From jason at bioteam.net Wed Oct 1 11:48:44 2008 From: jason at bioteam.net (jason) Date: Wed, 01 Oct 2008 23:48:44 +0800 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48DC9D40.5030604@genesilico.pl> References: <48DC9D40.5030604@genesilico.pl> Message-ID: <48E39BDC.3030806@bioteam.net> Hi, all I am trying to set up some moby services for testing. What I have is a bunch of binaries such as blast, hmmer, and emboss program running on my system? One step in the service registration is generating service meta data. I guess others already register some of these binaries as services. Is there a way I can find out what binary is registered in the Moby Central? If I can, I could fetch those service meta data from moby central, change the authority and service URL, and register my services. Otherwise, I need to inspect and register the binaries one by one. It is daunting task. thanks -jason From jason at bioteam.net Wed Oct 1 22:27:54 2008 From: jason at bioteam.net (jason) Date: Thu, 02 Oct 2008 10:27:54 +0800 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E39BDC.3030806@bioteam.net> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> Message-ID: <48E431AA.30503@bioteam.net> Hi, Any suggestion on this one? Help is appreciated. -jason jason wrote: > Hi, all > > I am trying to set up some moby services for testing. What I have is a > bunch of binaries such as blast, hmmer, and emboss program running on > my system? One step in the service registration is generating service > meta data. I guess others already register some of these binaries as > services. Is there a way I can find out what binary is registered in > the Moby Central? If I can, I could fetch those service meta data from > moby central, change the authority and service URL, and register my > services. Otherwise, I need to inspect and register the binaries one > by one. It is daunting task. > > thanks > > -jason > > > > From sebastien.carrere at toulouse.inra.fr Thu Oct 2 04:58:19 2008 From: sebastien.carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 02 Oct 2008 10:58:19 +0200 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E431AA.30503@bioteam.net> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> <48E431AA.30503@bioteam.net> Message-ID: <48E48D2B.6020000@toulouse.inra.fr> Hi Jason, We developped a lightweight framework in Toulouse (France), called PlayMoby. http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby The aim of this framework is to deploy easily BioMoby web-services for command line applications running on UNIX-like systems using a Mobyle program description (http://bioweb2.pasteur.fr/projects/mobyle/). You have an exemple on how to write a perl wrapper for Blast (blastp_swissprot) in the "Sample scripts" section (http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#samples). We deploy and survey around 120 web-services deployed with PlayMoby and if you need another exemple based on EMBOSS program, you can ask me sources for one of the following program: http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/external/services/mobycentral_bioworkflow.rss Hope this help, Sebastien jason a ?crit : > Hi, > Any suggestion on this one? > Help is appreciated. > > -jason > > jason wrote: >> Hi, all >> >> I am trying to set up some moby services for testing. What I have is >> a bunch of binaries such as blast, hmmer, and emboss program running >> on my system? One step in the service registration is generating >> service meta data. I guess others already register some of these >> binaries as services. Is there a way I can find out what binary is >> registered in the Moby Central? If I can, I could fetch those service >> meta data from moby central, change the authority and service URL, >> and register my services. Otherwise, I need to inspect and register >> the binaries one by one. It is daunting task. >> >> thanks >> >> -jason >> >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From jerzyo at genesilico.pl Thu Oct 2 05:31:52 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 02 Oct 2008 11:31:52 +0200 Subject: [MOBY-dev] Problems with biomoby plugins in taverna Message-ID: <48E49508.7080909@genesilico.pl> I am trying to execute an attached workflow with simple input (attached) using executeworkflow.sh What I get is: $ ./executeworkflow.sh -inputdoc /tmp/workflows/1653746517794550_input.xmml /tmp/workflows/1653746517794550_workflow_scufl.xml Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects ... done Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/Namespaces Exception in thread "Thread-15" java.lang.LinkageError: loader constraint violation: loader (instance of net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) previously initiated loading for a different type with name "org/apache/commons/logging/Log" at org.biomoby.shared.MobyException.(MobyException.java:55) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1525) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:521) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280) at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67) And the system hangs (executeworkflow.sh produce no result, no progress report and does not terminate) - Why do I get such errors? - Why does the program hang? It should exit with non-zero value - Why such workflow does not hang in taverna GUI version (it doesn't prosuce any result anyway), I attach the progress report from Taverna GUI version - Why This workflow hangs executeworkflow.sh system? Most of the others work ok. Jerzy Orlowski -------------- next part -------------- A non-text attachment was scrubbed... Name: 1653746517794550_input.xmml Type: text/xml Size: 601 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1653746517794550_workflow_scufl.xml Type: text/xml Size: 2953 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: progress.xml Type: text/xml Size: 115 bytes Desc: not available URL: From jerzyo at genesilico.pl Thu Oct 2 05:57:02 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 02 Oct 2008 11:57:02 +0200 Subject: [MOBY-dev] MOBY-dev Digest, Vol 70, Issue 1 In-Reply-To: References: Message-ID: <48E49AEE.4040803@genesilico.pl> Thanks, I found it, I'll see if it works Jerzy moby-dev-request at lists.open-bio.org wrote: > Send MOBY-dev mailing list submissions to > moby-dev at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/moby-dev > or, via email, send a message with subject or body 'help' to > moby-dev-request at lists.open-bio.org > > You can reach the person managing the list at > moby-dev-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MOBY-dev digest..." > > > Today's Topics: > > 1. Re: Executing Moby Workflow straight from java > (Stian Soiland-Reyes) > 2. Re: Executing Moby Workflow straight from java (Jerzy Orlowski) > 3. decomposition of BioMoby Objects in Taverna (Jerzy Orlowski) > 4. Re: decomposition of BioMoby Objects in Taverna (Edward Kawas) > 5. Re: Executing Moby Workflow straight from java > (Stian Soiland-Reyes) > 6. correspondence between service and executable. (jason) > 7. Re: correspondence between service and executable. (jason) > 8. Re: correspondence between service and executable. > (Sebastien Carrere) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Sep 2008 10:54:47 +0100 > From: "Stian Soiland-Reyes" > Subject: Re: [MOBY-dev] Executing Moby Workflow straight from java > To: "Core developer announcements" > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > On Wed, Sep 24, 2008 at 16:55, Jerzy Orlowski wrote: > > I suggest as well to move the discussion to the taverna-hackers list ( > http://taverna.sourceforge.net/lists ) > >> I am trying to use your code, but I get strange erros like: >> >> The constructor EngineImpl(EngineConfiguration) is undefined >> >> Perhaps I am working on different versions of the code (some from taverna, >> some from ogasadai and some from freefluo). > > If you want to be sure to get it to work with Taverna 1.7.1, use > http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo/NO-VERSION/freefluo-NO-VERSION.jar > and http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1/freefluo-taverna-exts-1.7.1.jar > > The other projects are likely to have code in either too new or too old version. > > >> Where can I find source code or javadoc for >> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes? > > Note that this version of Freefluo was never released officially by > the Freefluo project, but it can be checked out from their CVS using a > date range. > > Look at the thread of http://markmail.org/message/dnrqdicmbzbfjjl5 if > you really want to build Freefluo from source. > > From pieter.neerincx at gmail.com Thu Oct 2 09:05:47 2008 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Thu, 2 Oct 2008 15:05:47 +0200 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E48D2B.6020000@toulouse.inra.fr> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> <48E431AA.30503@bioteam.net> <48E48D2B.6020000@toulouse.inra.fr> Message-ID: <1F1457E2-03B7-4815-B6DF-8269B479E8E9@gmail.com> Hi Jason, PlayMoby as advertised below looks like a good starting point to wrap existing tools into BioMoby web services. Looks a little like SOAPLAB, but in BioMoby lingua :). But be aware that there is no such thing as *THE* BioMoby service definition for a certain existing binary. Take for example a look at BLAST. In the official public BioMoby Central registry you will find as many different BLAST services as there are service authorities providing BLAST services. Some groups might only provide blastp for alignment with protein sequences. Therefore they might have hardcoded their service to use blastp. Others might provide both blastp & blastn (and blastx, tblastx, etc.) for alignment with protein and nucleotide sequences and use an optional parameter (secondary article in BioMoby) to specify which blast program to use. Similar things you will find for many more BLAST parameters... Then there's the issue of what you align you sequences with: some might provide the complete INSDC (DDBJ/EMBL/Genbank) database while others only provide subsections like only ESTs or only certain species of interest. And then there dozens of other blastable databases a service might, might partially or might not suport. Some might limit the size of you BLAST jobs by only providing a synchronous BLAST service while others might have implemented an asynchronous one allowing for longer runtimes. Finally there is the issue of output formats. NCBI BLAST has 12 different output formats. Officially a Biomoby service is registered with a certain output. This can not change dynamically based on a parameter. So one might choose to register 12 services for the 12 different output formats. The 12 BLAST output formats are not native BioMoby object structures though. BioMoby allows you to wrap existing "legacy" data formats. In that case you might wrap your BLAST output and use a parameter to specify the format although it is a bit of a hack. You could also design a native BioMoby object structure for BLAST output and write a converter... For other tools similar design choices for different input formats will result in different service implementations. And then off course you might use WU-BLAST instead of NCBI BLAST resulting in yet another service implementation... Personally I'm guilty of registering one of those "yet another" BLAST services, because at the time I wrote none of the existing services suited my needs. Right now your best bet is to investigate what is already registered in BioMoby Central and see if there is something that suits your needs. If so, recycle, or if not, implement yet another... It would be nice if we would have a standardised way of wrapping existing stuff into BioMoby services and Object structures. I am thinking of how PostScript works. PostScript is best known as a page description language in the electronic and desktop publishing areas. Most PostScript drivers implement "everything". For a printer driver this means, the driver supports an unlimited high resolution on an unlimited large piece of paper. Off course there is no single printer out there that can printed on a never-ending piece of paper. Therefore manufactures supply PPD (PostScript Printer Definition) files that specify the limits a printer can handle. For example max 1200 dpi and A4 paper. To print you always use the unlimited driver in combination with a PPD for a specific device. If I convert this to our BLAST example all BioMoby BLAST services would be registered with the same input, same output and same optional parameters, but service providers would be albe to specify limits on those. This would require not only standardising on BioMoby object structures, but also on naming of parmeters + their values and for example on naming + version numbering of databases.... hence it would require some level of curation of the BioMoby Central ontologies. Cheers, Pi On 02 Oct 2008, at 10:58, Sebastien Carrere wrote: > Hi Jason, > > We developped a lightweight framework in Toulouse (France), called > PlayMoby. > http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby > > The aim of this framework is to deploy easily BioMoby web-services > for command line applications running on UNIX-like systems using a > Mobyle program description (http://bioweb2.pasteur.fr/projects/ > mobyle/). > > You have an exemple on how to write a perl wrapper for Blast > (blastp_swissprot) in the "Sample scripts" section (http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#samples > ). > > We deploy and survey around 120 web-services deployed with PlayMoby > and if you need another exemple based on EMBOSS program, you can ask > me sources for one of the following program: > http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/external/services/mobycentral_bioworkflow.rss > > Hope this help, > > Sebastien > > jason a ?crit : >> Hi, >> Any suggestion on this one? >> Help is appreciated. >> >> -jason >> >> jason wrote: >>> Hi, all >>> >>> I am trying to set up some moby services for testing. What I have >>> is a bunch of binaries such as blast, hmmer, and emboss program >>> running on my system? One step in the service registration is >>> generating service meta data. I guess others already register >>> some of these binaries as services. Is there a way I can find out >>> what binary is registered in the Moby Central? If I can, I could >>> fetch those service meta data from moby central, change the >>> authority and service URL, and register my services. Otherwise, I >>> need to inspect and register the binaries one by one. It is >>> daunting task. >>> >>> thanks >>> >>> -jason >>> >>> >>> >>> >> _______________________________________________ >> 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 ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From soiland-reyes at cs.manchester.ac.uk Thu Oct 2 09:26:19 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Thu, 2 Oct 2008 14:26:19 +0100 Subject: [MOBY-dev] Problems with biomoby plugins in taverna In-Reply-To: <48E49508.7080909@genesilico.pl> References: <48E49508.7080909@genesilico.pl> Message-ID: On Thu, Oct 2, 2008 at 10:31, Jerzy Orlowski wrote: > What I get is: > Fetching namespace ontology from > http://biomoby.org/RESOURCES/MOBY-S/Namespaces > Exception in thread "Thread-15" java.lang.LinkageError: loader constraint > violation: loader (instance of > net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) previously > initiated loading for a different type with name > "org/apache/commons/logging/Log" > at org.biomoby.shared.MobyException.(MobyException.java:55) > - Why do I get such errors? This might be related to a Raven-related bug with LinkageError we had earlier, http://www.mygrid.org.uk/dev/issues/browse/TAV-480 although it then would say "duplicate class definition". > - Why does the program hang? It should exit with non-zero value Because the thread running your Biomoby activity fails with a fatal error, and the workflow never finishes. The program is waiting for the workflow to finish, but Freefluo doesn't catch LinkageError's which are RuntimeErrors. (Normally you shouldn't catch RuntimeErrors) > - Why such workflow does not hang in taverna GUI version (it doesn't prosuce > any result anyway), I attach the progress report from Taverna GUI version Probably because classes are initialised in a different order within the GUI, for instance by the scavengers browsing the service. The issue happens because of a threading conflict with the classloaders. > - Why This workflow hangs executeworkflow.sh system? Most of the others work > ok. Does it always happen with this workflow..? Which distribution of Taverna are you using for this? I am able to reproduce this with Taverna 1.7.1. I've noted this as a new bug http://www.mygrid.org.uk/dev/issues/browse/TAV-773 and am quickly investigating it with a debugger. It doesn't seem like a concurrency problem, actually, but perhaps there's twoo different org.apache.commons.logging.Log instances on the classpath.. this needs further investigation. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From soiland-reyes at cs.manchester.ac.uk Thu Oct 2 09:44:23 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Thu, 2 Oct 2008 14:44:23 +0100 Subject: [MOBY-dev] Problems with biomoby plugins in taverna In-Reply-To: References: <48E49508.7080909@genesilico.pl> Message-ID: On Thu, Oct 2, 2008 at 14:26, Stian Soiland-Reyes wrote: > this needs further investigation. > A BioMoby exception happens as it's calling runDecypherBlastp with: 20 YKSLTNDWEDHLAVKHFSVE Swissprot 10 If you want a silly workaround I would try to avoid getting that exception! :-) Then when this happens, he needs to initialise the MobyException class, which tries to access org.apache.commons.logging.Log - but somehow this fails. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From jason at bioteam.net Fri Oct 3 12:55:13 2008 From: jason at bioteam.net (jason) Date: Sat, 04 Oct 2008 00:55:13 +0800 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <1F1457E2-03B7-4815-B6DF-8269B479E8E9@gmail.com> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> <48E431AA.30503@bioteam.net> <48E48D2B.6020000@toulouse.inra.fr> <1F1457E2-03B7-4815-B6DF-8269B479E8E9@gmail.com> Message-ID: <48E64E71.2080708@bioteam.net> Hi, Pieter, Sebastien I pull all the services information from Moby Registery using "worker.getServices().". Then I checked the cached services directory. The xml files are very useful for me to find out what service is available for which application. For example, I want to know whether someone wrapped hmmsearch before. I use this command "grep -i hmmsearch *" thanks for the help -jason Pieter Neerincx wrote: > Hi Jason, > > PlayMoby as advertised below looks like a good starting point to wrap > existing tools into BioMoby web services. Looks a little like SOAPLAB, > but in BioMoby lingua :). > > But be aware that there is no such thing as *THE* BioMoby service > definition for a certain existing binary. Take for example a look at > BLAST. In the official public BioMoby Central registry you will find > as many different BLAST services as there are service authorities > providing BLAST services. > Some groups might only provide blastp for alignment with protein > sequences. Therefore they might have hardcoded their service to use > blastp. Others might provide both blastp & blastn (and blastx, > tblastx, etc.) for alignment with protein and nucleotide sequences and > use an optional parameter (secondary article in BioMoby) to specify > which blast program to use. Similar things you will find for many more > BLAST parameters... > Then there's the issue of what you align you sequences with: some > might provide the complete INSDC (DDBJ/EMBL/Genbank) database while > others only provide subsections like only ESTs or only certain species > of interest. And then there dozens of other blastable databases a > service might, might partially or might not suport. Some might > limit the size of you BLAST jobs by only providing a synchronous BLAST > service while others might have implemented an asynchronous one > allowing for longer runtimes. > Finally there is the issue of output formats. NCBI BLAST has 12 > different output formats. Officially a Biomoby service is registered > with a certain output. This can not change dynamically based on a > parameter. So one might choose to register 12 services for the 12 > different output formats. The 12 BLAST output formats are not native > BioMoby object structures though. BioMoby allows you to wrap existing > "legacy" data formats. In that case you might wrap your BLAST output > and use a parameter to specify the format although it is a bit of a > hack. You could also design a native BioMoby object structure for > BLAST output and write a converter... For other tools similar design > choices for different input formats will result in different service > implementations. And then off course you might use WU-BLAST instead of > NCBI BLAST resulting in yet another service implementation... > > Personally I'm guilty of registering one of those "yet another" BLAST > services, because at the time I wrote none of the existing services > suited my needs. Right now your best bet is to investigate what is > already registered in BioMoby Central and see if there is something > that suits your needs. If so, recycle, or if not, implement yet > another... > > It would be nice if we would have a standardised way of wrapping > existing stuff into BioMoby services and Object structures. I am > thinking of how PostScript works. PostScript is best known as a page > description language in the electronic and desktop publishing areas. > Most PostScript drivers implement "everything". For a printer driver > this means, the driver supports an unlimited high resolution on an > unlimited large piece of paper. Off course there is no single printer > out there that can printed on a never-ending piece of paper. Therefore > manufactures supply PPD (PostScript Printer Definition) files that > specify the limits a printer can handle. For example max 1200 dpi and > A4 paper. To print you always use the unlimited driver in combination > with a PPD for a specific device. If I convert this to our BLAST > example all BioMoby BLAST services would be registered with the same > input, same output and same optional parameters, but service providers > would be albe to specify limits on those. This would require not only > standardising on BioMoby object structures, but also on naming of > parmeters + their values and for example on naming + version numbering > of databases.... hence it would require some level of curation of the > BioMoby Central ontologies. > > Cheers, > > Pi > > > On 02 Oct 2008, at 10:58, Sebastien Carrere wrote: > >> Hi Jason, >> >> We developped a lightweight framework in Toulouse (France), called >> PlayMoby. >> http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby >> >> The aim of this framework is to deploy easily BioMoby web-services >> for command line applications running on UNIX-like systems using a >> Mobyle program description (http://bioweb2.pasteur.fr/projects/mobyle/). >> >> You have an exemple on how to write a perl wrapper for Blast >> (blastp_swissprot) in the "Sample scripts" section >> (http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#samples). >> >> We deploy and survey around 120 web-services deployed with PlayMoby >> and if you need another exemple based on EMBOSS program, you can ask >> me sources for one of the following program: >> http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/external/services/mobycentral_bioworkflow.rss >> >> >> Hope this help, >> >> Sebastien >> >> jason a ?crit : >>> Hi, >>> Any suggestion on this one? >>> Help is appreciated. >>> >>> -jason >>> >>> jason wrote: >>>> Hi, all >>>> >>>> I am trying to set up some moby services for testing. What I have >>>> is a bunch of binaries such as blast, hmmer, and emboss program >>>> running on my system? One step in the service registration is >>>> generating service meta data. I guess others already register some >>>> of these binaries as services. Is there a way I can find out what >>>> binary is registered in the Moby Central? If I can, I could fetch >>>> those service meta data from moby central, change the authority and >>>> service URL, and register my services. Otherwise, I need to inspect >>>> and register the binaries one by one. It is daunting task. >>>> >>>> thanks >>>> >>>> -jason >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: +31 (0)317-483 060 > mobile: +31 (0)6-143 66 783 > e-mail: 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 From srramirez at uma.es Thu Oct 2 03:48:15 2008 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Thu, 02 Oct 2008 09:48:15 +0200 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E39BDC.3030806@bioteam.net> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> Message-ID: <48E47CBF.8080607@uma.es> Hi Jason, As you said, there are registered services with the same binaries that you have. Why don't you, instead of register a new service, make a mirror of the existing ones?. In our group we are preparing an proposal to make MOBY support these. The document is available in this link (http://chirimoyo.ac.uma.es/proposals/BioMOBY_Mirroring.pdf). The implementation is almost finished and could be a good opportunity for discuss a protocol for request a new mirror, ask the owner for the code, etc. This protocol can help you to search for the services you are interesting in, because although you can use the API provided for MOBY, the service could not have the information about the binary used in it, maybe in the name but is not sure. What do you think?. jason wrote: > Hi, all > > I am trying to set up some moby services for testing. What I have is a > bunch of binaries such as blast, hmmer, and emboss program running on > my system? One step in the service registration is generating service > meta data. I guess others already register some of these binaries as > services. Is there a way I can find out what binary is registered in > the Moby Central? If I can, I could fetch those service meta data from > moby central, change the authority and service URL, and register my > services. Otherwise, I need to inspect and register the binaries one > by one. It is daunting task. > > thanks > > -jason > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From mccarthy at elmonline.ca Mon Oct 6 17:08:57 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 14:08:57 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems Message-ID: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> Hi, I'm trying to invoke an asynchronous service in jMoby and the call to invokeService never returns. I know that the service in question (the "runEmbossPatmatmotifsFromID" service at the authority "www.cnb.uam.es") works, because I can execute exactly the query I'm testing from dashboard and it works (I'm using UniProt:P15923 if anyone would like to play along at home...) The first problem seems to be that AnalysisEvent.createFromXML is returning an empty array of AnalysisEvent objects and all of the error detection assumes that a failure to parse will result in a null pointer. That said, even if the error were properly detected, I'd still have a problem because the parser would just die with an exception. So the second problem is the failure to parse the XML returned by the service. Here's the offending XML: http://www.w3.org/2005/08/addressing/anonymous urn:www.sve.man.ac.uk-84286358931187206910812790 http://docs.oasis-open.org/wsrf/fault soap:Server Application error 2008-10-06T20:07:18Z Property status_1 does not exist Now, even if this XML were parsed successfully, I'd still have a problem because it seems the service is trying to return an error complaining about the polling request. So the third problem is actually sending the service data it can use. I tried to find another asynchronous service to test, but the only other asynchronous services that take simple Moby objects (just namespace and id) are by the same authority and produce the same problems. So, is there something I can do to fix these problems I'm experiencing? Any insight at all would be welcome. Thanks, Luke From martin.senger at gmail.com Mon Oct 6 22:05:35 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 10:05:35 +0800 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> Message-ID: <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> > I'm trying to invoke an asynchronous service in jMoby and the call to > invokeService never returns. Just to clarify: jMoby (at least the Moses part) has no support for asynchronous services implemented yet. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From mccarthy at elmonline.ca Mon Oct 6 22:47:30 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 19:47:30 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> Message-ID: <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> On 6-Oct-08, at 7:05 PM, Martin Senger wrote: >> I'm trying to invoke an asynchronous service in jMoby and the call to >> invokeService never returns. > > Just to clarify: jMoby (at least the Moses part) has no support for > asynchronous services implemented yet. It sure looks like it does. MobyRequest.performAsyncSOAPRequest (called by MobyRequest.invokeService) doesn't do what I think it does? (perform an asynchronous service call) Cheers, Luke From martin.senger at gmail.com Mon Oct 6 22:54:45 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 10:54:45 +0800 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> Message-ID: <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> > MobyRequest.performAsyncSOAPRequest MobyRequest is not Moses that I was referring to. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From mccarthy at elmonline.ca Mon Oct 6 22:59:02 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 19:59:02 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> Message-ID: <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> On 6-Oct-08, at 7:54 PM, Martin Senger wrote: >> MobyRequest.performAsyncSOAPRequest > > MobyRequest is not Moses that I was referring to. When did we start talking about Moses? From martin.senger at gmail.com Mon Oct 6 23:06:02 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 11:06:02 +0800 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> Message-ID: <4d93f07c0810062006pf970971mf9d32954f496b838@mail.gmail.com> > When did we start talking about Moses? I did; see my email. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From mccarthy at elmonline.ca Mon Oct 6 23:13:27 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 20:13:27 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <4d93f07c0810062006pf970971mf9d32954f496b838@mail.gmail.com> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> <4d93f07c0810062006pf970971mf9d32954f496b838@mail.gmail.com> Message-ID: <43096C13-94FD-4423-A53C-1977EF41BD60@elmonline.ca> On 6-Oct-08, at 8:06 PM, Martin Senger wrote: >> When did we start talking about Moses? > > I did; see my email. Maybe I didn't make my point: I'm not. If you're answering questions about Moses, I've asked the wrong question. If that's the case, please let me know how to phrase it differently. When I use MobyRequest.invokeService to access an asynchronous service, it never returns from the call. The three causes that my digging has uncovered are related in my original post. From srramirez at uma.es Tue Oct 7 02:56:29 2008 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Tue, 07 Oct 2008 08:56:29 +0200 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> Message-ID: <48EB081D.30504@uma.es> Hello Luke, Has Martin said, jmoby is not abel to run Asynchronous Services for now. You can use MOWServ (www.inag.org/MOWServ) or jOrca (www.bitlab-es.com/jorca) for call them. If you are looking for a programmatic solution, maybe I can offer you some classes for call it in Java and C++. Best Regards, Sergio Luke McCarthy wrote: > On 6-Oct-08, at 7:05 PM, Martin Senger wrote: > >>> I'm trying to invoke an asynchronous service in jMoby and the call to >>> invokeService never returns. >> >> Just to clarify: jMoby (at least the Moses part) has no support for >> asynchronous services implemented yet. > > It sure looks like it does. MobyRequest.performAsyncSOAPRequest > (called by MobyRequest.invokeService) doesn't do what I think it > does? (perform an asynchronous service call) > > Cheers, > > Luke > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From edward.kawas at gmail.com Tue Oct 7 09:24:38 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 7 Oct 2008 06:24:38 -0700 Subject: [MOBY-dev] taverna-for-moby.jar Message-ID: <48eb6325.1ed6720a.27ad.ffffd92a@mx.google.com> Hello, Any ideas why jmoby depends on the above jar file? Thanks, Eddie From martin.senger at gmail.com Tue Oct 7 09:42:44 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 21:42:44 +0800 Subject: [MOBY-dev] taverna-for-moby.jar In-Reply-To: <48eb6325.1ed6720a.27ad.ffffd92a@mx.google.com> References: <48eb6325.1ed6720a.27ad.ffffd92a@mx.google.com> Message-ID: <4d93f07c0810070642j23d4eb81o2c30dd23fdb9d829@mail.gmail.com> > Any ideas why jmoby depends on the above jar file? Because there is some code for creating moby graphs that also produces scufl definitions - and for that I needed some code from taverna. At least, this is what I remember about it. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Tue Oct 7 10:32:02 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 07 Oct 2008 08:32:02 -0600 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> Message-ID: <48EB72E2.9090303@ucalgary.ca> Hi Luke, MobyRequest is my code. I'll look into the error handling for you. For clarification of others on the list, he's making a client call, not a server side call. jMoby supports this through MobyRequest (though it seems flakey if there's exceptions by Luke's analysis). Paul Luke McCarthy wrote: > Hi, > > I'm trying to invoke an asynchronous service in jMoby and the call to > invokeService never returns. I know that the service in question (the > "runEmbossPatmatmotifsFromID" service at the authority > "www.cnb.uam.es") works, because I can execute exactly the query I'm > testing from dashboard and it works (I'm using UniProt:P15923 if > anyone would like to play along at home...) > > The first problem seems to be that AnalysisEvent.createFromXML is > returning an empty array of AnalysisEvent objects and all of the error > detection assumes that a failure to parse will result in a null pointer. > > That said, even if the error were properly detected, I'd still have a > problem because the parser would just die with an exception. So the > second problem is the failure to parse the XML returned by the > service. Here's the offending XML: > > > xmlns:wsse="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-secext-1.0.xsd" > xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" > xmlns:wsrl="http://docs.oasis-open.org/wsrf/rl-2" > xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:mobyws="http://biomoby.org/" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > xmlns:wsrp="http://docs.oasis-open.org/wsrf/rp-2" > xmlns:wsa="http://www.w3.org/2005/08/addressing"> > > wsu:Id="To">http://www.w3.org/2005/08/addressing/anonymous > wsu:Id="MessageID">urn:www.sve.man.ac.uk-84286358931187206910812790 > > wsu:Id="Action">http://docs.oasis-open.org/wsrf/fault > > > > soap:Server > Application error > > xmlns:wsbf="http://docs.oasis-open.org/wsrf/bf-2"> > 2008-10-06T20:07:18Z > Property status_1 does not > exist > > > > > > > Now, even if this XML were parsed successfully, I'd still have a > problem because it seems the service is trying to return an error > complaining about the polling request. So the third problem is > actually sending the service data it can use. > > I tried to find another asynchronous service to test, but the only > other asynchronous services that take simple Moby objects (just > namespace and id) are by the same authority and produce the same > problems. > > So, is there something I can do to fix these problems I'm > experiencing? Any insight at all would be welcome. Thanks, > > Luke > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From py at pingoured.fr Wed Oct 15 12:21:16 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 15 Oct 2008 18:21:16 +0200 Subject: [MOBY-dev] Some stats Message-ID: <48F6187C.8010108@pingoured.fr> Dear list, I am preparing a presentation that I will give in my lab. In this presentation I will present BioMoby in general and thus would like to give some statistics about it: How many authorities do we have ? How many registered services do we have ? How many datatypes ? How many contributors ? How many people on the mailing lists ? I already found some numbers [1] but the presentation is a bit old (2006) and I would like to update them. I know that this is not really the place where to ask since it has nothing related to development, I could also have asked privately, but I though some other people might be interested and it might be interesting to have this archive somewhere :) Thanks in advance for your help, Best regards, Pierre [1] http://biomoby.open-bio.org/TIGR_Brief.ppt From edward.kawas at gmail.com Wed Oct 15 12:39:01 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 15 Oct 2008 09:39:01 -0700 Subject: [MOBY-dev] Some stats In-Reply-To: <48F6187C.8010108@pingoured.fr> References: <48F6187C.8010108@pingoured.fr> Message-ID: <48f61cab.15528c0a.2725.2676@mx.google.com> Hi Pierre, Here are some stats for services (and providers) http://moby.ucalgary.ca/moby/ValidateService?getStats=true To get the other information (number of datatypes, etc), you could easily use the api and count the results. That way you could get the most up to date information. If you have problems with this, let me know and I can help you. 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 Pierre-Yves Chibon Sent: October-15-08 9:21 AM To: MOBY-dev at lists.open-bio.org Subject: [MOBY-dev] Some stats Dear list, I am preparing a presentation that I will give in my lab. In this presentation I will present BioMoby in general and thus would like to give some statistics about it: How many authorities do we have ? How many registered services do we have ? How many datatypes ? How many contributors ? How many people on the mailing lists ? I already found some numbers [1] but the presentation is a bit old (2006) and I would like to update them. I know that this is not really the place where to ask since it has nothing related to development, I could also have asked privately, but I though some other people might be interested and it might be interesting to have this archive somewhere :) Thanks in advance for your help, Best regards, Pierre [1] http://biomoby.open-bio.org/TIGR_Brief.ppt _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From py at pingoured.fr Wed Oct 15 16:01:56 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 15 Oct 2008 22:01:56 +0200 Subject: [MOBY-dev] Some stats In-Reply-To: <48f61cab.15528c0a.2725.2676@mx.google.com> References: <48F6187C.8010108@pingoured.fr> <48f61cab.15528c0a.2725.2676@mx.google.com> Message-ID: <48F64C34.70800@pingoured.fr> Edward Kawas wrote: > Hi Pierre, > > Here are some stats for services (and providers) > http://moby.ucalgary.ca/moby/ValidateService?getStats=true Thanks a lot for your quick answer. I am a bit surprise by these results: "There are 92 service providers, with at least one registered service, registered with this registry. Of these service providers, there are 45 that don't have at least one working service." Those 45 services providers are they in the testing repository or are there services really not working ? Could you help me on the part concerning the development ? (Number of developers to the core) Thanks again for your help, Best regards, Pierre From markw at illuminae.com Wed Oct 15 16:14:35 2008 From: markw at illuminae.com (Mark) Date: Wed, 15 Oct 2008 13:14:35 -0700 Subject: [MOBY-dev] Some stats In-Reply-To: <48F64C34.70800@pingoured.fr> References: <48F6187C.8010108@pingoured.fr> <48f61cab.15528c0a.2725.2676@mx.google.com> <48F64C34.70800@pingoured.fr> Message-ID: Hi Pierre, It'll be a mixture - some of the 45 will be providers who never intended their services to be "live", but registered them in the live registry anyway. Others are providers who have moved away from their institutes and the services have gone offline and they forgot to de-register them. The moby 1.0 manuscript had ~42 authors, and these represent people who have either directly contributed code or have been involved in planning/funding the project. There are ~10 people worldwide who are actively contributing code at the moment (beyond the code required for services) there are 135 members of the moby-dev mailing list (developers), and 221 members on the moby-l mailing list (discussion). Hope that helps! M On Wed, 15 Oct 2008 13:01:56 -0700, Pierre-Yves Chibon wrote: > Edward Kawas wrote: >> Hi Pierre, >> Here are some stats for services (and providers) >> http://moby.ucalgary.ca/moby/ValidateService?getStats=true > > Thanks a lot for your quick answer. > > I am a bit surprise by these results: > > "There are 92 service providers, with at least one registered service, > registered with this registry. > Of these service providers, there are 45 that don't have at least one > working service." > > Those 45 services providers are they in the testing repository or are > there services really not working ? > > Could you help me on the part concerning the development ? (Number of > developers to the core) > > > Thanks again for your help, > > Best regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Oct 16 09:04:01 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 16 Oct 2008 06:04:01 -0700 Subject: [MOBY-dev] Some stats In-Reply-To: <48F64C34.70800@pingoured.fr> References: <48F6187C.8010108@pingoured.fr> <48f61cab.15528c0a.2725.2676@mx.google.com> <48F64C34.70800@pingoured.fr> Message-ID: <48f73bca.02578c0a.5968.6db3@mx.google.com> Hi Pierre, Those 45 that don't have any working services may be old service providers that no longer have any registered services or their services really no longer work (respond to a ping, etc). Perhaps Mark can help you with your second question. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: October-15-08 1:02 PM To: Core developer announcements Subject: Re: [MOBY-dev] Some stats Edward Kawas wrote: > Hi Pierre, > > Here are some stats for services (and providers) > http://moby.ucalgary.ca/moby/ValidateService?getStats=true Thanks a lot for your quick answer. I am a bit surprise by these results: "There are 92 service providers, with at least one registered service, registered with this registry. Of these service providers, there are 45 that don't have at least one working service." Those 45 services providers are they in the testing repository or are there services really not working ? Could you help me on the part concerning the development ? (Number of developers to the core) Thanks again for your help, Best regards, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Oct 22 01:09:33 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 22 Oct 2008 06:09:33 +0100 Subject: [MOBY-dev] what license is BioMoby and jMoby? Message-ID: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> I have got this question from a jMoby user: I know that BioMoby is an open source project. Could you tell me which > license is used to generate jMoby Code? > and I found that I did not know how to answer. Do we have anywhere such policy? I personally usually used the Apache license - but I have not expressed it verbally in any of the jMoby code. I would like to do it now - and even though I am planning to add it only to the Java sources I wrote myself I need some consensus from the others. So what is your opinion? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From sneumann at ipb-halle.de Wed Oct 22 02:48:23 2008 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Wed, 22 Oct 2008 08:48:23 +0200 Subject: [MOBY-dev] what license is BioMoby and jMoby? In-Reply-To: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> References: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> Message-ID: <1224658103.7986.350.camel@lathan.ipb-sub.ipb-halle.de> On Wed, 2008-10-22 at 06:09 +0100, Martin Senger wrote: > I know that BioMoby is an open source project. Could you tell me which > > license is used to generate jMoby Code? A proper license audit would also involve checking the myriad of licenses pulled in via the maven repository, and check their compatibility. A useful starting point is the fedora compatibility matrix towards the end of http://fedoraproject.org/wiki/Licensing Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From Dominique.Jeannin at avignon.inra.fr Wed Oct 22 05:07:51 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 22 Oct 2008 11:07:51 +0200 Subject: [MOBY-dev] ant install crashes Message-ID: <48FEED67.2010403@avignon.inra.fr> Hello I updated the jMoby project by CVS, I launched the "ant install" command right after and I have just got this compilation error : [...] compile-datatypes: [javac] Compiling 834 source files to /home/gafl/djeannin/workspace/jMoby/build/others/datatypes [javac] /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithObjectValues.java:107: getMoby_values() in org.biomoby.shared.datatypes.GCP_FeatureWithObjectValues cannot override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] [javac] required: org.biomoby.shared.datatypes.GCP_Value[] [javac] public GCP_SimpleIdentifier[] getMoby_values() { [javac] ^ [javac] /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithSimpleValues.java:93: getMoby_values() in org.biomoby.shared.datatypes.GCP_FeatureWithSimpleValues cannot override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.MobyString [javac] required: org.biomoby.shared.datatypes.GCP_Value[] [javac] public MobyString getMoby_values() { [javac] ^ [javac] /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FullBiblioReference.java:121: getMoby_metaData() in org.biomoby.shared.datatypes.GCP_FullBiblioReference cannot override getMoby_metaData() in org.biomoby.shared.datatypes.GCP_BiblioReference; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] [javac] required: org.biomoby.shared.datatypes.GCP_SimpleFeature [javac] public GCP_SimpleIdentifier[] getMoby_metaData() { [javac] ^ [javac] 3 errors BUILD FAILED /home/gafl/djeannin/workspace/jMoby/xmls/install.xml:114: The following error occurred while executing this line: /home/gafl/djeannin/workspace/jMoby/xmls/mosesBuild.xml:286: Compile failed; see the compiler error output for details. Total time: 2 minutes 2 seconds Has anyone seen this before ? Best regards, Dominique From martin.senger at gmail.com Wed Oct 22 05:28:48 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 22 Oct 2008 10:28:48 +0100 Subject: [MOBY-dev] ant install crashes In-Reply-To: <48FEED67.2010403@avignon.inra.fr> References: <48FEED67.2010403@avignon.inra.fr> Message-ID: <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> I think that the problem may happen when you have previously generated Moses datatypes and/or skeletons - and when they have since changed in the registry. The 'ant install' should take care about removing them - but it perhaps does not now. I will check it later today - and if I find that this is the case I will update the 'ant install' appropriately. You can try it now by removing manually directories 'generated/datatypes/' and 'generated/skeletons/' and running 'ant install' again. Does it work now? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From Dominique.Jeannin at avignon.inra.fr Wed Oct 22 05:40:49 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 22 Oct 2008 11:40:49 +0200 Subject: [MOBY-dev] ant install crashes In-Reply-To: <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> References: <48FEED67.2010403@avignon.inra.fr> <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> Message-ID: <48FEF521.8090905@avignon.inra.fr> Martin Senger a ?crit : > I think that the problem may happen when you have previously generated Moses > datatypes and/or skeletons - and when they have since changed in the > registry. The 'ant install' should take care about removing them - but it > perhaps does not now. I will check it later today - and if I find that this > is the case I will update the 'ant install' appropriately. You can try it > now by removing manually directories 'generated/datatypes/' and > 'generated/skeletons/' and running 'ant install' again. Does it work now? > > Cheers, > Martin > > Thanks for the reply. It works. I remove the two folders, whereas my office mate run "ant clean" and "ant clean-datatypes", both method worked. Thanks again. Best regards, Dominique From groscurt at mpiz-koeln.mpg.de Wed Oct 22 05:41:06 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 22 Oct 2008 11:41:06 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <48FEED67.2010403@avignon.inra.fr> References: <48FEED67.2010403@avignon.inra.fr> Message-ID: <48FEF532.6080804@mpiz-koeln.mpg.de> Hi, first you dont need to do an "ant install" after you made an update. the install feature is only used for the first time you work with jmoby. second i just made an update and run ant install and dont get that error - and for me it was 739 datatypes to compile not 834.... this made me think and i had a look at the generated datatypes. On the production central we have a lot of test__xxx datatypes which is weird on the production on the first place funnily they are all registered by "sarah.connor at treminator.com" ... so - do the machines have taken over now ? Are we at a point someone made a bad joke or do have bots taken over the registration ;-) ? Cheers andreas Dominique Jeannin wrote: > Hello > > I updated the jMoby project by CVS, I launched the "ant install" > command right after and I have just got this compilation error : > > [...] > compile-datatypes: > [javac] Compiling 834 source files to > /home/gafl/djeannin/workspace/jMoby/build/others/datatypes > [javac] > /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithObjectValues.java:107: > getMoby_values() in > org.biomoby.shared.datatypes.GCP_FeatureWithObjectValues cannot > override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; > attempting to use incompatible return type > [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] > [javac] required: org.biomoby.shared.datatypes.GCP_Value[] > [javac] public GCP_SimpleIdentifier[] getMoby_values() { > [javac] ^ > [javac] > /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithSimpleValues.java:93: > getMoby_values() in > org.biomoby.shared.datatypes.GCP_FeatureWithSimpleValues cannot > override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; > attempting to use incompatible return type > [javac] found : org.biomoby.shared.datatypes.MobyString > [javac] required: org.biomoby.shared.datatypes.GCP_Value[] > [javac] public MobyString getMoby_values() { > [javac] ^ > [javac] > /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FullBiblioReference.java:121: > getMoby_metaData() in > org.biomoby.shared.datatypes.GCP_FullBiblioReference cannot override > getMoby_metaData() in > org.biomoby.shared.datatypes.GCP_BiblioReference; attempting to use > incompatible return type > [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] > [javac] required: org.biomoby.shared.datatypes.GCP_SimpleFeature > [javac] public GCP_SimpleIdentifier[] getMoby_metaData() { > [javac] ^ > [javac] 3 errors > > BUILD FAILED > /home/gafl/djeannin/workspace/jMoby/xmls/install.xml:114: The > following error occurred while executing this line: > /home/gafl/djeannin/workspace/jMoby/xmls/mosesBuild.xml:286: Compile > failed; see the compiler error output for details. > > Total time: 2 minutes 2 seconds > > Has anyone seen this before ? > > Best regards, > > Dominique > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From py at pingoured.fr Wed Oct 22 07:09:19 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 22 Oct 2008 13:09:19 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <48FEF532.6080804@mpiz-koeln.mpg.de> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> Message-ID: <48FF09DF.6080003@pingoured.fr> Andreas Groscurth wrote: > Hi, > > first you dont need to do an "ant install" after you made an update. the > install feature is only used for the first time you work with jmoby. > > second i just made an update and run ant install and dont get that error > - and for me it was 739 datatypes to compile not 834.... > > > this made me think and i had a look at the generated datatypes. On the > production central we have a lot of test__xxx datatypes which is weird > on the production on the first place > > funnily they are all registered by "sarah.connor at treminator.com" ... so > - do the machines have taken over now ? > > Are we at a point someone made a bad joke or do have bots taken over the > registration ;-) ? To me the datatype "testHydrophobicity" and its children are even worse to me... (ze.ze does not exist on google on the contrary to treminator.com which does not seems to be very biology related that's true...) But I think this is another topic. Regards, Pierre From py at pingoured.fr Wed Oct 22 08:01:46 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 22 Oct 2008 14:01:46 +0200 Subject: [MOBY-dev] dashboard build failed Message-ID: <48FF162A.70507@pingoured.fr> Dear all, Quite often when I run "ant dashboard" I got a Build Failed (see at the end of this mail for the full example). I normally get rid of it by doing an 'ant all'. I have looked a bit on the BioMoby website, I found the FAQ for the dashboard [1] but there seem to be nothing about such issue. Is that a known issue ? Is there a common/quick way to fix it (else than 'ant all') ? Anyway I think that it might be interesting to add this in the FAQ. Thanks for your help, Regards, Pierre [1] http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html ------------------------------------------------------------------------ $ ant dashboard Buildfile: build.xml checkmaven: initmaven: init: config: compile: moses-init: samples-init: dashboard-init: dashboard-config: dashboard: [Dashboard] Exception in thread "main" java.lang.Error: Unresolved compilation problem: [Dashboard] [Dashboard] at org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:985) BUILD FAILED /home/pierrey/workspace/jMoby/xmls/dashboardBuild.xml:50: Java returned: 1 From groscurt at mpiz-koeln.mpg.de Wed Oct 22 08:12:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 22 Oct 2008 14:12:55 +0200 Subject: [MOBY-dev] dashboard build failed In-Reply-To: <48FF162A.70507@pingoured.fr> References: <48FF162A.70507@pingoured.fr> Message-ID: <48FF18C7.3040802@mpiz-koeln.mpg.de> do you change anything in the code ? this is a normal java error that you have errors in your source code and therfore it cannot be compiled. As this is not the case with the code from jmoby in the cvs this error can only come up if you change something in the code ?! cheers Andreas Pierre-Yves Chibon wrote: > Dear all, > > Quite often when I run "ant dashboard" I got a Build Failed (see at > the end of this mail for the full example). I normally get rid of it > by doing an 'ant all'. > > I have looked a bit on the BioMoby website, I found the FAQ for the > dashboard [1] but there seem to be nothing about such issue. > > Is that a known issue ? Is there a common/quick way to fix it (else > than 'ant all') ? > > Anyway I think that it might be interesting to add this in the FAQ. > > Thanks for your help, > > Regards, > > Pierre > > [1] > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html > > > ------------------------------------------------------------------------ > $ ant dashboard > Buildfile: build.xml > > checkmaven: > > initmaven: > > init: > > config: > > compile: > > moses-init: > > samples-init: > > dashboard-init: > > dashboard-config: > > dashboard: > [Dashboard] Exception in thread "main" java.lang.Error: Unresolved > compilation problem: > [Dashboard] > [Dashboard] at > org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:985) > > BUILD FAILED > /home/pierrey/workspace/jMoby/xmls/dashboardBuild.xml:50: Java > returned: 1 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From martin.senger at gmail.com Wed Oct 22 17:33:18 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Oct 2008 05:33:18 +0800 Subject: [MOBY-dev] dashboard build failed In-Reply-To: <48FF162A.70507@pingoured.fr> References: <48FF162A.70507@pingoured.fr> Message-ID: <4d93f07c0810221433n1be41009m4afc9d17a4ed5c08@mail.gmail.com> > Is that a known issue ? Is there a common/quick way to fix it (else than > 'ant all') ? No, it is not a known issue. The probable cause is that you have some stale class on your classpath - which may happen (I think) when/if you change java compiler. The fix should be to clean everything (ant clean) and then do it again (ant dashboard). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Wed Oct 22 21:20:28 2008 From: markw at illuminae.com (Mark) Date: Wed, 22 Oct 2008 18:20:28 -0700 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <48FF09DF.6080003@pingoured.fr> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: Sorry, it's been a LONG time since I curated the production registry. By the "rules" of the production registry, I have assumed the authority to delete any service or ontology node that includes the word 'test' in its name or it's service description (though I have to be careful, since 'test' is a legitimate analytical activity, so I do take care when I do this!)... I hate doing it, though, since I know that sometimes people use the production registry for workshops, etc, and I might be deleting something that is really actively being used (even if only for a couple of days...) I'll go through the registry in the next few days and clean it up. Mark On Wed, 22 Oct 2008 04:09:19 -0700, Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> first you dont need to do an "ant install" after you made an update. >> the install feature is only used for the first time you work with jmoby. >> second i just made an update and run ant install and dont get that >> error - and for me it was 739 datatypes to compile not 834.... >> this made me think and i had a look at the generated datatypes. On >> the production central we have a lot of test__xxx datatypes which is >> weird on the production on the first place >> funnily they are all registered by "sarah.connor at treminator.com" ... >> so - do the machines have taken over now ? >> Are we at a point someone made a bad joke or do have bots taken over >> the registration ;-) ? > > To me the datatype "testHydrophobicity" and its children are even worse > to me... (ze.ze does not exist on google on the contrary to > treminator.com which does not seems to be very biology related that's > true...) > > But I think this is another topic. > > Regards, > > Pierre > _______________________________________________ > 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 Oct 22 21:27:18 2008 From: markw at illuminae.com (Mark) Date: Wed, 22 Oct 2008 18:27:18 -0700 Subject: [MOBY-dev] what license is BioMoby and jMoby? In-Reply-To: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> References: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> Message-ID: I believe I am using the Artistic License for the Perl code. M On Tue, 21 Oct 2008 22:09:33 -0700, Martin Senger wrote: > I have got this question from a jMoby user: > > I know that BioMoby is an open source project. Could you tell me which >> license is used to generate jMoby Code? >> > > and I found that I did not know how to answer. Do we have anywhere such > policy? I personally usually used the Apache license - but I have not > expressed it verbally in any of the jMoby code. I would like to do it > now - > and even though I am planning to add it only to the Java sources I wrote > myself I need some consensus from the others. So what is your opinion? > > Thanks, > Martin > From martin.senger at gmail.com Wed Oct 22 21:27:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Oct 2008 09:27:21 +0800 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> > to delete any service or ontology node that includes the word 'test' in its > name or it's service description Please let me remind you that the last agreement was that services with the URL pointing to a localhost will stay, as well. [The clients creating statistics should ignore such services.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Wed Oct 22 21:32:34 2008 From: markw at illuminae.com (Mark) Date: Wed, 22 Oct 2008 18:32:34 -0700 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> Message-ID: right :-) On Wed, 22 Oct 2008 18:27:21 -0700, Martin Senger wrote: >> to delete any service or ontology node that includes the word 'test' in >> its >> name or it's service description > > > Please let me remind you that the last agreement was that services with > the > URL pointing to a localhost will stay, as well. [The clients creating > statistics should ignore such services.] > > Cheers, > Martin > From sneumann at ipb-halle.de Thu Oct 23 03:30:23 2008 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Thu, 23 Oct 2008 09:30:23 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: <1224747026.7986.365.camel@lathan.ipb-sub.ipb-halle.de> On Wed, 2008-10-22 at 18:20 -0700, Mark wrote: > I'll go through the registry in the next few days and clean it up. Any way of keeping a Least-recently-used list or (access statistics in general) for service queries to the central registry ? Then a $(grep test) service unused for >1 year (or whatever) can go without second thought. In addition, we could have some (mildly misleading) statistics about the most heavily used services, like a "hall of fame". Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From py at pingoured.fr Thu Oct 23 03:41:41 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 23 Oct 2008 09:41:41 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: <49002AB5.9000106@pingoured.fr> Mark wrote: > I hate doing it, though, since I know that sometimes people > use the production registry for workshops, etc, and I might be deleting > something that is really actively being used (even if only for a couple > of days...) I am getting confused there, isn't it the goal of the testing registry ? Maybe I misunderstood the difference between the production registry and the testing registry, can someone give me some light about this ? Thanks, Regards, Pierre From groscurt at mpiz-koeln.mpg.de Thu Oct 23 04:09:36 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 23 Oct 2008 10:09:36 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <49002AB5.9000106@pingoured.fr> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <49002AB5.9000106@pingoured.fr> Message-ID: <49003140.4090208@mpiz-koeln.mpg.de> In my point of view you are absolutely right... the test central should be used for everything which is non productional. This includes demonstrating the registry at workshops or the first steps one is deploying web services. The production should only be used for stable and fully working services. i think the problem is that you cant force people to do so and you cant prevent that. cheers andreas Pierre-Yves Chibon wrote: > Mark wrote: >> I hate doing it, though, since I know that sometimes people use >> the production registry for workshops, etc, and I might be deleting >> something that is really actively being used (even if only for a >> couple of days...) > > I am getting confused there, isn't it the goal of the testing registry ? > > Maybe I misunderstood the difference between the production registry > and the testing registry, can someone give me some light about this ? > > Thanks, > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From groscurt at mpiz-koeln.mpg.de Thu Oct 23 04:12:28 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 23 Oct 2008 10:12:28 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <1224747026.7986.365.camel@lathan.ipb-sub.ipb-halle.de> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <1224747026.7986.365.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <490031EC.8080202@mpiz-koeln.mpg.de> The problem of course of the moby registry is that querying a service does not mean calling it also. so a service which would get into the Hall of Fame because it was often asked could never have been called. So in my point of view this Hall of Fame could be misleading as also the number of calls do not say anything about the quality of the service. But i admit, it would be nice to see what services are asked frequently ;-) Cheers Andreas Steffen Neumann wrote: > On Wed, 2008-10-22 at 18:20 -0700, Mark wrote: > >> I'll go through the registry in the next few days and clean it up. >> > Any way of keeping a Least-recently-used list > or (access statistics in general) for service queries > to the central registry ? > > Then a $(grep test) service unused for >1 year (or whatever) > can go without second thought. In addition, we could have > some (mildly misleading) statistics about the most heavily > used services, like a "hall of fame". > > Yours, > Steffen > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From groscurt at mpiz-koeln.mpg.de Thu Oct 23 04:13:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 23 Oct 2008 10:13:09 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> Message-ID: <49003215.4000305@mpiz-koeln.mpg.de> So service registered at production with pointing to a localhost do remain there ? is this correct ? and if so, why ? cheers andreas Mark wrote: > right :-) > > > > On Wed, 22 Oct 2008 18:27:21 -0700, Martin Senger > wrote: > >>> to delete any service or ontology node that includes the word 'test' >>> in its >>> name or it's service description >> >> >> Please let me remind you that the last agreement was that services >> with the >> URL pointing to a localhost will stay, as well. [The clients creating >> statistics should ignore such services.] >> >> Cheers, >> Martin >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From martin.senger at gmail.com Thu Oct 23 04:23:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Oct 2008 16:23:21 +0800 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <49003140.4090208@mpiz-koeln.mpg.de> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <49002AB5.9000106@pingoured.fr> <49003140.4090208@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0810230123u7deee79bib38f5df79a09c74@mail.gmail.com> > In my point of view you are absolutely right... the test central should be > used for everything which is non productional. In theory, it is right. But from my experiences, the duplication of moby registries has been pain in the neck. Because moby does not have (yet?) a proper and well defined notion of registry mirroring or registry federation, registering the same entities twice in two (or more) different registries may cause problems. I am talking from the experience of the Canadian and IRRI registry. In our project, we are using quite a huge set of data types and they can cause incompabilites if they are not mirrored exactly. And doing so is not easy for a big project. Bottom line is that the same entity (such as a data type) should have the same LSID in both registries. But it does not - because these registries do not know about each other. >From this reasons, I still prefer to allow having services registered with the localhost in the main registry. This way I do not step on my own toes if I need to have different versions of the same entity in the main and in the testing (or IRRI, in my case) registry. 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 23 20:40:04 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 24 Oct 2008 08:40:04 +0800 Subject: [MOBY-dev] what license is BioMoby and jMoby? In-Reply-To: References: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> Message-ID: <4d93f07c0810231740x2ca07f78k68ab40147fa65c4e@mail.gmail.com> I have updated jMoby documentation (it will take couple of hours to propagate there) with the following: What license jMoby uses: Unless individual jMoby parts define it differently, the code is licensed under the Apache License. And the LICENSE file contains: Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Thu Oct 23 21:42:27 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 24 Oct 2008 09:42:27 +0800 Subject: [MOBY-dev] ant install crashes In-Reply-To: <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> References: <48FEED67.2010403@avignon.inra.fr> <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> Message-ID: <4d93f07c0810231842s19a74aedl39dbe210d3b1ea28@mail.gmail.com> > The 'ant install' should take care about removing them - but it perhaps > does not now. I will check it later today I have fixed the 'ant install'. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From soiland-reyes at cs.manchester.ac.uk Fri Oct 24 06:14:13 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 24 Oct 2008 11:14:13 +0100 Subject: [MOBY-dev] /home/senger reference in deployed log4j.properties Message-ID: Hi! jmoby-1.1.1.jar from http://biomoby.org/m2repo/org/biomoby/jmoby/1.1.1/ seems to contain a log4j.properties file that includes lines like: log4j.appender.A2=org.apache.log4j.FileAppender log4j.appender.A2.file=/home/senger/moby-live/Java/jMoby.log log4j.appender.A2=org.apache.log4j.RollingFileAppender log4j.appender.A2.MaxFileSize=500KB log4j.appender.A2.MaxBackupIndex=9 log4j.appender.A2.layout=org.apache.log4j.PatternLayout log4j.appender.A2.layout.ConversionPattern=%d{ISO8601} %-4r [%t] %-5p %c{1} %x- %m%n This causes various error messages about /home/senger/moby-live not existing when trying to use jmoby in Taverna's unit tests. Is it possible to not include this log4j property file and let whoever uses jmoby decide what kind of logging to do..? -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From martin.senger at gmail.com Fri Oct 24 06:31:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 24 Oct 2008 18:31:31 +0800 Subject: [MOBY-dev] /home/senger reference in deployed log4j.properties In-Reply-To: References: Message-ID: <4d93f07c0810240331y7691b231lf52982ea85bd0856@mail.gmail.com> > log4j.appender.A2.file=/home/senger/moby-live/Java/jMoby.log This is obviously wrong. Actually, IMO, in the jar file deployed to a maven repository should be no log4j.properties file at all. Or, at least, it should have a property pointing to a log file that could be set from outside (as jMoby has it in its war files deployed to Tomcat). I will look at it. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Sat Oct 25 10:31:42 2008 From: martin.senger at gmail.com (Martin Senger) Date: Sat, 25 Oct 2008 22:31:42 +0800 Subject: [MOBY-dev] /home/senger reference in deployed log4j.properties In-Reply-To: <4d93f07c0810240331y7691b231lf52982ea85bd0856@mail.gmail.com> References: <4d93f07c0810240331y7691b231lf52982ea85bd0856@mail.gmail.com> Message-ID: <4d93f07c0810250731l1f51cbf7x2b1b5591d1e55c73@mail.gmail.com> > > log4j.appender.A2.file=/home/senger/moby-live/Java/jMoby.log > > > This is obviously wrong. Actually, IMO, in the jar file deployed to a maven > repository should be no log4j.properties file at all. > I have fixed this, committed - but I have not yet deployed a new jMoby jar file to Maven - because I am waiting for some further advices how to do define dependencies on axis. I will inform you when a new deployed version of jMoby is out. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Wed Oct 29 13:11:25 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 29 Oct 2008 11:11:25 -0600 Subject: [MOBY-dev] Ontology XML problems again? Message-ID: <4908993D.8060305@ucalgary.ca> Am I the only one getting a "premature end of file" when updating the registry cache in Dashboard? From edward.kawas at gmail.com Wed Oct 29 13:32:03 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 29 Oct 2008 10:32:03 -0700 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <4908993D.8060305@ucalgary.ca> References: <4908993D.8060305@ucalgary.ca> Message-ID: <49089e1c.09d7720a.6964.fffffc72@mx.google.com> For which registry? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: October-29-08 10:11 AM To: mobydev Subject: [MOBY-dev] Ontology XML problems again? Am I the only one getting a "premature end of file" when updating the registry cache in Dashboard? _______________________________________________ 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 Oct 29 13:32:03 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 29 Oct 2008 10:32:03 -0700 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <4908993D.8060305@ucalgary.ca> References: <4908993D.8060305@ucalgary.ca> Message-ID: <49089e1c.09d7720a.6964.fffffc72@mx.google.com> For which registry? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: October-29-08 10:11 AM To: mobydev Subject: [MOBY-dev] Ontology XML problems again? Am I the only one getting a "premature end of file" when updating the registry cache in Dashboard? _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Oct 29 13:34:58 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 29 Oct 2008 11:34:58 -0600 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <49089e1c.09d7720a.6964.fffffc72@mx.google.com> References: <4908993D.8060305@ucalgary.ca> <49089e1c.09d7720a.6964.fffffc72@mx.google.com> Message-ID: <49089EC2.4040602@ucalgary.ca> The default. Edward Kawas wrote: > For which registry? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: October-29-08 10:11 AM > To: mobydev > Subject: [MOBY-dev] Ontology XML problems again? > > Am I the only one getting a "premature end of file" when updating the > registry cache in Dashboard? > _______________________________________________ > 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 Oct 29 14:15:39 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 29 Oct 2008 11:15:39 -0700 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <49089EC2.4040602@ucalgary.ca> References: <4908993D.8060305@ucalgary.ca> <49089e1c.09d7720a.6964.fffffc72@mx.google.com> <49089EC2.4040602@ucalgary.ca> Message-ID: <4908a856.1c048e0a.2c9d.537e@mx.google.com> Works for me ... try clearing your cache. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: October-29-08 10:35 AM To: Core developer announcements Subject: Re: [MOBY-dev] Ontology XML problems again? The default. Edward Kawas wrote: > For which registry? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: October-29-08 10:11 AM > To: mobydev > Subject: [MOBY-dev] Ontology XML problems again? > > Am I the only one getting a "premature end of file" when updating the > registry cache in Dashboard? > _______________________________________________ > 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 kenny.billiau at psb.ugent.be Thu Oct 30 09:32:53 2008 From: kenny.billiau at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 14:32:53 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever Message-ID: Hi, this is my first question, so I hope I'm sending this to the right maillinglist. I recently installed the BioMoby packages and generated my service using the moses-* perl scripts. So myCache is filled without problems and I'm using the testing registry. I'm using perl 5.8.5. Distribution E/EK/EKAWAS/MOBY-1.05.tar.gz Distribution E/EK/EKAWAS/MOBY-Client-1.02.tar.gz Distribution E/EK/EKAWAS/MOSES-MOBY-0.86.tar.gz I can provide the xml files I use to test these services too. $ moses-generate-services.pl psb.ugent.be $ moses-generate-services.pl -b psb.ugent.be All works well. I'm only interested in the BogasGetRegion and the BogasSaveRegion. If I test BogasGetRegion with following command (1), all works fine: $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasGetRegion ~/tmp/moby.xml $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasSaveRegion ~/tmp/mobysave.xml But If I test BogasSaveRegion (2), something goes seriously wrong. The command as above is used, and the response from command (1) is fed to this one. Nothing is done with the results in BogasSaveRegion, I simply generated the perl modules and send the xml file to it. This is the error message: ===================================== --- TRANSPORT ERROR --- 500 read timeout syntax error at line 1, column 0, byte 0 at /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/XML/Parser.pm line 187 500 read timeout ===================================== The timeout for apache is set to 10 minutes, but the transport error occures after 180secs. If I truncate the response from (1) enough, i get a response for (2) back within those 180 secs. But still, as the XML file from (1) only is 250KB, it seems unreasonably long. If I look at what get's into to log, the script seems to do all it's number crunching in the generated Base.pm (here called BogasSaveRegionBase.pm). Generating the parser works, parsing itself goes slow beyong belief: $self->default_throw_with_stack (0) unless $in_testing_mode; my $in_package; eval { my $parser = $self->create_parser( lowestKnownDataTypes => { 'locus_id' => 'String','date' => 'DateTime','region' => 'Region', }, loadDataTypes => [ qw( String DateTime Region Boolean ) ] ) ; # does not get beyond this point in a reasonable amount of time. $in_package = $parser->parse ( method => $in_testing_mode ? 'file' : 'string', data => $data ) ; }; I tried to put the webservice through dprof, with these results (unfortunatly, Apache::DProf seems to die on me, but invoking the mod_perl envirnment with -d:DProf works): [davebowman at hal2000 ~]$ dprofpp -F /tmp/tmon.out XML:: LibXML::parse_string has 1 unstacked calls in outer XML:: SAX::Base::end_element has 1 unstacked calls in outer BOGAS::Moby::BogasSaveRegionBase::BogasSaveRegion has 1 unstacked calls in outer XML::SAX::Base::parse has 1 unstacked calls in outer Exporter::Heavy::heavy_export has 16 unstacked calls in outer Config::Simple::import_from has 1 unstacked calls in outer SOAP::Server::handle has 1 unstacked calls in outer MOSES::MOBY:: Parser::callMethod has 1 unstacked calls in outer MOSES::MOBY:: Base::as_string has 1 unstacked calls in outer Config::Simple::verbose has 1 unstacked calls in outer utf8::AUTOLOAD has -1 unstacked calls in outer HTTP::Message::__ANON__ has 3 unstacked calls in outer Dumpvalue::unwrap has 8 unstacked calls in outer XML::LibXML::_parse_sax_string has 1 unstacked calls in outer MOSES::MOBY::Parser::parse has 1 unstacked calls in outer XML::LibXML::SAX::_parse has 1 unstacked calls in outer Config::Simple::vars has 1 unstacked calls in outer MOSES::MOBY::Parser::end_element has 1 unstacked calls in outer SOAP::Transport::HTTP::Server::handle has 1 unstacked calls in outer AutoLoader::AUTOLOAD has -3 unstacked calls in outer XML::SAX::Base::parse_string has 1 unstacked calls in outer Fcntl::AUTOLOAD has -6 unstacked calls in outer Dumpvalue:: dumpValue has 1 unstacked calls in outer Dumpvalue:: DumpElem has 7 unstacked calls in outer HTTP::Message::AUTOLOAD has -3 unstacked calls in outer Fcntl::__ANON__ has 6 unstacked calls in outer XML::SAX::Base::__ANON__ has 1 unstacked calls in outer Exporter::export has -16 unstacked calls in outer utf8::SWASHNEW has 1 unstacked calls in outer SOAP::Transport::HTTP::CGI::handle has 1 unstacked calls in outer XML::LibXML::SAX::_parse_string has 1 unstacked calls in outer Faking 32 exit timestamp(s). Total Elapsed Time = -34.8210 Seconds User+System Time = 0 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 0.00 140.6 140.64 486940 0.0003 0.0003 IO::Scalar::print 0.00 3.553 3.975 449046 0.0000 0.0000 Dumpvalue::stringify 0.00 2.551 2.551 574503 0.0000 0.0000 File::Spec::Unix::canonpath 0.00 2.005 147.07 232696 0.0000 0.0006 Dumpvalue::unwrap 0.00 1.177 1.177 423816 0.0000 0.0000 overload::mycan 0.00 1.019 1.019 743 0.0014 0.0014 MOSES::MOBY::Cache::Registries::in it 0.00 0.959 3.885 742 0.0013 0.0052 MOSES::MOBY::Generators::Utils::fi nd_file 0.00 0.581 2.989 286495 0.0000 0.0000 File::Spec::Unix::catfile 0.00 0.450 146.88 230026 0.0000 0.0006 Dumpvalue::DumpElem 0.00 0.367 0.607 56930 0.0000 0.0000 MOSES::MOBY::Base::__ANON__ 0.00 0.257 1.876 1925 0.0001 0.0010 MOSES::MOBY::Cache::Central::get_d atatype 0.00 0.246 0.246 1925 0.0001 0.0001 MOSES::MOBY::Cache::Central::_clea n 0.00 0.234 155.05 1 0.2342 155.05 XML::LibXML::_parse_sax_string 0.00 0.218 0.218 11242 0.0000 0.0000 XML::LibXML::Node::_childNodes 0.00 0.143 0.143 108644 0.0000 0.0000 XML::LibXML::Node::nodeName These results don't make me anymuch wiser. I tried switching xml parsers by changing then in the mobyservices.cfg, with no result. Does anyone know what the problem is? Or how to debug this? Am I missing something obvious here? -Kenny ================================================================== Kenny Billiau Web Developer 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 kenny.billiau at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== From edward.kawas at gmail.com Thu Oct 30 10:12:05 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 07:12:05 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: References: Message-ID: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> Hi, This is the right list! Could you send me the XML for your second service? 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 Kenny Billiau Sent: October-30-08 6:33 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] XML parsing takes forever Hi, this is my first question, so I hope I'm sending this to the right maillinglist. I recently installed the BioMoby packages and generated my service using the moses-* perl scripts. So myCache is filled without problems and I'm using the testing registry. I'm using perl 5.8.5. Distribution E/EK/EKAWAS/MOBY-1.05.tar.gz Distribution E/EK/EKAWAS/MOBY-Client-1.02.tar.gz Distribution E/EK/EKAWAS/MOSES-MOBY-0.86.tar.gz I can provide the xml files I use to test these services too. $ moses-generate-services.pl psb.ugent.be $ moses-generate-services.pl -b psb.ugent.be All works well. I'm only interested in the BogasGetRegion and the BogasSaveRegion. If I test BogasGetRegion with following command (1), all works fine: $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasGetRegion ~/tmp/moby.xml $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasSaveRegion ~/tmp/mobysave.xml But If I test BogasSaveRegion (2), something goes seriously wrong. The command as above is used, and the response from command (1) is fed to this one. Nothing is done with the results in BogasSaveRegion, I simply generated the perl modules and send the xml file to it. This is the error message: ===================================== --- TRANSPORT ERROR --- 500 read timeout syntax error at line 1, column 0, byte 0 at /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/XML/Parser.pm line 187 500 read timeout ===================================== The timeout for apache is set to 10 minutes, but the transport error occures after 180secs. If I truncate the response from (1) enough, i get a response for (2) back within those 180 secs. But still, as the XML file from (1) only is 250KB, it seems unreasonably long. If I look at what get's into to log, the script seems to do all it's number crunching in the generated Base.pm (here called BogasSaveRegionBase.pm). Generating the parser works, parsing itself goes slow beyong belief: $self->default_throw_with_stack (0) unless $in_testing_mode; my $in_package; eval { my $parser = $self->create_parser( lowestKnownDataTypes => { 'locus_id' => 'String','date' => 'DateTime','region' => 'Region', }, loadDataTypes => [ qw( String DateTime Region Boolean ) ] ) ; # does not get beyond this point in a reasonable amount of time. $in_package = $parser->parse ( method => $in_testing_mode ? 'file' : 'string', data => $data ) ; }; I tried to put the webservice through dprof, with these results (unfortunatly, Apache::DProf seems to die on me, but invoking the mod_perl envirnment with -d:DProf works): [davebowman at hal2000 ~]$ dprofpp -F /tmp/tmon.out XML:: LibXML::parse_string has 1 unstacked calls in outer XML:: SAX::Base::end_element has 1 unstacked calls in outer BOGAS::Moby::BogasSaveRegionBase::BogasSaveRegion has 1 unstacked calls in outer XML::SAX::Base::parse has 1 unstacked calls in outer Exporter::Heavy::heavy_export has 16 unstacked calls in outer Config::Simple::import_from has 1 unstacked calls in outer SOAP::Server::handle has 1 unstacked calls in outer MOSES::MOBY:: Parser::callMethod has 1 unstacked calls in outer MOSES::MOBY:: Base::as_string has 1 unstacked calls in outer Config::Simple::verbose has 1 unstacked calls in outer utf8::AUTOLOAD has -1 unstacked calls in outer HTTP::Message::__ANON__ has 3 unstacked calls in outer Dumpvalue::unwrap has 8 unstacked calls in outer XML::LibXML::_parse_sax_string has 1 unstacked calls in outer MOSES::MOBY::Parser::parse has 1 unstacked calls in outer XML::LibXML::SAX::_parse has 1 unstacked calls in outer Config::Simple::vars has 1 unstacked calls in outer MOSES::MOBY::Parser::end_element has 1 unstacked calls in outer SOAP::Transport::HTTP::Server::handle has 1 unstacked calls in outer AutoLoader::AUTOLOAD has -3 unstacked calls in outer XML::SAX::Base::parse_string has 1 unstacked calls in outer Fcntl::AUTOLOAD has -6 unstacked calls in outer Dumpvalue:: dumpValue has 1 unstacked calls in outer Dumpvalue:: DumpElem has 7 unstacked calls in outer HTTP::Message::AUTOLOAD has -3 unstacked calls in outer Fcntl::__ANON__ has 6 unstacked calls in outer XML::SAX::Base::__ANON__ has 1 unstacked calls in outer Exporter::export has -16 unstacked calls in outer utf8::SWASHNEW has 1 unstacked calls in outer SOAP::Transport::HTTP::CGI::handle has 1 unstacked calls in outer XML::LibXML::SAX::_parse_string has 1 unstacked calls in outer Faking 32 exit timestamp(s). Total Elapsed Time = -34.8210 Seconds User+System Time = 0 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 0.00 140.6 140.64 486940 0.0003 0.0003 IO::Scalar::print 0.00 3.553 3.975 449046 0.0000 0.0000 Dumpvalue::stringify 0.00 2.551 2.551 574503 0.0000 0.0000 File::Spec::Unix::canonpath 0.00 2.005 147.07 232696 0.0000 0.0006 Dumpvalue::unwrap 0.00 1.177 1.177 423816 0.0000 0.0000 overload::mycan 0.00 1.019 1.019 743 0.0014 0.0014 MOSES::MOBY::Cache::Registries::in it 0.00 0.959 3.885 742 0.0013 0.0052 MOSES::MOBY::Generators::Utils::fi nd_file 0.00 0.581 2.989 286495 0.0000 0.0000 File::Spec::Unix::catfile 0.00 0.450 146.88 230026 0.0000 0.0006 Dumpvalue::DumpElem 0.00 0.367 0.607 56930 0.0000 0.0000 MOSES::MOBY::Base::__ANON__ 0.00 0.257 1.876 1925 0.0001 0.0010 MOSES::MOBY::Cache::Central::get_d atatype 0.00 0.246 0.246 1925 0.0001 0.0001 MOSES::MOBY::Cache::Central::_clea n 0.00 0.234 155.05 1 0.2342 155.05 XML::LibXML::_parse_sax_string 0.00 0.218 0.218 11242 0.0000 0.0000 XML::LibXML::Node::_childNodes 0.00 0.143 0.143 108644 0.0000 0.0000 XML::LibXML::Node::nodeName These results don't make me anymuch wiser. I tried switching xml parsers by changing then in the mobyservices.cfg, with no result. Does anyone know what the problem is? Or how to debug this? Am I missing something obvious here? -Kenny ================================================================== Kenny Billiau Web Developer 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 kenny.billiau at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From kebil at psb.ugent.be Thu Oct 30 08:30:08 2008 From: kebil at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 13:30:08 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <4908a856.1c048e0a.2c9d.537e@mx.google.com> References: <4908993D.8060305@ucalgary.ca> <49089e1c.09d7720a.6964.fffffc72@mx.google.com> <49089EC2.4040602@ucalgary.ca> <4908a856.1c048e0a.2c9d.537e@mx.google.com> Message-ID: Hi, this is my first question, so I hope I'm sending this to the right maillinglist. I recently installed the BioMoby packages and generated my service using the moses-* perl scripts. So myCache is filled without problems and I'm using the testing registry. I'm using perl 5.8.5. Distribution E/EK/EKAWAS/MOBY-1.05.tar.gz Distribution E/EK/EKAWAS/MOBY-Client-1.02.tar.gz Distribution E/EK/EKAWAS/MOSES-MOBY-0.86.tar.gz I can provide the xml files I use to test these services too. $ moses-generate-services.pl psb.ugent.be $ moses-generate-services.pl -b psb.ugent.be All works well. I'm only interested in the BogasGetRegion and the BogasSaveRegion. If I test BogasGetRegion with following command (1), all works fine: $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasGetRegion ~/tmp/moby.xml $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasSaveRegion ~/tmp/mobysave.xml But If I test BogasSaveRegion (2), something goes seriously wrong. The command as above is used, and the response from command (1) is fed to this one. Nothing is done with the results in BogasSaveRegion, I simply generated the perl modules and send the xml file to it. This is the error message: ===================================== --- TRANSPORT ERROR --- 500 read timeout syntax error at line 1, column 0, byte 0 at /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/XML/Parser.pm line 187 500 read timeout ===================================== The timeout for apache is set to 10 minutes, but the transport error occures after 180secs. If I truncate the response from (1) enough, i get a response for (2) back within those 180 secs. But still, as the XML file from (1) only is 250KB, it seems unreasonably long. If I look at what get's into to log, the script seems to do all it's number crunching in the generated Base.pm (here called BogasSaveRegionBase.pm). Generating the parser works, parsing itself goes slow beyong belief: $self->default_throw_with_stack (0) unless $in_testing_mode; my $in_package; eval { my $parser = $self->create_parser( lowestKnownDataTypes => { 'locus_id' => 'String','date' => 'DateTime','region' => 'Region', }, loadDataTypes => [ qw( String DateTime Region Boolean ) ] ); # does not get beyond this point in a reasonable amount of time. $in_package = $parser->parse ( method => $in_testing_mode ? 'file' : 'string', data => $data ); }; I tried to put the webservice through dprof, with these results (unfortunatly, Apache::DProf seems to die on me, but invoking the mod_perl envirnment with -d:DProf works): [davebowman at hal2000 ~]$ dprofpp -F /tmp/tmon.out XML::LibXML::parse_string has 1 unstacked calls in outer XML::SAX::Base::end_element has 1 unstacked calls in outer BOGAS::Moby::BogasSaveRegionBase::BogasSaveRegion has 1 unstacked calls in outer XML::SAX::Base::parse has 1 unstacked calls in outer Exporter::Heavy::heavy_export has 16 unstacked calls in outer Config::Simple::import_from has 1 unstacked calls in outer SOAP::Server::handle has 1 unstacked calls in outer MOSES::MOBY::Parser::callMethod has 1 unstacked calls in outer MOSES::MOBY::Base::as_string has 1 unstacked calls in outer Config::Simple::verbose has 1 unstacked calls in outer utf8::AUTOLOAD has -1 unstacked calls in outer HTTP::Message::__ANON__ has 3 unstacked calls in outer Dumpvalue::unwrap has 8 unstacked calls in outer XML::LibXML::_parse_sax_string has 1 unstacked calls in outer MOSES::MOBY::Parser::parse has 1 unstacked calls in outer XML::LibXML::SAX::_parse has 1 unstacked calls in outer Config::Simple::vars has 1 unstacked calls in outer MOSES::MOBY::Parser::end_element has 1 unstacked calls in outer SOAP::Transport::HTTP::Server::handle has 1 unstacked calls in outer AutoLoader::AUTOLOAD has -3 unstacked calls in outer XML::SAX::Base::parse_string has 1 unstacked calls in outer Fcntl::AUTOLOAD has -6 unstacked calls in outer Dumpvalue::dumpValue has 1 unstacked calls in outer Dumpvalue::DumpElem has 7 unstacked calls in outer HTTP::Message::AUTOLOAD has -3 unstacked calls in outer Fcntl::__ANON__ has 6 unstacked calls in outer XML::SAX::Base::__ANON__ has 1 unstacked calls in outer Exporter::export has -16 unstacked calls in outer utf8::SWASHNEW has 1 unstacked calls in outer SOAP::Transport::HTTP::CGI::handle has 1 unstacked calls in outer XML::LibXML::SAX::_parse_string has 1 unstacked calls in outer Faking 32 exit timestamp(s). Total Elapsed Time = -34.8210 Seconds User+System Time = 0 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 0.00 140.6 140.64 486940 0.0003 0.0003 IO::Scalar::print 0.00 3.553 3.975 449046 0.0000 0.0000 Dumpvalue::stringify 0.00 2.551 2.551 574503 0.0000 0.0000 File::Spec::Unix::canonpath 0.00 2.005 147.07 232696 0.0000 0.0006 Dumpvalue::unwrap 0.00 1.177 1.177 423816 0.0000 0.0000 overload::mycan 0.00 1.019 1.019 743 0.0014 0.0014 MOSES::MOBY::Cache::Registries::in it 0.00 0.959 3.885 742 0.0013 0.0052 MOSES::MOBY::Generators::Utils::fi nd_file 0.00 0.581 2.989 286495 0.0000 0.0000 File::Spec::Unix::catfile 0.00 0.450 146.88 230026 0.0000 0.0006 Dumpvalue::DumpElem 0.00 0.367 0.607 56930 0.0000 0.0000 MOSES::MOBY::Base::__ANON__ 0.00 0.257 1.876 1925 0.0001 0.0010 MOSES::MOBY::Cache::Central::get_d atatype 0.00 0.246 0.246 1925 0.0001 0.0001 MOSES::MOBY::Cache::Central::_clea n 0.00 0.234 155.05 1 0.2342 155.05 XML::LibXML::_parse_sax_string 0.00 0.218 0.218 11242 0.0000 0.0000 XML::LibXML::Node::_childNodes 0.00 0.143 0.143 108644 0.0000 0.0000 XML::LibXML::Node::nodeName These results don't make me anymuch wiser. I tried switching xml parsers by changing then in the mobyservices.cfg, with no result. Does anyone know what the problem is? Or how to debug this? Am I missing something obvious here? -Kenny ================================================================== Kenny Billiau Web Developer 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 kenny.billiau at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== From kenny.billiau at psb.ugent.be Thu Oct 30 11:17:18 2008 From: kenny.billiau at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 16:17:18 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever Message-ID: Hi, here you go, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > Hi, > > This is the right list! Could you send me the XML for your second service? > > Thanks, > > Eddie -------------- next part -------------- A non-text attachment was scrubbed... Name: mobysave.xml Type: text/xml Size: 200385 bytes Desc: URL: From kebil at psb.ugent.be Thu Oct 30 11:03:00 2008 From: kebil at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 16:03:00 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> Message-ID: Hi, here you go, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > Hi, > > This is the right list! Could you send me the XML for your second service? > > Thanks, > > Eddie -------------- next part -------------- A non-text attachment was scrubbed... Name: mobysave.xml Type: text/xml Size: 200385 bytes Desc: URL: From edward.kawas at gmail.com Thu Oct 30 14:39:14 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 11:39:14 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> Message-ID: <4909ff61.27f8720a.750d.76c6@mx.google.com> So this one might take some time... from what I can see, our parser goes into an infinite loop (although, I am not certain about that ...). I will play around with this XML file and get back to you. 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 Kenny Billiau Sent: October-30-08 8:03 AM To: Core developer announcements Subject: Re: [MOBY-dev] XML parsing takes forever Hi, here you go, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > Hi, > > This is the right list! Could you send me the XML for your second service? > > Thanks, > > Eddie From kenny.billiau at psb.ugent.be Thu Oct 30 14:55:50 2008 From: kenny.billiau at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 19:55:50 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <4909ff61.27f8720a.750d.76c6@mx.google.com> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> Message-ID: Hi, thx for helping to investigate the problem! I'm pretty sure the parser gets out of it's mess. When you truncate the XML file by removing all but a few ElementContainers, it takes awhile, but it actually returns without error. And memory consuption doesn't seem to be a problem either, as mostly 'top' reveals that the invoked webservice script uses a steady amount of memory. thx, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > So this one might take some time... from what I can see, our parser goes > into an infinite loop (although, I am not certain about that ...). > > I will play around with this XML file and get back to you. > > 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 Kenny Billiau > Sent: October-30-08 8:03 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > here you go, > > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> Hi, >> >> This is the right list! Could you send me the XML for your second service? >> >> Thanks, >> >> Eddie > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- From edward.kawas at gmail.com Thu Oct 30 14:58:39 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 11:58:39 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> Message-ID: <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> I think that you are right about the parser not going into an infinite loop. For some reason, the SAX parser seems to be really slow (although, I don't want to say that until I know for sure). Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau Sent: October-30-08 11:56 AM To: Core developer announcements Subject: Re: [MOBY-dev] XML parsing takes forever Hi, thx for helping to investigate the problem! I'm pretty sure the parser gets out of it's mess. When you truncate the XML file by removing all but a few ElementContainers, it takes awhile, but it actually returns without error. And memory consuption doesn't seem to be a problem either, as mostly 'top' reveals that the invoked webservice script uses a steady amount of memory. thx, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > So this one might take some time... from what I can see, our parser goes > into an infinite loop (although, I am not certain about that ...). > > I will play around with this XML file and get back to you. > > 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 Kenny Billiau > Sent: October-30-08 8:03 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > here you go, > > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> Hi, >> >> This is the right list! Could you send me the XML for your second service? >> >> Thanks, >> >> Eddie > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jmfernandez at cnio.es Thu Oct 30 15:54:33 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 30 Oct 2008 20:54:33 +0100 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> Message-ID: <490A10F9.5050408@cnio.es> Hi everybody, I'm using the XML::LibXML SAX parser for other projects and tasks, and it can be really, really slow. You don't realize that until you are parsing a large file from a pipe, and you see that most of the time the program which is parsing is CPU (and not I/O) bounded. Best Regards, Jos? Mar?a Edward Kawas wrote: > I think that you are right about the parser not going into an infinite loop. > For some reason, the SAX parser seems to be really slow (although, I don't > want to say that until I know for sure). > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau > Sent: October-30-08 11:56 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > thx for helping to investigate the problem! > > I'm pretty sure the parser gets out of it's mess. When you truncate the > XML file by removing all but a few ElementContainers, it takes awhile, but > it actually returns without error. > > And memory consuption doesn't seem to be a problem either, as mostly 'top' > reveals that the invoked webservice script uses a steady amount of memory. > > thx, > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> So this one might take some time... from what I can see, our parser goes >> into an infinite loop (although, I am not certain about that ...). >> >> I will play around with this XML file and get back to you. >> >> 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 Kenny Billiau >> Sent: October-30-08 8:03 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] XML parsing takes forever >> >> Hi, >> >> here you go, >> >> Kenny >> >> On Thu, 30 Oct 2008, Edward Kawas wrote: >> >>> Hi, >>> >>> This is the right list! Could you send me the XML for your second > service? >>> Thanks, >>> >>> Eddie >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Thu Oct 30 16:39:08 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 13:39:08 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <490A10F9.5050408@cnio.es> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> <490A10F9.5050408@cnio.es> Message-ID: <490a1b7c.0fba720a.690e.4995@mx.google.com> Now I can confirm that it is slow parsing and not an infinite loop! The XML file took over an hour on my virtual machine to parse. I will see what I can do with other SAX parsers for Perl. 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 Jos? Mar?a Fern?ndez Gonz?lez Sent: October-30-08 12:55 PM To: Core developer announcements Subject: Re: [MOBY-dev] XML parsing takes forever Hi everybody, I'm using the XML::LibXML SAX parser for other projects and tasks, and it can be really, really slow. You don't realize that until you are parsing a large file from a pipe, and you see that most of the time the program which is parsing is CPU (and not I/O) bounded. Best Regards, Jos? Mar?a Edward Kawas wrote: > I think that you are right about the parser not going into an infinite loop. > For some reason, the SAX parser seems to be really slow (although, I don't > want to say that until I know for sure). > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau > Sent: October-30-08 11:56 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > thx for helping to investigate the problem! > > I'm pretty sure the parser gets out of it's mess. When you truncate the > XML file by removing all but a few ElementContainers, it takes awhile, but > it actually returns without error. > > And memory consuption doesn't seem to be a problem either, as mostly 'top' > reveals that the invoked webservice script uses a steady amount of memory. > > thx, > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> So this one might take some time... from what I can see, our parser goes >> into an infinite loop (although, I am not certain about that ...). >> >> I will play around with this XML file and get back to you. >> >> 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 Kenny Billiau >> Sent: October-30-08 8:03 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] XML parsing takes forever >> >> Hi, >> >> here you go, >> >> Kenny >> >> On Thu, 30 Oct 2008, Edward Kawas wrote: >> >>> Hi, >>> >>> This is the right list! Could you send me the XML for your second > service? >>> Thanks, >>> >>> Eddie >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jason at bioteam.net Wed Oct 1 15:48:44 2008 From: jason at bioteam.net (jason) Date: Wed, 01 Oct 2008 23:48:44 +0800 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48DC9D40.5030604@genesilico.pl> References: <48DC9D40.5030604@genesilico.pl> Message-ID: <48E39BDC.3030806@bioteam.net> Hi, all I am trying to set up some moby services for testing. What I have is a bunch of binaries such as blast, hmmer, and emboss program running on my system? One step in the service registration is generating service meta data. I guess others already register some of these binaries as services. Is there a way I can find out what binary is registered in the Moby Central? If I can, I could fetch those service meta data from moby central, change the authority and service URL, and register my services. Otherwise, I need to inspect and register the binaries one by one. It is daunting task. thanks -jason From jason at bioteam.net Thu Oct 2 02:27:54 2008 From: jason at bioteam.net (jason) Date: Thu, 02 Oct 2008 10:27:54 +0800 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E39BDC.3030806@bioteam.net> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> Message-ID: <48E431AA.30503@bioteam.net> Hi, Any suggestion on this one? Help is appreciated. -jason jason wrote: > Hi, all > > I am trying to set up some moby services for testing. What I have is a > bunch of binaries such as blast, hmmer, and emboss program running on > my system? One step in the service registration is generating service > meta data. I guess others already register some of these binaries as > services. Is there a way I can find out what binary is registered in > the Moby Central? If I can, I could fetch those service meta data from > moby central, change the authority and service URL, and register my > services. Otherwise, I need to inspect and register the binaries one > by one. It is daunting task. > > thanks > > -jason > > > > From sebastien.carrere at toulouse.inra.fr Thu Oct 2 08:58:19 2008 From: sebastien.carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 02 Oct 2008 10:58:19 +0200 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E431AA.30503@bioteam.net> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> <48E431AA.30503@bioteam.net> Message-ID: <48E48D2B.6020000@toulouse.inra.fr> Hi Jason, We developped a lightweight framework in Toulouse (France), called PlayMoby. http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby The aim of this framework is to deploy easily BioMoby web-services for command line applications running on UNIX-like systems using a Mobyle program description (http://bioweb2.pasteur.fr/projects/mobyle/). You have an exemple on how to write a perl wrapper for Blast (blastp_swissprot) in the "Sample scripts" section (http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#samples). We deploy and survey around 120 web-services deployed with PlayMoby and if you need another exemple based on EMBOSS program, you can ask me sources for one of the following program: http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/external/services/mobycentral_bioworkflow.rss Hope this help, Sebastien jason a ?crit : > Hi, > Any suggestion on this one? > Help is appreciated. > > -jason > > jason wrote: >> Hi, all >> >> I am trying to set up some moby services for testing. What I have is >> a bunch of binaries such as blast, hmmer, and emboss program running >> on my system? One step in the service registration is generating >> service meta data. I guess others already register some of these >> binaries as services. Is there a way I can find out what binary is >> registered in the Moby Central? If I can, I could fetch those service >> meta data from moby central, change the authority and service URL, >> and register my services. Otherwise, I need to inspect and register >> the binaries one by one. It is daunting task. >> >> thanks >> >> -jason >> >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From jerzyo at genesilico.pl Thu Oct 2 09:31:52 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 02 Oct 2008 11:31:52 +0200 Subject: [MOBY-dev] Problems with biomoby plugins in taverna Message-ID: <48E49508.7080909@genesilico.pl> I am trying to execute an attached workflow with simple input (attached) using executeworkflow.sh What I get is: $ ./executeworkflow.sh -inputdoc /tmp/workflows/1653746517794550_input.xmml /tmp/workflows/1653746517794550_workflow_scufl.xml Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects ... done Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/Namespaces Exception in thread "Thread-15" java.lang.LinkageError: loader constraint violation: loader (instance of net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) previously initiated loading for a different type with name "org/apache/commons/logging/Log" at org.biomoby.shared.MobyException.(MobyException.java:55) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1525) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:521) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280) at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67) And the system hangs (executeworkflow.sh produce no result, no progress report and does not terminate) - Why do I get such errors? - Why does the program hang? It should exit with non-zero value - Why such workflow does not hang in taverna GUI version (it doesn't prosuce any result anyway), I attach the progress report from Taverna GUI version - Why This workflow hangs executeworkflow.sh system? Most of the others work ok. Jerzy Orlowski -------------- next part -------------- A non-text attachment was scrubbed... Name: 1653746517794550_input.xmml Type: text/xml Size: 601 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1653746517794550_workflow_scufl.xml Type: text/xml Size: 2953 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: progress.xml Type: text/xml Size: 115 bytes Desc: not available URL: From jerzyo at genesilico.pl Thu Oct 2 09:57:02 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 02 Oct 2008 11:57:02 +0200 Subject: [MOBY-dev] MOBY-dev Digest, Vol 70, Issue 1 In-Reply-To: References: Message-ID: <48E49AEE.4040803@genesilico.pl> Thanks, I found it, I'll see if it works Jerzy moby-dev-request at lists.open-bio.org wrote: > Send MOBY-dev mailing list submissions to > moby-dev at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/moby-dev > or, via email, send a message with subject or body 'help' to > moby-dev-request at lists.open-bio.org > > You can reach the person managing the list at > moby-dev-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of MOBY-dev digest..." > > > Today's Topics: > > 1. Re: Executing Moby Workflow straight from java > (Stian Soiland-Reyes) > 2. Re: Executing Moby Workflow straight from java (Jerzy Orlowski) > 3. decomposition of BioMoby Objects in Taverna (Jerzy Orlowski) > 4. Re: decomposition of BioMoby Objects in Taverna (Edward Kawas) > 5. Re: Executing Moby Workflow straight from java > (Stian Soiland-Reyes) > 6. correspondence between service and executable. (jason) > 7. Re: correspondence between service and executable. (jason) > 8. Re: correspondence between service and executable. > (Sebastien Carrere) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Sep 2008 10:54:47 +0100 > From: "Stian Soiland-Reyes" > Subject: Re: [MOBY-dev] Executing Moby Workflow straight from java > To: "Core developer announcements" > Message-ID: > > Content-Type: text/plain; charset=UTF-8 > > On Wed, Sep 24, 2008 at 16:55, Jerzy Orlowski wrote: > > I suggest as well to move the discussion to the taverna-hackers list ( > http://taverna.sourceforge.net/lists ) > >> I am trying to use your code, but I get strange erros like: >> >> The constructor EngineImpl(EngineConfiguration) is undefined >> >> Perhaps I am working on different versions of the code (some from taverna, >> some from ogasadai and some from freefluo). > > If you want to be sure to get it to work with Taverna 1.7.1, use > http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo/NO-VERSION/freefluo-NO-VERSION.jar > and http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1/freefluo-taverna-exts-1.7.1.jar > > The other projects are likely to have code in either too new or too old version. > > >> Where can I find source code or javadoc for >> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes? > > Note that this version of Freefluo was never released officially by > the Freefluo project, but it can be checked out from their CVS using a > date range. > > Look at the thread of http://markmail.org/message/dnrqdicmbzbfjjl5 if > you really want to build Freefluo from source. > > From pieter.neerincx at gmail.com Thu Oct 2 13:05:47 2008 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Thu, 2 Oct 2008 15:05:47 +0200 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E48D2B.6020000@toulouse.inra.fr> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> <48E431AA.30503@bioteam.net> <48E48D2B.6020000@toulouse.inra.fr> Message-ID: <1F1457E2-03B7-4815-B6DF-8269B479E8E9@gmail.com> Hi Jason, PlayMoby as advertised below looks like a good starting point to wrap existing tools into BioMoby web services. Looks a little like SOAPLAB, but in BioMoby lingua :). But be aware that there is no such thing as *THE* BioMoby service definition for a certain existing binary. Take for example a look at BLAST. In the official public BioMoby Central registry you will find as many different BLAST services as there are service authorities providing BLAST services. Some groups might only provide blastp for alignment with protein sequences. Therefore they might have hardcoded their service to use blastp. Others might provide both blastp & blastn (and blastx, tblastx, etc.) for alignment with protein and nucleotide sequences and use an optional parameter (secondary article in BioMoby) to specify which blast program to use. Similar things you will find for many more BLAST parameters... Then there's the issue of what you align you sequences with: some might provide the complete INSDC (DDBJ/EMBL/Genbank) database while others only provide subsections like only ESTs or only certain species of interest. And then there dozens of other blastable databases a service might, might partially or might not suport. Some might limit the size of you BLAST jobs by only providing a synchronous BLAST service while others might have implemented an asynchronous one allowing for longer runtimes. Finally there is the issue of output formats. NCBI BLAST has 12 different output formats. Officially a Biomoby service is registered with a certain output. This can not change dynamically based on a parameter. So one might choose to register 12 services for the 12 different output formats. The 12 BLAST output formats are not native BioMoby object structures though. BioMoby allows you to wrap existing "legacy" data formats. In that case you might wrap your BLAST output and use a parameter to specify the format although it is a bit of a hack. You could also design a native BioMoby object structure for BLAST output and write a converter... For other tools similar design choices for different input formats will result in different service implementations. And then off course you might use WU-BLAST instead of NCBI BLAST resulting in yet another service implementation... Personally I'm guilty of registering one of those "yet another" BLAST services, because at the time I wrote none of the existing services suited my needs. Right now your best bet is to investigate what is already registered in BioMoby Central and see if there is something that suits your needs. If so, recycle, or if not, implement yet another... It would be nice if we would have a standardised way of wrapping existing stuff into BioMoby services and Object structures. I am thinking of how PostScript works. PostScript is best known as a page description language in the electronic and desktop publishing areas. Most PostScript drivers implement "everything". For a printer driver this means, the driver supports an unlimited high resolution on an unlimited large piece of paper. Off course there is no single printer out there that can printed on a never-ending piece of paper. Therefore manufactures supply PPD (PostScript Printer Definition) files that specify the limits a printer can handle. For example max 1200 dpi and A4 paper. To print you always use the unlimited driver in combination with a PPD for a specific device. If I convert this to our BLAST example all BioMoby BLAST services would be registered with the same input, same output and same optional parameters, but service providers would be albe to specify limits on those. This would require not only standardising on BioMoby object structures, but also on naming of parmeters + their values and for example on naming + version numbering of databases.... hence it would require some level of curation of the BioMoby Central ontologies. Cheers, Pi On 02 Oct 2008, at 10:58, Sebastien Carrere wrote: > Hi Jason, > > We developped a lightweight framework in Toulouse (France), called > PlayMoby. > http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby > > The aim of this framework is to deploy easily BioMoby web-services > for command line applications running on UNIX-like systems using a > Mobyle program description (http://bioweb2.pasteur.fr/projects/ > mobyle/). > > You have an exemple on how to write a perl wrapper for Blast > (blastp_swissprot) in the "Sample scripts" section (http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#samples > ). > > We deploy and survey around 120 web-services deployed with PlayMoby > and if you need another exemple based on EMBOSS program, you can ask > me sources for one of the following program: > http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/external/services/mobycentral_bioworkflow.rss > > Hope this help, > > Sebastien > > jason a ?crit : >> Hi, >> Any suggestion on this one? >> Help is appreciated. >> >> -jason >> >> jason wrote: >>> Hi, all >>> >>> I am trying to set up some moby services for testing. What I have >>> is a bunch of binaries such as blast, hmmer, and emboss program >>> running on my system? One step in the service registration is >>> generating service meta data. I guess others already register >>> some of these binaries as services. Is there a way I can find out >>> what binary is registered in the Moby Central? If I can, I could >>> fetch those service meta data from moby central, change the >>> authority and service URL, and register my services. Otherwise, I >>> need to inspect and register the binaries one by one. It is >>> daunting task. >>> >>> thanks >>> >>> -jason >>> >>> >>> >>> >> _______________________________________________ >> 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 ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From soiland-reyes at cs.manchester.ac.uk Thu Oct 2 13:26:19 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Thu, 2 Oct 2008 14:26:19 +0100 Subject: [MOBY-dev] Problems with biomoby plugins in taverna In-Reply-To: <48E49508.7080909@genesilico.pl> References: <48E49508.7080909@genesilico.pl> Message-ID: On Thu, Oct 2, 2008 at 10:31, Jerzy Orlowski wrote: > What I get is: > Fetching namespace ontology from > http://biomoby.org/RESOURCES/MOBY-S/Namespaces > Exception in thread "Thread-15" java.lang.LinkageError: loader constraint > violation: loader (instance of > net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) previously > initiated loading for a different type with name > "org/apache/commons/logging/Log" > at org.biomoby.shared.MobyException.(MobyException.java:55) > - Why do I get such errors? This might be related to a Raven-related bug with LinkageError we had earlier, http://www.mygrid.org.uk/dev/issues/browse/TAV-480 although it then would say "duplicate class definition". > - Why does the program hang? It should exit with non-zero value Because the thread running your Biomoby activity fails with a fatal error, and the workflow never finishes. The program is waiting for the workflow to finish, but Freefluo doesn't catch LinkageError's which are RuntimeErrors. (Normally you shouldn't catch RuntimeErrors) > - Why such workflow does not hang in taverna GUI version (it doesn't prosuce > any result anyway), I attach the progress report from Taverna GUI version Probably because classes are initialised in a different order within the GUI, for instance by the scavengers browsing the service. The issue happens because of a threading conflict with the classloaders. > - Why This workflow hangs executeworkflow.sh system? Most of the others work > ok. Does it always happen with this workflow..? Which distribution of Taverna are you using for this? I am able to reproduce this with Taverna 1.7.1. I've noted this as a new bug http://www.mygrid.org.uk/dev/issues/browse/TAV-773 and am quickly investigating it with a debugger. It doesn't seem like a concurrency problem, actually, but perhaps there's twoo different org.apache.commons.logging.Log instances on the classpath.. this needs further investigation. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From soiland-reyes at cs.manchester.ac.uk Thu Oct 2 13:44:23 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Thu, 2 Oct 2008 14:44:23 +0100 Subject: [MOBY-dev] Problems with biomoby plugins in taverna In-Reply-To: References: <48E49508.7080909@genesilico.pl> Message-ID: On Thu, Oct 2, 2008 at 14:26, Stian Soiland-Reyes wrote: > this needs further investigation. > A BioMoby exception happens as it's calling runDecypherBlastp with: 20 YKSLTNDWEDHLAVKHFSVE Swissprot 10 If you want a silly workaround I would try to avoid getting that exception! :-) Then when this happens, he needs to initialise the MobyException class, which tries to access org.apache.commons.logging.Log - but somehow this fails. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From jason at bioteam.net Fri Oct 3 16:55:13 2008 From: jason at bioteam.net (jason) Date: Sat, 04 Oct 2008 00:55:13 +0800 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <1F1457E2-03B7-4815-B6DF-8269B479E8E9@gmail.com> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> <48E431AA.30503@bioteam.net> <48E48D2B.6020000@toulouse.inra.fr> <1F1457E2-03B7-4815-B6DF-8269B479E8E9@gmail.com> Message-ID: <48E64E71.2080708@bioteam.net> Hi, Pieter, Sebastien I pull all the services information from Moby Registery using "worker.getServices().". Then I checked the cached services directory. The xml files are very useful for me to find out what service is available for which application. For example, I want to know whether someone wrapped hmmsearch before. I use this command "grep -i hmmsearch *" thanks for the help -jason Pieter Neerincx wrote: > Hi Jason, > > PlayMoby as advertised below looks like a good starting point to wrap > existing tools into BioMoby web services. Looks a little like SOAPLAB, > but in BioMoby lingua :). > > But be aware that there is no such thing as *THE* BioMoby service > definition for a certain existing binary. Take for example a look at > BLAST. In the official public BioMoby Central registry you will find > as many different BLAST services as there are service authorities > providing BLAST services. > Some groups might only provide blastp for alignment with protein > sequences. Therefore they might have hardcoded their service to use > blastp. Others might provide both blastp & blastn (and blastx, > tblastx, etc.) for alignment with protein and nucleotide sequences and > use an optional parameter (secondary article in BioMoby) to specify > which blast program to use. Similar things you will find for many more > BLAST parameters... > Then there's the issue of what you align you sequences with: some > might provide the complete INSDC (DDBJ/EMBL/Genbank) database while > others only provide subsections like only ESTs or only certain species > of interest. And then there dozens of other blastable databases a > service might, might partially or might not suport. Some might > limit the size of you BLAST jobs by only providing a synchronous BLAST > service while others might have implemented an asynchronous one > allowing for longer runtimes. > Finally there is the issue of output formats. NCBI BLAST has 12 > different output formats. Officially a Biomoby service is registered > with a certain output. This can not change dynamically based on a > parameter. So one might choose to register 12 services for the 12 > different output formats. The 12 BLAST output formats are not native > BioMoby object structures though. BioMoby allows you to wrap existing > "legacy" data formats. In that case you might wrap your BLAST output > and use a parameter to specify the format although it is a bit of a > hack. You could also design a native BioMoby object structure for > BLAST output and write a converter... For other tools similar design > choices for different input formats will result in different service > implementations. And then off course you might use WU-BLAST instead of > NCBI BLAST resulting in yet another service implementation... > > Personally I'm guilty of registering one of those "yet another" BLAST > services, because at the time I wrote none of the existing services > suited my needs. Right now your best bet is to investigate what is > already registered in BioMoby Central and see if there is something > that suits your needs. If so, recycle, or if not, implement yet > another... > > It would be nice if we would have a standardised way of wrapping > existing stuff into BioMoby services and Object structures. I am > thinking of how PostScript works. PostScript is best known as a page > description language in the electronic and desktop publishing areas. > Most PostScript drivers implement "everything". For a printer driver > this means, the driver supports an unlimited high resolution on an > unlimited large piece of paper. Off course there is no single printer > out there that can printed on a never-ending piece of paper. Therefore > manufactures supply PPD (PostScript Printer Definition) files that > specify the limits a printer can handle. For example max 1200 dpi and > A4 paper. To print you always use the unlimited driver in combination > with a PPD for a specific device. If I convert this to our BLAST > example all BioMoby BLAST services would be registered with the same > input, same output and same optional parameters, but service providers > would be albe to specify limits on those. This would require not only > standardising on BioMoby object structures, but also on naming of > parmeters + their values and for example on naming + version numbering > of databases.... hence it would require some level of curation of the > BioMoby Central ontologies. > > Cheers, > > Pi > > > On 02 Oct 2008, at 10:58, Sebastien Carrere wrote: > >> Hi Jason, >> >> We developped a lightweight framework in Toulouse (France), called >> PlayMoby. >> http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby >> >> The aim of this framework is to deploy easily BioMoby web-services >> for command line applications running on UNIX-like systems using a >> Mobyle program description (http://bioweb2.pasteur.fr/projects/mobyle/). >> >> You have an exemple on how to write a perl wrapper for Blast >> (blastp_swissprot) in the "Sample scripts" section >> (http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/#samples). >> >> We deploy and survey around 120 web-services deployed with PlayMoby >> and if you need another exemple based on EMBOSS program, you can ask >> me sources for one of the following program: >> http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/external/services/mobycentral_bioworkflow.rss >> >> >> Hope this help, >> >> Sebastien >> >> jason a ?crit : >>> Hi, >>> Any suggestion on this one? >>> Help is appreciated. >>> >>> -jason >>> >>> jason wrote: >>>> Hi, all >>>> >>>> I am trying to set up some moby services for testing. What I have >>>> is a bunch of binaries such as blast, hmmer, and emboss program >>>> running on my system? One step in the service registration is >>>> generating service meta data. I guess others already register some >>>> of these binaries as services. Is there a way I can find out what >>>> binary is registered in the Moby Central? If I can, I could fetch >>>> those service meta data from moby central, change the authority and >>>> service URL, and register my services. Otherwise, I need to inspect >>>> and register the binaries one by one. It is daunting task. >>>> >>>> thanks >>>> >>>> -jason >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: +31 (0)317-483 060 > mobile: +31 (0)6-143 66 783 > e-mail: 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 From srramirez at uma.es Thu Oct 2 07:48:15 2008 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Thu, 02 Oct 2008 09:48:15 +0200 Subject: [MOBY-dev] correspondence between service and executable. In-Reply-To: <48E39BDC.3030806@bioteam.net> References: <48DC9D40.5030604@genesilico.pl> <48E39BDC.3030806@bioteam.net> Message-ID: <48E47CBF.8080607@uma.es> Hi Jason, As you said, there are registered services with the same binaries that you have. Why don't you, instead of register a new service, make a mirror of the existing ones?. In our group we are preparing an proposal to make MOBY support these. The document is available in this link (http://chirimoyo.ac.uma.es/proposals/BioMOBY_Mirroring.pdf). The implementation is almost finished and could be a good opportunity for discuss a protocol for request a new mirror, ask the owner for the code, etc. This protocol can help you to search for the services you are interesting in, because although you can use the API provided for MOBY, the service could not have the information about the binary used in it, maybe in the name but is not sure. What do you think?. jason wrote: > Hi, all > > I am trying to set up some moby services for testing. What I have is a > bunch of binaries such as blast, hmmer, and emboss program running on > my system? One step in the service registration is generating service > meta data. I guess others already register some of these binaries as > services. Is there a way I can find out what binary is registered in > the Moby Central? If I can, I could fetch those service meta data from > moby central, change the authority and service URL, and register my > services. Otherwise, I need to inspect and register the binaries one > by one. It is daunting task. > > thanks > > -jason > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From mccarthy at elmonline.ca Mon Oct 6 21:08:57 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 14:08:57 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems Message-ID: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> Hi, I'm trying to invoke an asynchronous service in jMoby and the call to invokeService never returns. I know that the service in question (the "runEmbossPatmatmotifsFromID" service at the authority "www.cnb.uam.es") works, because I can execute exactly the query I'm testing from dashboard and it works (I'm using UniProt:P15923 if anyone would like to play along at home...) The first problem seems to be that AnalysisEvent.createFromXML is returning an empty array of AnalysisEvent objects and all of the error detection assumes that a failure to parse will result in a null pointer. That said, even if the error were properly detected, I'd still have a problem because the parser would just die with an exception. So the second problem is the failure to parse the XML returned by the service. Here's the offending XML: http://www.w3.org/2005/08/addressing/anonymous urn:www.sve.man.ac.uk-84286358931187206910812790 http://docs.oasis-open.org/wsrf/fault soap:Server Application error 2008-10-06T20:07:18Z Property status_1 does not exist Now, even if this XML were parsed successfully, I'd still have a problem because it seems the service is trying to return an error complaining about the polling request. So the third problem is actually sending the service data it can use. I tried to find another asynchronous service to test, but the only other asynchronous services that take simple Moby objects (just namespace and id) are by the same authority and produce the same problems. So, is there something I can do to fix these problems I'm experiencing? Any insight at all would be welcome. Thanks, Luke From martin.senger at gmail.com Tue Oct 7 02:05:35 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 10:05:35 +0800 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> Message-ID: <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> > I'm trying to invoke an asynchronous service in jMoby and the call to > invokeService never returns. Just to clarify: jMoby (at least the Moses part) has no support for asynchronous services implemented yet. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From mccarthy at elmonline.ca Tue Oct 7 02:47:30 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 19:47:30 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> Message-ID: <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> On 6-Oct-08, at 7:05 PM, Martin Senger wrote: >> I'm trying to invoke an asynchronous service in jMoby and the call to >> invokeService never returns. > > Just to clarify: jMoby (at least the Moses part) has no support for > asynchronous services implemented yet. It sure looks like it does. MobyRequest.performAsyncSOAPRequest (called by MobyRequest.invokeService) doesn't do what I think it does? (perform an asynchronous service call) Cheers, Luke From martin.senger at gmail.com Tue Oct 7 02:54:45 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 10:54:45 +0800 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> Message-ID: <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> > MobyRequest.performAsyncSOAPRequest MobyRequest is not Moses that I was referring to. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From mccarthy at elmonline.ca Tue Oct 7 02:59:02 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 19:59:02 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> Message-ID: <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> On 6-Oct-08, at 7:54 PM, Martin Senger wrote: >> MobyRequest.performAsyncSOAPRequest > > MobyRequest is not Moses that I was referring to. When did we start talking about Moses? From martin.senger at gmail.com Tue Oct 7 03:06:02 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 11:06:02 +0800 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> Message-ID: <4d93f07c0810062006pf970971mf9d32954f496b838@mail.gmail.com> > When did we start talking about Moses? I did; see my email. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From mccarthy at elmonline.ca Tue Oct 7 03:13:27 2008 From: mccarthy at elmonline.ca (Luke McCarthy) Date: Mon, 6 Oct 2008 20:13:27 -0700 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <4d93f07c0810062006pf970971mf9d32954f496b838@mail.gmail.com> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> <4d93f07c0810061954h5b66c343yebdbc6f1c448cd7d@mail.gmail.com> <8C549216-2EB3-4FC0-99CA-B518CC8A063E@elmonline.ca> <4d93f07c0810062006pf970971mf9d32954f496b838@mail.gmail.com> Message-ID: <43096C13-94FD-4423-A53C-1977EF41BD60@elmonline.ca> On 6-Oct-08, at 8:06 PM, Martin Senger wrote: >> When did we start talking about Moses? > > I did; see my email. Maybe I didn't make my point: I'm not. If you're answering questions about Moses, I've asked the wrong question. If that's the case, please let me know how to phrase it differently. When I use MobyRequest.invokeService to access an asynchronous service, it never returns from the call. The three causes that my digging has uncovered are related in my original post. From srramirez at uma.es Tue Oct 7 06:56:29 2008 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Tue, 07 Oct 2008 08:56:29 +0200 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> <4d93f07c0810061905g592508cdv78210d829de84817@mail.gmail.com> <86FCCF35-1CAB-4E78-A721-0AC230ADC225@elmonline.ca> Message-ID: <48EB081D.30504@uma.es> Hello Luke, Has Martin said, jmoby is not abel to run Asynchronous Services for now. You can use MOWServ (www.inag.org/MOWServ) or jOrca (www.bitlab-es.com/jorca) for call them. If you are looking for a programmatic solution, maybe I can offer you some classes for call it in Java and C++. Best Regards, Sergio Luke McCarthy wrote: > On 6-Oct-08, at 7:05 PM, Martin Senger wrote: > >>> I'm trying to invoke an asynchronous service in jMoby and the call to >>> invokeService never returns. >> >> Just to clarify: jMoby (at least the Moses part) has no support for >> asynchronous services implemented yet. > > It sure looks like it does. MobyRequest.performAsyncSOAPRequest > (called by MobyRequest.invokeService) doesn't do what I think it > does? (perform an asynchronous service call) > > Cheers, > > Luke > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From edward.kawas at gmail.com Tue Oct 7 13:24:38 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 7 Oct 2008 06:24:38 -0700 Subject: [MOBY-dev] taverna-for-moby.jar Message-ID: <48eb6325.1ed6720a.27ad.ffffd92a@mx.google.com> Hello, Any ideas why jmoby depends on the above jar file? Thanks, Eddie From martin.senger at gmail.com Tue Oct 7 13:42:44 2008 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 7 Oct 2008 21:42:44 +0800 Subject: [MOBY-dev] taverna-for-moby.jar In-Reply-To: <48eb6325.1ed6720a.27ad.ffffd92a@mx.google.com> References: <48eb6325.1ed6720a.27ad.ffffd92a@mx.google.com> Message-ID: <4d93f07c0810070642j23d4eb81o2c30dd23fdb9d829@mail.gmail.com> > Any ideas why jmoby depends on the above jar file? Because there is some code for creating moby graphs that also produces scufl definitions - and for that I needed some code from taverna. At least, this is what I remember about it. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Tue Oct 7 14:32:02 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 07 Oct 2008 08:32:02 -0600 Subject: [MOBY-dev] jMoby: Asynchronous service invocation problems In-Reply-To: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> References: <803A85A5-EA1E-48DA-811B-FCE7DB72494A@elmonline.ca> Message-ID: <48EB72E2.9090303@ucalgary.ca> Hi Luke, MobyRequest is my code. I'll look into the error handling for you. For clarification of others on the list, he's making a client call, not a server side call. jMoby supports this through MobyRequest (though it seems flakey if there's exceptions by Luke's analysis). Paul Luke McCarthy wrote: > Hi, > > I'm trying to invoke an asynchronous service in jMoby and the call to > invokeService never returns. I know that the service in question (the > "runEmbossPatmatmotifsFromID" service at the authority > "www.cnb.uam.es") works, because I can execute exactly the query I'm > testing from dashboard and it works (I'm using UniProt:P15923 if > anyone would like to play along at home...) > > The first problem seems to be that AnalysisEvent.createFromXML is > returning an empty array of AnalysisEvent objects and all of the error > detection assumes that a failure to parse will result in a null pointer. > > That said, even if the error were properly detected, I'd still have a > problem because the parser would just die with an exception. So the > second problem is the failure to parse the XML returned by the > service. Here's the offending XML: > > > xmlns:wsse="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-secext-1.0.xsd" > xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" > xmlns:wsrl="http://docs.oasis-open.org/wsrf/rl-2" > xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/" > xmlns:mobyws="http://biomoby.org/" > xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" > xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" > xmlns:xsd="http://www.w3.org/2001/XMLSchema" > xmlns:wsrp="http://docs.oasis-open.org/wsrf/rp-2" > xmlns:wsa="http://www.w3.org/2005/08/addressing"> > > wsu:Id="To">http://www.w3.org/2005/08/addressing/anonymous > wsu:Id="MessageID">urn:www.sve.man.ac.uk-84286358931187206910812790 > > wsu:Id="Action">http://docs.oasis-open.org/wsrf/fault > > > > soap:Server > Application error > > xmlns:wsbf="http://docs.oasis-open.org/wsrf/bf-2"> > 2008-10-06T20:07:18Z > Property status_1 does not > exist > > > > > > > Now, even if this XML were parsed successfully, I'd still have a > problem because it seems the service is trying to return an error > complaining about the polling request. So the third problem is > actually sending the service data it can use. > > I tried to find another asynchronous service to test, but the only > other asynchronous services that take simple Moby objects (just > namespace and id) are by the same authority and produce the same > problems. > > So, is there something I can do to fix these problems I'm > experiencing? Any insight at all would be welcome. Thanks, > > Luke > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From py at pingoured.fr Wed Oct 15 16:21:16 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 15 Oct 2008 18:21:16 +0200 Subject: [MOBY-dev] Some stats Message-ID: <48F6187C.8010108@pingoured.fr> Dear list, I am preparing a presentation that I will give in my lab. In this presentation I will present BioMoby in general and thus would like to give some statistics about it: How many authorities do we have ? How many registered services do we have ? How many datatypes ? How many contributors ? How many people on the mailing lists ? I already found some numbers [1] but the presentation is a bit old (2006) and I would like to update them. I know that this is not really the place where to ask since it has nothing related to development, I could also have asked privately, but I though some other people might be interested and it might be interesting to have this archive somewhere :) Thanks in advance for your help, Best regards, Pierre [1] http://biomoby.open-bio.org/TIGR_Brief.ppt From edward.kawas at gmail.com Wed Oct 15 16:39:01 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 15 Oct 2008 09:39:01 -0700 Subject: [MOBY-dev] Some stats In-Reply-To: <48F6187C.8010108@pingoured.fr> References: <48F6187C.8010108@pingoured.fr> Message-ID: <48f61cab.15528c0a.2725.2676@mx.google.com> Hi Pierre, Here are some stats for services (and providers) http://moby.ucalgary.ca/moby/ValidateService?getStats=true To get the other information (number of datatypes, etc), you could easily use the api and count the results. That way you could get the most up to date information. If you have problems with this, let me know and I can help you. 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 Pierre-Yves Chibon Sent: October-15-08 9:21 AM To: MOBY-dev at lists.open-bio.org Subject: [MOBY-dev] Some stats Dear list, I am preparing a presentation that I will give in my lab. In this presentation I will present BioMoby in general and thus would like to give some statistics about it: How many authorities do we have ? How many registered services do we have ? How many datatypes ? How many contributors ? How many people on the mailing lists ? I already found some numbers [1] but the presentation is a bit old (2006) and I would like to update them. I know that this is not really the place where to ask since it has nothing related to development, I could also have asked privately, but I though some other people might be interested and it might be interesting to have this archive somewhere :) Thanks in advance for your help, Best regards, Pierre [1] http://biomoby.open-bio.org/TIGR_Brief.ppt _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From py at pingoured.fr Wed Oct 15 20:01:56 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 15 Oct 2008 22:01:56 +0200 Subject: [MOBY-dev] Some stats In-Reply-To: <48f61cab.15528c0a.2725.2676@mx.google.com> References: <48F6187C.8010108@pingoured.fr> <48f61cab.15528c0a.2725.2676@mx.google.com> Message-ID: <48F64C34.70800@pingoured.fr> Edward Kawas wrote: > Hi Pierre, > > Here are some stats for services (and providers) > http://moby.ucalgary.ca/moby/ValidateService?getStats=true Thanks a lot for your quick answer. I am a bit surprise by these results: "There are 92 service providers, with at least one registered service, registered with this registry. Of these service providers, there are 45 that don't have at least one working service." Those 45 services providers are they in the testing repository or are there services really not working ? Could you help me on the part concerning the development ? (Number of developers to the core) Thanks again for your help, Best regards, Pierre From markw at illuminae.com Wed Oct 15 20:14:35 2008 From: markw at illuminae.com (Mark) Date: Wed, 15 Oct 2008 13:14:35 -0700 Subject: [MOBY-dev] Some stats In-Reply-To: <48F64C34.70800@pingoured.fr> References: <48F6187C.8010108@pingoured.fr> <48f61cab.15528c0a.2725.2676@mx.google.com> <48F64C34.70800@pingoured.fr> Message-ID: Hi Pierre, It'll be a mixture - some of the 45 will be providers who never intended their services to be "live", but registered them in the live registry anyway. Others are providers who have moved away from their institutes and the services have gone offline and they forgot to de-register them. The moby 1.0 manuscript had ~42 authors, and these represent people who have either directly contributed code or have been involved in planning/funding the project. There are ~10 people worldwide who are actively contributing code at the moment (beyond the code required for services) there are 135 members of the moby-dev mailing list (developers), and 221 members on the moby-l mailing list (discussion). Hope that helps! M On Wed, 15 Oct 2008 13:01:56 -0700, Pierre-Yves Chibon wrote: > Edward Kawas wrote: >> Hi Pierre, >> Here are some stats for services (and providers) >> http://moby.ucalgary.ca/moby/ValidateService?getStats=true > > Thanks a lot for your quick answer. > > I am a bit surprise by these results: > > "There are 92 service providers, with at least one registered service, > registered with this registry. > Of these service providers, there are 45 that don't have at least one > working service." > > Those 45 services providers are they in the testing repository or are > there services really not working ? > > Could you help me on the part concerning the development ? (Number of > developers to the core) > > > Thanks again for your help, > > Best regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Oct 16 13:04:01 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 16 Oct 2008 06:04:01 -0700 Subject: [MOBY-dev] Some stats In-Reply-To: <48F64C34.70800@pingoured.fr> References: <48F6187C.8010108@pingoured.fr> <48f61cab.15528c0a.2725.2676@mx.google.com> <48F64C34.70800@pingoured.fr> Message-ID: <48f73bca.02578c0a.5968.6db3@mx.google.com> Hi Pierre, Those 45 that don't have any working services may be old service providers that no longer have any registered services or their services really no longer work (respond to a ping, etc). Perhaps Mark can help you with your second question. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: October-15-08 1:02 PM To: Core developer announcements Subject: Re: [MOBY-dev] Some stats Edward Kawas wrote: > Hi Pierre, > > Here are some stats for services (and providers) > http://moby.ucalgary.ca/moby/ValidateService?getStats=true Thanks a lot for your quick answer. I am a bit surprise by these results: "There are 92 service providers, with at least one registered service, registered with this registry. Of these service providers, there are 45 that don't have at least one working service." Those 45 services providers are they in the testing repository or are there services really not working ? Could you help me on the part concerning the development ? (Number of developers to the core) Thanks again for your help, Best regards, Pierre _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From martin.senger at gmail.com Wed Oct 22 05:09:33 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 22 Oct 2008 06:09:33 +0100 Subject: [MOBY-dev] what license is BioMoby and jMoby? Message-ID: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> I have got this question from a jMoby user: I know that BioMoby is an open source project. Could you tell me which > license is used to generate jMoby Code? > and I found that I did not know how to answer. Do we have anywhere such policy? I personally usually used the Apache license - but I have not expressed it verbally in any of the jMoby code. I would like to do it now - and even though I am planning to add it only to the Java sources I wrote myself I need some consensus from the others. So what is your opinion? Thanks, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From sneumann at ipb-halle.de Wed Oct 22 06:48:23 2008 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Wed, 22 Oct 2008 08:48:23 +0200 Subject: [MOBY-dev] what license is BioMoby and jMoby? In-Reply-To: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> References: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> Message-ID: <1224658103.7986.350.camel@lathan.ipb-sub.ipb-halle.de> On Wed, 2008-10-22 at 06:09 +0100, Martin Senger wrote: > I know that BioMoby is an open source project. Could you tell me which > > license is used to generate jMoby Code? A proper license audit would also involve checking the myriad of licenses pulled in via the maven repository, and check their compatibility. A useful starting point is the fedora compatibility matrix towards the end of http://fedoraproject.org/wiki/Licensing Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From Dominique.Jeannin at avignon.inra.fr Wed Oct 22 09:07:51 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 22 Oct 2008 11:07:51 +0200 Subject: [MOBY-dev] ant install crashes Message-ID: <48FEED67.2010403@avignon.inra.fr> Hello I updated the jMoby project by CVS, I launched the "ant install" command right after and I have just got this compilation error : [...] compile-datatypes: [javac] Compiling 834 source files to /home/gafl/djeannin/workspace/jMoby/build/others/datatypes [javac] /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithObjectValues.java:107: getMoby_values() in org.biomoby.shared.datatypes.GCP_FeatureWithObjectValues cannot override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] [javac] required: org.biomoby.shared.datatypes.GCP_Value[] [javac] public GCP_SimpleIdentifier[] getMoby_values() { [javac] ^ [javac] /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithSimpleValues.java:93: getMoby_values() in org.biomoby.shared.datatypes.GCP_FeatureWithSimpleValues cannot override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.MobyString [javac] required: org.biomoby.shared.datatypes.GCP_Value[] [javac] public MobyString getMoby_values() { [javac] ^ [javac] /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FullBiblioReference.java:121: getMoby_metaData() in org.biomoby.shared.datatypes.GCP_FullBiblioReference cannot override getMoby_metaData() in org.biomoby.shared.datatypes.GCP_BiblioReference; attempting to use incompatible return type [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] [javac] required: org.biomoby.shared.datatypes.GCP_SimpleFeature [javac] public GCP_SimpleIdentifier[] getMoby_metaData() { [javac] ^ [javac] 3 errors BUILD FAILED /home/gafl/djeannin/workspace/jMoby/xmls/install.xml:114: The following error occurred while executing this line: /home/gafl/djeannin/workspace/jMoby/xmls/mosesBuild.xml:286: Compile failed; see the compiler error output for details. Total time: 2 minutes 2 seconds Has anyone seen this before ? Best regards, Dominique From martin.senger at gmail.com Wed Oct 22 09:28:48 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 22 Oct 2008 10:28:48 +0100 Subject: [MOBY-dev] ant install crashes In-Reply-To: <48FEED67.2010403@avignon.inra.fr> References: <48FEED67.2010403@avignon.inra.fr> Message-ID: <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> I think that the problem may happen when you have previously generated Moses datatypes and/or skeletons - and when they have since changed in the registry. The 'ant install' should take care about removing them - but it perhaps does not now. I will check it later today - and if I find that this is the case I will update the 'ant install' appropriately. You can try it now by removing manually directories 'generated/datatypes/' and 'generated/skeletons/' and running 'ant install' again. Does it work now? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From Dominique.Jeannin at avignon.inra.fr Wed Oct 22 09:40:49 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 22 Oct 2008 11:40:49 +0200 Subject: [MOBY-dev] ant install crashes In-Reply-To: <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> References: <48FEED67.2010403@avignon.inra.fr> <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> Message-ID: <48FEF521.8090905@avignon.inra.fr> Martin Senger a ?crit : > I think that the problem may happen when you have previously generated Moses > datatypes and/or skeletons - and when they have since changed in the > registry. The 'ant install' should take care about removing them - but it > perhaps does not now. I will check it later today - and if I find that this > is the case I will update the 'ant install' appropriately. You can try it > now by removing manually directories 'generated/datatypes/' and > 'generated/skeletons/' and running 'ant install' again. Does it work now? > > Cheers, > Martin > > Thanks for the reply. It works. I remove the two folders, whereas my office mate run "ant clean" and "ant clean-datatypes", both method worked. Thanks again. Best regards, Dominique From groscurt at mpiz-koeln.mpg.de Wed Oct 22 09:41:06 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 22 Oct 2008 11:41:06 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <48FEED67.2010403@avignon.inra.fr> References: <48FEED67.2010403@avignon.inra.fr> Message-ID: <48FEF532.6080804@mpiz-koeln.mpg.de> Hi, first you dont need to do an "ant install" after you made an update. the install feature is only used for the first time you work with jmoby. second i just made an update and run ant install and dont get that error - and for me it was 739 datatypes to compile not 834.... this made me think and i had a look at the generated datatypes. On the production central we have a lot of test__xxx datatypes which is weird on the production on the first place funnily they are all registered by "sarah.connor at treminator.com" ... so - do the machines have taken over now ? Are we at a point someone made a bad joke or do have bots taken over the registration ;-) ? Cheers andreas Dominique Jeannin wrote: > Hello > > I updated the jMoby project by CVS, I launched the "ant install" > command right after and I have just got this compilation error : > > [...] > compile-datatypes: > [javac] Compiling 834 source files to > /home/gafl/djeannin/workspace/jMoby/build/others/datatypes > [javac] > /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithObjectValues.java:107: > getMoby_values() in > org.biomoby.shared.datatypes.GCP_FeatureWithObjectValues cannot > override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; > attempting to use incompatible return type > [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] > [javac] required: org.biomoby.shared.datatypes.GCP_Value[] > [javac] public GCP_SimpleIdentifier[] getMoby_values() { > [javac] ^ > [javac] > /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FeatureWithSimpleValues.java:93: > getMoby_values() in > org.biomoby.shared.datatypes.GCP_FeatureWithSimpleValues cannot > override getMoby_values() in org.biomoby.shared.datatypes.GCP_Feature; > attempting to use incompatible return type > [javac] found : org.biomoby.shared.datatypes.MobyString > [javac] required: org.biomoby.shared.datatypes.GCP_Value[] > [javac] public MobyString getMoby_values() { > [javac] ^ > [javac] > /home/gafl/djeannin/workspace/jMoby/generated/datatypes/org/biomoby/shared/datatypes/GCP_FullBiblioReference.java:121: > getMoby_metaData() in > org.biomoby.shared.datatypes.GCP_FullBiblioReference cannot override > getMoby_metaData() in > org.biomoby.shared.datatypes.GCP_BiblioReference; attempting to use > incompatible return type > [javac] found : org.biomoby.shared.datatypes.GCP_SimpleIdentifier[] > [javac] required: org.biomoby.shared.datatypes.GCP_SimpleFeature > [javac] public GCP_SimpleIdentifier[] getMoby_metaData() { > [javac] ^ > [javac] 3 errors > > BUILD FAILED > /home/gafl/djeannin/workspace/jMoby/xmls/install.xml:114: The > following error occurred while executing this line: > /home/gafl/djeannin/workspace/jMoby/xmls/mosesBuild.xml:286: Compile > failed; see the compiler error output for details. > > Total time: 2 minutes 2 seconds > > Has anyone seen this before ? > > Best regards, > > Dominique > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From py at pingoured.fr Wed Oct 22 11:09:19 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 22 Oct 2008 13:09:19 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <48FEF532.6080804@mpiz-koeln.mpg.de> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> Message-ID: <48FF09DF.6080003@pingoured.fr> Andreas Groscurth wrote: > Hi, > > first you dont need to do an "ant install" after you made an update. the > install feature is only used for the first time you work with jmoby. > > second i just made an update and run ant install and dont get that error > - and for me it was 739 datatypes to compile not 834.... > > > this made me think and i had a look at the generated datatypes. On the > production central we have a lot of test__xxx datatypes which is weird > on the production on the first place > > funnily they are all registered by "sarah.connor at treminator.com" ... so > - do the machines have taken over now ? > > Are we at a point someone made a bad joke or do have bots taken over the > registration ;-) ? To me the datatype "testHydrophobicity" and its children are even worse to me... (ze.ze does not exist on google on the contrary to treminator.com which does not seems to be very biology related that's true...) But I think this is another topic. Regards, Pierre From py at pingoured.fr Wed Oct 22 12:01:46 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 22 Oct 2008 14:01:46 +0200 Subject: [MOBY-dev] dashboard build failed Message-ID: <48FF162A.70507@pingoured.fr> Dear all, Quite often when I run "ant dashboard" I got a Build Failed (see at the end of this mail for the full example). I normally get rid of it by doing an 'ant all'. I have looked a bit on the BioMoby website, I found the FAQ for the dashboard [1] but there seem to be nothing about such issue. Is that a known issue ? Is there a common/quick way to fix it (else than 'ant all') ? Anyway I think that it might be interesting to add this in the FAQ. Thanks for your help, Regards, Pierre [1] http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html ------------------------------------------------------------------------ $ ant dashboard Buildfile: build.xml checkmaven: initmaven: init: config: compile: moses-init: samples-init: dashboard-init: dashboard-config: dashboard: [Dashboard] Exception in thread "main" java.lang.Error: Unresolved compilation problem: [Dashboard] [Dashboard] at org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:985) BUILD FAILED /home/pierrey/workspace/jMoby/xmls/dashboardBuild.xml:50: Java returned: 1 From groscurt at mpiz-koeln.mpg.de Wed Oct 22 12:12:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 22 Oct 2008 14:12:55 +0200 Subject: [MOBY-dev] dashboard build failed In-Reply-To: <48FF162A.70507@pingoured.fr> References: <48FF162A.70507@pingoured.fr> Message-ID: <48FF18C7.3040802@mpiz-koeln.mpg.de> do you change anything in the code ? this is a normal java error that you have errors in your source code and therfore it cannot be compiled. As this is not the case with the code from jmoby in the cvs this error can only come up if you change something in the code ?! cheers Andreas Pierre-Yves Chibon wrote: > Dear all, > > Quite often when I run "ant dashboard" I got a Build Failed (see at > the end of this mail for the full example). I normally get rid of it > by doing an 'ant all'. > > I have looked a bit on the BioMoby website, I found the FAQ for the > dashboard [1] but there seem to be nothing about such issue. > > Is that a known issue ? Is there a common/quick way to fix it (else > than 'ant all') ? > > Anyway I think that it might be interesting to add this in the FAQ. > > Thanks for your help, > > Regards, > > Pierre > > [1] > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html > > > ------------------------------------------------------------------------ > $ ant dashboard > Buildfile: build.xml > > checkmaven: > > initmaven: > > init: > > config: > > compile: > > moses-init: > > samples-init: > > dashboard-init: > > dashboard-config: > > dashboard: > [Dashboard] Exception in thread "main" java.lang.Error: Unresolved > compilation problem: > [Dashboard] > [Dashboard] at > org.biomoby.service.dashboard.Dashboard.main(Dashboard.java:985) > > BUILD FAILED > /home/pierrey/workspace/jMoby/xmls/dashboardBuild.xml:50: Java > returned: 1 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From martin.senger at gmail.com Wed Oct 22 21:33:18 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Oct 2008 05:33:18 +0800 Subject: [MOBY-dev] dashboard build failed In-Reply-To: <48FF162A.70507@pingoured.fr> References: <48FF162A.70507@pingoured.fr> Message-ID: <4d93f07c0810221433n1be41009m4afc9d17a4ed5c08@mail.gmail.com> > Is that a known issue ? Is there a common/quick way to fix it (else than > 'ant all') ? No, it is not a known issue. The probable cause is that you have some stale class on your classpath - which may happen (I think) when/if you change java compiler. The fix should be to clean everything (ant clean) and then do it again (ant dashboard). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Thu Oct 23 01:20:28 2008 From: markw at illuminae.com (Mark) Date: Wed, 22 Oct 2008 18:20:28 -0700 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <48FF09DF.6080003@pingoured.fr> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: Sorry, it's been a LONG time since I curated the production registry. By the "rules" of the production registry, I have assumed the authority to delete any service or ontology node that includes the word 'test' in its name or it's service description (though I have to be careful, since 'test' is a legitimate analytical activity, so I do take care when I do this!)... I hate doing it, though, since I know that sometimes people use the production registry for workshops, etc, and I might be deleting something that is really actively being used (even if only for a couple of days...) I'll go through the registry in the next few days and clean it up. Mark On Wed, 22 Oct 2008 04:09:19 -0700, Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> first you dont need to do an "ant install" after you made an update. >> the install feature is only used for the first time you work with jmoby. >> second i just made an update and run ant install and dont get that >> error - and for me it was 739 datatypes to compile not 834.... >> this made me think and i had a look at the generated datatypes. On >> the production central we have a lot of test__xxx datatypes which is >> weird on the production on the first place >> funnily they are all registered by "sarah.connor at treminator.com" ... >> so - do the machines have taken over now ? >> Are we at a point someone made a bad joke or do have bots taken over >> the registration ;-) ? > > To me the datatype "testHydrophobicity" and its children are even worse > to me... (ze.ze does not exist on google on the contrary to > treminator.com which does not seems to be very biology related that's > true...) > > But I think this is another topic. > > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Oct 23 01:27:18 2008 From: markw at illuminae.com (Mark) Date: Wed, 22 Oct 2008 18:27:18 -0700 Subject: [MOBY-dev] what license is BioMoby and jMoby? In-Reply-To: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> References: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> Message-ID: I believe I am using the Artistic License for the Perl code. M On Tue, 21 Oct 2008 22:09:33 -0700, Martin Senger wrote: > I have got this question from a jMoby user: > > I know that BioMoby is an open source project. Could you tell me which >> license is used to generate jMoby Code? >> > > and I found that I did not know how to answer. Do we have anywhere such > policy? I personally usually used the Apache license - but I have not > expressed it verbally in any of the jMoby code. I would like to do it > now - > and even though I am planning to add it only to the Java sources I wrote > myself I need some consensus from the others. So what is your opinion? > > Thanks, > Martin > From martin.senger at gmail.com Thu Oct 23 01:27:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Oct 2008 09:27:21 +0800 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> > to delete any service or ontology node that includes the word 'test' in its > name or it's service description Please let me remind you that the last agreement was that services with the URL pointing to a localhost will stay, as well. [The clients creating statistics should ignore such services.] Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Thu Oct 23 01:32:34 2008 From: markw at illuminae.com (Mark) Date: Wed, 22 Oct 2008 18:32:34 -0700 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> Message-ID: right :-) On Wed, 22 Oct 2008 18:27:21 -0700, Martin Senger wrote: >> to delete any service or ontology node that includes the word 'test' in >> its >> name or it's service description > > > Please let me remind you that the last agreement was that services with > the > URL pointing to a localhost will stay, as well. [The clients creating > statistics should ignore such services.] > > Cheers, > Martin > From sneumann at ipb-halle.de Thu Oct 23 07:30:23 2008 From: sneumann at ipb-halle.de (Steffen Neumann) Date: Thu, 23 Oct 2008 09:30:23 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: <1224747026.7986.365.camel@lathan.ipb-sub.ipb-halle.de> On Wed, 2008-10-22 at 18:20 -0700, Mark wrote: > I'll go through the registry in the next few days and clean it up. Any way of keeping a Least-recently-used list or (access statistics in general) for service queries to the central registry ? Then a $(grep test) service unused for >1 year (or whatever) can go without second thought. In addition, we could have some (mildly misleading) statistics about the most heavily used services, like a "hall of fame". Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 From py at pingoured.fr Thu Oct 23 07:41:41 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 23 Oct 2008 09:41:41 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> Message-ID: <49002AB5.9000106@pingoured.fr> Mark wrote: > I hate doing it, though, since I know that sometimes people > use the production registry for workshops, etc, and I might be deleting > something that is really actively being used (even if only for a couple > of days...) I am getting confused there, isn't it the goal of the testing registry ? Maybe I misunderstood the difference between the production registry and the testing registry, can someone give me some light about this ? Thanks, Regards, Pierre From groscurt at mpiz-koeln.mpg.de Thu Oct 23 08:09:36 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 23 Oct 2008 10:09:36 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <49002AB5.9000106@pingoured.fr> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <49002AB5.9000106@pingoured.fr> Message-ID: <49003140.4090208@mpiz-koeln.mpg.de> In my point of view you are absolutely right... the test central should be used for everything which is non productional. This includes demonstrating the registry at workshops or the first steps one is deploying web services. The production should only be used for stable and fully working services. i think the problem is that you cant force people to do so and you cant prevent that. cheers andreas Pierre-Yves Chibon wrote: > Mark wrote: >> I hate doing it, though, since I know that sometimes people use >> the production registry for workshops, etc, and I might be deleting >> something that is really actively being used (even if only for a >> couple of days...) > > I am getting confused there, isn't it the goal of the testing registry ? > > Maybe I misunderstood the difference between the production registry > and the testing registry, can someone give me some light about this ? > > Thanks, > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From groscurt at mpiz-koeln.mpg.de Thu Oct 23 08:12:28 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 23 Oct 2008 10:12:28 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <1224747026.7986.365.camel@lathan.ipb-sub.ipb-halle.de> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <1224747026.7986.365.camel@lathan.ipb-sub.ipb-halle.de> Message-ID: <490031EC.8080202@mpiz-koeln.mpg.de> The problem of course of the moby registry is that querying a service does not mean calling it also. so a service which would get into the Hall of Fame because it was often asked could never have been called. So in my point of view this Hall of Fame could be misleading as also the number of calls do not say anything about the quality of the service. But i admit, it would be nice to see what services are asked frequently ;-) Cheers Andreas Steffen Neumann wrote: > On Wed, 2008-10-22 at 18:20 -0700, Mark wrote: > >> I'll go through the registry in the next few days and clean it up. >> > Any way of keeping a Least-recently-used list > or (access statistics in general) for service queries > to the central registry ? > > Then a $(grep test) service unused for >1 year (or whatever) > can go without second thought. In addition, we could have > some (mildly misleading) statistics about the most heavily > used services, like a "hall of fame". > > Yours, > Steffen > > -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From groscurt at mpiz-koeln.mpg.de Thu Oct 23 08:13:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 23 Oct 2008 10:13:09 +0200 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <4d93f07c0810221827r66f45631y432bfeca296227e8@mail.gmail.com> Message-ID: <49003215.4000305@mpiz-koeln.mpg.de> So service registered at production with pointing to a localhost do remain there ? is this correct ? and if so, why ? cheers andreas Mark wrote: > right :-) > > > > On Wed, 22 Oct 2008 18:27:21 -0700, Martin Senger > wrote: > >>> to delete any service or ontology node that includes the word 'test' >>> in its >>> name or it's service description >> >> >> Please let me remind you that the last agreement was that services >> with the >> URL pointing to a localhost will stay, as well. [The clients creating >> statistics should ignore such services.] >> >> Cheers, >> Martin >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- ===================================================== Dipl. Bioinf. Andreas Groscurth Bioinformatics Software Developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ===================================================== From martin.senger at gmail.com Thu Oct 23 08:23:21 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 23 Oct 2008 16:23:21 +0800 Subject: [MOBY-dev] ant install crashes... does moby have bots? In-Reply-To: <49003140.4090208@mpiz-koeln.mpg.de> References: <48FEED67.2010403@avignon.inra.fr> <48FEF532.6080804@mpiz-koeln.mpg.de> <48FF09DF.6080003@pingoured.fr> <49002AB5.9000106@pingoured.fr> <49003140.4090208@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0810230123u7deee79bib38f5df79a09c74@mail.gmail.com> > In my point of view you are absolutely right... the test central should be > used for everything which is non productional. In theory, it is right. But from my experiences, the duplication of moby registries has been pain in the neck. Because moby does not have (yet?) a proper and well defined notion of registry mirroring or registry federation, registering the same entities twice in two (or more) different registries may cause problems. I am talking from the experience of the Canadian and IRRI registry. In our project, we are using quite a huge set of data types and they can cause incompabilites if they are not mirrored exactly. And doing so is not easy for a big project. Bottom line is that the same entity (such as a data type) should have the same LSID in both registries. But it does not - because these registries do not know about each other. >From this reasons, I still prefer to allow having services registered with the localhost in the main registry. This way I do not step on my own toes if I need to have different versions of the same entity in the main and in the testing (or IRRI, in my case) registry. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Oct 24 00:40:04 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 24 Oct 2008 08:40:04 +0800 Subject: [MOBY-dev] what license is BioMoby and jMoby? In-Reply-To: References: <4d93f07c0810212209g31988541v4ec949b785b150db@mail.gmail.com> Message-ID: <4d93f07c0810231740x2ca07f78k68ab40147fa65c4e@mail.gmail.com> I have updated jMoby documentation (it will take couple of hours to propagate there) with the following: What license jMoby uses: Unless individual jMoby parts define it differently, the code is licensed under the Apache License. And the LICENSE file contains: Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Fri Oct 24 01:42:27 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 24 Oct 2008 09:42:27 +0800 Subject: [MOBY-dev] ant install crashes In-Reply-To: <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> References: <48FEED67.2010403@avignon.inra.fr> <4d93f07c0810220228v2e8ce256o716d2e241431d4f0@mail.gmail.com> Message-ID: <4d93f07c0810231842s19a74aedl39dbe210d3b1ea28@mail.gmail.com> > The 'ant install' should take care about removing them - but it perhaps > does not now. I will check it later today I have fixed the 'ant install'. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From soiland-reyes at cs.manchester.ac.uk Fri Oct 24 10:14:13 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 24 Oct 2008 11:14:13 +0100 Subject: [MOBY-dev] /home/senger reference in deployed log4j.properties Message-ID: Hi! jmoby-1.1.1.jar from http://biomoby.org/m2repo/org/biomoby/jmoby/1.1.1/ seems to contain a log4j.properties file that includes lines like: log4j.appender.A2=org.apache.log4j.FileAppender log4j.appender.A2.file=/home/senger/moby-live/Java/jMoby.log log4j.appender.A2=org.apache.log4j.RollingFileAppender log4j.appender.A2.MaxFileSize=500KB log4j.appender.A2.MaxBackupIndex=9 log4j.appender.A2.layout=org.apache.log4j.PatternLayout log4j.appender.A2.layout.ConversionPattern=%d{ISO8601} %-4r [%t] %-5p %c{1} %x- %m%n This causes various error messages about /home/senger/moby-live not existing when trying to use jmoby in Taverna's unit tests. Is it possible to not include this log4j property file and let whoever uses jmoby decide what kind of logging to do..? -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From martin.senger at gmail.com Fri Oct 24 10:31:31 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 24 Oct 2008 18:31:31 +0800 Subject: [MOBY-dev] /home/senger reference in deployed log4j.properties In-Reply-To: References: Message-ID: <4d93f07c0810240331y7691b231lf52982ea85bd0856@mail.gmail.com> > log4j.appender.A2.file=/home/senger/moby-live/Java/jMoby.log This is obviously wrong. Actually, IMO, in the jar file deployed to a maven repository should be no log4j.properties file at all. Or, at least, it should have a property pointing to a log file that could be set from outside (as jMoby has it in its war files deployed to Tomcat). I will look at it. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Sat Oct 25 14:31:42 2008 From: martin.senger at gmail.com (Martin Senger) Date: Sat, 25 Oct 2008 22:31:42 +0800 Subject: [MOBY-dev] /home/senger reference in deployed log4j.properties In-Reply-To: <4d93f07c0810240331y7691b231lf52982ea85bd0856@mail.gmail.com> References: <4d93f07c0810240331y7691b231lf52982ea85bd0856@mail.gmail.com> Message-ID: <4d93f07c0810250731l1f51cbf7x2b1b5591d1e55c73@mail.gmail.com> > > log4j.appender.A2.file=/home/senger/moby-live/Java/jMoby.log > > > This is obviously wrong. Actually, IMO, in the jar file deployed to a maven > repository should be no log4j.properties file at all. > I have fixed this, committed - but I have not yet deployed a new jMoby jar file to Maven - because I am waiting for some further advices how to do define dependencies on axis. I will inform you when a new deployed version of jMoby is out. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Wed Oct 29 17:11:25 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 29 Oct 2008 11:11:25 -0600 Subject: [MOBY-dev] Ontology XML problems again? Message-ID: <4908993D.8060305@ucalgary.ca> Am I the only one getting a "premature end of file" when updating the registry cache in Dashboard? From edward.kawas at gmail.com Wed Oct 29 17:32:03 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 29 Oct 2008 10:32:03 -0700 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <4908993D.8060305@ucalgary.ca> References: <4908993D.8060305@ucalgary.ca> Message-ID: <49089e1c.09d7720a.6964.fffffc72@mx.google.com> For which registry? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: October-29-08 10:11 AM To: mobydev Subject: [MOBY-dev] Ontology XML problems again? Am I the only one getting a "premature end of file" when updating the registry cache in Dashboard? _______________________________________________ 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 Oct 29 17:32:03 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 29 Oct 2008 10:32:03 -0700 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <4908993D.8060305@ucalgary.ca> References: <4908993D.8060305@ucalgary.ca> Message-ID: <49089e1c.09d7720a.6964.fffffc72@mx.google.com> For which registry? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: October-29-08 10:11 AM To: mobydev Subject: [MOBY-dev] Ontology XML problems again? Am I the only one getting a "premature end of file" when updating the registry cache in Dashboard? _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Oct 29 17:34:58 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 29 Oct 2008 11:34:58 -0600 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <49089e1c.09d7720a.6964.fffffc72@mx.google.com> References: <4908993D.8060305@ucalgary.ca> <49089e1c.09d7720a.6964.fffffc72@mx.google.com> Message-ID: <49089EC2.4040602@ucalgary.ca> The default. Edward Kawas wrote: > For which registry? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: October-29-08 10:11 AM > To: mobydev > Subject: [MOBY-dev] Ontology XML problems again? > > Am I the only one getting a "premature end of file" when updating the > registry cache in Dashboard? > _______________________________________________ > 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 Oct 29 18:15:39 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 29 Oct 2008 11:15:39 -0700 Subject: [MOBY-dev] Ontology XML problems again? In-Reply-To: <49089EC2.4040602@ucalgary.ca> References: <4908993D.8060305@ucalgary.ca> <49089e1c.09d7720a.6964.fffffc72@mx.google.com> <49089EC2.4040602@ucalgary.ca> Message-ID: <4908a856.1c048e0a.2c9d.537e@mx.google.com> Works for me ... try clearing your cache. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: October-29-08 10:35 AM To: Core developer announcements Subject: Re: [MOBY-dev] Ontology XML problems again? The default. Edward Kawas wrote: > For which registry? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon > Sent: October-29-08 10:11 AM > To: mobydev > Subject: [MOBY-dev] Ontology XML problems again? > > Am I the only one getting a "premature end of file" when updating the > registry cache in Dashboard? > _______________________________________________ > 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 kenny.billiau at psb.ugent.be Thu Oct 30 13:32:53 2008 From: kenny.billiau at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 14:32:53 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever Message-ID: Hi, this is my first question, so I hope I'm sending this to the right maillinglist. I recently installed the BioMoby packages and generated my service using the moses-* perl scripts. So myCache is filled without problems and I'm using the testing registry. I'm using perl 5.8.5. Distribution E/EK/EKAWAS/MOBY-1.05.tar.gz Distribution E/EK/EKAWAS/MOBY-Client-1.02.tar.gz Distribution E/EK/EKAWAS/MOSES-MOBY-0.86.tar.gz I can provide the xml files I use to test these services too. $ moses-generate-services.pl psb.ugent.be $ moses-generate-services.pl -b psb.ugent.be All works well. I'm only interested in the BogasGetRegion and the BogasSaveRegion. If I test BogasGetRegion with following command (1), all works fine: $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasGetRegion ~/tmp/moby.xml $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasSaveRegion ~/tmp/mobysave.xml But If I test BogasSaveRegion (2), something goes seriously wrong. The command as above is used, and the response from command (1) is fed to this one. Nothing is done with the results in BogasSaveRegion, I simply generated the perl modules and send the xml file to it. This is the error message: ===================================== --- TRANSPORT ERROR --- 500 read timeout syntax error at line 1, column 0, byte 0 at /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/XML/Parser.pm line 187 500 read timeout ===================================== The timeout for apache is set to 10 minutes, but the transport error occures after 180secs. If I truncate the response from (1) enough, i get a response for (2) back within those 180 secs. But still, as the XML file from (1) only is 250KB, it seems unreasonably long. If I look at what get's into to log, the script seems to do all it's number crunching in the generated Base.pm (here called BogasSaveRegionBase.pm). Generating the parser works, parsing itself goes slow beyong belief: $self->default_throw_with_stack (0) unless $in_testing_mode; my $in_package; eval { my $parser = $self->create_parser( lowestKnownDataTypes => { 'locus_id' => 'String','date' => 'DateTime','region' => 'Region', }, loadDataTypes => [ qw( String DateTime Region Boolean ) ] ) ; # does not get beyond this point in a reasonable amount of time. $in_package = $parser->parse ( method => $in_testing_mode ? 'file' : 'string', data => $data ) ; }; I tried to put the webservice through dprof, with these results (unfortunatly, Apache::DProf seems to die on me, but invoking the mod_perl envirnment with -d:DProf works): [davebowman at hal2000 ~]$ dprofpp -F /tmp/tmon.out XML:: LibXML::parse_string has 1 unstacked calls in outer XML:: SAX::Base::end_element has 1 unstacked calls in outer BOGAS::Moby::BogasSaveRegionBase::BogasSaveRegion has 1 unstacked calls in outer XML::SAX::Base::parse has 1 unstacked calls in outer Exporter::Heavy::heavy_export has 16 unstacked calls in outer Config::Simple::import_from has 1 unstacked calls in outer SOAP::Server::handle has 1 unstacked calls in outer MOSES::MOBY:: Parser::callMethod has 1 unstacked calls in outer MOSES::MOBY:: Base::as_string has 1 unstacked calls in outer Config::Simple::verbose has 1 unstacked calls in outer utf8::AUTOLOAD has -1 unstacked calls in outer HTTP::Message::__ANON__ has 3 unstacked calls in outer Dumpvalue::unwrap has 8 unstacked calls in outer XML::LibXML::_parse_sax_string has 1 unstacked calls in outer MOSES::MOBY::Parser::parse has 1 unstacked calls in outer XML::LibXML::SAX::_parse has 1 unstacked calls in outer Config::Simple::vars has 1 unstacked calls in outer MOSES::MOBY::Parser::end_element has 1 unstacked calls in outer SOAP::Transport::HTTP::Server::handle has 1 unstacked calls in outer AutoLoader::AUTOLOAD has -3 unstacked calls in outer XML::SAX::Base::parse_string has 1 unstacked calls in outer Fcntl::AUTOLOAD has -6 unstacked calls in outer Dumpvalue:: dumpValue has 1 unstacked calls in outer Dumpvalue:: DumpElem has 7 unstacked calls in outer HTTP::Message::AUTOLOAD has -3 unstacked calls in outer Fcntl::__ANON__ has 6 unstacked calls in outer XML::SAX::Base::__ANON__ has 1 unstacked calls in outer Exporter::export has -16 unstacked calls in outer utf8::SWASHNEW has 1 unstacked calls in outer SOAP::Transport::HTTP::CGI::handle has 1 unstacked calls in outer XML::LibXML::SAX::_parse_string has 1 unstacked calls in outer Faking 32 exit timestamp(s). Total Elapsed Time = -34.8210 Seconds User+System Time = 0 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 0.00 140.6 140.64 486940 0.0003 0.0003 IO::Scalar::print 0.00 3.553 3.975 449046 0.0000 0.0000 Dumpvalue::stringify 0.00 2.551 2.551 574503 0.0000 0.0000 File::Spec::Unix::canonpath 0.00 2.005 147.07 232696 0.0000 0.0006 Dumpvalue::unwrap 0.00 1.177 1.177 423816 0.0000 0.0000 overload::mycan 0.00 1.019 1.019 743 0.0014 0.0014 MOSES::MOBY::Cache::Registries::in it 0.00 0.959 3.885 742 0.0013 0.0052 MOSES::MOBY::Generators::Utils::fi nd_file 0.00 0.581 2.989 286495 0.0000 0.0000 File::Spec::Unix::catfile 0.00 0.450 146.88 230026 0.0000 0.0006 Dumpvalue::DumpElem 0.00 0.367 0.607 56930 0.0000 0.0000 MOSES::MOBY::Base::__ANON__ 0.00 0.257 1.876 1925 0.0001 0.0010 MOSES::MOBY::Cache::Central::get_d atatype 0.00 0.246 0.246 1925 0.0001 0.0001 MOSES::MOBY::Cache::Central::_clea n 0.00 0.234 155.05 1 0.2342 155.05 XML::LibXML::_parse_sax_string 0.00 0.218 0.218 11242 0.0000 0.0000 XML::LibXML::Node::_childNodes 0.00 0.143 0.143 108644 0.0000 0.0000 XML::LibXML::Node::nodeName These results don't make me anymuch wiser. I tried switching xml parsers by changing then in the mobyservices.cfg, with no result. Does anyone know what the problem is? Or how to debug this? Am I missing something obvious here? -Kenny ================================================================== Kenny Billiau Web Developer 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 kenny.billiau at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== From edward.kawas at gmail.com Thu Oct 30 14:12:05 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 07:12:05 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: References: Message-ID: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> Hi, This is the right list! Could you send me the XML for your second service? 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 Kenny Billiau Sent: October-30-08 6:33 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] XML parsing takes forever Hi, this is my first question, so I hope I'm sending this to the right maillinglist. I recently installed the BioMoby packages and generated my service using the moses-* perl scripts. So myCache is filled without problems and I'm using the testing registry. I'm using perl 5.8.5. Distribution E/EK/EKAWAS/MOBY-1.05.tar.gz Distribution E/EK/EKAWAS/MOBY-Client-1.02.tar.gz Distribution E/EK/EKAWAS/MOSES-MOBY-0.86.tar.gz I can provide the xml files I use to test these services too. $ moses-generate-services.pl psb.ugent.be $ moses-generate-services.pl -b psb.ugent.be All works well. I'm only interested in the BogasGetRegion and the BogasSaveRegion. If I test BogasGetRegion with following command (1), all works fine: $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasGetRegion ~/tmp/moby.xml $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasSaveRegion ~/tmp/mobysave.xml But If I test BogasSaveRegion (2), something goes seriously wrong. The command as above is used, and the response from command (1) is fed to this one. Nothing is done with the results in BogasSaveRegion, I simply generated the perl modules and send the xml file to it. This is the error message: ===================================== --- TRANSPORT ERROR --- 500 read timeout syntax error at line 1, column 0, byte 0 at /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/XML/Parser.pm line 187 500 read timeout ===================================== The timeout for apache is set to 10 minutes, but the transport error occures after 180secs. If I truncate the response from (1) enough, i get a response for (2) back within those 180 secs. But still, as the XML file from (1) only is 250KB, it seems unreasonably long. If I look at what get's into to log, the script seems to do all it's number crunching in the generated Base.pm (here called BogasSaveRegionBase.pm). Generating the parser works, parsing itself goes slow beyong belief: $self->default_throw_with_stack (0) unless $in_testing_mode; my $in_package; eval { my $parser = $self->create_parser( lowestKnownDataTypes => { 'locus_id' => 'String','date' => 'DateTime','region' => 'Region', }, loadDataTypes => [ qw( String DateTime Region Boolean ) ] ) ; # does not get beyond this point in a reasonable amount of time. $in_package = $parser->parse ( method => $in_testing_mode ? 'file' : 'string', data => $data ) ; }; I tried to put the webservice through dprof, with these results (unfortunatly, Apache::DProf seems to die on me, but invoking the mod_perl envirnment with -d:DProf works): [davebowman at hal2000 ~]$ dprofpp -F /tmp/tmon.out XML:: LibXML::parse_string has 1 unstacked calls in outer XML:: SAX::Base::end_element has 1 unstacked calls in outer BOGAS::Moby::BogasSaveRegionBase::BogasSaveRegion has 1 unstacked calls in outer XML::SAX::Base::parse has 1 unstacked calls in outer Exporter::Heavy::heavy_export has 16 unstacked calls in outer Config::Simple::import_from has 1 unstacked calls in outer SOAP::Server::handle has 1 unstacked calls in outer MOSES::MOBY:: Parser::callMethod has 1 unstacked calls in outer MOSES::MOBY:: Base::as_string has 1 unstacked calls in outer Config::Simple::verbose has 1 unstacked calls in outer utf8::AUTOLOAD has -1 unstacked calls in outer HTTP::Message::__ANON__ has 3 unstacked calls in outer Dumpvalue::unwrap has 8 unstacked calls in outer XML::LibXML::_parse_sax_string has 1 unstacked calls in outer MOSES::MOBY::Parser::parse has 1 unstacked calls in outer XML::LibXML::SAX::_parse has 1 unstacked calls in outer Config::Simple::vars has 1 unstacked calls in outer MOSES::MOBY::Parser::end_element has 1 unstacked calls in outer SOAP::Transport::HTTP::Server::handle has 1 unstacked calls in outer AutoLoader::AUTOLOAD has -3 unstacked calls in outer XML::SAX::Base::parse_string has 1 unstacked calls in outer Fcntl::AUTOLOAD has -6 unstacked calls in outer Dumpvalue:: dumpValue has 1 unstacked calls in outer Dumpvalue:: DumpElem has 7 unstacked calls in outer HTTP::Message::AUTOLOAD has -3 unstacked calls in outer Fcntl::__ANON__ has 6 unstacked calls in outer XML::SAX::Base::__ANON__ has 1 unstacked calls in outer Exporter::export has -16 unstacked calls in outer utf8::SWASHNEW has 1 unstacked calls in outer SOAP::Transport::HTTP::CGI::handle has 1 unstacked calls in outer XML::LibXML::SAX::_parse_string has 1 unstacked calls in outer Faking 32 exit timestamp(s). Total Elapsed Time = -34.8210 Seconds User+System Time = 0 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 0.00 140.6 140.64 486940 0.0003 0.0003 IO::Scalar::print 0.00 3.553 3.975 449046 0.0000 0.0000 Dumpvalue::stringify 0.00 2.551 2.551 574503 0.0000 0.0000 File::Spec::Unix::canonpath 0.00 2.005 147.07 232696 0.0000 0.0006 Dumpvalue::unwrap 0.00 1.177 1.177 423816 0.0000 0.0000 overload::mycan 0.00 1.019 1.019 743 0.0014 0.0014 MOSES::MOBY::Cache::Registries::in it 0.00 0.959 3.885 742 0.0013 0.0052 MOSES::MOBY::Generators::Utils::fi nd_file 0.00 0.581 2.989 286495 0.0000 0.0000 File::Spec::Unix::catfile 0.00 0.450 146.88 230026 0.0000 0.0006 Dumpvalue::DumpElem 0.00 0.367 0.607 56930 0.0000 0.0000 MOSES::MOBY::Base::__ANON__ 0.00 0.257 1.876 1925 0.0001 0.0010 MOSES::MOBY::Cache::Central::get_d atatype 0.00 0.246 0.246 1925 0.0001 0.0001 MOSES::MOBY::Cache::Central::_clea n 0.00 0.234 155.05 1 0.2342 155.05 XML::LibXML::_parse_sax_string 0.00 0.218 0.218 11242 0.0000 0.0000 XML::LibXML::Node::_childNodes 0.00 0.143 0.143 108644 0.0000 0.0000 XML::LibXML::Node::nodeName These results don't make me anymuch wiser. I tried switching xml parsers by changing then in the mobyservices.cfg, with no result. Does anyone know what the problem is? Or how to debug this? Am I missing something obvious here? -Kenny ================================================================== Kenny Billiau Web Developer 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 kenny.billiau at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From kebil at psb.ugent.be Thu Oct 30 12:30:08 2008 From: kebil at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 13:30:08 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <4908a856.1c048e0a.2c9d.537e@mx.google.com> References: <4908993D.8060305@ucalgary.ca> <49089e1c.09d7720a.6964.fffffc72@mx.google.com> <49089EC2.4040602@ucalgary.ca> <4908a856.1c048e0a.2c9d.537e@mx.google.com> Message-ID: Hi, this is my first question, so I hope I'm sending this to the right maillinglist. I recently installed the BioMoby packages and generated my service using the moses-* perl scripts. So myCache is filled without problems and I'm using the testing registry. I'm using perl 5.8.5. Distribution E/EK/EKAWAS/MOBY-1.05.tar.gz Distribution E/EK/EKAWAS/MOBY-Client-1.02.tar.gz Distribution E/EK/EKAWAS/MOSES-MOBY-0.86.tar.gz I can provide the xml files I use to test these services too. $ moses-generate-services.pl psb.ugent.be $ moses-generate-services.pl -b psb.ugent.be All works well. I'm only interested in the BogasGetRegion and the BogasSaveRegion. If I test BogasGetRegion with following command (1), all works fine: $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasGetRegion ~/tmp/moby.xml $ moses-testing-service.pl -e http://hal2000/sandbox/BOGAS_dev/trunk/www/ws/moby.pl BogasSaveRegion ~/tmp/mobysave.xml But If I test BogasSaveRegion (2), something goes seriously wrong. The command as above is used, and the response from command (1) is fed to this one. Nothing is done with the results in BogasSaveRegion, I simply generated the perl modules and send the xml file to it. This is the error message: ===================================== --- TRANSPORT ERROR --- 500 read timeout syntax error at line 1, column 0, byte 0 at /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi/XML/Parser.pm line 187 500 read timeout ===================================== The timeout for apache is set to 10 minutes, but the transport error occures after 180secs. If I truncate the response from (1) enough, i get a response for (2) back within those 180 secs. But still, as the XML file from (1) only is 250KB, it seems unreasonably long. If I look at what get's into to log, the script seems to do all it's number crunching in the generated Base.pm (here called BogasSaveRegionBase.pm). Generating the parser works, parsing itself goes slow beyong belief: $self->default_throw_with_stack (0) unless $in_testing_mode; my $in_package; eval { my $parser = $self->create_parser( lowestKnownDataTypes => { 'locus_id' => 'String','date' => 'DateTime','region' => 'Region', }, loadDataTypes => [ qw( String DateTime Region Boolean ) ] ); # does not get beyond this point in a reasonable amount of time. $in_package = $parser->parse ( method => $in_testing_mode ? 'file' : 'string', data => $data ); }; I tried to put the webservice through dprof, with these results (unfortunatly, Apache::DProf seems to die on me, but invoking the mod_perl envirnment with -d:DProf works): [davebowman at hal2000 ~]$ dprofpp -F /tmp/tmon.out XML::LibXML::parse_string has 1 unstacked calls in outer XML::SAX::Base::end_element has 1 unstacked calls in outer BOGAS::Moby::BogasSaveRegionBase::BogasSaveRegion has 1 unstacked calls in outer XML::SAX::Base::parse has 1 unstacked calls in outer Exporter::Heavy::heavy_export has 16 unstacked calls in outer Config::Simple::import_from has 1 unstacked calls in outer SOAP::Server::handle has 1 unstacked calls in outer MOSES::MOBY::Parser::callMethod has 1 unstacked calls in outer MOSES::MOBY::Base::as_string has 1 unstacked calls in outer Config::Simple::verbose has 1 unstacked calls in outer utf8::AUTOLOAD has -1 unstacked calls in outer HTTP::Message::__ANON__ has 3 unstacked calls in outer Dumpvalue::unwrap has 8 unstacked calls in outer XML::LibXML::_parse_sax_string has 1 unstacked calls in outer MOSES::MOBY::Parser::parse has 1 unstacked calls in outer XML::LibXML::SAX::_parse has 1 unstacked calls in outer Config::Simple::vars has 1 unstacked calls in outer MOSES::MOBY::Parser::end_element has 1 unstacked calls in outer SOAP::Transport::HTTP::Server::handle has 1 unstacked calls in outer AutoLoader::AUTOLOAD has -3 unstacked calls in outer XML::SAX::Base::parse_string has 1 unstacked calls in outer Fcntl::AUTOLOAD has -6 unstacked calls in outer Dumpvalue::dumpValue has 1 unstacked calls in outer Dumpvalue::DumpElem has 7 unstacked calls in outer HTTP::Message::AUTOLOAD has -3 unstacked calls in outer Fcntl::__ANON__ has 6 unstacked calls in outer XML::SAX::Base::__ANON__ has 1 unstacked calls in outer Exporter::export has -16 unstacked calls in outer utf8::SWASHNEW has 1 unstacked calls in outer SOAP::Transport::HTTP::CGI::handle has 1 unstacked calls in outer XML::LibXML::SAX::_parse_string has 1 unstacked calls in outer Faking 32 exit timestamp(s). Total Elapsed Time = -34.8210 Seconds User+System Time = 0 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 0.00 140.6 140.64 486940 0.0003 0.0003 IO::Scalar::print 0.00 3.553 3.975 449046 0.0000 0.0000 Dumpvalue::stringify 0.00 2.551 2.551 574503 0.0000 0.0000 File::Spec::Unix::canonpath 0.00 2.005 147.07 232696 0.0000 0.0006 Dumpvalue::unwrap 0.00 1.177 1.177 423816 0.0000 0.0000 overload::mycan 0.00 1.019 1.019 743 0.0014 0.0014 MOSES::MOBY::Cache::Registries::in it 0.00 0.959 3.885 742 0.0013 0.0052 MOSES::MOBY::Generators::Utils::fi nd_file 0.00 0.581 2.989 286495 0.0000 0.0000 File::Spec::Unix::catfile 0.00 0.450 146.88 230026 0.0000 0.0006 Dumpvalue::DumpElem 0.00 0.367 0.607 56930 0.0000 0.0000 MOSES::MOBY::Base::__ANON__ 0.00 0.257 1.876 1925 0.0001 0.0010 MOSES::MOBY::Cache::Central::get_d atatype 0.00 0.246 0.246 1925 0.0001 0.0001 MOSES::MOBY::Cache::Central::_clea n 0.00 0.234 155.05 1 0.2342 155.05 XML::LibXML::_parse_sax_string 0.00 0.218 0.218 11242 0.0000 0.0000 XML::LibXML::Node::_childNodes 0.00 0.143 0.143 108644 0.0000 0.0000 XML::LibXML::Node::nodeName These results don't make me anymuch wiser. I tried switching xml parsers by changing then in the mobyservices.cfg, with no result. Does anyone know what the problem is? Or how to debug this? Am I missing something obvious here? -Kenny ================================================================== Kenny Billiau Web Developer 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 kenny.billiau at psb.ugent.be http://bioinformatics.psb.ugent.be ================================================================== From kenny.billiau at psb.ugent.be Thu Oct 30 15:17:18 2008 From: kenny.billiau at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 16:17:18 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever Message-ID: Hi, here you go, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > Hi, > > This is the right list! Could you send me the XML for your second service? > > Thanks, > > Eddie -------------- next part -------------- A non-text attachment was scrubbed... Name: mobysave.xml Type: text/xml Size: 200385 bytes Desc: URL: From kebil at psb.ugent.be Thu Oct 30 15:03:00 2008 From: kebil at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 16:03:00 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> Message-ID: Hi, here you go, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > Hi, > > This is the right list! Could you send me the XML for your second service? > > Thanks, > > Eddie -------------- next part -------------- A non-text attachment was scrubbed... Name: mobysave.xml Type: text/xml Size: 200385 bytes Desc: URL: From edward.kawas at gmail.com Thu Oct 30 18:39:14 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 11:39:14 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> Message-ID: <4909ff61.27f8720a.750d.76c6@mx.google.com> So this one might take some time... from what I can see, our parser goes into an infinite loop (although, I am not certain about that ...). I will play around with this XML file and get back to you. 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 Kenny Billiau Sent: October-30-08 8:03 AM To: Core developer announcements Subject: Re: [MOBY-dev] XML parsing takes forever Hi, here you go, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > Hi, > > This is the right list! Could you send me the XML for your second service? > > Thanks, > > Eddie From kenny.billiau at psb.ugent.be Thu Oct 30 18:55:50 2008 From: kenny.billiau at psb.ugent.be (Kenny Billiau) Date: Thu, 30 Oct 2008 19:55:50 +0100 (CET) Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <4909ff61.27f8720a.750d.76c6@mx.google.com> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> Message-ID: Hi, thx for helping to investigate the problem! I'm pretty sure the parser gets out of it's mess. When you truncate the XML file by removing all but a few ElementContainers, it takes awhile, but it actually returns without error. And memory consuption doesn't seem to be a problem either, as mostly 'top' reveals that the invoked webservice script uses a steady amount of memory. thx, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > So this one might take some time... from what I can see, our parser goes > into an infinite loop (although, I am not certain about that ...). > > I will play around with this XML file and get back to you. > > 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 Kenny Billiau > Sent: October-30-08 8:03 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > here you go, > > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> Hi, >> >> This is the right list! Could you send me the XML for your second service? >> >> Thanks, >> >> Eddie > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- From edward.kawas at gmail.com Thu Oct 30 18:58:39 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 11:58:39 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> Message-ID: <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> I think that you are right about the parser not going into an infinite loop. For some reason, the SAX parser seems to be really slow (although, I don't want to say that until I know for sure). Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau Sent: October-30-08 11:56 AM To: Core developer announcements Subject: Re: [MOBY-dev] XML parsing takes forever Hi, thx for helping to investigate the problem! I'm pretty sure the parser gets out of it's mess. When you truncate the XML file by removing all but a few ElementContainers, it takes awhile, but it actually returns without error. And memory consuption doesn't seem to be a problem either, as mostly 'top' reveals that the invoked webservice script uses a steady amount of memory. thx, Kenny On Thu, 30 Oct 2008, Edward Kawas wrote: > So this one might take some time... from what I can see, our parser goes > into an infinite loop (although, I am not certain about that ...). > > I will play around with this XML file and get back to you. > > 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 Kenny Billiau > Sent: October-30-08 8:03 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > here you go, > > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> Hi, >> >> This is the right list! Could you send me the XML for your second service? >> >> Thanks, >> >> Eddie > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jmfernandez at cnio.es Thu Oct 30 19:54:33 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 30 Oct 2008 20:54:33 +0100 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> Message-ID: <490A10F9.5050408@cnio.es> Hi everybody, I'm using the XML::LibXML SAX parser for other projects and tasks, and it can be really, really slow. You don't realize that until you are parsing a large file from a pipe, and you see that most of the time the program which is parsing is CPU (and not I/O) bounded. Best Regards, Jos? Mar?a Edward Kawas wrote: > I think that you are right about the parser not going into an infinite loop. > For some reason, the SAX parser seems to be really slow (although, I don't > want to say that until I know for sure). > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau > Sent: October-30-08 11:56 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > thx for helping to investigate the problem! > > I'm pretty sure the parser gets out of it's mess. When you truncate the > XML file by removing all but a few ElementContainers, it takes awhile, but > it actually returns without error. > > And memory consuption doesn't seem to be a problem either, as mostly 'top' > reveals that the invoked webservice script uses a steady amount of memory. > > thx, > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> So this one might take some time... from what I can see, our parser goes >> into an infinite loop (although, I am not certain about that ...). >> >> I will play around with this XML file and get back to you. >> >> 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 Kenny Billiau >> Sent: October-30-08 8:03 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] XML parsing takes forever >> >> Hi, >> >> here you go, >> >> Kenny >> >> On Thu, 30 Oct 2008, Edward Kawas wrote: >> >>> Hi, >>> >>> This is the right list! Could you send me the XML for your second > service? >>> Thanks, >>> >>> Eddie >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Thu Oct 30 20:39:08 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 30 Oct 2008 13:39:08 -0700 Subject: [MOBY-dev] XML parsing takes forever In-Reply-To: <490A10F9.5050408@cnio.es> References: <4909c0c3.27b38c0a.1e6e.fffff90d@mx.google.com> <4909ff61.27f8720a.750d.76c6@mx.google.com> <490a03ee.22ba720a.17d1.ffff9006@mx.google.com> <490A10F9.5050408@cnio.es> Message-ID: <490a1b7c.0fba720a.690e.4995@mx.google.com> Now I can confirm that it is slow parsing and not an infinite loop! The XML file took over an hour on my virtual machine to parse. I will see what I can do with other SAX parsers for Perl. 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 Jos? Mar?a Fern?ndez Gonz?lez Sent: October-30-08 12:55 PM To: Core developer announcements Subject: Re: [MOBY-dev] XML parsing takes forever Hi everybody, I'm using the XML::LibXML SAX parser for other projects and tasks, and it can be really, really slow. You don't realize that until you are parsing a large file from a pipe, and you see that most of the time the program which is parsing is CPU (and not I/O) bounded. Best Regards, Jos? Mar?a Edward Kawas wrote: > I think that you are right about the parser not going into an infinite loop. > For some reason, the SAX parser seems to be really slow (although, I don't > want to say that until I know for sure). > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Kenny Billiau > Sent: October-30-08 11:56 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] XML parsing takes forever > > Hi, > > thx for helping to investigate the problem! > > I'm pretty sure the parser gets out of it's mess. When you truncate the > XML file by removing all but a few ElementContainers, it takes awhile, but > it actually returns without error. > > And memory consuption doesn't seem to be a problem either, as mostly 'top' > reveals that the invoked webservice script uses a steady amount of memory. > > thx, > Kenny > > On Thu, 30 Oct 2008, Edward Kawas wrote: > >> So this one might take some time... from what I can see, our parser goes >> into an infinite loop (although, I am not certain about that ...). >> >> I will play around with this XML file and get back to you. >> >> 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 Kenny Billiau >> Sent: October-30-08 8:03 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] XML parsing takes forever >> >> Hi, >> >> here you go, >> >> Kenny >> >> On Thu, 30 Oct 2008, Edward Kawas wrote: >> >>> Hi, >>> >>> This is the right list! Could you send me the XML for your second > service? >>> Thanks, >>> >>> Eddie >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev