having more people use jMOBY in > their current work, we should keep it in the back of our minds that they > may not be using the jMOBY CVS checkout as their primary development > directory. > Definitely. It would be useful for all of us if you can write a page (and link it from the main jMoby's index.html) explaining how to squeeze jar files into smaller ones, depending on your needs. Regards, Martin From gordonp at ucalgary.ca Fri Apr 28 17:09:31 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 15:09:31 -0600 Subject: [MOBY-dev] Shims Message-ID: <4452848B.2080500@ucalgary.ca> Hi everyone, This is a very general question, especially for non-native-English speakers. I was going to add a top-level "Shim" category of services to the ontology, but I'm pretty sure most non-native-English speakers would have no idea what this means. I'm borrowing the term from D Hull, R Stevens, P Lord, C Wroe, C Goble (2004). Treating shimantic web syndrome with ontologies. First AKT workshop on Semantic Web Services (AKT-SWS04). Essentially, I'm tired of having a DNASequence, and not being able to directly call BLAST services because they take FASTA_NA. Services in the "Shim" category would be something like the Conversion category, but specifically they would convert between MOBY data types for the purpose of service compatibility. Having all such services in one category would make it easier to do these transformations automagically for the user. But do people think this is a good name, or what would they suggest? shim: A thin slip, usually of metal, used to fill up a space between parts subject to wear, to align or adjust the level of rails, etc. (Oxford English Dictionary) From markw at illuminae.com Fri Apr 28 17:23:05 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 28 Apr 2006 14:23:05 -0700 Subject: [MOBY-dev] Shims In-Reply-To: <4452848B.2080500@ucalgary.ca> References: <4452848B.2080500@ucalgary.ca> Message-ID: I think it is already there, isn't it? There is a "conversion" category for sure, which is intended for that purpose. M On Fri, 28 Apr 2006 14:09:31 -0700, Paul Gordon wrote: > Hi everyone, > > This is a very general question, especially for non-native-English > speakers. I was going to add a top-level "Shim" category of services > to the ontology, but I'm pretty sure most non-native-English speakers > would have no idea what this means. I'm borrowing the term from > > D Hull, R Stevens, P Lord, C Wroe, C Goble (2004). Treating shimantic > web syndrome with ontologies. First AKT workshop on Semantic Web > Services (AKT-SWS04). > > Essentially, I'm tired of having a DNASequence, and not being able to > directly call BLAST services because they take FASTA_NA. Services in > the "Shim" category would be something like the Conversion category, but > specifically they would convert between MOBY data types for the purpose > of service compatibility. Having all such services in one category > would make it easier to do these transformations automagically for the > user. But do people think this is a good name, or what would they > suggest? > > shim: A thin slip, usually of metal, used to fill up a space between > parts subject to wear, to align or adjust the level of rails, etc. > (Oxford English Dictionary) > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Fri Apr 28 18:44:04 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 16:44:04 -0600 Subject: [MOBY-dev] Shims In-Reply-To: References: <4452848B.2080500@ucalgary.ca> Message-ID: <44529AB4.9010602@ucalgary.ca> Mark Wilkinson wrote: > I think it is already there, isn't it? There is a "conversion" category > for sure, which is intended for that purpose. > But that's not how it's being used now. That why I said... >> Services in >> the "Shim" category would be something like the Conversion category, but >> specifically they would convert between MOBY data types for the purpose >> of service compatibility. From ssoiland at cs.man.ac.uk Sat Apr 29 08:30:01 2006 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Sat, 29 Apr 2006 13:30:01 +0100 Subject: [MOBY-dev] Shims In-Reply-To: <4452848B.2080500@ucalgary.ca> References: <4452848B.2080500@ucalgary.ca> Message-ID: <09EDCBE0-BDD0-4ED1-8B10-F496F989AE7B@cs.man.ac.uk> On 28. apr. 2006, at 22:09, Paul Gordon wrote: > This is a very general question, especially for non-native-English > speakers. I was going to add a top-level "Shim" category of services > to the ontology, but I'm pretty sure most non-native-English speakers > would have no idea what this means. I'm borrowing the term from As a non-native speaker I had to look up the term itself. However, we are using the term "shim" in mygrid/Taverna for the very same concept of making services with nearly-the-same-datatypes work together. However, I wish there could be a better word to present to the user what this category would be. I would assume many like me to just assume this had something to do with "the shim system" which I didn't know anything about, and so I would never explore it. "Conversion" is much better, even if its already in use. Maybe look into what really are the different conversions, and call the shimming "Format conversion" or something. -- Stian Soiland, myGrid project School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From senger at ebi.ac.uk Sat Apr 29 17:26:05 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sat, 29 Apr 2006 22:26:05 +0100 (BST) Subject: [MOBY-dev] logging ip requests from moby MoSeS genereated service In-Reply-To: <442AB936.2080901@mmb.pcb.ub.es> Message-ID: Hi, > I need to log some data about the use of the webservices generated by > MoSeS. One of the things is the IP address of the caller. Is there any > sensible way to do it from the webservice implementing class? > I have added it there (into org.biomoby.service.BaseService). Now you can call from your implementation class (because it inherits from the BaseService via generated skeleton): String remoteAddr = getCallerAddr(); Be aware, however, that it may not return an address on the real Biomoby client, but of some proxy which is in between. But for that, I am helpless. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From carole at cs.man.ac.uk Sat Apr 29 18:25:57 2006 From: carole at cs.man.ac.uk (Carole Goble) Date: Sat, 29 Apr 2006 23:25:57 +0100 Subject: [MOBY-dev] Shims In-Reply-To: <09EDCBE0-BDD0-4ED1-8B10-F496F989AE7B@cs.man.ac.uk> References: <4452848B.2080500@ucalgary.ca> <09EDCBE0-BDD0-4ED1-8B10-F496F989AE7B@cs.man.ac.uk> Message-ID: <4453E7F5.3000609@cs.man.ac.uk> Stian as the person who coined the term shim it is there precisely because there are a whole range of words that have been used. mediator, adaptor, conversion etc. not all shims are conversions. the new term gives a fresh start. By the way, the first shim paper not by manchester is now published Adapters, shims, and glue--service interoperability for in silico experiments U. Radetzki, U. Leser, S. C. Schulze-Rauschenbach, J. Zimmermann, J. Lussem, T. Bode, and A. B. Cremers Bioinformatics 2006 22: 1137-1143. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/9/1137?etoc Carole > On 28. apr. 2006, at 22:09, Paul Gordon wrote: > > >> This is a very general question, especially for non-native-English >> speakers. I was going to add a top-level "Shim" category of services >> to the ontology, but I'm pretty sure most non-native-English speakers >> would have no idea what this means. I'm borrowing the term from >> > > As a non-native speaker I had to look up the term itself. However, we > are using the term "shim" in mygrid/Taverna for the very same concept > of making services with nearly-the-same-datatypes work together. > However, I wish there could be a better word to present to the user > what this category would be. I would assume many like me to just > assume this had something to do with "the shim system" which I didn't > know anything about, and so I would never explore it. > > "Conversion" is much better, even if its already in use. Maybe look > into what really are the different conversions, and call the shimming > "Format conversion" or something. > > From heese at mpiz-koeln.mpg.de Tue Apr 4 10:34:58 2006 From: heese at mpiz-koeln.mpg.de (heese at mpiz-koeln.mpg.de) Date: Tue, 4 Apr 2006 12:34:58 +0200 (CEST) Subject: [MOBY-dev] RDF file generation for test registry Message-ID: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi, these are 3 questions for Eddie, but the answers might be interesting for others, that's why I post it to the whole list. I'm quite new in the BioMoby business, so I hope my questions havn't been asked before (at least I didn't find anything). 1. Is there a page available equivalent to http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm to create/update an rdf document for services registered in the TestCentral at (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? 2. I registered a couple of services at the TestCentral the old way without giving a RDF signature URL. Now I wanted to deregister them the old way but it failed since you generated an rdf last week that included my services. Can you please deregister them, so I can regain control over them? I will use an RDF file for registration next time, I promise :) ... 3. Is it correct that the "getSignatureForm"-script is only meant to help people updating their already working Services, i.e. generating an RDF file for those? And that in future one should generate an RDF file by hand and then use only the agent to register it? Or will it always be possible to first register the old way, then use "getSignatureForm" to update the RDF? Thanks, maren From dgpisano at cnb.uam.es Tue Apr 4 11:04:18 2006 From: dgpisano at cnb.uam.es (David Gonzalez Pisano) Date: Tue, 4 Apr 2006 13:04:18 +0200 Subject: [MOBY-dev] Object naming inconsistencies Message-ID: Hi, Gonzalo Claros from INB at Malaga and some other members have found some inconsistencies in the moby ontology datatypes names. Looking at an BioMOBY ontology release from 05/10/04, we deduced that it was recommended to use compound names with the underscore "_" to separate words. However, right now, we can find strange cases like: text_plain text-plain PMUT-Text PMUT_Text PDB-Text text-formatted text_formatted text-html text_html and so on When differences are in final datatypes (PMUT_Text, PDB-Text, etc) it is not so disturbing,, but when the alternate names correspond to key nodes like text_formatted, plain_text or text_html, the name difference can affect implementations (INB implementations and your own services, that's why we ask here). At INB, we are considering using the underscore "_" in any case, but we would like to maintain compatibility with BioMOBY Central in Canada. So, which will be considered the main root object, the one with "-" or the one with "-"? What are you using? Cheers, David From gordonp at ucalgary.ca Tue Apr 4 13:49:13 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 04 Apr 2006 07:49:13 -0600 Subject: [MOBY-dev] Object naming inconsistencies In-Reply-To: References: Message-ID: <44327959.7030801@ucalgary.ca> May I humbly suggest that we use the hyphen ('-'), as this at the very least feigns the desire to use the existing standards in HTTP content-type headers/MIME/etc... > Hi, > > Gonzalo Claros from INB at Malaga and some other members have found > some inconsistencies in the moby ontology datatypes names. Looking at > an BioMOBY ontology release from 05/10/04, we deduced that it was > recommended to use compound names with the underscore "_" to separate > words. However, right now, we can find strange cases like: > > text_plain > text-plain > PMUT-Text > PMUT_Text > PDB-Text > text-formatted > text_formatted > text-html > text_html > > and so on > > When differences are in final datatypes (PMUT_Text, PDB-Text, etc) it > is not so disturbing,, but when the alternate names correspond to key > nodes like text_formatted, plain_text or text_html, the name > difference can affect implementations (INB implementations and your > own services, that's why we ask here). > > At INB, we are considering using the underscore "_" in any case, but > we would like to maintain compatibility with BioMOBY Central in > Canada. So, which will be considered the main root object, the one > with "-" or the one with "-"? What are you using? > > Cheers, > > David > > _______________________________________________ > 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 Apr 4 15:56:50 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 04 Apr 2006 08:56:50 -0700 Subject: [MOBY-dev] [moby] RDF file generation for test registry In-Reply-To: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> References: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <1144166210.5952.14.camel@bioinfo.icapture.ubc.ca> On Tue, 2006-04-04 at 12:34 +0200, heese at mpiz-koeln.mpg.de wrote: > my services. Can you please deregister them, so I can regain control over > them? I will use an RDF file for registration next time, I promise :) ... The RDF signature migration has been a painfully slow process for a number of reasons - partly the desire to coordinate with other efforts who are on a different schedule, and in part because the desire to create an RDF document that is both extensible *and* computable ("reason-able") is very strong. On the other hand, removing the ability of a script kiddie to delete the entire registry was also a high priority, so we currently find ourselves "in limbo". The latest hiccup was my discovery last week that the Dublin Core RDF is ~OWL Full, and we use Dublin Core in our RDF signature. This means that we could not use a reasoner to do request/service mapping... which is one of the useful features of moving to an RDF-based service description (a la S-MOBY). Matthew H at Manchester has just given me a heads-up of a "patched" version of the Dublin Core that we can use instead of the native one, and this should allow us to use a DL reasoner. I'm trying to find time to test this in reality using a few signature RDF's, but my own time is quite limited these days as we approach the end of the school term. It's just a lack of hands for what it turning out to be a more difficult task than we had first imagined! Eddie can answer the other comments. M From edward.kawas at gmail.com Tue Apr 4 14:02:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 4 Apr 2006 07:02:57 -0700 Subject: [MOBY-dev] RDF file generation for test registry In-Reply-To: <43559.195.37.46.17.1144146898.squirrel@mpizmail.mpiz-koeln.mpg.de> Message-ID: <001501c657f0$7b294e70$6500a8c0@notebook> > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > heese at mpiz-koeln.mpg.de > Sent: Tuesday, April 04, 2006 3:35 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] RDF file generation for test registry > > Hi, > > these are 3 questions for Eddie, but the answers might be > interesting for others, that's why I post it to the whole list. > > I'm quite new in the BioMoby business, so I hope my questions > havn't been asked before (at least I didn't find anything). > > 1. Is there a page available equivalent to > http://mobycentral.icapture.ubc.ca/servlets/forms/getSignature > Form to create/update an rdf document for services registered > in the TestCentral at > (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? There is no such page for the test registry. I can make one if you wish though. > > 2. I registered a couple of services at the TestCentral the > old way without giving a RDF signature URL. Now I wanted to > deregister them the old way but it failed since you generated > an rdf last week that included my services. Can you please > deregister them, so I can regain control over them? I will > use an RDF file for registration next time, I promise :) ... > Sure I can, let me know the service name/authority and I will remove them. > 3. Is it correct that the "getSignatureForm"-script is only > meant to help people updating their already working Services, > i.e. generating an RDF file for those? And that in future one > should generate an RDF file by hand and then use only the > agent to register it? Or will it always be possible to first > register the old way, then use "getSignatureForm" to update the RDF? > Correct, the script is only for people updating their already working services. In the future, the RDF will be returned to you so long as you provide a signature url. If no signatureURL is provided, then I guess that you could use the getSignatureForm. I wouldn't be generating this stuff by hand ;-) Eddie > Thanks, > maren > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From senger at ebi.ac.uk Wed Apr 5 17:25:12 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 5 Apr 2006 18:25:12 +0100 (BST) Subject: [MOBY-dev] RDF file generation for test registry In-Reply-To: <001501c657f0$7b294e70$6500a8c0@notebook> Message-ID: > > in the TestCentral at > > (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? > > There is no such page for the test registry. I can make one if you > wish though. > If such page is useful (and obviously it is), its code should be well documented and provided within the moby central distribution. Each moby central provider should be instructed how to set her/his registry in order to provide this information. (Ideally, the URL of such page should be return by a call in the Moby API - as it is for RESOURCE). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Wed Apr 5 15:59:08 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 5 Apr 2006 16:59:08 +0100 (BST) Subject: [MOBY-dev] jMoby seems not to compile In-Reply-To: <4433D329.1060109@mmb.pcb.ub.es> Message-ID: > Perhaps I'm committing some mistake but I think I've updated my local > copy from the last version in the CVS and when I try to compile jMoby by > doing "build-dev.sh all" I get the following error: > Thanks for spotting it. Somebody (Paul?) changed MobyRequest but did not make './build-dev clean compile'. For now, I have removed HelloMOBY2.java. Please (whoever) put it back when you fix it. Thanks. Eddie, could you please fix these warnings? [javac] Issued 2 semantic warnings compiling "/home/senger/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RDFConfigure.java": [javac] 190. Model model = ModelFactory.createDefaultModel(); [javac] ^---^ [javac] *** Semantic Warning: Local "model" shadows a field of the same name in "org.biomoby.client.rdf.builder.RDFConfigure". [javac] 359. Model model = ModelFactory.createDefaultModel(); [javac] ^---^ [javac] *** Semantic Warning: Local "model" shadows a field of the same name in "org.biomoby.client.rdf.builder.RDFConfigure". [javac] Compiling 19 source files to /home/senger/moby-live/Java/build/Clients Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Thu Apr 6 13:43:31 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 06 Apr 2006 07:43:31 -0600 Subject: [MOBY-dev] jMoby seems not to compile In-Reply-To: References: Message-ID: <44351B03.6050106@ucalgary.ca> Oops, sorry! My first bad CVS commit. I've fixed this now. >> Perhaps I'm committing some mistake but I think I've updated my local >> copy from the last version in the CVS and when I try to compile jMoby by >> doing "build-dev.sh all" I get the following error: >> >> > Thanks for spotting it. Somebody (Paul?) changed MobyRequest but did > not make './build-dev clean compile'. For now, I have removed > HelloMOBY2.java. Please (whoever) put it back when you fix it. Thanks. > > Eddie, could you please fix these warnings? > > [javac] Issued 2 semantic warnings compiling > "/home/senger/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RDFConfigure.java": > > [javac] 190. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > > > [javac] 359. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > [javac] Compiling 19 source files to > /home/senger/moby-live/Java/build/Clients > > > Thanks, > Martin > > From gordonp at ucalgary.ca Thu Apr 6 13:43:31 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 06 Apr 2006 07:43:31 -0600 Subject: [MOBY-dev] jMoby seems not to compile In-Reply-To: References: Message-ID: <44351B03.6050106@ucalgary.ca> Oops, sorry! My first bad CVS commit. I've fixed this now. >> Perhaps I'm committing some mistake but I think I've updated my local >> copy from the last version in the CVS and when I try to compile jMoby by >> doing "build-dev.sh all" I get the following error: >> >> > Thanks for spotting it. Somebody (Paul?) changed MobyRequest but did > not make './build-dev clean compile'. For now, I have removed > HelloMOBY2.java. Please (whoever) put it back when you fix it. Thanks. > > Eddie, could you please fix these warnings? > > [javac] Issued 2 semantic warnings compiling > "/home/senger/moby-live/Java/src/main/org/biomoby/client/rdf/builder/RDFConfigure.java": > > [javac] 190. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > > > [javac] 359. Model model = > ModelFactory.createDefaultModel(); > [javac] ^---^ > [javac] *** Semantic Warning: Local "model" shadows a field of the > same name in "org.biomoby.client.rdf.builder.RDFConfigure". > [javac] Compiling 19 source files to > /home/senger/moby-live/Java/build/Clients > > > Thanks, > Martin > > From edward.kawas at gmail.com Thu Apr 6 23:28:40 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 6 Apr 2006 16:28:40 -0700 Subject: [MOBY-dev] Quick poll Message-ID: <004c01c659d1$d716f240$6500a8c0@notebook> Hi, Just out of curiosity, who is using the RDFs that mobycentral is currently generating. If you are using them, what tasks are you using them for. I ask, because the RDF that is generated by mobycentral is different than the one that is generated by the test machine. The difference lies on the fact that mobycentral identifies resources based on URIs, while the test registry uses LSIDs. There are some other changes, but mainly additions (for instance, object ontology rdf now has more information in it, like the authority of the creator, the creators email address, etc). We are hoping to deploy the new RDF onto mobycentral very soon, and I just want to get a head count of who it is that will yell (beat up, etc) at me ;-) Thanks, Eddie From akerhornou at imim.es Fri Apr 7 09:04:00 2006 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Fri, 07 Apr 2006 11:04:00 +0200 Subject: [MOBY-dev] Quick poll In-Reply-To: <004c01c659d1$d716f240$6500a8c0@notebook> References: <004c01c659d1$d716f240$6500a8c0@notebook> Message-ID: <44362B00.7020301@imim.es> Hi Eddie, I have updated my services, and they all have a signature URL. I have a RDF document that includes in it all my services in there, http://genome.imim.es/webservices/RDFs/services.rdf i don't use the RDF, i guess in future i could use it for parameters and input objects validation - this way validatino could be done on the fly generically. Also, quick question, is the agent on ? Is it going to check the RDF document on a regular basis, and being able to update the central registry if i modify the specs of my services? regards, Arnaud Edward Kawas wrote: > Hi, > > Just out of curiosity, who is using the RDFs that mobycentral is currently > generating. If you are using them, what tasks are you using them for. > > I ask, because the RDF that is generated by mobycentral is different than the > one that is generated by the test machine. The difference lies on the fact that > mobycentral identifies resources based on URIs, while the test registry uses > LSIDs. There are some other changes, but mainly additions (for instance, object > ontology rdf now has more information in it, like the authority of the creator, > the creators email address, etc). > > We are hoping to deploy the new RDF onto mobycentral very soon, and I just want > to get a head count of who it is that will yell (beat up, etc) at me ;-) > > Thanks, > > Eddie > > > From heese at mpiz-koeln.mpg.de Fri Apr 7 12:59:45 2006 From: heese at mpiz-koeln.mpg.de (heese at mpiz-koeln.mpg.de) Date: Fri, 7 Apr 2006 14:59:45 +0200 (CEST) Subject: [MOBY-dev] RDF file generation for test registry Message-ID: <1062.80.135.69.229.1144414785.squirrel@mpizmail.mpiz-koeln.mpg.de> Hi Eddi, thanks for the answers, I just found them in the archives, since I somehow kicked myself out of the mailing list trying to switch from digest to normal mode - but now I'm back in ... > > 1. Is there a page available equivalent to > http://mobycentral.icapture.ubc.ca/servlets/forms/getSignature > Form to create/update an rdf document for services registered > in the TestCentral at > (bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl)? > There is no such page for the test registry. I can make one if you wish >though. I think it would be a nice feature, since I havn't found another way to get an RDF for several services in one go (so far I used the dashboard to register my services & get the RDF). In fact, I havn't been able to get a valid RDF document for the TestRegistry at all. When I used the dasboard, the RDF I recieved was empty (just the RDF-tags). Then I tried to take the detour over the MobyCentral registry (i.e. I registered the same service there (via dashboard), got an RDF with content, and tried to use this RDF for the TestRestigry as well. But since the RDFs for MobyCentralRegistry and TestRegistry aren't alike (I wasn't aware of that), it obviously didn't work either. So, what would be the correct way to generate a valid RDF-document for the Test registry at the moment? > > 2. I registered a couple of services at the TestCentral the > old way without giving a RDF signature URL. Now I wanted to > deregister them the old way but it failed since you generated > an rdf last week that included my services. Can you please > deregister them, so I can regain control over them? I will > use an RDF file for registration next time, I promise :) ... > > Sure I can, let me know the service name/authority and I will remove them. Please remove all services with the authority mpiz-koeln.mpg.de starting with MH_ from the TestRegistry and if there is another one with the authority mpiz-koeln.mpg.de that has your RDF signature URL, please remove that one as well (I'm not at work right now, so I cannot look up the name, sorry). Thanks, maren From edward.kawas at gmail.com Fri Apr 7 14:03:37 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 7 Apr 2006 07:03:37 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <44362B00.7020301@imim.es> Message-ID: <000501c65a4c$12691a10$6500a8c0@notebook> Hi, The agent isnt on yet (on mobycentral that is, it is running on the test registry). We want to make sure that the RDF is 100% correct before the agent is deployed. 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 > Arnaud Kerhornou > Sent: Friday, April 07, 2006 2:04 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > Hi Eddie, > > I have updated my services, and they all have a signature > URL. I have a RDF document that includes in it all my > services in there, http://genome.imim.es/webservices/RDFs/services.rdf > > i don't use the RDF, i guess in future i could use it for > parameters and input objects validation - this way validatino > could be done on the fly generically. > > Also, quick question, is the agent on ? Is it going to check > the RDF document on a regular basis, and being able to update > the central registry if i modify the specs of my services? > > regards, > Arnaud > > Edward Kawas wrote: > > Hi, > > > > Just out of curiosity, who is using the RDFs that mobycentral is > > currently generating. If you are using them, what tasks are > you using them for. > > > > I ask, because the RDF that is generated by mobycentral is > different > > than the one that is generated by the test machine. The difference > > lies on the fact that mobycentral identifies resources > based on URIs, > > while the test registry uses LSIDs. There are some other > changes, but > > mainly additions (for instance, object ontology rdf now has more > > information in it, like the authority of the creator, the > creators email address, etc). > > > > We are hoping to deploy the new RDF onto mobycentral very > soon, and I > > just want to get a head count of who it is that will yell (beat up, > > etc) at me ;-) > > > > Thanks, > > > > Eddie > > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From joecker at mpiz-koeln.mpg.de Fri Apr 7 14:03:32 2006 From: joecker at mpiz-koeln.mpg.de (Anika Joecker) Date: Fri, 7 Apr 2006 16:03:32 +0200 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: References: Message-ID: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Hello, I implemented a JMOBY webservice, which returns a BioMoby BLAST-Text object. Content, namespace and ID are added by JMOBY API like this: BLAST_Text text = new BLAST_Text(); text.setId("output"); text.setNamespace("BLAST"); text.set_content(result); By executing my BioMoby service I found, that some tags (XML namespaces) in the output XML file were prefixed with "moby:" and all JMoby primitives were not. For example: <-- here Because of that I've got some problems by parsing the XML output with Java JDOM. So my questions are: Why have the primitives no "moby" XML namespace? Is it possible to change the JMoby api so that all primitives get a "moby" XML namespace too? Thanks, Anika From gordonp at ucalgary.ca Fri Apr 7 15:16:35 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 09:16:35 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: <44368253.5020705@ucalgary.ca> Him They do. In the top level tag, http://www.biomoby.org/moby is defined as the default namespace. If the tags don't have that namespace in your DOM, you might want to make sure that you've set the parser's namespace awareness option to "on". Cheers, Paul > Hello, > > I implemented a JMOBY webservice, which returns a BioMoby BLAST-Text object. > Content, namespace and ID are added by JMOBY API like this: > > BLAST_Text text = new BLAST_Text(); > text.setId("output"); > text.setNamespace("BLAST"); > text.set_content(result); > > By executing my BioMoby service I found, that some tags (XML namespaces) in > the output XML file were prefixed with "moby:" and all JMoby primitives were > not. > For example: > > > xmlns='http://www.biomoby.org/moby'> > > > > > <-- here > > > Because of that I've got some problems by parsing the XML output with Java > JDOM. > So my questions are: > > Why have the primitives no "moby" XML namespace? > Is it possible to change the JMoby api so that all primitives get a "moby" XML > namespace too? > > Thanks, > Anika > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Fri Apr 7 15:22:20 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 09:22:20 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: <443683AC.8050704@ucalgary.ca> Hi all, Not directly related to the question below, I would like to *strongly* encourage people using formatted output such as GFF, BLAST, etc. to explicitly add a xml:space="preserve" attribute to their string objects. Otherwise an XML parser (or XSLT stylesheet as I use) can irreversibly collapse all those nice formatting whitespace characters into a single space to produce very ugly results. I've added this to org.biomoby.shared.MobyDataString, but haven't commited yet since I'm waiting for Ediie's RDF stuff to go live... Cheers, Paul > Hello, > > I implemented a JMOBY webservice, which returns a BioMoby BLAST-Text object. > Content, namespace and ID are added by JMOBY API like this: > > BLAST_Text text = new BLAST_Text(); > text.setId("output"); > text.setNamespace("BLAST"); > text.set_content(result); > > By executing my BioMoby service I found, that some tags (XML namespaces) in > the output XML file were prefixed with "moby:" and all JMoby primitives were > not. > For example: > > > xmlns='http://www.biomoby.org/moby'> > > > > > <-- here > > > Because of that I've got some problems by parsing the XML output with Java > JDOM. > So my questions are: > > Why have the primitives no "moby" XML namespace? > Is it possible to change the JMoby api so that all primitives get a "moby" XML > namespace too? > > Thanks, > Anika > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Fri Apr 7 15:24:51 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 09:24:51 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <443683AC.8050704@ucalgary.ca> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> <443683AC.8050704@ucalgary.ca> Message-ID: <44368443.6060802@ucalgary.ca> Oops. I meant org.biomoby.shared.data.MobyDataString. > org.biomoby.shared.MobyDataString, but haven't commited yet since I'm > From martin.senger at gmail.com Fri Apr 7 15:02:01 2006 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 07 Apr 2006 16:02:01 +0100 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: <44367EE9.10008@gmail.com> Hi, > By executing my BioMoby service I found, that some tags (XML namespaces) in > the output XML file were prefixed with "moby:" and all JMoby primitives were > not. > > Because of that I've got some problems by parsing the XML output with Java > JDOM. > So my questions are: > > Why have the primitives no "moby" XML namespace? > Is it possible to change the JMoby api so that all primitives get a "moby" XML > namespace too? > I had similar problems. When I was using JDOM I was always asked two questions: first using a local name, second with the moby namespace. I have even added two methods in (jMoby) org.biomoby.shared.Utils: * Get a child by 'name' from 'parent'. It tries first a child * without any namespace, then with {@link #MOBY_NS}.

* public static Element getChild (Element parent, String name); * Get text of a child 'name' from 'parent'. It tries first a * child without any namespace, then with {@link #MOBY_NS}.

* public static String getChildText (Element parent, String name); But I wonder if this is a correct way to do it. Anybody (perhaps Paul?) knows more about how to treat namespaces? Also, (Mark, Eddie?) what is in the Moby API about namepaces? Are they mandatory or not? I can surely add namespaces to primitive types as well... But I would rather first wait for the answers... Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Apr 7 16:42:43 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Apr 2006 10:42:43 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <44367EE9.10008@gmail.com> References: <200604071603.33008.joecker@mpiz-koeln.mpg.de> <44367EE9.10008@gmail.com> Message-ID: <44369683.2040904@ucalgary.ca> This must be a bug in JDOM, because the namespaces in the actual document are correct. Attributes is another story though, as by default, these do not have namespaces. > I had similar problems. When I was using JDOM I was always asked > two questions: first using a local name, second with the moby namespace. > I have even added two methods in (jMoby) org.biomoby.shared.Utils: > > > * Get a child by 'name' from 'parent'. It tries first a child > * without any namespace, then with {@link #MOBY_NS}.

> * > public static Element getChild (Element parent, String name); > > * Get text of a child 'name' from 'parent'. It tries first a > * child without any namespace, then with {@link #MOBY_NS}.

> * > public static String getChildText (Element parent, String name); > > But I wonder if this is a correct way to do it. Anybody (perhaps > Paul?) knows more about how to treat namespaces? > Also, (Mark, Eddie?) what is in the Moby API about namepaces? Are > they mandatory or not? > I can surely add namespaces to primitive types as well... But I > would rather first wait for the answers... > > Cheers, > Martin > > From senger at ebi.ac.uk Mon Apr 10 09:12:04 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 10 Apr 2006 10:12:04 +0100 (BST) Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: <200604071603.33008.joecker@mpiz-koeln.mpg.de> Message-ID: > Because of that I've got some problems by parsing the XML output with Java > JDOM. > Just from curiosity: why would you need to parse XML at all? From your example, I understand, that you are using jMoby generated classes (Moses) - and for them you could use jMoby's XML parser (class MobyParser). Please let me know if you have any questions regarding how to use Moses and its parser. With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Mon Apr 10 10:30:53 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 10 Apr 2006 11:30:53 +0100 (BST) Subject: [MOBY-dev] namespaces in Moby (and generally) Message-ID: Hi all (and perhaps especially Paul), I am unsure if I am doing namespace things properly in jMoby. Perhaps somebody can enlighten me on the topic. Thanks in advance. When I am parsing a moby XML I assume that the elements and attributes either do not have any namespace attached, or that they have the namespace exactly like this: http://www.biomoby.org/moby. But I have this namespace hard-coded (actually taken from one of Paul's classes in jMoby). Is this correct, or should I rather read the parsed XML, and find there the namespace definition (in this case in the MOBY element: ... and to use the string that is defined there? For example, recently I was in a discussion with Ivan from INB, his message started as: ... Thanks and with regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Mon Apr 10 16:13:05 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Apr 2006 10:13:05 -0600 Subject: [MOBY-dev] Prefixes for generated moby objects In-Reply-To: References: Message-ID: <443A8411.1030509@ucalgary.ca> Ditto for me, if you are using org.biomoby.shared.data.MobyDataUtils. You should never have to touch the XML directly... With two different implementations of data parsing in jMOBY, you shouldn't need to create a third :-) >> Because of that I've got some problems by parsing the XML output with Java >> JDOM. >> >> > Just from curiosity: why would you need to parse XML at all? From your > example, I understand, that you are using jMoby generated classes > (Moses) - and for them you could use jMoby's XML parser (class > MobyParser). Please let me know if you have any questions regarding how to > use Moses and its parser. > > With regards, > Martin > > From gordonp at ucalgary.ca Mon Apr 10 16:48:58 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Apr 2006 10:48:58 -0600 Subject: [MOBY-dev] namespaces in Moby (and generally) In-Reply-To: References: Message-ID: <443A8C7A.6060605@ucalgary.ca> The moby namespace is defined here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InputMessage.html So Ivan's is incorrect as far as I can see...no disrespect to the Spanish. I've noticed they have the most inconsistencies with the API, but that's because they are also producing most of the services that actually work! :-) It'd be great if we could all get together again some time, now that we have a lot of clients and servers, and work out these interoperability kinks more efficiently... Martin Senger wrote: > Hi all (and perhaps especially Paul), > I am unsure if I am doing namespace things properly in jMoby. Perhaps > somebody can enlighten me on the topic. Thanks in advance. > When I am parsing a moby XML I assume that the elements and attributes > either do not have any namespace attached, or that they have the namespace > exactly like this: http://www.biomoby.org/moby. > But I have this namespace hard-coded (actually taken from one of Paul's > classes in jMoby). Is this correct, or should I rather read the parsed > XML, and find there the namespace definition (in this case in the MOBY > element: > > ... > > and to use the string that is defined there? For example, recently I was > in a discussion with Ivan from INB, his message started as: > > ... > > Thanks and with regards, > Martin > > From gordonp at ucalgary.ca Mon Apr 10 23:20:36 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Apr 2006 17:20:36 -0600 Subject: [MOBY-dev] Quick poll In-Reply-To: <000501c65a4c$12691a10$6500a8c0@notebook> References: <000501c65a4c$12691a10$6500a8c0@notebook> Message-ID: <443AE844.5040301@ucalgary.ca> Umm.. the test server has reverted to http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID based. Is this intentional? It breaks all my code :-( > Hi, > > The agent isnt on yet (on mobycentral that is, it is running on the test > registry). We want to make sure that the RDF is 100% correct before the agent is > deployed. > > 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 >> Arnaud Kerhornou >> Sent: Friday, April 07, 2006 2:04 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Quick poll >> >> Hi Eddie, >> >> I have updated my services, and they all have a signature >> URL. I have a RDF document that includes in it all my >> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >> >> i don't use the RDF, i guess in future i could use it for >> parameters and input objects validation - this way validatino >> could be done on the fly generically. >> >> Also, quick question, is the agent on ? Is it going to check >> the RDF document on a regular basis, and being able to update >> the central registry if i modify the specs of my services? >> >> regards, >> Arnaud >> >> Edward Kawas wrote: >> >>> Hi, >>> >>> Just out of curiosity, who is using the RDFs that mobycentral is >>> currently generating. If you are using them, what tasks are >>> >> you using them for. >> >>> I ask, because the RDF that is generated by mobycentral is >>> >> different >> >>> than the one that is generated by the test machine. The difference >>> lies on the fact that mobycentral identifies resources >>> >> based on URIs, >> >>> while the test registry uses LSIDs. There are some other >>> >> changes, but >> >>> mainly additions (for instance, object ontology rdf now has more >>> information in it, like the authority of the creator, the >>> >> creators email address, etc). >> >>> We are hoping to deploy the new RDF onto mobycentral very >>> >> soon, and I >> >>> just want to get a head count of who it is that will yell (beat up, >>> etc) at me ;-) >>> >>> Thanks, >>> >>> Eddie >>> >>> >>> >>> >> _______________________________________________ >> 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 Mon Apr 10 23:39:05 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 10 Apr 2006 16:39:05 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443AE844.5040301@ucalgary.ca> References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> Message-ID: More specifics please. which ontology are you looking at? On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon wrote: > Umm.. the test server has reverted to > http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID > based. Is this intentional? It breaks all my code :-( >> Hi, >> >> The agent isnt on yet (on mobycentral that is, it is running on the test >> registry). We want to make sure that the RDF is 100% correct before the >> agent is >> deployed. >> >> 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 >>> Arnaud Kerhornou >>> Sent: Friday, April 07, 2006 2:04 AM >>> To: Core developer announcements >>> Subject: Re: [MOBY-dev] Quick poll >>> >>> Hi Eddie, >>> >>> I have updated my services, and they all have a signature >>> URL. I have a RDF document that includes in it all my >>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>> >>> i don't use the RDF, i guess in future i could use it for >>> parameters and input objects validation - this way validatino >>> could be done on the fly generically. >>> >>> Also, quick question, is the agent on ? Is it going to check >>> the RDF document on a regular basis, and being able to update >>> the central registry if i modify the specs of my services? >>> >>> regards, >>> Arnaud >>> >>> Edward Kawas wrote: >>> >>>> Hi, >>>> >>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>> currently generating. If you are using them, what tasks are >>>> >>> you using them for. >>> >>>> I ask, because the RDF that is generated by mobycentral is >>>> >>> different >>> >>>> than the one that is generated by the test machine. The difference >>>> lies on the fact that mobycentral identifies resources >>>> >>> based on URIs, >>> >>>> while the test registry uses LSIDs. There are some other >>>> >>> changes, but >>> >>>> mainly additions (for instance, object ontology rdf now has more >>>> information in it, like the authority of the creator, the >>>> >>> creators email address, etc). >>> >>>> We are hoping to deploy the new RDF onto mobycentral very >>>> >>> soon, and I >>> >>>> just want to get a head count of who it is that will yell (beat up, >>>> etc) at me ;-) >>>> >>>> Thanks, >>>> >>>> Eddie >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From markw at illuminae.com Mon Apr 10 23:44:07 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 10 Apr 2006 16:44:07 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443AE844.5040301@ucalgary.ca> References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> Message-ID: Hi Paul, Can you send us a copy of what you are seeing, and the URL that you retrieved it from? From our perspective, it is still LSID-based... ?? M On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon wrote: > Umm.. the test server has reverted to > http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID > based. Is this intentional? It breaks all my code :-( >> Hi, >> >> The agent isnt on yet (on mobycentral that is, it is running on the test >> registry). We want to make sure that the RDF is 100% correct before the >> agent is >> deployed. >> >> 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 >>> Arnaud Kerhornou >>> Sent: Friday, April 07, 2006 2:04 AM >>> To: Core developer announcements >>> Subject: Re: [MOBY-dev] Quick poll >>> >>> Hi Eddie, >>> >>> I have updated my services, and they all have a signature >>> URL. I have a RDF document that includes in it all my >>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>> >>> i don't use the RDF, i guess in future i could use it for >>> parameters and input objects validation - this way validatino >>> could be done on the fly generically. >>> >>> Also, quick question, is the agent on ? Is it going to check >>> the RDF document on a regular basis, and being able to update >>> the central registry if i modify the specs of my services? >>> >>> regards, >>> Arnaud >>> >>> Edward Kawas wrote: >>> >>>> Hi, >>>> >>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>> currently generating. If you are using them, what tasks are >>>> >>> you using them for. >>> >>>> I ask, because the RDF that is generated by mobycentral is >>>> >>> different >>> >>>> than the one that is generated by the test machine. The difference >>>> lies on the fact that mobycentral identifies resources >>>> >>> based on URIs, >>> >>>> while the test registry uses LSIDs. There are some other >>>> >>> changes, but >>> >>>> mainly additions (for instance, object ontology rdf now has more >>>> information in it, like the authority of the creator, the >>>> >>> creators email address, etc). >>> >>>> We are hoping to deploy the new RDF onto mobycentral very >>>> >>> soon, and I >>> >>>> just want to get a head count of who it is that will yell (beat up, >>>> etc) at me ;-) >>>> >>>> Thanks, >>>> >>>> Eddie >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From edward.kawas at gmail.com Mon Apr 10 23:28:22 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 10 Apr 2006 16:28:22 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443AE844.5040301@ucalgary.ca> Message-ID: <000a01c65cf6$763a24b0$636fa8c0@notebook> Hi Paul, I am seeing LSIDs, what ontology are you talking about? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Monday, April 10, 2006 4:21 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > Umm.. the test server has reverted to > http://www.w3.org/2000/01/rdf-schema#label type RDF instead > of LSID based. Is this intentional? It breaks all my code :-( > > Hi, > > > > The agent isnt on yet (on mobycentral that is, it is running on the > > test registry). We want to make sure that the RDF is 100% correct > > before the agent is deployed. > > > > 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 Arnaud > >> Kerhornou > >> Sent: Friday, April 07, 2006 2:04 AM > >> To: Core developer announcements > >> Subject: Re: [MOBY-dev] Quick poll > >> > >> Hi Eddie, > >> > >> I have updated my services, and they all have a signature > URL. I have > >> a RDF document that includes in it all my services in there, > >> http://genome.imim.es/webservices/RDFs/services.rdf > >> > >> i don't use the RDF, i guess in future i could use it for > parameters > >> and input objects validation - this way validatino could > be done on > >> the fly generically. > >> > >> Also, quick question, is the agent on ? Is it going to > check the RDF > >> document on a regular basis, and being able to update the central > >> registry if i modify the specs of my services? > >> > >> regards, > >> Arnaud > >> > >> Edward Kawas wrote: > >> > >>> Hi, > >>> > >>> Just out of curiosity, who is using the RDFs that mobycentral is > >>> currently generating. If you are using them, what tasks are > >>> > >> you using them for. > >> > >>> I ask, because the RDF that is generated by mobycentral is > >>> > >> different > >> > >>> than the one that is generated by the test machine. The > difference > >>> lies on the fact that mobycentral identifies resources > >>> > >> based on URIs, > >> > >>> while the test registry uses LSIDs. There are some other > >>> > >> changes, but > >> > >>> mainly additions (for instance, object ontology rdf now has more > >>> information in it, like the authority of the creator, the > >>> > >> creators email address, etc). > >> > >>> We are hoping to deploy the new RDF onto mobycentral very > >>> > >> soon, and I > >> > >>> just want to get a head count of who it is that will yell > (beat up, > >>> etc) at me ;-) > >>> > >>> Thanks, > >>> > >>> Eddie > >>> > >>> > >>> > >>> > >> _______________________________________________ > >> 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 gordonp at ucalgary.ca Tue Apr 11 14:09:36 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 11 Apr 2006 08:09:36 -0600 Subject: [MOBY-dev] Quick poll In-Reply-To: References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> Message-ID: <443BB8A0.60303@ucalgary.ca> It is in the Object ontology, but only the last two lines I guess, which look like: In the file http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects Which causes the following error (so the problem might actually be that org.biomoby.shared.extended.DataTypeParser should ignore this field but doesn't?): Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeParser.java:173) > Hi Paul, > > Can you send us a copy of what you are seeing, and the URL that you > retrieved it from? From our perspective, it is still LSID-based... > > ?? > > M > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > wrote: > > >> Umm.. the test server has reverted to >> http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID >> based. Is this intentional? It breaks all my code :-( >> >>> Hi, >>> >>> The agent isnt on yet (on mobycentral that is, it is running on the test >>> registry). We want to make sure that the RDF is 100% correct before the >>> agent is >>> deployed. >>> >>> 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 >>>> Arnaud Kerhornou >>>> Sent: Friday, April 07, 2006 2:04 AM >>>> To: Core developer announcements >>>> Subject: Re: [MOBY-dev] Quick poll >>>> >>>> Hi Eddie, >>>> >>>> I have updated my services, and they all have a signature >>>> URL. I have a RDF document that includes in it all my >>>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>>> >>>> i don't use the RDF, i guess in future i could use it for >>>> parameters and input objects validation - this way validatino >>>> could be done on the fly generically. >>>> >>>> Also, quick question, is the agent on ? Is it going to check >>>> the RDF document on a regular basis, and being able to update >>>> the central registry if i modify the specs of my services? >>>> >>>> regards, >>>> Arnaud >>>> >>>> Edward Kawas wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>>> currently generating. If you are using them, what tasks are >>>>> >>>>> >>>> you using them for. >>>> >>>> >>>>> I ask, because the RDF that is generated by mobycentral is >>>>> >>>>> >>>> different >>>> >>>> >>>>> than the one that is generated by the test machine. The difference >>>>> lies on the fact that mobycentral identifies resources >>>>> >>>>> >>>> based on URIs, >>>> >>>> >>>>> while the test registry uses LSIDs. There are some other >>>>> >>>>> >>>> changes, but >>>> >>>> >>>>> mainly additions (for instance, object ontology rdf now has more >>>>> information in it, like the authority of the creator, the >>>>> >>>>> >>>> creators email address, etc). >>>> >>>> >>>>> We are hoping to deploy the new RDF onto mobycentral very >>>>> >>>>> >>>> soon, and I >>>> >>>> >>>>> just want to get a head count of who it is that will yell (beat up, >>>>> etc) at me ;-) >>>>> >>>>> Thanks, >>>>> >>>>> Eddie >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 edward.kawas at gmail.com Tue Apr 11 14:11:59 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 11 Apr 2006 07:11:59 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443BB8A0.60303@ucalgary.ca> Message-ID: <000f01c65d71$e6f3c1e0$6600a8c0@notebook> Hi Paul, I will update the parsers in a moment and let you know. We made some changes yesterday to the RDF to make our ontologies owl-dl (actually Mark is trying to make owl-dl and I just code the changes ;-). Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: Tuesday, April 11, 2006 7:10 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > It is in the Object ontology, but only the last two lines I > guess, which look like: > > rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"> > > In the file > http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects > > Which causes the following error (so the problem might > actually be that org.biomoby.shared.extended.DataTypeParser > should ignore this field but > doesn't?): > > Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: > Expected an LSID as a URI, instead got > http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > org.biomoby.shared.MobyException: Expected an LSID as a URI, > instead got http://www.w3.org/2000/01/rdf-schema#comment 200 > : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > at > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFro > mRDF(DataTypeParser.java:173) > > > Hi Paul, > > > > Can you send us a copy of what you are seeing, and the URL that you > > retrieved it from? From our perspective, it is still LSID-based... > > > > ?? > > > > M > > > > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > > > wrote: > > > > > >> Umm.. the test server has reverted to > >> http://www.w3.org/2000/01/rdf-schema#label type RDF > instead of LSID > >> based. Is this intentional? It breaks all my code :-( > >> > >>> Hi, > >>> > >>> The agent isnt on yet (on mobycentral that is, it is > running on the > >>> test registry). We want to make sure that the RDF is 100% correct > >>> before the agent is deployed. > >>> > >>> 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 Arnaud > >>>> Kerhornou > >>>> Sent: Friday, April 07, 2006 2:04 AM > >>>> To: Core developer announcements > >>>> Subject: Re: [MOBY-dev] Quick poll > >>>> > >>>> Hi Eddie, > >>>> > >>>> I have updated my services, and they all have a signature URL. I > >>>> have a RDF document that includes in it all my services > in there, > >>>> http://genome.imim.es/webservices/RDFs/services.rdf > >>>> > >>>> i don't use the RDF, i guess in future i could use it for > >>>> parameters and input objects validation - this way > validatino could > >>>> be done on the fly generically. > >>>> > >>>> Also, quick question, is the agent on ? Is it going to check the > >>>> RDF document on a regular basis, and being able to update the > >>>> central registry if i modify the specs of my services? > >>>> > >>>> regards, > >>>> Arnaud > >>>> > >>>> Edward Kawas wrote: > >>>> > >>>> > >>>>> Hi, > >>>>> > >>>>> Just out of curiosity, who is using the RDFs that > mobycentral is > >>>>> currently generating. If you are using them, what tasks are > >>>>> > >>>>> > >>>> you using them for. > >>>> > >>>> > >>>>> I ask, because the RDF that is generated by mobycentral is > >>>>> > >>>>> > >>>> different > >>>> > >>>> > >>>>> than the one that is generated by the test machine. The > difference > >>>>> lies on the fact that mobycentral identifies resources > >>>>> > >>>>> > >>>> based on URIs, > >>>> > >>>> > >>>>> while the test registry uses LSIDs. There are some other > >>>>> > >>>>> > >>>> changes, but > >>>> > >>>> > >>>>> mainly additions (for instance, object ontology rdf now > has more > >>>>> information in it, like the authority of the creator, the > >>>>> > >>>>> > >>>> creators email address, etc). > >>>> > >>>> > >>>>> We are hoping to deploy the new RDF onto mobycentral very > >>>>> > >>>>> > >>>> soon, and I > >>>> > >>>> > >>>>> just want to get a head count of who it is that will yell (beat > >>>>> up, > >>>>> etc) at me ;-) > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Eddie > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>> _______________________________________________ > >>>> 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 From edward.kawas at gmail.com Tue Apr 11 14:57:57 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 11 Apr 2006 07:57:57 -0700 Subject: [MOBY-dev] Quick poll In-Reply-To: <443BB8A0.60303@ucalgary.ca> Message-ID: <001401c65d78$528f2790$6600a8c0@notebook> Hi Paul, The RDF parsers have been updated. Let me know if you run into any problems. 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 Paul Gordon > Sent: Tuesday, April 11, 2006 7:10 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Quick poll > > It is in the Object ontology, but only the last two lines I > guess, which look like: > > rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"> > > In the file > http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects > > Which causes the following error (so the problem might > actually be that org.biomoby.shared.extended.DataTypeParser > should ignore this field but > doesn't?): > > Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: > Expected an LSID as a URI, instead got > http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > org.biomoby.shared.MobyException: Expected an LSID as a URI, > instead got http://www.w3.org/2000/01/rdf-schema#comment 200 > : LSID must be of the > form: > urn:lsid::::[RevisionID], got: > urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] > > at > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFro > mRDF(DataTypeParser.java:173) > > > Hi Paul, > > > > Can you send us a copy of what you are seeing, and the URL that you > > retrieved it from? From our perspective, it is still LSID-based... > > > > ?? > > > > M > > > > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > > > wrote: > > > > > >> Umm.. the test server has reverted to > >> http://www.w3.org/2000/01/rdf-schema#label type RDF > instead of LSID > >> based. Is this intentional? It breaks all my code :-( > >> > >>> Hi, > >>> > >>> The agent isnt on yet (on mobycentral that is, it is > running on the > >>> test registry). We want to make sure that the RDF is 100% correct > >>> before the agent is deployed. > >>> > >>> 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 Arnaud > >>>> Kerhornou > >>>> Sent: Friday, April 07, 2006 2:04 AM > >>>> To: Core developer announcements > >>>> Subject: Re: [MOBY-dev] Quick poll > >>>> > >>>> Hi Eddie, > >>>> > >>>> I have updated my services, and they all have a signature URL. I > >>>> have a RDF document that includes in it all my services > in there, > >>>> http://genome.imim.es/webservices/RDFs/services.rdf > >>>> > >>>> i don't use the RDF, i guess in future i could use it for > >>>> parameters and input objects validation - this way > validatino could > >>>> be done on the fly generically. > >>>> > >>>> Also, quick question, is the agent on ? Is it going to check the > >>>> RDF document on a regular basis, and being able to update the > >>>> central registry if i modify the specs of my services? > >>>> > >>>> regards, > >>>> Arnaud > >>>> > >>>> Edward Kawas wrote: > >>>> > >>>> > >>>>> Hi, > >>>>> > >>>>> Just out of curiosity, who is using the RDFs that > mobycentral is > >>>>> currently generating. If you are using them, what tasks are > >>>>> > >>>>> > >>>> you using them for. > >>>> > >>>> > >>>>> I ask, because the RDF that is generated by mobycentral is > >>>>> > >>>>> > >>>> different > >>>> > >>>> > >>>>> than the one that is generated by the test machine. The > difference > >>>>> lies on the fact that mobycentral identifies resources > >>>>> > >>>>> > >>>> based on URIs, > >>>> > >>>> > >>>>> while the test registry uses LSIDs. There are some other > >>>>> > >>>>> > >>>> changes, but > >>>> > >>>> > >>>>> mainly additions (for instance, object ontology rdf now > has more > >>>>> information in it, like the authority of the creator, the > >>>>> > >>>>> > >>>> creators email address, etc). > >>>> > >>>> > >>>>> We are hoping to deploy the new RDF onto mobycentral very > >>>>> > >>>>> > >>>> soon, and I > >>>> > >>>> > >>>>> just want to get a head count of who it is that will yell (beat > >>>>> up, > >>>>> etc) at me ;-) > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Eddie > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>> _______________________________________________ > >>>> 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 From markw at illuminae.com Tue Apr 11 15:25:27 2006 From: markw at illuminae.com (mark wilkinson) Date: Tue, 11 Apr 2006 15:25:27 +0000 GMT Subject: [MOBY-dev] Quick poll In-Reply-To: <443BB8A0.60303@ucalgary.ca> References: <000501c65a4c$12691a10$6500a8c0@notebook> <443AE844.5040301@ucalgary.ca> <443BB8A0.60303@ucalgary.ca> Message-ID: <565197944-1144769236-cardhu_blackberry.rim.net-31034-@engine18-cell01> Yeah that's necessary. Your code needs to be clever and detect different types of uri's M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Tue, 11 Apr 2006 08:09:36 To:Core developer announcements Subject: Re: [MOBY-dev] Quick poll It is in the Object ontology, but only the last two lines I guess, which look like: In the file http://bioinfo.icapture.ubc.ca:8090/RESOURCES/MOBY-S/Objects Which causes the following error (so the problem might actually be that org.biomoby.shared.extended.DataTypeParser should ignore this field but doesn't?): Cannot parse MOBY Object Ontology: org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] org.biomoby.shared.MobyException: Expected an LSID as a URI, instead got http://www.w3.org/2000/01/rdf-schema#comment 200 : LSID must be of the form: urn:lsid::::[RevisionID], got: urn:lsid: not found: [http://www.w3.org/2000/01/rdf-schema#comment] at org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF(DataTypeParser.java:173) > Hi Paul, > > Can you send us a copy of what you are seeing, and the URL that you > retrieved it from? From our perspective, it is still LSID-based... > > ?? > > M > > > On Mon, 10 Apr 2006 16:20:36 -0700, Paul Gordon > wrote: > > >> Umm.. the test server has reverted to >> http://www.w3.org/2000/01/rdf-schema#label type RDF instead of LSID >> based. Is this intentional? It breaks all my code :-( >> >>> Hi, >>> >>> The agent isnt on yet (on mobycentral that is, it is running on the test >>> registry). We want to make sure that the RDF is 100% correct before the >>> agent is >>> deployed. >>> >>> 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 >>>> Arnaud Kerhornou >>>> Sent: Friday, April 07, 2006 2:04 AM >>>> To: Core developer announcements >>>> Subject: Re: [MOBY-dev] Quick poll >>>> >>>> Hi Eddie, >>>> >>>> I have updated my services, and they all have a signature >>>> URL. I have a RDF document that includes in it all my >>>> services in there, http://genome.imim.es/webservices/RDFs/services.rdf >>>> >>>> i don't use the RDF, i guess in future i could use it for >>>> parameters and input objects validation - this way validatino >>>> could be done on the fly generically. >>>> >>>> Also, quick question, is the agent on ? Is it going to check >>>> the RDF document on a regular basis, and being able to update >>>> the central registry if i modify the specs of my services? >>>> >>>> regards, >>>> Arnaud >>>> >>>> Edward Kawas wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Just out of curiosity, who is using the RDFs that mobycentral is >>>>> currently generating. If you are using them, what tasks are >>>>> >>>>> >>>> you using them for. >>>> >>>> >>>>> I ask, because the RDF that is generated by mobycentral is >>>>> >>>>> >>>> different >>>> >>>> >>>>> than the one that is generated by the test machine. The difference >>>>> lies on the fact that mobycentral identifies resources >>>>> >>>>> >>>> based on URIs, >>>> >>>> >>>>> while the test registry uses LSIDs. There are some other >>>>> >>>>> >>>> changes, but >>>> >>>> >>>>> mainly additions (for instance, object ontology rdf now has more >>>>> information in it, like the authority of the creator, the >>>>> >>>>> >>>> creators email address, etc). >>>> >>>> >>>>> We are hoping to deploy the new RDF onto mobycentral very >>>>> >>>>> >>>> soon, and I >>>> >>>> >>>>> just want to get a head count of who it is that will yell (beat up, >>>>> etc) at me ;-) >>>>> >>>>> Thanks, >>>>> >>>>> Eddie >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 From d.haase at gsf.de Thu Apr 13 07:58:19 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 13 Apr 2006 09:58:19 +0200 Subject: [MOBY-dev] Moby Collections in Taverna Message-ID: <200604130958.20054.d.haase@gsf.de> Hi all, I noticed that the handling of Moby collection outputs has changed in Taverna. Formerly (until version 1.2), a collection of n objects was processed with n invocations of the following step in the workflow. Now (version 1.3.1) this is done with only one invocation with n distinct queries (mobyData blocks). That's nice, because it reduces overhead. The downside is that for large collections this will inescapably lead to timeout problems. For our blast services for example I observed a limit of about 20 queries per invocation. I also found that the old multi-invocation behavior is still accessible by using the non-moby 'output' port. However I'm not sure if this is really the intended way... I think the optimal solution would be to have a 'max-number-of-queries-per-invocation' parameter to be set in the workflow definition. Is that feasible? Regards, dirk -- ---------------------------------------------------------- Dirk Haase phone +49 89 3187 3583 http://mips.gsf.de/~haase email d.haase at gsf.de From edward.kawas at gmail.com Thu Apr 13 13:56:30 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 13 Apr 2006 06:56:30 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604130958.20054.d.haase@gsf.de> Message-ID: <000b01c65f02$164e95a0$6700a8c0@notebook> Hi Dirk, The output port behaviour has been cloned for collections with a new port, Collection 'As Simples'. So that port now takes the n items in a collection and produces n simples that Taverna can iterate over. However, if that port isn't used and a collection is passed to a service that expects a simple, I transparently break apart the collection with n items into n invocations containing a simple and then invoke the service n times, rather than one time with a n invocation message. This was done, because I noticed that there were time out issues with very large collections. I haven't committed my changes in the Taverna cvs yet, so the only way to try these changes is to download an updated taverna-1.3.1.jar file from http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. I also have some example workflows at http://bioinfo.icapture.ubc.ca/ekawas/workflows/. Once I am ready, I will commit my changes and hopefully in the next release of Taverna (very soon I hear) the plugin will be updated. 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 Dirk Haase > Sent: Thursday, April 13, 2006 12:58 AM > To: Moby Developers > Subject: [MOBY-dev] Moby Collections in Taverna > > Hi all, > > I noticed that the handling of Moby collection outputs has > changed in Taverna. > Formerly (until version 1.2), a collection of n objects was > processed with n invocations of the following step in the workflow. > > Now (version 1.3.1) this is done with only one invocation > with n distinct queries (mobyData blocks). That's nice, > because it reduces overhead. The downside is that for large > collections this will inescapably lead to timeout problems. > For our blast services for example I observed a limit of > about 20 queries per invocation. > > I also found that the old multi-invocation behavior is still > accessible by using the non-moby 'output' port. However I'm > not sure if this is really the intended way... > > I think the optimal solution would be to have a > 'max-number-of-queries-per-invocation' parameter to be set in > the workflow definition. Is that feasible? > > Regards, > dirk > > -- > > ---------------------------------------------------------- > Dirk Haase phone +49 89 3187 3583 > http://mips.gsf.de/~haase email d.haase at gsf.de > _______________________________________________ > 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 Thu Apr 13 13:56:30 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 13 Apr 2006 06:56:30 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604130958.20054.d.haase@gsf.de> Message-ID: <000b01c65f02$164e95a0$6700a8c0@notebook> Hi Dirk, The output port behaviour has been cloned for collections with a new port, Collection 'As Simples'. So that port now takes the n items in a collection and produces n simples that Taverna can iterate over. However, if that port isn't used and a collection is passed to a service that expects a simple, I transparently break apart the collection with n items into n invocations containing a simple and then invoke the service n times, rather than one time with a n invocation message. This was done, because I noticed that there were time out issues with very large collections. I haven't committed my changes in the Taverna cvs yet, so the only way to try these changes is to download an updated taverna-1.3.1.jar file from http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.1.jar. I also have some example workflows at http://bioinfo.icapture.ubc.ca/ekawas/workflows/. Once I am ready, I will commit my changes and hopefully in the next release of Taverna (very soon I hear) the plugin will be updated. 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 Dirk Haase > Sent: Thursday, April 13, 2006 12:58 AM > To: Moby Developers > Subject: [MOBY-dev] Moby Collections in Taverna > > Hi all, > > I noticed that the handling of Moby collection outputs has > changed in Taverna. > Formerly (until version 1.2), a collection of n objects was > processed with n invocations of the following step in the workflow. > > Now (version 1.3.1) this is done with only one invocation > with n distinct queries (mobyData blocks). That's nice, > because it reduces overhead. The downside is that for large > collections this will inescapably lead to timeout problems. > For our blast services for example I observed a limit of > about 20 queries per invocation. > > I also found that the old multi-invocation behavior is still > accessible by using the non-moby 'output' port. However I'm > not sure if this is really the intended way... > > I think the optimal solution would be to have a > 'max-number-of-queries-per-invocation' parameter to be set in > the workflow definition. Is that feasible? > > Regards, > dirk > > -- > > ---------------------------------------------------------- > Dirk Haase phone +49 89 3187 3583 > http://mips.gsf.de/~haase email d.haase at gsf.de > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Apr 19 13:45:40 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 19 Apr 2006 15:45:40 +0200 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <000b01c65f02$164e95a0$6700a8c0@notebook> References: <000b01c65f02$164e95a0$6700a8c0@notebook> Message-ID: <200604191545.41064.d.haase@gsf.de> Hi Eddie, On Thursday 13 April 2006 15:56, Edward Kawas wrote: > Hi Dirk, > > The output port behaviour has been cloned for collections with a new port, > Collection 'As Simples'. So that port now takes the n items in a collection > and produces n simples that Taverna can iterate over. Wow, that's what I call a prompt fix! > However, if that port isn't used and a collection is passed to a service > that expects a simple, I transparently break apart the collection with n > items into n invocations containing a simple and then invoke the service n > times, rather than one time with a n invocation message. This was done, > because I noticed that there were time out issues with very large > collections. OK, I see this behavior when I use the 'output' port. For the old collection-type port 'Object(Collection - )' things are strange: it seems that only the first element in the collection is piped to the next service. However, I think this solution is very convenient. The drawback is that we now have three distinct types of output ports for moby services, this will confuse people. What I want to say is that good documentation is desperately needed ;-) Thanks, dirk From edward.kawas at gmail.com Wed Apr 19 14:52:47 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Apr 2006 07:52:47 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604191545.41064.d.haase@gsf.de> Message-ID: <000401c663c0$ed443a20$6500a8c0@notebook> One last thing, When creating new workflows, stay away from the ports labelled 'input' and 'output'. They are there only for legacy reasons. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, April 19, 2006 6:46 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > Hi Eddie, > > On Thursday 13 April 2006 15:56, Edward Kawas wrote: > > Hi Dirk, > > > > The output port behaviour has been cloned for collections > with a new > > port, Collection 'As Simples'. So that port now takes the n > items in a > > collection and produces n simples that Taverna can iterate over. > > Wow, that's what I call a prompt fix! > > > However, if that port isn't used and a collection is passed to a > > service that expects a simple, I transparently break apart the > > collection with n items into n invocations containing a simple and > > then invoke the service n times, rather than one time with a n > > invocation message. This was done, because I noticed that > there were > > time out issues with very large collections. > > OK, I see this behavior when I use the 'output' port. For the > old collection-type port 'Object(Collection - > )' things are > strange: it seems that only the first element in the > collection is piped to the next service. > > However, I think this solution is very convenient. The > drawback is that we now have three distinct types of output > ports for moby services, this will confuse people. What I > want to say is that good documentation is desperately needed ;-) > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Wed Apr 19 15:28:02 2006 From: d.haase at gsf.de (Dirk Haase) Date: Wed, 19 Apr 2006 17:28:02 +0200 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <000401c663c0$ed443a20$6500a8c0@notebook> References: <000401c663c0$ed443a20$6500a8c0@notebook> Message-ID: <200604191728.03047.d.haase@gsf.de> On Wednesday 19 April 2006 16:52, Edward Kawas wrote: > One last thing, > > When creating new workflows, stay away from the ports labelled 'input' and > 'output'. They are there only for legacy reasons. But currently I still need the 'output' for linking non-moby services/widgets, right? For example to use the 'Flatten' processor to merge lists of lists. From edward.kawas at gmail.com Wed Apr 19 15:30:25 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Apr 2006 08:30:25 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604191728.03047.d.haase@gsf.de> Message-ID: <000501c663c6$2f4eb6c0$6500a8c0@notebook> For the moby widgets, the output port isnt necessary. They should work with the other ports as well. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, April 19, 2006 8:28 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > On Wednesday 19 April 2006 16:52, Edward Kawas wrote: > > One last thing, > > > > When creating new workflows, stay away from the ports > labelled 'input' > > and 'output'. They are there only for legacy reasons. > > But currently I still need the 'output' for linking non-moby > services/widgets, right? For example to use the 'Flatten' > processor to merge lists of lists. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Apr 19 14:50:52 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Apr 2006 07:50:52 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604191545.41064.d.haase@gsf.de> Message-ID: <000301c663c0$a8d54e60$6500a8c0@notebook> Hi Dirk, You are right about the documentation and I plan on updating it today, but I want to outline what the behaviour is now: Service Output ----Connects to ---> Service Input 1 Simple Simple 2 Simple Collection 3 Collection Simple 4 Collection Collection 5 CollAsSimples Simples 6 CollAsSimples Collection Note that CollAsSimples transforms a collection into a list of simples. Case 1, 4 are straight forward - the output is passed to the input as is. Case 2, 6 - the simple (or a 'taverna list' of simples) are placed in a collection and passed to the service. Case 3 - the collection is broken down and each simple in the collection is passed to the downstream service one at a time (in a single invocation message). i.e. 1 2 3 4 Becomes 1 2 3 4 Case 5 - The collection became a list of simples and this case becomes similar to case 1. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Wednesday, April 19, 2006 6:46 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > Hi Eddie, > > On Thursday 13 April 2006 15:56, Edward Kawas wrote: > > Hi Dirk, > > > > The output port behaviour has been cloned for collections > with a new > > port, Collection 'As Simples'. So that port now takes the n > items in a > > collection and produces n simples that Taverna can iterate over. > > Wow, that's what I call a prompt fix! > > > However, if that port isn't used and a collection is passed to a > > service that expects a simple, I transparently break apart the > > collection with n items into n invocations containing a simple and > > then invoke the service n times, rather than one time with a n > > invocation message. This was done, because I noticed that > there were > > time out issues with very large collections. > > OK, I see this behavior when I use the 'output' port. For the > old collection-type port 'Object(Collection - > )' things are > strange: it seems that only the first element in the > collection is piped to the next service. > > However, I think this solution is very convenient. The > drawback is that we now have three distinct types of output > ports for moby services, this will confuse people. What I > want to say is that good documentation is desperately needed ;-) > > Thanks, > dirk > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Thu Apr 20 07:42:54 2006 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 20 Apr 2006 09:42:54 +0200 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <000301c663c0$a8d54e60$6500a8c0@notebook> References: <000301c663c0$a8d54e60$6500a8c0@notebook> Message-ID: <200604200942.55192.d.haase@gsf.de> Eddie, thanks for clarification, but if in case 3 (Collection -> Simple) a _single_ invocation message is sent wouldn't the XML rather look like: 1 2 3 4 On Wednesday 19 April 2006 16:50, Edward Kawas wrote: > Service Output ----Connects to ---> Service Input > 3 ?Collection???????????????????????????Simple > Case 3 - the collection is broken down and each simple in the collection is > passed to the downstream service one at a time (in a single invocation > message). i.e. > > > ? > ???????? > ????????????????1 > ???????? > ? > > > > ? > ???????? > ????????????????2 > ???????? > ? > > > > ? > ???????? > ????????????????3 > ???????? > ? > > > > ? > ???????? > ????????????????4 > ???????? > ? > From edward.kawas at gmail.com Thu Apr 20 13:42:53 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 20 Apr 2006 06:42:53 -0700 Subject: [MOBY-dev] Moby Collections in Taverna In-Reply-To: <200604200942.55192.d.haase@gsf.de> Message-ID: <000701c66480$53c48f60$6500a8c0@notebook> Hi, The message could look like that if I sent it all at once. But I don?t because conceivably, there could be hundreds of invocations and would most likely timeout. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase > Sent: Thursday, April 20, 2006 12:43 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Moby Collections in Taverna > > Eddie, > > thanks for clarification, but if in case 3 (Collection -> > Simple) a _single_ invocation message is sent wouldn't the > XML rather look like: > > > > > 1 > > > 2 > > > 3 > > > 4 > > > > > On Wednesday 19 April 2006 16:50, Edward Kawas wrote: > > Service Output ----Connects to ---> Service Input > > 3 ?Collection???????????????????????????Simple > > > Case 3 - the collection is broken down and each simple in the > > collection is passed to the downstream service one at a time (in a > > single invocation message). i.e. > > > > > > ? > > ???????? > > ????????????????1 > > ???????? > > ? > > > > > > > > ? > > ???????? > > ????????????????2 > > ???????? > > ? > > > > > > > > ? > > ???????? > > ????????????????3 > > ???????? > > ? > > > > > > > > ? > > ???????? > > ????????????????4 > > ???????? > > ? > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From senger at ebi.ac.uk Sun Apr 23 18:22:17 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sun, 23 Apr 2006 19:22:17 +0100 (BST) Subject: [MOBY-dev] jMoby does not compile Message-ID: Eddie! Quo usque tandem abutere, Catilina, patientia nostra? (We are *not*, at least not yet, using Java 1.5...) Martin PS: [javac] Found 4 semantic errors compiling "/home/senger/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/serviceInstanceCreationTool/ServiceInstanceEditorWindow.java": [javac] 172. this.setMaximumSize(new java.awt.Dimension(600, 550)); [javac] ^---------------------------------------------------^ [javac] *** Semantic Error: No accessible method with signature "setMaximumSize(java.awt.Dimension)" was found in type "org.biomoby.client.ui.graphical.applets.serviceInstanceCreationTool.ServiceInstanceEditorWindow". [javac] 173. this.setMinimumSize(new java.awt.Dimension(600, 550)); [javac] ^---------------------------------------------------^ [javac] *** Semantic Error: No accessible method with signature "setMinimumSize(java.awt.Dimension)" was found in type "org.biomoby.client.ui.graphical.applets.serviceInstanceCreationTool.ServiceInstanceEditorWindow". ...etc... -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Mon Apr 24 14:06:44 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Apr 2006 15:06:44 +0100 (BST) Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <444CDAD9.9020308@ucalgary.ca> Message-ID: > Should we require Java 1.5, or at least set some date, say August 2006, > at which we will require 1.5? > Fine with me (I have just decided to make a similar suggestion when your email came :-)). Perhaps middle of the year, June 30? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Mon Apr 24 14:06:44 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 24 Apr 2006 15:06:44 +0100 (BST) Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <444CDAD9.9020308@ucalgary.ca> Message-ID: > Should we require Java 1.5, or at least set some date, say August 2006, > at which we will require 1.5? > Fine with me (I have just decided to make a similar suggestion when your email came :-)). Perhaps middle of the year, June 30? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Mon Apr 24 14:16:41 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:16:41 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDDC9.1080805@ucalgary.ca> June 30th sounds good to me! Perhaps we should create a Java 1.4 branch in CVS after that date for fixes, but no code improvements. That way any 1.4 users can still have the basic functionality until they can upgrade, and we can start changing the code on the CVS trunk as much as we want right away... >> Should we require Java 1.5, or at least set some date, say August 2006, >> at which we will require 1.5? >> >> > Fine with me (I have just decided to make a similar suggestion when > your email came :-)). Perhaps middle of the year, June 30? > > Martin > > From gordonp at ucalgary.ca Mon Apr 24 14:16:41 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:16:41 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDDC9.1080805@ucalgary.ca> June 30th sounds good to me! Perhaps we should create a Java 1.4 branch in CVS after that date for fixes, but no code improvements. That way any 1.4 users can still have the basic functionality until they can upgrade, and we can start changing the code on the CVS trunk as much as we want right away... >> Should we require Java 1.5, or at least set some date, say August 2006, >> at which we will require 1.5? >> >> > Fine with me (I have just decided to make a similar suggestion when > your email came :-)). Perhaps middle of the year, June 30? > > Martin > > From gordonp at ucalgary.ca Mon Apr 24 14:04:09 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:04:09 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDAD9.9020308@ucalgary.ca> Maybe we should we open up the question: Should we require Java 1.5, or at least set some date, say August 2006, at which we will require 1.5? If we don't set something in stone, it will never happen. It's been out for 2 years now...Java 1.6 is going to be out soon! On the developer side there is virtually no reason not to use 1.5. Changing your 'enum' variables isn't hard. The only client side issue I've run in to is Mac OS X 10.3 or lower users (who aren't upgrading because they require legacy Mac OS 9 binary compatibility for old programs they still need). > Eddie! > Quo usque tandem abutere, Catilina, patientia nostra? > > (We are *not*, at least not yet, using Java 1.5...) > > From gordonp at ucalgary.ca Mon Apr 24 14:04:09 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 24 Apr 2006 08:04:09 -0600 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: References: Message-ID: <444CDAD9.9020308@ucalgary.ca> Maybe we should we open up the question: Should we require Java 1.5, or at least set some date, say August 2006, at which we will require 1.5? If we don't set something in stone, it will never happen. It's been out for 2 years now...Java 1.6 is going to be out soon! On the developer side there is virtually no reason not to use 1.5. Changing your 'enum' variables isn't hard. The only client side issue I've run in to is Mac OS X 10.3 or lower users (who aren't upgrading because they require legacy Mac OS 9 binary compatibility for old programs they still need). > Eddie! > Quo usque tandem abutere, Catilina, patientia nostra? > > (We are *not*, at least not yet, using Java 1.5...) > > From markw at illuminae.com Tue Apr 25 14:53:45 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 25 Apr 2006 07:53:45 -0700 Subject: [MOBY-dev] updating MOBY Central with input/output articleNames Message-ID: Hi all, A few months ago the spec for service registration was tightened such that all inputs and outputs require an articleName. This is now required also in Taverna workflows, and as such, many "illegitimate" services currently in the registry will not function with Taverna even though they are perfectly functional in reality. Given that these services are not looking for an articleName, it will do no harm to them if one were added. Thus the fastest way to bring all service registrations back into compliance with the API would be for me to manipulate the MOBY Central database directly and add "dummy" articleNames ("input", "output") to all inputs and outputs that are currently un-named. Would this bother anyone? Please let me know ASAP. Mark From senger at ebi.ac.uk Tue Apr 25 21:25:58 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 25 Apr 2006 22:25:58 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <444CDDC9.1080805@ucalgary.ca> Message-ID: If you disagree please say so. Your silence will be (in due time) considered as a yes vote. Thanks and regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Tue Apr 25 23:21:22 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 25 Apr 2006 16:21:22 -0700 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: Message-ID: <003001c668be$f8392f50$6700a8c0@notebook> If it means that my commits wont break things, I am in ;-) Ed > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Martin Senger > Sent: Tuesday, April 25, 2006 2:26 PM > To: Moby Developers > Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. > from June 30, 2006 > > If you disagree please say so. Your silence will be (in due > time) considered as a yes vote. > > Thanks and regards, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Apr 25 23:21:22 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 25 Apr 2006 16:21:22 -0700 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: Message-ID: <003001c668be$f8392f50$6700a8c0@notebook> If it means that my commits wont break things, I am in ;-) Ed > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of > Martin Senger > Sent: Tuesday, April 25, 2006 2:26 PM > To: Moby Developers > Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. > from June 30, 2006 > > If you disagree please say so. Your silence will be (in due > time) considered as a yes vote. > > Thanks and regards, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From senger at ebi.ac.uk Wed Apr 26 01:08:08 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 02:08:08 +0100 (BST) Subject: [MOBY-dev] BioMoby/BioCASE integration Message-ID: Dear all, Me and Milko (from IPGRI) have finished the first version of integrating BioCASE and BioMoby. The project is documented here (the same link is also available from the main jMoby page): http://moby.generationcp.org/bb_services/docs/index.html. There is only one service of this kind running, so much more testing is needed - but one has to start somewhere, right? Any comments welcome, With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Wed Apr 26 16:07:05 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 26 Apr 2006 10:07:05 -0600 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <003001c668be$f8392f50$6700a8c0@notebook> References: <003001c668be$f8392f50$6700a8c0@notebook> Message-ID: <444F9AA9.3020801@ucalgary.ca> Would anyone be opposed to creating a 'java15' branch right away? On June 30th, we can merge it back into the trunk. I suggest this for two reasons: 1) It allows me to commit a bunch of changes right away without affecting trunk users 2) We won't have to do as much work on the transition date if we know in advance that the java15 branch works nicely > If it means that my commits wont break things, I am in ;-) > > Ed > > >> -----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: Tuesday, April 25, 2006 2:26 PM >> To: Moby Developers >> Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. >> from June 30, 2006 >> >> If you disagree please say so. Your silence will be (in due >> time) considered as a yes vote. >> >> Thanks and regards, >> Martin >> >> -- >> Martin Senger >> email: martin.senger at gmail.com >> skype: martinsenger >> >> >> _______________________________________________ >> 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 senger at ebi.ac.uk Wed Apr 26 16:15:06 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 17:15:06 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <444F9AA9.3020801@ucalgary.ca> Message-ID: > Would anyone be opposed to creating a 'java15' branch right away? > I would like to continue to work on the HEAD (or is it called TRUNK?). Otherwise, I do not mind. But isn't it easier just to move to java 1.5. sooner? Is there anyone around still in need of pure 1.4? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Wed Apr 26 16:27:37 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 26 Apr 2006 10:27:37 -0600 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: References: Message-ID: <444F9F79.7030009@ucalgary.ca> True. Perhaps we are flattering ourselves by assuming there are so many jMOBY developers to appease :-) I think Martin, Eddie and myself account for 99% of the commits to jMOBY... In terms of jMOBY library *users*, if they need Java 1.4, we can put a 'preJava15' tag on the trunk right now, and they'll have to upgrade their Java before they can check out any newer code. The sooner we switch, the better! > I would like to continue to work on the HEAD (or is it called > TRUNK?). Otherwise, I do not mind. But isn't it easier just to move to > java 1.5. sooner? Is there anyone around still in need of pure 1.4? > > Martin > > From senger at ebi.ac.uk Wed Apr 26 16:51:57 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 17:51:57 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <444F9F79.7030009@ucalgary.ca> Message-ID: I agree. Let's wait for at least one confirming reply from Spain and from Germany. Anybody there to give us green light for Java 1.5. now? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Wed Apr 26 17:03:57 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Wed, 26 Apr 2006 18:03:57 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: Message-ID: Also we need a green light from Eddie because he needs to check whether jmoby.jar, created with java 1.5., will be allowed to put in taverna - I am not sure if they still use 1.4 or already switched to 1.5. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From d.haase at gsf.de Thu Apr 27 14:54:04 2006 From: d.haase at gsf.de (Haase, Dirk) Date: Thu, 27 Apr 2006 16:54:04 +0200 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 References: Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A0882@sw-rz010.gsf.de> Hmm, I don't know if you refer to us (Heiko, MIPS, me) when you say Germany... As we are not actively developing (we are only always complaining ;-) we give the greenest light possible. Regards, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Martin Senger Sent: Wed 4/26/2006 6:51 PM To: Paul Gordon Cc: Core developer announcements Subject: Re: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 I agree. Let's wait for at least one confirming reply from Spain and from Germany. Anybody there to give us green light for Java 1.5. now? Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ 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: winmail.dat Type: application/ms-tnef Size: 3128 bytes Desc: not available URL: From senger at ebi.ac.uk Fri Apr 28 00:24:11 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 01:24:11 +0100 (BST) Subject: [MOBY-dev] jMoby/Dashboard update Message-ID: Hi, Recently, I have made few fixes in Dashboard (and some in jMoby itself) so it is worth to cvs update. The main fixes were made thanks to Dirk who very nicely and accurately described some found bugs. Thanks. What has been changed: * the local cache default directory includes now a user name (on Windows that was true before, but on Unix/Mac the default was just /tmp) - this makes it easier to use Dashboard during workshops where people share the same machine * I tried to improve visibility of the progress bars when a local cache is loaded. I hope I have improved it - but still there are some situations when it still continues to load the cache behind the scene (e.g. if you add new panel during loading). Please let me know if you spot strange behaviour. Synchronizing entity trees showed to be, so far, the most challenging part of Dashboard (from the developer's point of view), so I will be glad to make it better any time. * The editing of various tables (e.g. editing article names in the registering service panel) is properly finished just by loosing focus, hitting ENTER is not needed any more. [ A side comment for Java developers: this was amazingly easy to fix once I found the solution on google. There is a single property to be set in a JTable constructor, and that's it!: putClientProperty ("terminateEditOnFocusLost", Boolean.TRUE); ] * The ant configuration file build.xml: - was splitted into more files to be easier maintained. - I have commented out some dependency rules in build.xml - search there for 'dependset' to see details - jmoby.jar now splitted (jmoby.jar and jmoby-dashboard.jar): I would like to separate into more jar files in the future (see my next email about) * small improvement in the deployment sub-panel in the pattern field (see {Service} at the end of the panel help page about it) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Fri Apr 28 00:32:50 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 01:32:50 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar Message-ID: Eddie (and others), I think about making more (splitted) jar files, not only jmoby.jar. I would like to have a lightweight version of jmoby.jar that can be used for biomoby service providers (for those implementing a moby service in a different directory etc.). For normal jMoby users this would not be any change. Could you perhaps identify what which from your packages do not need to be for those who are writting service implementation? I will then update the build.xml. (Look there and you will see I have in mind: search for jmoby-dashboard.) Think also about how many of these new jar files (and which ones) you will need to move to taverna (together with the lightweight jmoby.jar, of course). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Fri Apr 28 03:59:32 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 27 Apr 2006 20:59:32 -0700 Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: Message-ID: <000101c66a78$28e5b3c0$6500a8c0@notebook> Hi Martin, Most likely all of the classes in the package org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry are not needed by clients writing services. Classes in the package org.biomoby.shared.extended are used for parsing RDF and are probably no use to clients. Eddie > -----Original Message----- > From: Martin Senger [mailto:senger at ebi.ac.uk] > Sent: Thursday, April 27, 2006 5:33 PM > To: Edward Kawas > Cc: Moby Developers > Subject: splitting jmoby.jar > > Eddie (and others), > I think about making more (splitted) jar files, not only > jmoby.jar. I would like to have a lightweight version of > jmoby.jar that can be used for biomoby service providers (for > those implementing a moby service in a different directory > etc.). For normal jMoby users this would not be any change. > Could you perhaps identify what which from your packages > do not need to be for those who are writting service > implementation? I will then update the build.xml. (Look there > and you will see I have in mind: search for > jmoby-dashboard.) > Think also about how many of these new jar files (and > which ones) you will need to move to taverna (together with > the lightweight jmoby.jar, of course). > > Cheers, > Martin > > -- > Martin Senger > email: martin.senger at gmail.com > skype: martinsenger > > From ivanp at mmb.pcb.ub.es Fri Apr 28 08:51:09 2006 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 28 Apr 2006 10:51:09 +0200 Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: References: Message-ID: <4451D77D.10200@mmb.pcb.ub.es> Hi, Sorry for my delay in answering. I've been ill (and offline) the last days. Java 1.5 is welcome from Spain, in fact, we've working with 1.5 since it was launched. Regards, Iv?n P?rraga Garc?a Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es http://mmb.pcb.ub.es Martin Senger escribi?: > I agree. > Let's wait for at least one confirming reply from Spain and from > Germany. Anybody there to give us green light for Java 1.5. now? > > Martin > > From senger at ebi.ac.uk Fri Apr 28 10:35:30 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 11:35:30 +0100 (BST) Subject: [MOBY-dev] RFC: jMoby will start using Java 1.5. from June 30, 2006 In-Reply-To: <4451D77D.10200@mmb.pcb.ub.es> Message-ID: Eddie, how is going your Taverna 1.5.enquiries? It seems that we may make a tag 1.4, and start to use 1.5 when you give us a green light. Don't worry, however, it does not need to be *now*. Cheers, Martin > Sorry for my delay in answering. I've been ill (and offline) the last > days. Java 1.5 is welcome from Spain, in fact, we've working with 1.5 > since it was launched. > > Regards, > > Iv?n P?rraga Garc?a > Molecular Modelling & Bioinformatics Unit > INB - Instituto Nacional de Bioinform?tica > Josep Samitier 1-5 > 08028 Barcelona > Spain > tel.: +34 93 403 71 55 > fax.: +34 93 403 71 57 > e-mail: ivanp at mmb.pcb.ub.es > http://mmb.pcb.ub.es > > > > Martin Senger escribi?: > > I agree. > > Let's wait for at least one confirming reply from Spain and from > > Germany. Anybody there to give us green light for Java 1.5. now? > > > > Martin > > > > > -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Apr 28 14:01:44 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 08:01:44 -0600 Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <000101c66a78$28e5b3c0$6500a8c0@notebook> References: <000101c66a78$28e5b3c0$6500a8c0@notebook> Message-ID: <44522048.3010503@ucalgary.ca> Hi Ediie, Actually, I write clients, and use org.biomoby.shared.extended to type-check data, so yes a client may need these. In my Seahawk application (which uses Java 1.5), these are the MOBY directories I imported from src/main/org/biomoby: ./client ./client/rdf ./client/rdf/vocabulary ./registry ./registry/definitions ./registry/definitions/types ./registry/properties ./service ./service/generated ./shared ./shared/data ./shared/dom ./shared/dom/wrappers ./shared/parser ./shared/extended ./shared/schema If we are really interested in making truly lightweight JARs available, I may be able to help, should go to Java 1.5 sooner rather than later. I've made uncommitted changes to several classes so that MOBY doesn't absoluely require having the tulsoft, JDOM and ebi JARs around. Seahawk packs everything it needs to call MOBY Central and remote services into a 2.5 MB JAR file (including the relevant classes from Axis, Xerces, Xalan, Commons Logging, etc., etc.)... Regards, Paul > Hi Martin, > > Most likely all of the classes in the package > org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry are > not needed by clients writing services. > > Classes in the package org.biomoby.shared.extended are used for parsing RDF and > are probably no use to clients. > > Eddie > > >> -----Original Message----- >> From: Martin Senger [mailto:senger at ebi.ac.uk] >> Sent: Thursday, April 27, 2006 5:33 PM >> To: Edward Kawas >> Cc: Moby Developers >> Subject: splitting jmoby.jar >> >> Eddie (and others), >> I think about making more (splitted) jar files, not only >> jmoby.jar. I would like to have a lightweight version of >> jmoby.jar that can be used for biomoby service providers (for >> those implementing a moby service in a different directory >> etc.). For normal jMoby users this would not be any change. >> Could you perhaps identify what which from your packages >> do not need to be for those who are writting service >> implementation? I will then update the build.xml. (Look there >> and you will see I have in mind: search for >> jmoby-dashboard.) >> Think also about how many of these new jar files (and >> which ones) you will need to move to taverna (together with >> the lightweight jmoby.jar, of course). >> >> Cheers, >> Martin >> >> -- >> Martin Senger >> email: martin.senger at gmail.com >> skype: martinsenger >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From senger at ebi.ac.uk Fri Apr 28 14:08:38 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 15:08:38 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <44522048.3010503@ucalgary.ca> Message-ID: > Actually, I write clients > I am not talking about clients. My motivation for splitting is to make a lightweight jmoby.jar for service providers. That's all. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Apr 28 14:30:20 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 08:30:20 -0600 Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: References: Message-ID: <445226FC.7090203@ucalgary.ca> Right, I realize that. I was replying to Eddie's post: "Classes in the package org.biomoby.shared.extended are used for parsing RDF and are probably no use to clients." Perhaps he meant service providers, not clients? In any case, if we are interested in having more people use jMOBY in their current work, we should keep it in the back of our minds that they may not be using the jMOBY CVS checkout as their primary development directory. I, for example am in that boat, since my main program (Bluejay) has its own CVS directory. Self-contained JARs would make using jMOBY a lot easier for such situations. This is what I have done, and I am willing to provide these to others. The current option is for such developers to adopt the 50MB of JAR files in jMOBY's lib directory in their application deployments... Don't get me wrong, the current setup is great for people developing jMOBY code, but it's not ideal for people who just want to use jMOBY code in another application... My CAN$0.02, Paul Martin Senger wrote: >> Actually, I write clients >> >> > I am not talking about clients. My motivation for splitting is to make > a lightweight jmoby.jar for service providers. That's all. > > Martin > > From senger at ebi.ac.uk Fri Apr 28 15:43:03 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 16:43:03 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <000101c66a78$28e5b3c0$6500a8c0@notebook> Message-ID: > Most likely all of the classes in the package > org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry are > Okay, I splitted jmoby.jar into 3: jmoby-dashboard.jar has org.biomoby.service.dashboard, jmoby-others has org.biomoby.client.ui, org.biomoby.client.rdf, org.biomoby.registry, and jmoby.jar has the rest. Which means that if anybody wants to develop a service in a different directory (if it does directly in jMoby directiry, nothing changed), she needs to copy there only jmoby.jar (and few others third-party libraries - I have also created a short document "How to develop a BioMoby service" (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopment.html) to summarize what har files are needed. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From senger at ebi.ac.uk Fri Apr 28 15:45:35 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 28 Apr 2006 16:45:35 +0100 (BST) Subject: [MOBY-dev] splitting jmoby.jar In-Reply-To: <445226FC.7090203@ucalgary.ca> Message-ID: > Perhaps he meant service providers, not clients? > That was also my interpretation. > In any case, if we are interested in having more people use jMOBY in > their current work, we should keep it in the back of our minds that they > may not be using the jMOBY CVS checkout as their primary development > directory. > Definitely. It would be useful for all of us if you can write a page (and link it from the main jMoby's index.html) explaining how to squeeze jar files into smaller ones, depending on your needs. Regards, Martin From gordonp at ucalgary.ca Fri Apr 28 21:09:31 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 15:09:31 -0600 Subject: [MOBY-dev] Shims Message-ID: <4452848B.2080500@ucalgary.ca> Hi everyone, This is a very general question, especially for non-native-English speakers. I was going to add a top-level "Shim" category of services to the ontology, but I'm pretty sure most non-native-English speakers would have no idea what this means. I'm borrowing the term from D Hull, R Stevens, P Lord, C Wroe, C Goble (2004). Treating shimantic web syndrome with ontologies. First AKT workshop on Semantic Web Services (AKT-SWS04). Essentially, I'm tired of having a DNASequence, and not being able to directly call BLAST services because they take FASTA_NA. Services in the "Shim" category would be something like the Conversion category, but specifically they would convert between MOBY data types for the purpose of service compatibility. Having all such services in one category would make it easier to do these transformations automagically for the user. But do people think this is a good name, or what would they suggest? shim: A thin slip, usually of metal, used to fill up a space between parts subject to wear, to align or adjust the level of rails, etc. (Oxford English Dictionary) From markw at illuminae.com Fri Apr 28 21:23:05 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 28 Apr 2006 14:23:05 -0700 Subject: [MOBY-dev] Shims In-Reply-To: <4452848B.2080500@ucalgary.ca> References: <4452848B.2080500@ucalgary.ca> Message-ID: I think it is already there, isn't it? There is a "conversion" category for sure, which is intended for that purpose. M On Fri, 28 Apr 2006 14:09:31 -0700, Paul Gordon wrote: > Hi everyone, > > This is a very general question, especially for non-native-English > speakers. I was going to add a top-level "Shim" category of services > to the ontology, but I'm pretty sure most non-native-English speakers > would have no idea what this means. I'm borrowing the term from > > D Hull, R Stevens, P Lord, C Wroe, C Goble (2004). Treating shimantic > web syndrome with ontologies. First AKT workshop on Semantic Web > Services (AKT-SWS04). > > Essentially, I'm tired of having a DNASequence, and not being able to > directly call BLAST services because they take FASTA_NA. Services in > the "Shim" category would be something like the Conversion category, but > specifically they would convert between MOBY data types for the purpose > of service compatibility. Having all such services in one category > would make it easier to do these transformations automagically for the > user. But do people think this is a good name, or what would they > suggest? > > shim: A thin slip, usually of metal, used to fill up a space between > parts subject to wear, to align or adjust the level of rails, etc. > (Oxford English Dictionary) > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Fri Apr 28 22:44:04 2006 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 28 Apr 2006 16:44:04 -0600 Subject: [MOBY-dev] Shims In-Reply-To: References: <4452848B.2080500@ucalgary.ca> Message-ID: <44529AB4.9010602@ucalgary.ca> Mark Wilkinson wrote: > I think it is already there, isn't it? There is a "conversion" category > for sure, which is intended for that purpose. > But that's not how it's being used now. That why I said... >> Services in >> the "Shim" category would be something like the Conversion category, but >> specifically they would convert between MOBY data types for the purpose >> of service compatibility. From ssoiland at cs.man.ac.uk Sat Apr 29 12:30:01 2006 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Sat, 29 Apr 2006 13:30:01 +0100 Subject: [MOBY-dev] Shims In-Reply-To: <4452848B.2080500@ucalgary.ca> References: <4452848B.2080500@ucalgary.ca> Message-ID: <09EDCBE0-BDD0-4ED1-8B10-F496F989AE7B@cs.man.ac.uk> On 28. apr. 2006, at 22:09, Paul Gordon wrote: > This is a very general question, especially for non-native-English > speakers. I was going to add a top-level "Shim" category of services > to the ontology, but I'm pretty sure most non-native-English speakers > would have no idea what this means. I'm borrowing the term from As a non-native speaker I had to look up the term itself. However, we are using the term "shim" in mygrid/Taverna for the very same concept of making services with nearly-the-same-datatypes work together. However, I wish there could be a better word to present to the user what this category would be. I would assume many like me to just assume this had something to do with "the shim system" which I didn't know anything about, and so I would never explore it. "Conversion" is much better, even if its already in use. Maybe look into what really are the different conversions, and call the shimming "Format conversion" or something. -- Stian Soiland, myGrid project School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From senger at ebi.ac.uk Sat Apr 29 21:26:05 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Sat, 29 Apr 2006 22:26:05 +0100 (BST) Subject: [MOBY-dev] logging ip requests from moby MoSeS genereated service In-Reply-To: <442AB936.2080901@mmb.pcb.ub.es> Message-ID: Hi, > I need to log some data about the use of the webservices generated by > MoSeS. One of the things is the IP address of the caller. Is there any > sensible way to do it from the webservice implementing class? > I have added it there (into org.biomoby.service.BaseService). Now you can call from your implementation class (because it inherits from the BaseService via generated skeleton): String remoteAddr = getCallerAddr(); Be aware, however, that it may not return an address on the real Biomoby client, but of some proxy which is in between. But for that, I am helpless. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From carole at cs.man.ac.uk Sat Apr 29 22:25:57 2006 From: carole at cs.man.ac.uk (Carole Goble) Date: Sat, 29 Apr 2006 23:25:57 +0100 Subject: [MOBY-dev] Shims In-Reply-To: <09EDCBE0-BDD0-4ED1-8B10-F496F989AE7B@cs.man.ac.uk> References: <4452848B.2080500@ucalgary.ca> <09EDCBE0-BDD0-4ED1-8B10-F496F989AE7B@cs.man.ac.uk> Message-ID: <4453E7F5.3000609@cs.man.ac.uk> Stian as the person who coined the term shim it is there precisely because there are a whole range of words that have been used. mediator, adaptor, conversion etc. not all shims are conversions. the new term gives a fresh start. By the way, the first shim paper not by manchester is now published Adapters, shims, and glue--service interoperability for in silico experiments U. Radetzki, U. Leser, S. C. Schulze-Rauschenbach, J. Zimmermann, J. Lussem, T. Bode, and A. B. Cremers Bioinformatics 2006 22: 1137-1143. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/9/1137?etoc Carole > On 28. apr. 2006, at 22:09, Paul Gordon wrote: > > >> This is a very general question, especially for non-native-English >> speakers. I was going to add a top-level "Shim" category of services >> to the ontology, but I'm pretty sure most non-native-English speakers >> would have no idea what this means. I'm borrowing the term from >> > > As a non-native speaker I had to look up the term itself. However, we > are using the term "shim" in mygrid/Taverna for the very same concept > of making services with nearly-the-same-datatypes work together. > However, I wish there could be a better word to present to the user > what this category would be. I would assume many like me to just > assume this had something to do with "the shim system" which I didn't > know anything about, and so I would never explore it. > > "Conversion" is much better, even if its already in use. Maybe look > into what really are the different conversions, and call the shimming > "Format conversion" or something. > >