From pieter.neerincx at gmail.com Thu Oct 1 06:13:06 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Thu, 1 Oct 2009 12:13:06 +0200 Subject: [MOBY-dev] Public CVS problems In-Reply-To: <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Hi, I'm unable to connect to the CVS server today. The connection fails with a timeout. Am I the only one or is the CVS server down? Yesterday it was fine and other sites work as expected... Cheers, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Group Faculty of Science Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Thu Oct 1 07:24:43 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 1 Oct 2009 19:24:43 +0800 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: <4d93f07c0910010424x4c0b3d1ewf0e3b7d47ff9890f@mail.gmail.com> The same problem for me... Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Thu Oct 1 13:24:50 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 01 Oct 2009 19:24:50 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> Message-ID: <4AC4E5E2.8090906@bsc.es> Hello Martin, There is no JDK6 dependency in INB code. Libraries work with Java5 + JAX-WS 2.1 or with Java6u4+ (which has JAX-WS 2.1 included). The missing class is a part of "jaxws-api-2.1.jar" which is included in a moby build. It MUST contain W3CEndpointReferenceBuilder.class, if not, that means something wrong with maven repository... Kind Regards, Dmitry From martin.senger at gmail.com Thu Oct 1 14:00:00 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 02:00:00 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC4E5E2.8090906@bsc.es> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> <4AC4E5E2.8090906@bsc.es> Message-ID: <4d93f07c0910011100w41bd71e7ndbbdc26cb45c989d@mail.gmail.com> > There is no JDK6 dependency in INB code. Good; I have mentioned the Java 6 just to be sure that it was not the culprit. > The missing class is a part of "jaxws-api-2.1.jar" which is included in a > moby build. > It MUST contain W3CEndpointReferenceBuilder.class, if not, that means > something wrong with maven repository... > Well, you have to choose a repository that does not cause the problem. If you bring a new dependency to jMoby you have to solve it first - so other people can compile it. If you find that there is a problem with the maven repository (which I doubt - but it is possible; I have seen such cases in the past) you need to take the jar file (representing the new dependency), to create its pom file (defining its own dependencies) and deploy it to the openbio maven repository (I can deploy it for you if you do not have an access there). The missing class is a part of "jaxws-api-2.1.jar" which is included in a > moby build. > All dependencies have to be in xmls/project.pom (or in their consequent dependencies) - nowhere else (i.g. no additional dependency can be hard coded in the build.xml file - if it is what you meant by "moby build"). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Thu Oct 1 14:14:37 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 02:14:37 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910011100w41bd71e7ndbbdc26cb45c989d@mail.gmail.com> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> <4AC4E5E2.8090906@bsc.es> <4d93f07c0910011100w41bd71e7ndbbdc26cb45c989d@mail.gmail.com> Message-ID: <4d93f07c0910011114hfff0a34u55edd8b96fdfe4fe@mail.gmail.com> [cont.] My reply was general - regarding the way how to solve all dependencies. Tomorrow, when I boot into my linux box, I will try to be more specific and to help with your specific problem (unless you solve it before that, of course). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Thu Oct 1 14:17:18 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 01 Oct 2009 11:17:18 -0700 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Seems to be working now... are you still having problems? On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx wrote: > Hi, > > I'm unable to connect to the CVS server today. The connection fails with > a timeout. Am I the only one or is the CVS server down? Yesterday it was > fine and other sites work as expected... > -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From martin.senger at gmail.com Thu Oct 1 20:10:12 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 08:10:12 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC4E5E2.8090906@bsc.es> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> <4AC4E5E2.8090906@bsc.es> Message-ID: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> Hi again, The missing class is a part of "jaxws-api-2.1.jar" which is included in a > moby build. > It MUST contain W3CEndpointReferenceBuilder.class, if not, that means > something wrong with maven repository... > I have looked at the jaxws-api.jar (version 2.1) file. This file does not contain the class W3CEndpointReferenceBuilder. However, I found this class in the newer version, 2.1-1. Which means that you have to use the newer version perhaps? Let me know if you need any assistance with adding the new version into the xmls/project.pom file. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Thu Oct 1 21:21:06 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 02 Oct 2009 03:21:06 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> References: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> Message-ID: <4AC55582.70204@bsc.es> Hello Martin, I didn't change anything regarding the JAX-WS version I just got a clean cvs version and had rebuilt a maven repository to be sure the correct version of jax-ws is there... The version is 2.1 as far as I can see and does have the W3CEndpointReferenceBuilder.class: 4.0.0 javax.xml.ws jaxws-api 2.1 javax.xml.bind jaxb-api 2.1 Just finished to run a Dashboadrd, Dmitry From martin.senger at gmail.com Thu Oct 1 22:40:54 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 10:40:54 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC55582.70204@bsc.es> References: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> <4AC55582.70204@bsc.es> Message-ID: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> > The version is 2.1 as far as I can see and does have the > W3CEndpointReferenceBuilder.class: > That's not what I see. I am talking about the file "jaxws-api-2.1.jar" (from the directory: ".m2/repository/javax/xml/ws/jaxws-api/2.1" - where ever your local maven repository is located). My has size 33428. This file does not have W3CEndpointReferenceBuilder class. What file do you have in mind? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Fri Oct 2 03:04:50 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 02 Oct 2009 09:04:50 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> References: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> Message-ID: <4AC5A612.7020602@bsc.es> ... Very strange. As I said I just did a "clean" install to check. C:\Documents and Settings\dmitry\.m2\repository\javax\xml\ws\jaxws-api\2.1 Zip:jaxws-api-2.1.jar \javax\xml\ws\wsaddressing package-info.class W3CEndpointReference.class W3CEndpointReference$Address.class W3CEndpointReference$Elements.class W3CEndpointReferenceBuilder.class Here is a manifest file: Manifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_06-b05 (Sun Microsystems Inc.) Specification-Title: Java API for XML Web Services Specification-Version: 2.1 Implementation-Title: Java API for XML Web Services Standard Implement ation Implementation-Vendor: Sun Microsystems, Inc. Implementation-Vendor-Id: com.sun Extension-Name: javax.xml.ws The only thing I can think out is to remove jaxws-api directory and try to reload it... Dmitry From martin.senger at gmail.com Fri Oct 2 03:13:05 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 15:13:05 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC5A612.7020602@bsc.es> References: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> <4AC5A612.7020602@bsc.es> Message-ID: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> > ... Very strange. > Indeed, it is. In the jar file that I just downloaded from the central maven (just to be sure that I do not have a strange copy in my local repository) I see only these classes: -rw-r--r-- 742 22-Sep-2006 14:43:10 javax/xml/ws/wsaddressing/W3CEndpointReference$Address.class -rw-r--r-- 803 22-Sep-2006 14:43:10 javax/xml/ws/wsaddressing/W3CEndpointReference$Elements.class -rw-r--r-- 3551 22-Sep-2006 14:43:10 javax/xml/ws/wsaddressing/W3CEndpointReference.class The only thing I can think out is to remove jaxws-api directory and try to > reload it... Yes, please, do so (even though I am not sure in which order various maven repositories are contacted - you may still end up with the wrong file - if there is anywhere a wrong file). Other option is still to move to version 2.1-1. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From pieter.neerincx at gmail.com Fri Oct 2 05:05:45 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Fri, 2 Oct 2009 11:05:45 +0200 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Hi Mark, I'm still getting: cvs [login aborted]: connect to [cvs.open-bio.org]:2401 failed: Connection timed out If Martin has the same problem, maybe it's a transatlantic glitch... Cheers, Pi On 1?Oct?2009, at 8:17 PM, Mark Wilkinson wrote: > Seems to be working now... are you still having problems? > > > On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx > wrote: > >> Hi, >> >> I'm unable to connect to the CVS server today. The connection fails >> with a timeout. Am I the only one or is the CVS server down? >> Yesterday it was fine and other sites work as expected... >> > > > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary > Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Group Faculty of Science Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Fri Oct 2 05:12:04 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 17:12:04 +0800 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: <4d93f07c0910020212y3b66bb8dvc9fd321cd0d1b15b@mail.gmail.com> > > If Martin has the same problem, maybe it's a transatlantic glitch... > My problem occurs in the cron job - the cron job runs on an openbio server - which I guess is also in the North America. I have asked Chris - let's see what his view will be. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Fri Oct 2 05:39:32 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 02 Oct 2009 11:39:32 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> References: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> Message-ID: <4AC5CA54.9080307@bsc.es> It looks like a bug in maven (or rather repository problems) http://markmail.org/message/ybohzo74pxh45i7e#query:maven%20jax-ws%20W3CEndpointReferenceBuilder%20missing+page:1+mid:epcwtuzlbhcjkuol+state:results In any case I don't mind to pass to jax-ws 2.1.1... I keep reading... From markw at illuminae.com Fri Oct 2 10:56:03 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 02 Oct 2009 07:56:03 -0700 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Seems that it might be a transatlantic glitch... both the public and the private cvs servers are functioning normally for me. Is *anyone* else having this problem? if someone could try: cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login (password cvs) cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co moby-live Thanks! Mark On Fri, 02 Oct 2009 02:05:45 -0700, Pieter Neerincx wrote: > Hi Mark, > > I'm still getting: > > cvs [login aborted]: connect to [cvs.open-bio.org]:2401 failed: > Connection timed out > > If Martin has the same problem, maybe it's a transatlantic glitch... > > Cheers, > > Pi > > On 1?Oct?2009, at 8:17 PM, Mark Wilkinson wrote: > >> Seems to be working now... are you still having problems? >> >> >> On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx >> wrote: >> >>> Hi, >>> >>> I'm unable to connect to the CVS server today. The connection fails >>> with a timeout. Am I the only one or is the CVS server down? Yesterday >>> it was fine and other sites work as expected... >>> >> >> >> >> >> --Mark D Wilkinson, PI Bioinformatics >> Assistant Professor, Medical Genetics >> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research >> Providence Heart + Lung Institute >> University of British Columbia - St. Paul's Hospital >> Vancouver, BC, Canada >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > ------------------------------------------------------------- > Biomolecular Mass Spectrometry and Proteomics Group > Faculty of Science > Utrecht University > > Visiting address: > H.R. Kruyt building room O607 > Padualaan 8 > 3584 CH Utrecht > The Netherlands > > Mail address: > P.O. box 80.082 > 3508 TB Utrecht > The Netherlands > > phone: +31 (0)6-143 66 783 > email: pieter.neerincx at gmail.com > skype: pieter.online > ------------------------------------------------------------- > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From Sebastien.Carrere at toulouse.inra.fr Fri Oct 2 11:12:10 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 02 Oct 2009 17:12:10 +0200 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: <4AC6184A.6090900@toulouse.inra.fr> Bonjour, It's OK from Toulouse. Sebastien Mark Wilkinson wrote: > Seems that it might be a transatlantic glitch... both the public and > the private cvs servers are functioning normally for me. > > Is *anyone* else having this problem? if someone could try: > > cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login > (password cvs) > cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co moby-live > > > Thanks! > > Mark > > > > On Fri, 02 Oct 2009 02:05:45 -0700, Pieter Neerincx > wrote: > >> Hi Mark, >> >> I'm still getting: >> >> cvs [login aborted]: connect to [cvs.open-bio.org]:2401 failed: >> Connection timed out >> >> If Martin has the same problem, maybe it's a transatlantic glitch... >> >> Cheers, >> >> Pi >> >> On 1?Oct?2009, at 8:17 PM, Mark Wilkinson wrote: >> >>> Seems to be working now... are you still having problems? >>> >>> >>> On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx >>> wrote: >>> >>>> Hi, >>>> >>>> I'm unable to connect to the CVS server today. The connection fails >>>> with a timeout. Am I the only one or is the CVS server down? >>>> Yesterday it was fine and other sites work as expected... >>>> >>> >>> >>> >>> >>> --Mark D Wilkinson, PI Bioinformatics >>> Assistant Professor, Medical Genetics >>> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary >>> Research >>> Providence Heart + Lung Institute >>> University of British Columbia - St. Paul's Hospital >>> Vancouver, BC, Canada >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> ------------------------------------------------------------- >> Biomolecular Mass Spectrometry and Proteomics Group >> Faculty of Science >> Utrecht University >> >> Visiting address: >> H.R. Kruyt building room O607 >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> >> Mail address: >> P.O. box 80.082 >> 3508 TB Utrecht >> The Netherlands >> >> phone: +31 (0)6-143 66 783 >> email: pieter.neerincx at gmail.com >> skype: pieter.online >> ------------------------------------------------------------- >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 398 bytes Desc: not available URL: From martin.senger at gmail.com Sun Oct 4 19:34:42 2009 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 5 Oct 2009 07:34:42 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC5CA54.9080307@bsc.es> References: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> <4AC5CA54.9080307@bsc.es> Message-ID: <4d93f07c0910041634k6b044648n55cd4c7728fa47fd@mail.gmail.com> Sorry but I could not wait longer for the jMoby to be compilable. Therefore, I have updated myself the "xmls/project.pom" - in order to get there a newer version of jax-ws (that has the class missing in Dmitry's code). It compiles now. But it needs testing whether the newer version does what it is supposed to do. Please 'cvs update -dP'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Mon Oct 5 10:35:03 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 05 Oct 2009 16:35:03 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910041634k6b044648n55cd4c7728fa47fd@mail.gmail.com> References: <4d93f07c0910041634k6b044648n55cd4c7728fa47fd@mail.gmail.com> Message-ID: <4ACA0417.70703@bsc.es> Thank you Martin for modifying it. As I understand the problem was that there are two different repositories for JAX-WS 2.1 and by some reason sometimes it took one and sometimes another... Strange thing is that in maven1 repository contains a "wrong" jaxws-api-2.1.jar... Anyway I could confirm that I can compile everything with JAX-WS 2.1.1... Dmitry From pieter.neerincx at gmail.com Mon Oct 19 12:24:55 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Mon, 19 Oct 2009 18:24:55 +0200 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: <47BC0768.50905@bsc.es> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> Message-ID: <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Hi Moby developers, I was wondering if one of you can point me to an easy way to update the RDF for an already registered moby service? Generating the RDF the first time was easy. I used dashboard and there's also an online web form linked from the Biomoby website. But I cannot figure out how to update the RDF. The documentation tells me I have to update and then either call the RDF agent or simply wait for the next pass. The latter is easy, but I don't seem to be able to generate updated RDF for my service with the dashboard. When I modify my service I can save the service registration XML without registering, but I cannot save the RDF. The only way the RDF is generated and saved is to click the register service button, but that one fails because the service is already registered. Clicking unregister service first to reregister the updated version will fail of course too as you cannot unregister a service that was registered with an RDF signature URL. Likewise the online form the generate the RDF cannot be used, because it only works for existing services. I looked at the RDF to update it manually. I can patch most of it manually, but there are Description tags like this: Where do those numbers at the end of the rdf:about attribute value come from? As far as I can figure out the only way to get my service RDF updated is to remove the RDF, call the agent to unregister the service and then to re-register a new one, but I was hoping to find a more elegant approach :).... Cheers, Pi From edward.kawas at gmail.com Mon Oct 19 12:53:51 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 19 Oct 2009 09:53:51 -0700 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Message-ID: <4adc99a2.161bf30a.6792.1d86@mx.google.com> Hi Pieter, In Perl, look at MOBY::RDF::Parsers::ServiceParser. This module contains a method, createRDFModel, that consumes an array reference of MOBY::Client::ServiceInstance objects and produces RDF/XML for them all. In Java, look at org.biomoby.client.rdf.builder.ServiceInstanceRDF. This class can create RDF/XML for instances of MobyServices ... Hope that helps, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: October-19-09 9:25 AM To: Core developer announcements Subject: [MOBY-dev] Updating vs generating RDF Hi Moby developers, I was wondering if one of you can point me to an easy way to update the RDF for an already registered moby service? Generating the RDF the first time was easy. I used dashboard and there's also an online web form linked from the Biomoby website. But I cannot figure out how to update the RDF. The documentation tells me I have to update and then either call the RDF agent or simply wait for the next pass. The latter is easy, but I don't seem to be able to generate updated RDF for my service with the dashboard. When I modify my service I can save the service registration XML without registering, but I cannot save the RDF. The only way the RDF is generated and saved is to click the register service button, but that one fails because the service is already registered. Clicking unregister service first to reregister the updated version will fail of course too as you cannot unregister a service that was registered with an RDF signature URL. Likewise the online form the generate the RDF cannot be used, because it only works for existing services. I looked at the RDF to update it manually. I can patch most of it manually, but there are Description tags like this: Where do those numbers at the end of the rdf:about attribute value come from? As far as I can figure out the only way to get my service RDF updated is to remove the RDF, call the agent to unregister the service and then to re-register a new one, but I was hoping to find a more elegant approach :).... Cheers, Pi _______________________________________________ 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 Oct 19 12:39:31 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 19 Oct 2009 09:39:31 -0700 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Message-ID: Hi Pi! The answer to your question may be simple, or may be complex, depending on how dramatic your service interface changes are! In the RDF, the URIs that look like: http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances/e0578ca78558ba81463c3e9f59412c9b are simply hashes designed to be unique to that node, for that service provider, for that service. This ensures that we don't get node-collisions when we integrate RDF from multiple service providers (as was previously a problem with the auto-naming of bnodes that some RDF libraries did). So... if you need to edit the content of one of those nodes, just go ahead and edit the content, and leave the node ID intact. If you need to remove a node, go ahead and remove it, no problem. If you need to ADD a node, however, then you're going to have to generate a 100% unique ID for that node (unique within all of moby central). Eddie can tell you how he hashes things to generate that number. Editing the RDF can be done in any text editor, but you might prefer to do it in Protege or whatever your preferred RDF editor is. Cheers! Mark On Mon, 19 Oct 2009 09:24:55 -0700, Pieter Neerincx wrote: > Hi Moby developers, > > I was wondering if one of you can point me to an easy way to update the > RDF for an already registered moby service? > > Generating the RDF the first time was easy. I used dashboard and there's > also an online web form linked from the Biomoby website. But I cannot > figure out how to update the RDF. The documentation tells me I have to > update and then either call the RDF agent or simply wait for the next > pass. The latter is easy, but I don't seem to be able to generate > updated RDF for my service with the dashboard. When I modify my service > I can save the service registration XML without registering, but I > cannot save the RDF. The only way the RDF is generated and saved is to > click the register service button, but that one fails because the > service is already registered. Clicking unregister service first to > reregister the updated version will fail of course too as you cannot > unregister a service that was registered with an RDF signature URL. > Likewise the online form the generate the RDF cannot be used, because it > only works for existing services. > > I looked at the RDF to update it manually. I can patch most of it > manually, but there are Description tags like this: > > rdf:about="http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances/e0578ca78558ba81463c3e9f59412c9b"> > > Where do those numbers at the end of the rdf:about attribute value come > from? > > As far as I can figure out the only way to get my service RDF updated is > to remove the RDF, call the agent to unregister the service and then to > re-register a new one, but I was hoping to find a more elegant approach > :).... > > Cheers, > > Pi > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From pieter.neerincx at gmail.com Tue Oct 20 17:43:41 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Tue, 20 Oct 2009 23:43:41 +0200 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Message-ID: <540C29BF-772A-4896-97DF-0AD275166535@gmail.com> Hi Mark and Eddie, Thanks for the help! It's clear to me now where those seemingly random numbers come from :). Cheers, Pi On 19 Oct 2009, at 18:39, Mark Wilkinson wrote: > Hi Pi! > > The answer to your question may be simple, or may be complex, > depending on how dramatic your service interface changes are! > > In the RDF, the URIs that look like: > http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances/e0578ca78558ba81463c3e9f59412c9b > > are simply hashes designed to be unique to that node, for that > service provider, for that service. This ensures that we don't get > node-collisions when we integrate RDF from multiple service > providers (as was previously a problem with the auto-naming of > bnodes that some RDF libraries did). > > So... if you need to edit the content of one of those nodes, just go > ahead and edit the content, and leave the node ID intact. If you > need to remove a node, go ahead and remove it, no problem. If you > need to ADD a node, however, then you're going to have to generate a > 100% unique ID for that node (unique within all of moby central). > > Eddie can tell you how he hashes things to generate that number. > > Editing the RDF can be done in any text editor, but you might prefer > to do it in Protege or whatever your preferred RDF editor is. > > Cheers! > > Mark > > > > > On Mon, 19 Oct 2009 09:24:55 -0700, Pieter Neerincx > wrote: > >> Hi Moby developers, >> >> I was wondering if one of you can point me to an easy way to update >> the RDF for an already registered moby service? >> >> Generating the RDF the first time was easy. I used dashboard and >> there's also an online web form linked from the Biomoby website. >> But I cannot figure out how to update the RDF. The documentation >> tells me I have to update and then either call the RDF agent or >> simply wait for the next pass. The latter is easy, but I don't seem >> to be able to generate updated RDF for my service with the >> dashboard. When I modify my service I can save the service >> registration XML without registering, but I cannot save the RDF. >> The only way the RDF is generated and saved is to click the >> register service button, but that one fails because the service is >> already registered. Clicking unregister service first to reregister >> the updated version will fail of course too as you cannot >> unregister a service that was registered with an RDF signature URL. >> Likewise the online form the generate the RDF cannot be used, >> because it only works for existing services. >> >> I looked at the RDF to update it manually. I can patch most of it >> manually, but there are Description tags like this: >> >> >> >> Where do those numbers at the end of the rdf:about attribute value >> come from? >> >> As far as I can figure out the only way to get my service RDF >> updated is to remove the RDF, call the agent to unregister the >> service and then to re-register a new one, but I was hoping to find >> a more elegant approach :).... >> >> Cheers, >> >> Pi >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary > Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Thu Oct 1 02:21:36 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 1 Oct 2009 10:21:36 +0800 Subject: [MOBY-dev] jMoby does not compile Message-ID: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> Please correct the code asap - people cannot use jMoby when it does not compile. Please be aware that we are still using Java 5. There was a suggestion to switch to Java 6 but it was not yet broadly accepted. If this is the case of not compiling, please make effort to bring the broader consensus on this issue (you have my vote of support for Java 6). The errors are: compile: [javac] Compiling 476 source files to /home/senger/moby-live/Java/build/classes [javac] /home/senger/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java:18: cannot find symbol [javac] symbol : class W3CEndpointReferenceBuilder [javac] location: package javax.xml.ws.wsaddressing [javac] import javax.xml.ws.wsaddressing.W3CEndpointReferenceBuilder; [javac] ^ [javac] /home/senger/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java:51: cannot find symbol [javac] symbol : class W3CEndpointReferenceBuilder [javac] location: class org.inb.biomoby.shared.wsrf.MobyEndpointReference [javac] W3CEndpointReferenceBuilder wsaBuilder = new W3CEndpointReferenceBuilder(); [javac] ^ [javac] /home/senger/moby-live/Java/src/main/org/inb/biomoby/shared/wsrf/MobyEndpointReference.java:51: cannot find symbol [javac] symbol : class W3CEndpointReferenceBuilder [javac] location: class org.inb.biomoby.shared.wsrf.MobyEndpointReference [javac] W3CEndpointReferenceBuilder wsaBuilder = new W3CEndpointReferenceBuilder(); [javac] ^ [javac] Note: /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/PBERecorder.java uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 3 errors Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From pieter.neerincx at gmail.com Thu Oct 1 10:13:06 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Thu, 1 Oct 2009 12:13:06 +0200 Subject: [MOBY-dev] Public CVS problems In-Reply-To: <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Hi, I'm unable to connect to the CVS server today. The connection fails with a timeout. Am I the only one or is the CVS server down? Yesterday it was fine and other sites work as expected... Cheers, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Group Faculty of Science Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Thu Oct 1 11:24:43 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 1 Oct 2009 19:24:43 +0800 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: <4d93f07c0910010424x4c0b3d1ewf0e3b7d47ff9890f@mail.gmail.com> The same problem for me... Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Thu Oct 1 17:24:50 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Thu, 01 Oct 2009 19:24:50 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> Message-ID: <4AC4E5E2.8090906@bsc.es> Hello Martin, There is no JDK6 dependency in INB code. Libraries work with Java5 + JAX-WS 2.1 or with Java6u4+ (which has JAX-WS 2.1 included). The missing class is a part of "jaxws-api-2.1.jar" which is included in a moby build. It MUST contain W3CEndpointReferenceBuilder.class, if not, that means something wrong with maven repository... Kind Regards, Dmitry From martin.senger at gmail.com Thu Oct 1 18:00:00 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 02:00:00 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC4E5E2.8090906@bsc.es> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> <4AC4E5E2.8090906@bsc.es> Message-ID: <4d93f07c0910011100w41bd71e7ndbbdc26cb45c989d@mail.gmail.com> > There is no JDK6 dependency in INB code. Good; I have mentioned the Java 6 just to be sure that it was not the culprit. > The missing class is a part of "jaxws-api-2.1.jar" which is included in a > moby build. > It MUST contain W3CEndpointReferenceBuilder.class, if not, that means > something wrong with maven repository... > Well, you have to choose a repository that does not cause the problem. If you bring a new dependency to jMoby you have to solve it first - so other people can compile it. If you find that there is a problem with the maven repository (which I doubt - but it is possible; I have seen such cases in the past) you need to take the jar file (representing the new dependency), to create its pom file (defining its own dependencies) and deploy it to the openbio maven repository (I can deploy it for you if you do not have an access there). The missing class is a part of "jaxws-api-2.1.jar" which is included in a > moby build. > All dependencies have to be in xmls/project.pom (or in their consequent dependencies) - nowhere else (i.g. no additional dependency can be hard coded in the build.xml file - if it is what you meant by "moby build"). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Thu Oct 1 18:14:37 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 02:14:37 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910011100w41bd71e7ndbbdc26cb45c989d@mail.gmail.com> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> <4AC4E5E2.8090906@bsc.es> <4d93f07c0910011100w41bd71e7ndbbdc26cb45c989d@mail.gmail.com> Message-ID: <4d93f07c0910011114hfff0a34u55edd8b96fdfe4fe@mail.gmail.com> [cont.] My reply was general - regarding the way how to solve all dependencies. Tomorrow, when I boot into my linux box, I will try to be more specific and to help with your specific problem (unless you solve it before that, of course). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Thu Oct 1 18:17:18 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 01 Oct 2009 11:17:18 -0700 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Seems to be working now... are you still having problems? On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx wrote: > Hi, > > I'm unable to connect to the CVS server today. The connection fails with > a timeout. Am I the only one or is the CVS server down? Yesterday it was > fine and other sites work as expected... > -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From martin.senger at gmail.com Fri Oct 2 00:10:12 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 08:10:12 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC4E5E2.8090906@bsc.es> References: <4d93f07c0909301921x71a678f5sbb626013c946565c@mail.gmail.com> <4AC4E5E2.8090906@bsc.es> Message-ID: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> Hi again, The missing class is a part of "jaxws-api-2.1.jar" which is included in a > moby build. > It MUST contain W3CEndpointReferenceBuilder.class, if not, that means > something wrong with maven repository... > I have looked at the jaxws-api.jar (version 2.1) file. This file does not contain the class W3CEndpointReferenceBuilder. However, I found this class in the newer version, 2.1-1. Which means that you have to use the newer version perhaps? Let me know if you need any assistance with adding the new version into the xmls/project.pom file. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Fri Oct 2 01:21:06 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 02 Oct 2009 03:21:06 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> References: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> Message-ID: <4AC55582.70204@bsc.es> Hello Martin, I didn't change anything regarding the JAX-WS version I just got a clean cvs version and had rebuilt a maven repository to be sure the correct version of jax-ws is there... The version is 2.1 as far as I can see and does have the W3CEndpointReferenceBuilder.class: 4.0.0 javax.xml.ws jaxws-api 2.1 javax.xml.bind jaxb-api 2.1 Just finished to run a Dashboadrd, Dmitry From martin.senger at gmail.com Fri Oct 2 02:40:54 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 10:40:54 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC55582.70204@bsc.es> References: <4d93f07c0910011710x39e67bq97ce43dd49f284bb@mail.gmail.com> <4AC55582.70204@bsc.es> Message-ID: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> > The version is 2.1 as far as I can see and does have the > W3CEndpointReferenceBuilder.class: > That's not what I see. I am talking about the file "jaxws-api-2.1.jar" (from the directory: ".m2/repository/javax/xml/ws/jaxws-api/2.1" - where ever your local maven repository is located). My has size 33428. This file does not have W3CEndpointReferenceBuilder class. What file do you have in mind? Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Fri Oct 2 07:04:50 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 02 Oct 2009 09:04:50 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> References: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> Message-ID: <4AC5A612.7020602@bsc.es> ... Very strange. As I said I just did a "clean" install to check. C:\Documents and Settings\dmitry\.m2\repository\javax\xml\ws\jaxws-api\2.1 Zip:jaxws-api-2.1.jar \javax\xml\ws\wsaddressing package-info.class W3CEndpointReference.class W3CEndpointReference$Address.class W3CEndpointReference$Elements.class W3CEndpointReferenceBuilder.class Here is a manifest file: Manifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_06-b05 (Sun Microsystems Inc.) Specification-Title: Java API for XML Web Services Specification-Version: 2.1 Implementation-Title: Java API for XML Web Services Standard Implement ation Implementation-Vendor: Sun Microsystems, Inc. Implementation-Vendor-Id: com.sun Extension-Name: javax.xml.ws The only thing I can think out is to remove jaxws-api directory and try to reload it... Dmitry From martin.senger at gmail.com Fri Oct 2 07:13:05 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 15:13:05 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC5A612.7020602@bsc.es> References: <4d93f07c0910011940j5fb8d1c4ie5d23c2f97c4f912@mail.gmail.com> <4AC5A612.7020602@bsc.es> Message-ID: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> > ... Very strange. > Indeed, it is. In the jar file that I just downloaded from the central maven (just to be sure that I do not have a strange copy in my local repository) I see only these classes: -rw-r--r-- 742 22-Sep-2006 14:43:10 javax/xml/ws/wsaddressing/W3CEndpointReference$Address.class -rw-r--r-- 803 22-Sep-2006 14:43:10 javax/xml/ws/wsaddressing/W3CEndpointReference$Elements.class -rw-r--r-- 3551 22-Sep-2006 14:43:10 javax/xml/ws/wsaddressing/W3CEndpointReference.class The only thing I can think out is to remove jaxws-api directory and try to > reload it... Yes, please, do so (even though I am not sure in which order various maven repositories are contacted - you may still end up with the wrong file - if there is anywhere a wrong file). Other option is still to move to version 2.1-1. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From pieter.neerincx at gmail.com Fri Oct 2 09:05:45 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Fri, 2 Oct 2009 11:05:45 +0200 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Hi Mark, I'm still getting: cvs [login aborted]: connect to [cvs.open-bio.org]:2401 failed: Connection timed out If Martin has the same problem, maybe it's a transatlantic glitch... Cheers, Pi On 1?Oct?2009, at 8:17 PM, Mark Wilkinson wrote: > Seems to be working now... are you still having problems? > > > On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx > wrote: > >> Hi, >> >> I'm unable to connect to the CVS server today. The connection fails >> with a timeout. Am I the only one or is the CVS server down? >> Yesterday it was fine and other sites work as expected... >> > > > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary > Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Group Faculty of Science Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Fri Oct 2 09:12:04 2009 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Oct 2009 17:12:04 +0800 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: <4d93f07c0910020212y3b66bb8dvc9fd321cd0d1b15b@mail.gmail.com> > > If Martin has the same problem, maybe it's a transatlantic glitch... > My problem occurs in the cron job - the cron job runs on an openbio server - which I guess is also in the North America. I have asked Chris - let's see what his view will be. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Fri Oct 2 09:39:32 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Fri, 02 Oct 2009 11:39:32 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> References: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> Message-ID: <4AC5CA54.9080307@bsc.es> It looks like a bug in maven (or rather repository problems) http://markmail.org/message/ybohzo74pxh45i7e#query:maven%20jax-ws%20W3CEndpointReferenceBuilder%20missing+page:1+mid:epcwtuzlbhcjkuol+state:results In any case I don't mind to pass to jax-ws 2.1.1... I keep reading... From markw at illuminae.com Fri Oct 2 14:56:03 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 02 Oct 2009 07:56:03 -0700 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: Seems that it might be a transatlantic glitch... both the public and the private cvs servers are functioning normally for me. Is *anyone* else having this problem? if someone could try: cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login (password cvs) cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co moby-live Thanks! Mark On Fri, 02 Oct 2009 02:05:45 -0700, Pieter Neerincx wrote: > Hi Mark, > > I'm still getting: > > cvs [login aborted]: connect to [cvs.open-bio.org]:2401 failed: > Connection timed out > > If Martin has the same problem, maybe it's a transatlantic glitch... > > Cheers, > > Pi > > On 1?Oct?2009, at 8:17 PM, Mark Wilkinson wrote: > >> Seems to be working now... are you still having problems? >> >> >> On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx >> wrote: >> >>> Hi, >>> >>> I'm unable to connect to the CVS server today. The connection fails >>> with a timeout. Am I the only one or is the CVS server down? Yesterday >>> it was fine and other sites work as expected... >>> >> >> >> >> >> --Mark D Wilkinson, PI Bioinformatics >> Assistant Professor, Medical Genetics >> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research >> Providence Heart + Lung Institute >> University of British Columbia - St. Paul's Hospital >> Vancouver, BC, Canada >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > ------------------------------------------------------------- > Biomolecular Mass Spectrometry and Proteomics Group > Faculty of Science > Utrecht University > > Visiting address: > H.R. Kruyt building room O607 > Padualaan 8 > 3584 CH Utrecht > The Netherlands > > Mail address: > P.O. box 80.082 > 3508 TB Utrecht > The Netherlands > > phone: +31 (0)6-143 66 783 > email: pieter.neerincx at gmail.com > skype: pieter.online > ------------------------------------------------------------- > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From Sebastien.Carrere at toulouse.inra.fr Fri Oct 2 15:12:10 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 02 Oct 2009 17:12:10 +0200 Subject: [MOBY-dev] Public CVS problems In-Reply-To: References: <4A9EBD2D.2050908@ucalgary.ca> <4d93f07c0909021724u37bec823mcde104331fc59e30@mail.gmail.com> Message-ID: <4AC6184A.6090900@toulouse.inra.fr> Bonjour, It's OK from Toulouse. Sebastien Mark Wilkinson wrote: > Seems that it might be a transatlantic glitch... both the public and > the private cvs servers are functioning normally for me. > > Is *anyone* else having this problem? if someone could try: > > cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby login > (password cvs) > cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/moby co moby-live > > > Thanks! > > Mark > > > > On Fri, 02 Oct 2009 02:05:45 -0700, Pieter Neerincx > wrote: > >> Hi Mark, >> >> I'm still getting: >> >> cvs [login aborted]: connect to [cvs.open-bio.org]:2401 failed: >> Connection timed out >> >> If Martin has the same problem, maybe it's a transatlantic glitch... >> >> Cheers, >> >> Pi >> >> On 1?Oct?2009, at 8:17 PM, Mark Wilkinson wrote: >> >>> Seems to be working now... are you still having problems? >>> >>> >>> On Thu, 01 Oct 2009 03:13:06 -0700, Pieter Neerincx >>> wrote: >>> >>>> Hi, >>>> >>>> I'm unable to connect to the CVS server today. The connection fails >>>> with a timeout. Am I the only one or is the CVS server down? >>>> Yesterday it was fine and other sites work as expected... >>>> >>> >>> >>> >>> >>> --Mark D Wilkinson, PI Bioinformatics >>> Assistant Professor, Medical Genetics >>> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary >>> Research >>> Providence Heart + Lung Institute >>> University of British Columbia - St. Paul's Hospital >>> Vancouver, BC, Canada >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> ------------------------------------------------------------- >> Biomolecular Mass Spectrometry and Proteomics Group >> Faculty of Science >> Utrecht University >> >> Visiting address: >> H.R. Kruyt building room O607 >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> >> Mail address: >> P.O. box 80.082 >> 3508 TB Utrecht >> The Netherlands >> >> phone: +31 (0)6-143 66 783 >> email: pieter.neerincx at gmail.com >> skype: pieter.online >> ------------------------------------------------------------- >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 398 bytes Desc: not available URL: From martin.senger at gmail.com Sun Oct 4 23:34:42 2009 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 5 Oct 2009 07:34:42 +0800 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4AC5CA54.9080307@bsc.es> References: <4d93f07c0910020013t17068e07h54ca584375d7dab6@mail.gmail.com> <4AC5CA54.9080307@bsc.es> Message-ID: <4d93f07c0910041634k6b044648n55cd4c7728fa47fd@mail.gmail.com> Sorry but I could not wait longer for the jMoby to be compilable. Therefore, I have updated myself the "xmls/project.pom" - in order to get there a newer version of jax-ws (that has the class missing in Dmitry's code). It compiles now. But it needs testing whether the newer version does what it is supposed to do. Please 'cvs update -dP'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From dmitry.repchevski at bsc.es Mon Oct 5 14:35:03 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 05 Oct 2009 16:35:03 +0200 Subject: [MOBY-dev] jMoby does not compile In-Reply-To: <4d93f07c0910041634k6b044648n55cd4c7728fa47fd@mail.gmail.com> References: <4d93f07c0910041634k6b044648n55cd4c7728fa47fd@mail.gmail.com> Message-ID: <4ACA0417.70703@bsc.es> Thank you Martin for modifying it. As I understand the problem was that there are two different repositories for JAX-WS 2.1 and by some reason sometimes it took one and sometimes another... Strange thing is that in maven1 repository contains a "wrong" jaxws-api-2.1.jar... Anyway I could confirm that I can compile everything with JAX-WS 2.1.1... Dmitry From pieter.neerincx at gmail.com Mon Oct 19 16:24:55 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Mon, 19 Oct 2009 18:24:55 +0200 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: <47BC0768.50905@bsc.es> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> Message-ID: <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Hi Moby developers, I was wondering if one of you can point me to an easy way to update the RDF for an already registered moby service? Generating the RDF the first time was easy. I used dashboard and there's also an online web form linked from the Biomoby website. But I cannot figure out how to update the RDF. The documentation tells me I have to update and then either call the RDF agent or simply wait for the next pass. The latter is easy, but I don't seem to be able to generate updated RDF for my service with the dashboard. When I modify my service I can save the service registration XML without registering, but I cannot save the RDF. The only way the RDF is generated and saved is to click the register service button, but that one fails because the service is already registered. Clicking unregister service first to reregister the updated version will fail of course too as you cannot unregister a service that was registered with an RDF signature URL. Likewise the online form the generate the RDF cannot be used, because it only works for existing services. I looked at the RDF to update it manually. I can patch most of it manually, but there are Description tags like this: Where do those numbers at the end of the rdf:about attribute value come from? As far as I can figure out the only way to get my service RDF updated is to remove the RDF, call the agent to unregister the service and then to re-register a new one, but I was hoping to find a more elegant approach :).... Cheers, Pi From edward.kawas at gmail.com Mon Oct 19 16:53:51 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 19 Oct 2009 09:53:51 -0700 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Message-ID: <4adc99a2.161bf30a.6792.1d86@mx.google.com> Hi Pieter, In Perl, look at MOBY::RDF::Parsers::ServiceParser. This module contains a method, createRDFModel, that consumes an array reference of MOBY::Client::ServiceInstance objects and produces RDF/XML for them all. In Java, look at org.biomoby.client.rdf.builder.ServiceInstanceRDF. This class can create RDF/XML for instances of MobyServices ... Hope that helps, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: October-19-09 9:25 AM To: Core developer announcements Subject: [MOBY-dev] Updating vs generating RDF Hi Moby developers, I was wondering if one of you can point me to an easy way to update the RDF for an already registered moby service? Generating the RDF the first time was easy. I used dashboard and there's also an online web form linked from the Biomoby website. But I cannot figure out how to update the RDF. The documentation tells me I have to update and then either call the RDF agent or simply wait for the next pass. The latter is easy, but I don't seem to be able to generate updated RDF for my service with the dashboard. When I modify my service I can save the service registration XML without registering, but I cannot save the RDF. The only way the RDF is generated and saved is to click the register service button, but that one fails because the service is already registered. Clicking unregister service first to reregister the updated version will fail of course too as you cannot unregister a service that was registered with an RDF signature URL. Likewise the online form the generate the RDF cannot be used, because it only works for existing services. I looked at the RDF to update it manually. I can patch most of it manually, but there are Description tags like this: Where do those numbers at the end of the rdf:about attribute value come from? As far as I can figure out the only way to get my service RDF updated is to remove the RDF, call the agent to unregister the service and then to re-register a new one, but I was hoping to find a more elegant approach :).... Cheers, Pi _______________________________________________ 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 Oct 19 16:39:31 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 19 Oct 2009 09:39:31 -0700 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Message-ID: Hi Pi! The answer to your question may be simple, or may be complex, depending on how dramatic your service interface changes are! In the RDF, the URIs that look like: http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances/e0578ca78558ba81463c3e9f59412c9b are simply hashes designed to be unique to that node, for that service provider, for that service. This ensures that we don't get node-collisions when we integrate RDF from multiple service providers (as was previously a problem with the auto-naming of bnodes that some RDF libraries did). So... if you need to edit the content of one of those nodes, just go ahead and edit the content, and leave the node ID intact. If you need to remove a node, go ahead and remove it, no problem. If you need to ADD a node, however, then you're going to have to generate a 100% unique ID for that node (unique within all of moby central). Eddie can tell you how he hashes things to generate that number. Editing the RDF can be done in any text editor, but you might prefer to do it in Protege or whatever your preferred RDF editor is. Cheers! Mark On Mon, 19 Oct 2009 09:24:55 -0700, Pieter Neerincx wrote: > Hi Moby developers, > > I was wondering if one of you can point me to an easy way to update the > RDF for an already registered moby service? > > Generating the RDF the first time was easy. I used dashboard and there's > also an online web form linked from the Biomoby website. But I cannot > figure out how to update the RDF. The documentation tells me I have to > update and then either call the RDF agent or simply wait for the next > pass. The latter is easy, but I don't seem to be able to generate > updated RDF for my service with the dashboard. When I modify my service > I can save the service registration XML without registering, but I > cannot save the RDF. The only way the RDF is generated and saved is to > click the register service button, but that one fails because the > service is already registered. Clicking unregister service first to > reregister the updated version will fail of course too as you cannot > unregister a service that was registered with an RDF signature URL. > Likewise the online form the generate the RDF cannot be used, because it > only works for existing services. > > I looked at the RDF to update it manually. I can patch most of it > manually, but there are Description tags like this: > > rdf:about="http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances/e0578ca78558ba81463c3e9f59412c9b"> > > Where do those numbers at the end of the rdf:about attribute value come > from? > > As far as I can figure out the only way to get my service RDF updated is > to remove the RDF, call the agent to unregister the service and then to > re-register a new one, but I was hoping to find a more elegant approach > :).... > > Cheers, > > Pi > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From pieter.neerincx at gmail.com Tue Oct 20 21:43:41 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Tue, 20 Oct 2009 23:43:41 +0200 Subject: [MOBY-dev] Updating vs generating RDF In-Reply-To: References: <4d93f07c0802191655x5825fd7sadb76247a5b01b32@mail.gmail.com> <47BC0768.50905@bsc.es> <3806FE54-FCBD-4135-86C2-F8CB89CB1ABF@gmail.com> Message-ID: <540C29BF-772A-4896-97DF-0AD275166535@gmail.com> Hi Mark and Eddie, Thanks for the help! It's clear to me now where those seemingly random numbers come from :). Cheers, Pi On 19 Oct 2009, at 18:39, Mark Wilkinson wrote: > Hi Pi! > > The answer to your question may be simple, or may be complex, > depending on how dramatic your service interface changes are! > > In the RDF, the URIs that look like: > http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances/e0578ca78558ba81463c3e9f59412c9b > > are simply hashes designed to be unique to that node, for that > service provider, for that service. This ensures that we don't get > node-collisions when we integrate RDF from multiple service > providers (as was previously a problem with the auto-naming of > bnodes that some RDF libraries did). > > So... if you need to edit the content of one of those nodes, just go > ahead and edit the content, and leave the node ID intact. If you > need to remove a node, go ahead and remove it, no problem. If you > need to ADD a node, however, then you're going to have to generate a > 100% unique ID for that node (unique within all of moby central). > > Eddie can tell you how he hashes things to generate that number. > > Editing the RDF can be done in any text editor, but you might prefer > to do it in Protege or whatever your preferred RDF editor is. > > Cheers! > > Mark > > > > > On Mon, 19 Oct 2009 09:24:55 -0700, Pieter Neerincx > wrote: > >> Hi Moby developers, >> >> I was wondering if one of you can point me to an easy way to update >> the RDF for an already registered moby service? >> >> Generating the RDF the first time was easy. I used dashboard and >> there's also an online web form linked from the Biomoby website. >> But I cannot figure out how to update the RDF. The documentation >> tells me I have to update and then either call the RDF agent or >> simply wait for the next pass. The latter is easy, but I don't seem >> to be able to generate updated RDF for my service with the >> dashboard. When I modify my service I can save the service >> registration XML without registering, but I cannot save the RDF. >> The only way the RDF is generated and saved is to click the >> register service button, but that one fails because the service is >> already registered. Clicking unregister service first to reregister >> the updated version will fail of course too as you cannot >> unregister a service that was registered with an RDF signature URL. >> Likewise the online form the generate the RDF cannot be used, >> because it only works for existing services. >> >> I looked at the RDF to update it manually. I can patch most of it >> manually, but there are Description tags like this: >> >> >> >> Where do those numbers at the end of the rdf:about attribute value >> come from? >> >> As far as I can figure out the only way to get my service RDF >> updated is to remove the RDF, call the agent to unregister the >> service and then to re-register a new one, but I was hoping to find >> a more elegant approach :).... >> >> Cheers, >> >> Pi >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary > Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- mobile: +31 6 143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online -------------------------------------------------------------