From groscurt at mpiz-koeln.mpg.de Thu Jun 5 03:47:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 05 Jun 2008 09:47:56 +0200 Subject: [MOBY-l] Dashboard as Java WebStart In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> Message-ID: <48479A2C.5060507@mpiz-koeln.mpg.de> Hi all, I like to announce that we are now offering the Dashboard as a Java Webstart project and therefore as a standalone version. Now one can explore the functionality of Dashboard without checking out the full moby cvs code :-) You can find it at http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to test it if everything works normally. I created this by deleting more and more libraries which were stated in the classpath but apparently are not needed at all. The web start version of dashboard offers the possibilty of browsing the registries, registration and the simple clientn (of course the MoSeS Generator is skipped for this version). If you encounter any problems during testing let me know. If possible i would suggest to add this to the clients overview of the biomoby.org page - so that people can use it :-) Any comments / suggestions are welcome Andreas From jerzyo at genesilico.pl Fri Jun 6 16:18:18 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Fri, 06 Jun 2008 22:18:18 +0200 Subject: [MOBY-l] BioMoby Problems Message-ID: <48499B8A.8000707@genesilico.pl> Hi I am new to BioMoby and I am preparing a seminar aboutit in mt Institute. However, I find my interaction with Biomoby quite painful in a few points. Maybe You can help me or You can benefit anyhow. 1. I got completely lost in the number of services. I wanted try a simple example: make a blast file given an input protein. I found it not that easy. I was unable to run anything i Remora. In taverna i failed to do anythig myself, but I found a working workflows: http://www.ebi.ac.uk/Tools/webservices/tutorials/taverna I don't know why it is so complicated When I tried to make my own workflows in taverna, I was unable to put correct input in correct fields. The input types are not described, have no shown default values or examples. A "plain/text" field does not tell anything. The same problem I had in the jMoby dashboard. 2. Command line programs The second thing I wanted to do is to write a simple command line program that connects to any service and parse he result. I downloaded and compiled jMoby. However, the examples from: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CmdLineClients.html Did not work For I got error when searching for DragonDB For I had no errors, but the resut contained only the: This data is provided by <a HREF='http://seqhound.blueprint.org'>SeqHound</a>; <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract'>Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW. SeqHound: biological sequence and structure database as a platform forbioinformatics research. BMC Bioinformatics. 2002 Oct 25;3(1):32</a> part I also tried compiling some java code from: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/SimpleClient.html First, I had to set the classpath to moby-live/Java/build/classes (It took me a lot of time to find out where it is). Then I got an error: ../test/HelloMOBY2.java:5: HelloMOBY2 is not abstract and does not override abstract method start(org.biomoby.client.MobyRequestEvent) in org.biomoby.client.MobyRequestEventHandler public class HelloMOBY2 implements MobyRequestEventHandler{ ^ When I created This method (doing nothing) i managed to compile the code wit javac, but I got error with java: Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/axis/AxisFault at HelloMOBY2.main(HelloMOBY2.java:8) I got stucked Best Regards Jerzy Orlowski From edward.kawas at gmail.com Fri Jun 6 19:27:45 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 6 Jun 2008 16:27:45 -0700 Subject: [MOBY-l] BioMoby Problems In-Reply-To: <48499B8A.8000707@genesilico.pl> References: <48499B8A.8000707@genesilico.pl> Message-ID: <4849c803.29578c0a.788f.fffff8ea@mx.google.com> Hi Jerzy, The XML was incorrect for one of the commandline examples. I have updated the page to reflect what was wrong, but it may not be reflected in the online documentation right away. Basically, try running the command line client again but with DragonDB:Allele replaced by DragonDB_Allele. Also, have you taken a look at the page: http://moby.ucalgary.ca/gbrowse_moby ? Might be good in giving you working examples of how moby works. The second command line example had an error in it as well. Again, it might take a few hours to be reflected on line. For the second example, the line: articleName="" should read articleName="identifier". For information on what the datatypes for services are, or under what *namespace* the are can be used, examine the 'log' window in dashboard when you select services or datatypes. I am not sure about the answer to the last jmoby problem, so someone else may have to help you on that one. Let me know if I can help further. Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: June-06-08 1:18 PM To: moby-l at lists.open-bio.org Subject: [MOBY-l] BioMoby Problems Hi I am new to BioMoby and I am preparing a seminar aboutit in mt Institute. However, I find my interaction with Biomoby quite painful in a few points. Maybe You can help me or You can benefit anyhow. 1. I got completely lost in the number of services. I wanted try a simple example: make a blast file given an input protein. I found it not that easy. I was unable to run anything i Remora. In taverna i failed to do anythig myself, but I found a working workflows: http://www.ebi.ac.uk/Tools/webservices/tutorials/taverna I don't know why it is so complicated When I tried to make my own workflows in taverna, I was unable to put correct input in correct fields. The input types are not described, have no shown default values or examples. A "plain/text" field does not tell anything. The same problem I had in the jMoby dashboard. 2. Command line programs The second thing I wanted to do is to write a simple command line program that connects to any service and parse he result. I downloaded and compiled jMoby. However, the examples from: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CmdLineClients.h tml Did not work For I got error when searching for DragonDB For I had no errors, but the resut contained only the: This data is provided by <a HREF='http://seqhound.blueprint.org'>SeqHound</a>; <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubM ed&list_uids=12401134&dopt=Abstract'>Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW. SeqHound: biological sequence and structure database as a platform forbioinformatics research. BMC Bioinformatics. 2002 Oct 25;3(1):32</a> part I also tried compiling some java code from: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/SimpleClient.htm l First, I had to set the classpath to moby-live/Java/build/classes (It took me a lot of time to find out where it is). Then I got an error: ../test/HelloMOBY2.java:5: HelloMOBY2 is not abstract and does not override abstract method start(org.biomoby.client.MobyRequestEvent) in org.biomoby.client.MobyRequestEventHandler public class HelloMOBY2 implements MobyRequestEventHandler{ ^ When I created This method (doing nothing) i managed to compile the code wit javac, but I got error with java: Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/axis/AxisFault at HelloMOBY2.main(HelloMOBY2.java:8) I got stucked Best Regards Jerzy Orlowski _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From groscurt at mpiz-koeln.mpg.de Mon Jun 9 03:08:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 09 Jun 2008 09:08:56 +0200 Subject: [MOBY-l] BioMoby Problems In-Reply-To: <48499B8A.8000707@genesilico.pl> References: <48499B8A.8000707@genesilico.pl> Message-ID: <484CD708.4020603@mpiz-koeln.mpg.de> Hi Jerzy, what did you try to compile from SimpleClient ? Did you put the example of the client in a separate project or what ? For compiling jmoby you should not use javac - there is an ant file which does everything you need to do. Its handy, because it handles all classpaths for you. If you want to create your own little client (you can also use the ones in moby-live/Java/build/run !) - you need the jars from moby (mhm which are in the maven directory actually - see moby-live/Java/build/run/run-dashboard as an example) add them to your classpath of your java class and run your client. Although it might be too much examples - i like to point you to http://www.eu-sol.net/science/bioinformatics/tutorials/jmoby-step-by-step/writing-a-biomoby-client - where we offer another simple client for java as an eclipse project. It contains already all required libraries and offers some features you can read at the page For any further questions feel free to ask Andreas Jerzy Orlowski wrote: > I also tried compiling some java code from: > > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/SimpleClient.html > > > First, I had to set the classpath to moby-live/Java/build/classes (It > took me a lot of time to find out where it is). > Then I got an error: > > ../test/HelloMOBY2.java:5: HelloMOBY2 is not abstract and does not > override abstract method start(org.biomoby.client.MobyRequestEvent) in > org.biomoby.client.MobyRequestEventHandler > public class HelloMOBY2 implements MobyRequestEventHandler{ > ^ > > When I created This method (doing nothing) i managed to compile the > code wit javac, but I got error with java: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org/apache/axis/AxisFault > at HelloMOBY2.main(HelloMOBY2.java:8) > > I got stucked > > Best Regards > > Jerzy Orlowski > > > > > > > > > _______________________________________________ > moby-l mailing list > moby-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-l From jerzyo at genesilico.pl Mon Jun 9 05:51:29 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Mon, 09 Jun 2008 11:51:29 +0200 Subject: [MOBY-l] jMoby problems Message-ID: <484CFD21.9000507@genesilico.pl> Hi everybody I am quite new to Moby, so I apologize for any stupid questions. I am discussing by e-mail with several Moby developers and I think we should switch to the mailing list. The are several problems I experience with jMoby 1. How should I compile my own code (such as from http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/SimpleClient.html) Andreas Groscurth writes: jmoby you should not use javac - there is an ant file which does everything you need to do. How should I compile my own code with ant? 2. I have problems with creation input xml data for different services, one of the example is creating FASTA sequence for iANTNetBlast the input xml created by dashboard and working with cmd client is: >aaaaa DMGRLIEFSRRFGGIPV nr ncbi-blastp I tried different ways of making Simple And Composite mobyDataObjects, but It did not work. Could anyone help? Best Regards Jerzy Orlowski From edward.kawas at gmail.com Wed Jun 11 11:19:38 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 11 Jun 2008 08:19:38 -0700 Subject: [MOBY-l] [MOBY-dev] Dashboard as Java WebStart In-Reply-To: <48479A2C.5060507@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> <48479A2C.5060507@mpiz-koeln.mpg.de> Message-ID: <484fed0b.1f588c0a.5fe1.6929@mx.google.com> Hi Andreas, I recently created a new panel in dashboard for perl moses. How hard would it be to get that running? The panel runs command line scripts in the background, so I am not sure if the webstart sandbox allows that anyways... Good work by the way! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: June-05-08 12:48 AM To: Core developer announcements; moby-l at lists.open-bio.org Subject: [MOBY-dev] Dashboard as Java WebStart Hi all, I like to announce that we are now offering the Dashboard as a Java Webstart project and therefore as a standalone version. Now one can explore the functionality of Dashboard without checking out the full moby cvs code :-) You can find it at http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to test it if everything works normally. I created this by deleting more and more libraries which were stated in the classpath but apparently are not needed at all. The web start version of dashboard offers the possibilty of browsing the registries, registration and the simple clientn (of course the MoSeS Generator is skipped for this version). If you encounter any problems during testing let me know. If possible i would suggest to add this to the clients overview of the biomoby.org page - so that people can use it :-) Any comments / suggestions are welcome Andreas _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Wed Jun 11 11:33:07 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 11 Jun 2008 17:33:07 +0200 Subject: [MOBY-l] [MOBY-dev] Dashboard as Java WebStart In-Reply-To: <484fed0b.1f588c0a.5fe1.6929@mx.google.com> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> <48479A2C.5060507@mpiz-koeln.mpg.de> <484fed0b.1f588c0a.5fe1.6929@mx.google.com> Message-ID: <484FF033.30806@mpiz-koeln.mpg.de> Hi Eddie, is the panel already checked in the cvs ? whats it called ? ... apparently i missed that. Mhm - the question is how these command line scripts are available - if they are some .pl scripts or .sh scripts or something it could be not working at all - but i will check that. best andreas Edward Kawas wrote: > Hi Andreas, > > I recently created a new panel in dashboard for perl moses. How hard would > it be to get that running? The panel runs command line scripts in the > background, so I am not sure if the webstart sandbox allows that anyways... > > Good work by the way! > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: June-05-08 12:48 AM > To: Core developer announcements; moby-l at lists.open-bio.org > Subject: [MOBY-dev] Dashboard as Java WebStart > > Hi all, > > I like to announce that we are now offering the Dashboard as a Java > Webstart project and therefore as a standalone version. Now one can > explore the functionality of Dashboard without checking out the full > moby cvs code :-) > > You can find it at > http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to > test it if everything works normally. I created this by deleting more > and more libraries which were stated in the classpath but apparently are > not needed at all. The web start version of dashboard offers the > possibilty of browsing the registries, registration and the simple > clientn (of course the MoSeS Generator is skipped for this version). If > you encounter any problems during testing let me know. > > If possible i would suggest to add this to the clients overview of the > biomoby.org page - so that people can use it :-) > > Any comments / suggestions are welcome > > Andreas > _______________________________________________ > 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 Wed Jun 11 11:41:07 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 11 Jun 2008 08:41:07 -0700 Subject: [MOBY-l] [MOBY-dev] Dashboard as Java WebStart In-Reply-To: <484FF033.30806@mpiz-koeln.mpg.de> References: <200802071539.09914.groscurt@mpiz-koeln.mpg.de> <48479A2C.5060507@mpiz-koeln.mpg.de> <484fed0b.1f588c0a.5fe1.6929@mx.google.com> <484FF033.30806@mpiz-koeln.mpg.de> Message-ID: <484ff215.16538c0a.6767.ffffdab9@mx.google.com> Yeah, the panel is in the cvs. The documentation for it is in the cvs too (both the dashboard internal help and an external one). I should link them to other documents, so that google can find them. The external one is at: http://tinyurl.com/63ucu3 The command line scripts are installed (by make) when users install the perl module MOSES::MOBY from cpan (or the perl branch of the cvs). 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 Andreas Groscurth Sent: June-11-08 8:33 AM To: Core developer announcements Cc: moby-l at lists.open-bio.org Subject: Re: [MOBY-dev] Dashboard as Java WebStart Hi Eddie, is the panel already checked in the cvs ? whats it called ? ... apparently i missed that. Mhm - the question is how these command line scripts are available - if they are some .pl scripts or .sh scripts or something it could be not working at all - but i will check that. best andreas Edward Kawas wrote: > Hi Andreas, > > I recently created a new panel in dashboard for perl moses. How hard would > it be to get that running? The panel runs command line scripts in the > background, so I am not sure if the webstart sandbox allows that anyways... > > Good work by the way! > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: June-05-08 12:48 AM > To: Core developer announcements; moby-l at lists.open-bio.org > Subject: [MOBY-dev] Dashboard as Java WebStart > > Hi all, > > I like to announce that we are now offering the Dashboard as a Java > Webstart project and therefore as a standalone version. Now one can > explore the functionality of Dashboard without checking out the full > moby cvs code :-) > > You can find it at > http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to > test it if everything works normally. I created this by deleting more > and more libraries which were stated in the classpath but apparently are > not needed at all. The web start version of dashboard offers the > possibilty of browsing the registries, registration and the simple > clientn (of course the MoSeS Generator is skipped for this version). If > you encounter any problems during testing let me know. > > If possible i would suggest to add this to the clients overview of the > biomoby.org page - so that people can use it :-) > > Any comments / suggestions are welcome > > Andreas > _______________________________________________ > 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 Wed Jun 11 14:48:46 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 11 Jun 2008 11:48:46 -0700 Subject: [MOBY-l] Moby Dashboard WebStart Message-ID: Hi all, So Dashboard is now running both on Moby Central and from Andreas' machine in Germany: http://moby.ucalgary.ca/dashboard http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp I'll put a link on teh Moby homepage later today. this is *fantastic*! Thanks Andreas!! Mark -- 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 edward.kawas at gmail.com Wed Jun 11 15:12:36 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 11 Jun 2008 12:12:36 -0700 Subject: [MOBY-l] Moby Dashboard WebStart In-Reply-To: References: Message-ID: <485023a6.1f538c0a.2469.5aed@mx.google.com> What is the url of it on moby.ucalgary.ca? the one posted doesn't work. Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson Sent: June-11-08 11:49 AM To: moby-l at lists.open-bio.org Subject: [MOBY-l] Moby Dashboard WebStart Hi all, So Dashboard is now running both on Moby Central and from Andreas' machine in Germany: http://moby.ucalgary.ca/dashboard http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp I'll put a link on teh Moby homepage later today. this is *fantastic*! Thanks Andreas!! Mark -- 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-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Wed Jun 11 16:50:55 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 11 Jun 2008 13:50:55 -0700 Subject: [MOBY-l] Moby Dashboard WebStart In-Reply-To: <485023a6.1f538c0a.2469.5aed@mx.google.com> References: <485023a6.1f538c0a.2469.5aed@mx.google.com> Message-ID: Try again - I had the redirect wrong M On Wed, 11 Jun 2008 12:12:36 -0700, Edward Kawas wrote: > What is the url of it on moby.ucalgary.ca? the one posted doesn't work. > > Eddie > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: June-11-08 11:49 AM > To: moby-l at lists.open-bio.org > Subject: [MOBY-l] Moby Dashboard WebStart > > Hi all, > > So Dashboard is now running both on Moby Central and from Andreas' > machine > in Germany: > > http://moby.ucalgary.ca/dashboard > http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp > > I'll put a link on teh Moby homepage later today. this is *fantastic*! > > Thanks Andreas!! > > Mark > > > -- 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 edward.kawas at gmail.com Wed Jun 11 16:54:07 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 11 Jun 2008 13:54:07 -0700 Subject: [MOBY-l] Moby Dashboard WebStart In-Reply-To: References: <485023a6.1f538c0a.2469.5aed@mx.google.com> Message-ID: <48503b72.1f538c0a.2477.ffff8f3b@mx.google.com> It works now. Thanks! Eddie -----Original Message----- From: Mark Wilkinson [mailto:markw at illuminae.com] Sent: June-11-08 1:51 PM To: Edward Kawas; moby-l at lists.open-bio.org Subject: Re: [MOBY-l] Moby Dashboard WebStart Try again - I had the redirect wrong M On Wed, 11 Jun 2008 12:12:36 -0700, Edward Kawas wrote: > What is the url of it on moby.ucalgary.ca? the one posted doesn't work. > > Eddie > > -----Original Message----- > From: moby-l-bounces at lists.open-bio.org > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: June-11-08 11:49 AM > To: moby-l at lists.open-bio.org > Subject: [MOBY-l] Moby Dashboard WebStart > > Hi all, > > So Dashboard is now running both on Moby Central and from Andreas' > machine > in Germany: > > http://moby.ucalgary.ca/dashboard > http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp > > I'll put a link on teh Moby homepage later today. this is *fantastic*! > > Thanks Andreas!! > > Mark > > > -- 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 thpar at psb.ugent.be Thu Jun 12 09:23:18 2008 From: thpar at psb.ugent.be (Thomas Van Parys) Date: Thu, 12 Jun 2008 15:23:18 +0200 Subject: [MOBY-l] JMoby, using the testing registry Message-ID: <48512346.6070200@psb.ugent.be> Hi all, I'm not completely sure where to post JMoby bug reports. When making a java client for a service that's registered only at the testing central, I noticed that every now and then, the client still tries to connect to the default moby central. This is eg. the case when getting back a MobyDataComposite from a service. The type of the composite is looked up in the default central, rather than the testing central. This could also pose problems when trying to use a locally installed moby central. Unless I'm misusing the existing code of course, I believe the bug lies in org.biomoby.shared.data.MobyDataComposite.java (line 40) public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{ this(element.getLocalName(), getName(element), MobyPrefixResolver.getAttr(element, "namespace"), getId(element)); //.... } This will just ignore the supplied registry as it is set to null here: public MobyDataComposite(String typeName, String name, String namespace, String id){ this(typeName, name, namespace, id, (Registry) null); } (this then chooses the default registry). Bug is solved by changing it to public MobyDataComposite(org.w3c.dom.Element element, Registry registry) throws MobyException{ this(element.getLocalName(), getName(element), MobyPrefixResolver.getAttr(element, "namespace"), getId(element), registry); //.... } Also, when wanting to use a non-default registry, I have to supply it with every new moby object. Is there a workaround for this? eg. job.put("locus_id", new MobyDataString(locusId, registry)); regards, Thomas -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== From markw at illuminae.com Fri Jun 13 12:18:09 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 13 Jun 2008 09:18:09 -0700 Subject: [MOBY-l] Fwd: [MOBY-dev] Unit testing of BioMoby Services In-Reply-To: References: Message-ID: In response to the current discussion on automated testing of Moby services, I'm re-posting this email. YES! It needs to go into the formal API documentation. My bad! In the end, it became quite difficult to do the unit testing in perl because of the lack of support for OWL-RDF in Perl, so hopefully someone from the Java world will pick-up this ball and create the application that does it? M ------- Forwarded message ------- From: "Mark Wilkinson" To: "moby Core developer announcements" Cc: Subject: [MOBY-dev] Unit testing of BioMoby Services Date: Fri, 14 Mar 2008 15:04:16 -0700 Hi all, During the hackathon I was working on the OWL classes and predicates we need for the ability to create unit tests in the Service metadata coming from the Service provider. I just finished working things out with the myGrid team, and here are the predicates and classes we have agreed on: Namespace: http://www.mygrid.org.uk/mygrid-moby-service# Class: #unitTest usage: can have one or more unitTests per service #operation ObjectProperty: #hasUnitTest domain: #operation range: #unitTest DatatypeProperty: #exampleInput domain: #unitTest range: xsd#string content: the full SOAP payload XML of an invocation message DatatypeProperty: #validOutputXML domain: #unitTest range: xsd#string content: the full SOAP payload of the associated output message DatatypeProperty: #validREGEX domain: #unitTest range: xsd#string content: a regular expression that should match against the output SOAP Payload of this unitTest DatatypeProperty: #validXPath domain: #unitTest range: xsd#string content: an XPath expression that should match against the output SOAP Payload of this unitTest An example can be seen in the antirrhinum.net,getDragonAlleleLocus service, whose signature RDF is available here: http://moby.ucalgary.ca/signatures/antirrhinum.rdf I'm almost finished writing a little Perl script that will go through and test the services based on the Unit Test data - I'll put it in the CVS as soon as it's done. Cheers all! Mark -- 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