From gordonp at ucalgary.ca Mon Jun 1 17:52:24 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 01 Jun 2009 15:52:24 -0600 Subject: [MOBY-l] New Moby app In-Reply-To: References: Message-ID: <4A244D98.7010208@ucalgary.ca> Hi all, I just put together a little video to introduce a new Moby application I'm hoping to release in the next couple of weeks, called Daggoo. It lets users create Moby services from existing Web Services via a drag 'n' drop interface. In case you are interested, the video is on SciVee, and is also embedded on the upcoming Daggoo Web site... http://www.daggoo.net/ Once I've committed the code, I'll follow up with more details. Cheers, Paul From dxha at vt.edu Wed Jun 3 16:39:16 2009 From: dxha at vt.edu (Ha X. Dang) Date: Wed, 3 Jun 2009 16:39:16 -0400 Subject: [MOBY-l] Dead services Message-ID: <000301c9e48b$5d1e3e60$175abb20$@edu> Hi, Does anyone know if the services listed by Taverna are still alive or not? It seems to me that Taverna retrieve even dead services posted here (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices). Thanks. //Ha From edward.kawas at gmail.com Wed Jun 3 17:46:25 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 3 Jun 2009 14:46:25 -0700 Subject: [MOBY-l] Dead services In-Reply-To: <000301c9e48b$5d1e3e60$175abb20$@edu> References: <000301c9e48b$5d1e3e60$175abb20$@edu> Message-ID: <4a26ef3b.25bc720a.3884.ffffcffe@mx.google.com> Hi Ha, Taverna retrieves all services from a biomoby registry. In the future, we may be able to filter out the dead ones, but as of today, that isn't done. Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ha X. Dang Sent: June-03-09 1:39 PM To: 'mobyl' Subject: [MOBY-l] Dead services Hi, Does anyone know if the services listed by Taverna are still alive or not? It seems to me that Taverna retrieve even dead services posted here (http://moby.ucalgary.ca/moby/ValidateService?getDeadServices). Thanks. //Ha _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l From markw at illuminae.com Wed Jun 3 19:24:08 2009 From: markw at illuminae.com (Mark) Date: Wed, 03 Jun 2009 16:24:08 -0700 Subject: [MOBY-l] Dead services In-Reply-To: <4a26ef3b.25bc720a.3884.ffffcffe@mx.google.com> References: <000301c9e48b$5d1e3e60$175abb20$@edu> <4a26ef3b.25bc720a.3884.ffffcffe@mx.google.com> Message-ID: I think that's pretty important... On Wed, 03 Jun 2009 14:46:25 -0700, Edward Kawas wrote: > Hi Ha, > > Taverna retrieves all services from a biomoby registry. In the future, we > may be able to filter out the dead ones, but as of today, that isn't > done. From phillip.lord at newcastle.ac.uk Thu Jun 4 12:32:52 2009 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Thu, 04 Jun 2009 17:32:52 +0100 Subject: [MOBY-l] Bio-Ontologies programme released Message-ID: <87ws7sarij.fsf@newcastle.ac.uk> ** Call for Participation Bio-Ontologies: Knowledge in Biology provides a forum for discussion of the latest and most cutting-edge research in ontologies and more generally the organisation, presentation and dissemination of knowledge in biology. We are pleased to announce the programme for Bio-Ontologies 2009: Knowledge in Biology, at SIG at Intelligent Systems for Molecular Biology, with papers and posters on a wide range of topics. ** Programme This year's keynote speaker will by Barend Mons (http://en.wikipedia.org/wiki/Barend_Mons). This year's panel will be - Barend Mons - Andrew Su - Dawn Field The full programme is now available at: http://bio-ontologies.org.uk/programme.html *** Organisers Phillip Lord, Newcastle University Susanna-Assunta Sansone, EBI Nigam Shah, Stanford Susie Stephens, Eli Lilly Larisa Soldatova, University of Wales, Aberystwyth ** Registration All registration will be handled by ISCB. Further details are available http://www.iscb.org/ismbeccb2009/registration.php ** Bio-Ontologies 2008 Papers from last years SIG have now been published in BMC Bioinformatics. http://www.biomedcentral.com/1471-2105/10?issue=S5 -- Phillip Lord, Phone: +44 (0) 191 222 7827 Lecturer in Bioinformatics, Email: phillip.lord at newcastle.ac.uk School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord Room 914 Claremont Tower, skype: russet_apples Newcastle University, msn: msn at russet.org.uk NE1 7RU From markw at illuminae.com Mon Jun 15 11:48:39 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 15 Jun 2009 08:48:39 -0700 Subject: [MOBY-l] BioXSD... 8 years later... Message-ID: I had to chuckle when I read that, last month, the BioXSD project (part of EMBRACE) proposed that "The availability of a set of canonical data types would increase the interoperability of Web services within our field." [1] ...8 years after it was done... and done WITH SEMANTICS to boot! :-) Cheers all! Mark [1] http://vit-embnet.unil.ch/EMBRACE-AGM/EMBRCE_AGM2009_Posters.pdf -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From phillip.lord at newcastle.ac.uk Mon Jun 15 12:53:35 2009 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Mon, 15 Jun 2009 17:53:35 +0100 Subject: [MOBY-l] BioXSD... 8 years later... In-Reply-To: (Mark Wilkinson's message of "Mon, 15 Jun 2009 08:48:39 -0700") References: Message-ID: <87iqixsak0.fsf@newcastle.ac.uk> This reminds me of the bio* days; you'd go to BOSC to see which new language now had interfaces for DNA sequence. The great thing about standards is that there are so many to choose from. Phil "Mark Wilkinson" writes: > I had to chuckle when I read that, last month, the BioXSD project (part of > EMBRACE) proposed that "The availability of a set of canonical data types > would increase the interoperability of Web services within our field." [1] > > ...8 years after it was done... and done WITH SEMANTICS to boot! :-) > > Cheers all! > > Mark > > > [1] http://vit-embnet.unil.ch/EMBRACE-AGM/EMBRCE_AGM2009_Posters.pdf > From dmitry.repchevski at bsc.es Mon Jun 15 22:36:09 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 15 Jun 2009 19:36:09 -0700 Subject: [MOBY-l] BioXSD... 8 years later... In-Reply-To: References: Message-ID: <4A370519.8020304@bsc.es> I am the one who applauds the initiative... Even though I'm a little bit skeptical... Is there any additional information to read about? As you may know we (INB/BSC) already converted all Moby ontology to XSD schema and even have a WSDL proxy to our Moby services (based on this schema). Concerning SAWSDL this is a way to go without any doubts... the only pitfall is that it's based on WSDL 2.0 and Java has no yet even a draft of API that implements it (Perl?). It would take two or three years to have such an API (being optimist). So at the time being this is nothing but a nice declaration of intentions. Cheers, Dmitry From markw at illuminae.com Tue Jun 16 09:57:46 2009 From: markw at illuminae.com (Mark) Date: Tue, 16 Jun 2009 06:57:46 -0700 Subject: [MOBY-l] BioXSD... 8 years later... In-Reply-To: <4A370519.8020304@bsc.es> References: <4A370519.8020304@bsc.es> Message-ID: On Mon, 15 Jun 2009 19:36:09 -0700, Dmitry Repchevsky wrote: > I am the one who applauds the initiative... > Even though I'm a little bit skeptical... Well... in addition to moby, there have been other efforts to create a consensus around XML schema... for example, Hobit (http://hobit.sourceforge.net/documentation.html) Given the history of such projects, I'd say skepticism is warranted! It seems to me that ANY project that requires people to agree on anything - at least, agreement at this level - is unlikely to succeed, unless you have a very big stick, or an even bigger carrot! [1] Personally, i think the sooner we stop using XML schema and start using OWL/RDF, the better! We cannot get interoperability without semantics. Moving from moby to XML Schema is simply a step backwards... but you and I seldom agree on our world-view ;-) :-) Cheers! M [1] http://en.wikipedia.org/wiki/Carrot_and_stick From dmitry.repchevski at bsc.es Tue Jun 16 19:59:09 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 16 Jun 2009 16:59:09 -0700 Subject: [MOBY-l] BioXSD... 8 years later... In-Reply-To: References: Message-ID: <4A3831CD.4040404@bsc.es> > > It seems to me that ANY project that requires people to agree on anything > - at least, agreement at this level - is unlikely to succeed, unless you > have a very big stick, or an even bigger carrot! I think we are doomed to support this one because it comes from EBI... :-\ > We cannot get interoperability without semantics. Wrong... we can not do reasoning without semantics... > Moving from moby to XML Schema is simply a step backwards... I disagree... The only semantics Moby has is orthogonal to Moby format itself, so in this case using Schema is to standardize the serialization and fix web-services' part, keeping the ontology intact. > I seldom agree on our world-view ... :-) I agree with your disagreement ;-) . There is no perfect solution and in many cases I disagree with myself... :-D > Personally, i think the sooner we stop using XML schema and start using > OWL/RDF, the better! This is one of the possibility, but in this case what to do with SOAP? There is no way Web-services move to OWL anytime soon, SAWSDL is the reasonable compromise (IMHO). Another possibility could be the REST, but this means to reinvent the wheel in many senses. OWL itself yet to have the formal description based on Schema (owl2). Dmitry From markw at illuminae.com Tue Jun 16 15:46:21 2009 From: markw at illuminae.com (Mark) Date: Tue, 16 Jun 2009 12:46:21 -0700 Subject: [MOBY-l] SADI and CardioSHARE relative to Re: BioXSD... 8 years later... In-Reply-To: <4A3831CD.4040404@bsc.es> References: <4A3831CD.4040404@bsc.es> Message-ID: On Tue, 16 Jun 2009 16:59:09 -0700, Dmitry Repchevsky wrote: >> We cannot get interoperability without semantics. > Wrong... we can not do reasoning without semantics... we cannot get (automated) interoperability without reasoning :-) (Unless we have universal agreement on data-types... which I guess is what BioXSD is trying to achieve... good luck to them!) >> Moving from moby to XML Schema is simply a step backwards... > I disagree... The only semantics Moby has is orthogonal to Moby format > itself, so in this case using Schema is to standardize the serialization > and fix web-services' part, keeping the ontology intact. In some ways I agree with you, but in others not... In MOBY we do allow inheritence of has and has-a objects within a Moby object. This situation cannot (sensibly) be represented in XML Schema; however, having said that, I don't think that anyone has ever USED this "feature" of Moby, so... it likely doesn't matter :-) My understanding from Eddie is that there are a couple of Moby objects that cannot be represented in XML Schema without breaking the rules of Schema, so there is a bit of a limitation there. Does your XML Schema mapping allow me to send more complex objects into a service that claims to consume only parent-type objects? It seems that this schema-mapping would be extremely difficult to do, since you cannot predict the structure of the incoming XML... >> I seldom agree on our world-view > ... :-) I agree with your disagreement ;-) . There is no perfect > solution and in many cases I disagree with myself... :-D Then we do agree! LOL! There is no perfect solution :-D >> Personally, i think the sooner we stop using XML schema and start using >> OWL/RDF, the better! > This is one of the possibility, but in this case what to do with SOAP? > There is no way Web-services move to OWL anytime soon, SAWSDL is the > reasonable compromise (IMHO). Another possibility could be the REST, but > this means to reinvent the wheel in many senses. OWL itself yet to have > the formal description based on Schema (owl2). Have a look at what we're doing with SADI and CardioSHARE: http://sadiframework.org and a presentation that explains it at: http://bioontology.org/videos/semanticwebservices.html I think we are starting to get close to a VERY simple solution to OWL/RDF based Web Services, and a registry model (if you can call it a "registry"...) that behaves in a manner we think is quite intuitive for biologists... This is what I hope we will replace MOBY with in the next year or two. Mark From dmitry.repchevski at bsc.es Wed Jun 17 03:19:33 2009 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 17 Jun 2009 00:19:33 -0700 Subject: [MOBY-l] SADI and CardioSHARE relative to Re: BioXSD... 8 years later... In-Reply-To: References: Message-ID: <4A389905.3080208@bsc.es> > > ... Unless we have universal agreement on data-types... which I guess is what BioXSD > is trying to achieve... good luck to them! > In MOBY we do allow inheritence of has and has-a objects within a Moby object. This situation > cannot (sensibly) be represented in XML Schema. Don't understand here... In XML schema "has"/"hasa" are represented as elements within a complex type. Such a type has a name and a schema type, you can substitute it by a child element... maybe I just don't understand your statement... > My understanding from Eddie is that there are a > couple of Moby objects that cannot be represented in XML Schema without > breaking the rules of Schema, so there is a bit of a limitation there. > So far I have converted whole inab ontology tree without any issues... :-) > Does your XML Schema mapping allow me to send more complex objects into a > service that claims to consume only parent-type objects? That's not the schema itself. Such an object should be casted without a problem by JAXB... here is just an example from "Moby Schema": Because in XML tag encoding (using schema) is done using element name (not the type), the resulting object for say: would be: 11 ATCATCATCAT if we substitute AminoAcidSequence with say AnnotatedAminoacidSequece there will be some additional tags, but in a time of decoding we will lose it... If you want your service provide a support to both AminoAcidSequence AND NucleotideSequence there is a possibility to use "SeeAlso" Tag. Actually this tag can be put onto the father so in ontology compile time all parents would know their children explicitly. There is a possibility (I did it once) in JAXB to inject a custom classloader. Such a classloader can DYNAMICALLY obtain the needed information (for example from registry), generate java code, compile it (java6 allows it) and load on-the-fly. This way there is no need in compiled ontology at all... > you cannot predict the structure of the incoming XML... > I prefer JAXB developers to break their heads with it :D > I think we are starting to get close to a VERY simple solution to OWL/RDF based Web Services, and a registry model. Being software engineer I'm twice skeptical... ;-) do you have more technical information? I seen some of these slides in your presentation last Falls. By the way, even before doing "MobyXSD" (contrary to BioXSD ;-) ) I discussed a lot with Jose Maria about OWL2. I tried to generate "MobyOWL2". There is no problem in it, apart that in Moby Ontology plenty of classes (MobyObjects) share the names with their attributes ("has"/"hasa"). This is absolutely forbidden in OWL... apart of those "problematic" object I was able not only to create it, but work with it in Protege! The message that i'ts possible to keep the ontology in OWL and use XSD as a serialization level for the services. Using dynamic compilation trick it's possible to transparently generate appropriate java objects... just some thoughts... Best regards, Dmitry. P.S. I'm working on adding moby-async services support to my proxy. The idea is to use WSA-Addressing, So if a client provides a callback the service works asynchronously, if not, as usual. http://inb.bsc.es/documents/java/nemus/index.html http://inb.bsc.es/documents/java/nemus/executor/wsdl_executor.html From phillip.lord at newcastle.ac.uk Wed Jun 17 05:56:53 2009 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Wed, 17 Jun 2009 10:56:53 +0100 Subject: [MOBY-l] BioXSD... 8 years later... In-Reply-To: <4A3831CD.4040404@bsc.es> (Dmitry Repchevsky's message of "Tue, 16 Jun 2009 16:59:09 -0700") References: <4A3831CD.4040404@bsc.es> Message-ID: <87y6rrji8q.fsf@newcastle.ac.uk> Dmitry Repchevsky writes: >> >> It seems to me that ANY project that requires people to agree on anything - >> at least, agreement at this level - is unlikely to succeed, unless you >> have a very big stick, or an even bigger carrot! > I think we are doomed to support this one because it comes from EBI... :-\ I wouldn't be so sure of that. It depends how willing the developers are to spend the 5 years pushing it. > >> We cannot get interoperability without semantics. > Wrong... we can not do reasoning without semantics... Unless there is an agreed upon semantics, then no interoperability. Now, whether you need the semantics expressed in a common language like OWL, or whether you need a common syntax and just agree on the semantics in another way is a different issue. For myself, I see OWL and RDF as another tool to be used; not a magic bullet but another spanner to be used when it fits. Phil From soiland-reyes at cs.manchester.ac.uk Mon Jun 29 11:32:39 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Mon, 29 Jun 2009 16:32:39 +0100 Subject: [MOBY-l] java.lang.OutOfMemoryError: PermGen space from getJpegFromAnnotatedImage Message-ID: Hi! I am getting this exception from the BioMoby service: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage As far as I understand this happens on server-side, I've tried increasing the PermGen space in Taverna to be sure. This happens with Taverna 1.7.1 and 2.1.x running the Fetch Dragon Images workflow [2] (I'm going through the example workflows[1] before releasing Taverna 2.1b2 - we would very much have a BioMoby workflow included!) [1] http://www.myexperiment.org/packs/14 [2] http://www.myexperiment.org/workflows/162 Do you know how to avoid this problem - or another similar workflow we could put in instead? ERROR 2009-06-29 16:24:24,682 java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space ERROR 2009-06-29 16:24:24,721 Error invoking biomoby service for biomoby. A MobyException caught org.biomoby.shared.MobyException: ===ERROR=== Fault details: [ns1:hostname: null] Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException Fault actor: null When calling: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549) at org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask.java:710) at org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.java:1226) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:585) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:524) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:443) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIteration(ProcessorTask.java:962) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(ProcessorTask.java:95) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(ProcessorTask.java:835) Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(SAXParser.java:375) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696) at org.apache.axis.Message.getSOAPEnvelope(Message.java:435) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206) at org.apache.axis.client.Call.invokeEngine(Call.java:2784) at org.apache.axis.client.Call.invoke(Call.java:2767) at org.apache.axis.client.Call.invoke(Call.java:2443) at org.apache.axis.client.Call.invoke(Call.java:2366) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247) ... 10 more ERROR 2009-06-29 16:24:24,725 Task failed while iterating Thread[Processor worker getJpegFromAnnotatedImage #0,6,main] uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Task failed due to problem invoking biomoby service. ===ERROR=== Fault details: [ns1:hostname: null] Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException Fault actor: null When calling: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage =========== at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:664) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:585) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:524) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:443) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIteration(ProcessorTask.java:962) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(ProcessorTask.java:95) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(ProcessorTask.java:835) Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [ns1:hostname: null] Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException Fault actor: null When calling: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549) at org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask.java:710) at org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.java:1226) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646) ... 6 more Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(SAXParser.java:375) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696) at org.apache.axis.Message.getSOAPEnvelope(Message.java:435) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206) at org.apache.axis.client.Call.invokeEngine(Call.java:2784) at org.apache.axis.client.Call.invoke(Call.java:2767) at org.apache.axis.client.Call.invoke(Call.java:2443) at org.apache.axis.client.Call.invoke(Call.java:2366) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247) ... 10 more -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From edward.kawas at gmail.com Mon Jun 29 12:14:49 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 29 Jun 2009 09:14:49 -0700 Subject: [MOBY-l] java.lang.OutOfMemoryError: PermGen space from getJpegFromAnnotatedImage In-Reply-To: References: Message-ID: <4a48e87d.09f8720a.10e5.7449@mx.google.com> Hi Stian, A workflow that excluded the service 'getJpegFromAnnotatedImage', but included a parser to extract the jpeg content would work nicely. I am having problems running the workbench at the moment, so I make the change at the moment, but I have included (attached) a similar workflow that could replace the one on myExperiment. Thanks, Eddie -----Original Message----- From: moby-l-bounces at lists.open-bio.org [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Stian Soiland-Reyes Sent: June-29-09 8:33 AM To: moby-l at biomoby.org Subject: [MOBY-l] java.lang.OutOfMemoryError: PermGen space from getJpegFromAnnotatedImage Hi! I am getting this exception from the BioMoby service: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage As far as I understand this happens on server-side, I've tried increasing the PermGen space in Taverna to be sure. This happens with Taverna 1.7.1 and 2.1.x running the Fetch Dragon Images workflow [2] (I'm going through the example workflows[1] before releasing Taverna 2.1b2 - we would very much have a BioMoby workflow included!) [1] http://www.myexperiment.org/packs/14 [2] http://www.myexperiment.org/workflows/162 Do you know how to avoid this problem - or another similar workflow we could put in instead? ERROR 2009-06-29 16:24:24,682 java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space ERROR 2009-06-29 16:24:24,721 Error invoking biomoby service for biomoby. A MobyException caught org.biomoby.shared.MobyException: ===ERROR=== Fault details: [ns1:hostname: null] Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException Fault actor: null When calling: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549) at org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask .java:710) at org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.jav a:1226) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenera teTemplates(ProcessorTask.java:585) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocation WithRetryLogic(ProcessorTask.java:524) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(P rocessorTask.java:443) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIter ation(ProcessorTask.java:962) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(P rocessorTask.java:95) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(Proces sorTask.java:835) Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2 22) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12 9) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo ntext.java:1087) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc her.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(SAXParser.java:375) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext .java:227) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696) at org.apache.axis.Message.getSOAPEnvelope(Message.java:435) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChe cker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206) at org.apache.axis.client.Call.invokeEngine(Call.java:2784) at org.apache.axis.client.Call.invoke(Call.java:2767) at org.apache.axis.client.Call.invoke(Call.java:2443) at org.apache.axis.client.Call.invoke(Call.java:2366) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247) ... 10 more ERROR 2009-06-29 16:24:24,725 Task failed while iterating Thread[Processor worker getJpegFromAnnotatedImage #0,6,main] uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException: Task failed due to problem invoking biomoby service. ===ERROR=== Fault details: [ns1:hostname: null] Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException Fault actor: null When calling: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage =========== at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:664) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenera teTemplates(ProcessorTask.java:585) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocation WithRetryLogic(ProcessorTask.java:524) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(P rocessorTask.java:443) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingleIter ation(ProcessorTask.java:962) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access$100(P rocessorTask.java:95) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run(Proces sorTask.java:835) Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [ns1:hostname: null] Fault string: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.generalException Fault actor: null When calling: http://es-01.chibi.ubc.ca/mobyservices/services/getJpegFromAnnotatedImage =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1549) at org.biomoby.client.taverna.plugin.BiomobyTask.executeMobyService(BiomobyTask .java:710) at org.biomoby.client.taverna.plugin.BiomobyTask.executeService(BiomobyTask.jav a:1226) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:646) ... 6 more Caused by: java.lang.OutOfMemoryError: PermGen space; nested exception is: java.lang.OutOfMemoryError: PermGen space at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2 22) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12 9) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo ntext.java:1087) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc her.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(SAXParser.java:375) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext .java:227) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696) at org.apache.axis.Message.getSOAPEnvelope(Message.java:435) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChe cker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206) at org.apache.axis.client.Call.invokeEngine(Call.java:2784) at org.apache.axis.client.Call.invoke(Call.java:2767) at org.apache.axis.client.Call.invoke(Call.java:2443) at org.apache.axis.client.Call.invoke(Call.java:2366) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247) ... 10 more -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester _______________________________________________ moby-l mailing list moby-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-l