From jerzyo at genesilico.pl Mon Sep 1 06:01:45 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Mon, 01 Sep 2008 12:01:45 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? Message-ID: <48BBBD89.6020803@genesilico.pl> Hello I am searchng for a java class representing a BioMoby workflow: I found some classes that represent connections: datatype -> service service -> datatype datatype -> datatype in org.biomoby.client. (There is even a class for drawing graphs using graphviz, but unfortunately without datatype -> datatype connections.) I do not find find any class that these connections gathers them together as a workflow and enables execution of this workflow given some inputs. Does such class exist in jMoby? Or should I run my workflows using Taverna libraries (How should I do it)? If it does not exist I will probably write it but maybe somebody is already doing it. Jerzy Orlowski From serr at ac.uma.es Mon Sep 1 06:10:53 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Mon, 01 Sep 2008 12:10:53 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBBD89.6020803@genesilico.pl> References: <48BBBD89.6020803@genesilico.pl> Message-ID: <48BBBFAD.7060401@ac.uma.es> Hello Jerzy Unfortunately, moby can not handle workflows by itself for now. Normally you use taverna for building workflows. I'm trying to learn how to use Taverna libraries to run workflows. There is a taverna class (workflowlauncher or similar) available in the web page for taverna, but I couldn't make it work. I'm also very interesting in this topic. Greetings, Sergio Jerzy Orlowski wrote: > Hello > > I am searchng for a java class representing a BioMoby workflow: > > I found some classes that represent connections: > datatype -> service > service -> datatype > datatype -> datatype > in org.biomoby.client. > (There is even a class for drawing graphs using graphviz, but > unfortunately without datatype -> datatype connections.) > > I do not find find any class that these connections gathers them > together as a workflow and enables execution of this workflow given > some inputs. > > Does such class exist in jMoby? Or should I run my workflows using > Taverna libraries (How should I do it)? > If it does not exist I will probably write it but maybe somebody is > already doing it. > > Jerzy Orlowski > > _______________________________________________ > 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 groscurt at mpiz-koeln.mpg.de Mon Sep 1 06:44:58 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 01 Sep 2008 12:44:58 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBBFAD.7060401@ac.uma.es> References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es> Message-ID: <48BBC7AA.2060002@mpiz-koeln.mpg.de> Hi Sergio, if you follow the mail list correspondance of the taverna list http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results you will find the same question with answer and links to your problem. best andreas Sergio Ramirez Ramirez wrote: > Hello Jerzy > > Unfortunately, moby can not handle workflows by itself for now. > Normally you use taverna for building workflows. > I'm trying to learn how to use Taverna libraries to run workflows. > There is a taverna class (workflowlauncher or similar) available in > the web page for taverna, but I couldn't make it work. > > I'm also very interesting in this topic. > Greetings, Sergio > > Jerzy Orlowski wrote: >> Hello >> >> I am searchng for a java class representing a BioMoby workflow: >> >> I found some classes that represent connections: >> datatype -> service >> service -> datatype >> datatype -> datatype >> in org.biomoby.client. >> (There is even a class for drawing graphs using graphviz, but >> unfortunately without datatype -> datatype connections.) >> >> I do not find find any class that these connections gathers them >> together as a workflow and enables execution of this workflow given >> some inputs. >> >> Does such class exist in jMoby? Or should I run my workflows using >> Taverna libraries (How should I do it)? >> If it does not exist I will probably write it but maybe somebody is >> already doing it. >> >> Jerzy Orlowski >> >> _______________________________________________ >> 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 serr at ac.uma.es Mon Sep 1 07:15:17 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Mon, 01 Sep 2008 13:15:17 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBC7AA.2060002@mpiz-koeln.mpg.de> References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es> <48BBC7AA.2060002@mpiz-koeln.mpg.de> Message-ID: <48BBCEC5.1070505@ac.uma.es> Thank you very much Best Sergio. Andreas Groscurth wrote: > Hi Sergio, > > if you follow the mail list correspondance of the taverna list > > http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results > > > you will find the same question with answer and links to your problem. > > best > andreas > > Sergio Ramirez Ramirez wrote: >> Hello Jerzy >> >> Unfortunately, moby can not handle workflows by itself for now. >> Normally you use taverna for building workflows. >> I'm trying to learn how to use Taverna libraries to run workflows. >> There is a taverna class (workflowlauncher or similar) available in >> the web page for taverna, but I couldn't make it work. >> >> I'm also very interesting in this topic. >> Greetings, Sergio >> >> Jerzy Orlowski wrote: >>> Hello >>> >>> I am searchng for a java class representing a BioMoby workflow: >>> >>> I found some classes that represent connections: >>> datatype -> service >>> service -> datatype >>> datatype -> datatype >>> in org.biomoby.client. >>> (There is even a class for drawing graphs using graphviz, but >>> unfortunately without datatype -> datatype connections.) >>> >>> I do not find find any class that these connections gathers them >>> together as a workflow and enables execution of this workflow given >>> some inputs. >>> >>> Does such class exist in jMoby? Or should I run my workflows using >>> Taverna libraries (How should I do it)? >>> If it does not exist I will probably write it but maybe somebody is >>> already doing it. >>> >>> Jerzy Orlowski >>> >>> _______________________________________________ >>> 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 MichaelGerlich at gmx.de Wed Sep 3 05:17:42 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Wed, 3 Sep 2008 11:17:42 +0200 Subject: [MOBY-dev] Problems calling a Moby service with secondary parameters Message-ID: <000001c90da5$eb498a40$c1dc9ec0$@de> Hi all, I'm working on a simple java app (client) that calls some Biomoby services I wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist" registered under authority "ipb-halle.de" takes additional 2 secondary parameters that modify its query behavior and the resulting number of outputs. Now when I try to add both secondary parameters to the input, the service call fails with the following message: Exception in thread "main" org.biomoby.shared.MobyException: Service get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but takes 2 (query 1). Extra secondary parameters must have been specified at org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java :928) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275) at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86) My code is like that: Central worker = new CentralImpl(); templateService = new MobyService("get_DBLinks_From_Peaklist", authority); // authority = "ipb-halle.de" validServices = worker.findService(templateService); comp = new MobyDataComposite(new MobyDataType("MSPeakRel")); comp.put("relInt", new MobyDataInt(999)); comp.put("mz", new MobyDataFloat(273.069)); MobyDataSecondaryInstance[] secParams = new MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length]; for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) { secParams[i] = new MobyDataSecondaryInstance(new MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()), validServices[0].getSecondaryInputs()[i].getDefaultValue()); } mr.setService(validServices[0]); mr.setInput(comp); mr.setSecondaryInput(secParams); System.out.println(mr.invokeService().toString()); The setSecondaryInput() function takes an array that consists of all parameters and applies them to all inputs. Now there are 2 parameters and an array of length 2 - with the default values for both parameters (I defined default values for both parameters). Some hints what I'm doing wrong? Another question - my input is of type MSPeakRel and is defined as collection. How do I manage to add multiple inputs - in this case, they would represent a complete peaklist of (m/z value, relative intensity) for querying a database? Best wishes, Michael From jason.e.stewart at gmail.com Mon Sep 8 07:06:59 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Mon, 8 Sep 2008 16:36:59 +0530 Subject: [MOBY-dev] SOAP::Lite claims support for document/literal Message-ID: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> Hey Moby-devs, The version of SOAP::Lite in CVS claims to support Document/literal encoding - I need help determing if this support is sufficient. Can you look this over? =head3 DOCUMENT/LITERAL SOAP web services using the document/literal message encoding are usually described by some Web Service Definition. Our web service has the following WSDL description: The XML message (inside the SOAP Envelope) look like this: Kutter Martin Hello Martin Kutter! You can call this web service with the following client code: use SOAP::Lite; my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); $soap->on_action( sub { "urn:HelloWorld#sayHello" }); $soap->autotype(0); $soap->default_ns('urn:HelloWorld'); my $som = $soap->call("sayHello", SOAP::Data->name('name')->value( 'Kutter' ), SOAP::Data->name('givenName')->value('Martin'), ); die $som->fault->{ faultstring } if ($som->fault); print $som->result, "\n"; =head2 Differences between the implementations You may have noticed that there's no between the rpc/literal and the document/literal example's implementation. In fact, from SOAP::Lite's point of view, the only differences between rpc/literal and document/literal that parameters are always named. In our example, the rpc/literal variant already used named parameters (by using a single complexType only as positional parameter), so there's no difference at all. The differences would have been bigger if the rpc/literal example had used more than one positional parameter, but this is quite unlikely to happen in the future: Current interoperability standards (like the WS-I basic profile) mandate the use of a single complexType as only parameter in rpc/literal calls. -- snip -- Help me on this one - is this valid? Is it sufficient for what MOBY and the rest of the Perl world needs? I suggest that I test this claim against: * perl SOAP::Lite client = axis Java server * java client = perl SOAP::Lite server I could use some suggestions for how to make these tests useful. Cheers, jas. From edward.kawas at gmail.com Mon Sep 8 11:16:08 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 8 Sep 2008 08:16:08 -0700 Subject: [MOBY-dev] SOAP::Lite claims support for document/literal In-Reply-To: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> Message-ID: <48c541bc.2a528c0a.2895.3efe@mx.google.com> Hi Jason, One of the problems that I have with soap lite and trying to perform doc/lit requests/responses is the inability to use attributes in the request. Since that statement doesn't make too much sense (to some it might have ;-), I will provide an example: I modified the wsdl that you sent to include an attribute in the givenName element, so that a request now looks like: Joe Blow Joe The server side code is simply: sub sayHello { SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) ); } So all that I am doing is dumping whatever is sent to the server. The response is $VAR1 = [ 'HelloWorld', 'Joe Blow', 'Joe' ]; I do believe that this is one of the biggest stumbling blocks so far. Because numerous Moby api calls use attributes. One such example is the retrieveService call. My dispatcher code is below! Eddie ------ CODE START ----- #!/usr/bin/perl -w # _________________________________________________________________ use SOAP::Transport::HTTP; if ($ENV{REQUEST_METHOD} eq "GET") { if (lc($ENV{QUERY_STRING} || "") eq "wsdl") { require CGI; my $q = CGI->new(); my $wsdl = HelloWorld::wsdl(); my $c = length($wsdl); print $q->header(-type=>'application/xml',-Content-length=>$c); print "$wsdl"; } } else { my $x = new SOAP::Transport::HTTP::CGI; $x->dispatch_to('/var/www/cgi-bin', 'HelloWorld'); $x->handle; } package HelloWorld; use Data::Dumper; sub sayHello { SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) ); } sub wsdl { return < EOF } 1; ------ CODE END ------ -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jason Stewart Sent: September-08-08 4:07 AM To: Core developer announcements Subject: [MOBY-dev] SOAP::Lite claims support for document/literal Hey Moby-devs, The version of SOAP::Lite in CVS claims to support Document/literal encoding - I need help determing if this support is sufficient. Can you look this over? =head3 DOCUMENT/LITERAL SOAP web services using the document/literal message encoding are usually described by some Web Service Definition. Our web service has the following WSDL description: The XML message (inside the SOAP Envelope) look like this: Kutter Martin Hello Martin Kutter! You can call this web service with the following client code: use SOAP::Lite; my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); $soap->on_action( sub { "urn:HelloWorld#sayHello" }); $soap->autotype(0); $soap->default_ns('urn:HelloWorld'); my $som = $soap->call("sayHello", SOAP::Data->name('name')->value( 'Kutter' ), SOAP::Data->name('givenName')->value('Martin'), ); die $som->fault->{ faultstring } if ($som->fault); print $som->result, "\n"; =head2 Differences between the implementations You may have noticed that there's no between the rpc/literal and the document/literal example's implementation. In fact, from SOAP::Lite's point of view, the only differences between rpc/literal and document/literal that parameters are always named. In our example, the rpc/literal variant already used named parameters (by using a single complexType only as positional parameter), so there's no difference at all. The differences would have been bigger if the rpc/literal example had used more than one positional parameter, but this is quite unlikely to happen in the future: Current interoperability standards (like the WS-I basic profile) mandate the use of a single complexType as only parameter in rpc/literal calls. -- snip -- Help me on this one - is this valid? Is it sufficient for what MOBY and the rest of the Perl world needs? I suggest that I test this claim against: * perl SOAP::Lite client = axis Java server * java client = perl SOAP::Lite server I could use some suggestions for how to make these tests useful. Cheers, jas. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jason.e.stewart at gmail.com Mon Sep 8 12:00:18 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Mon, 8 Sep 2008 21:30:18 +0530 Subject: [MOBY-dev] SOAP::Lite claims support for document/literal In-Reply-To: <48c541bc.2a528c0a.2895.3efe@mx.google.com> References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> <48c541bc.2a528c0a.2895.3efe@mx.google.com> Message-ID: <41c1ade50809080900l4d681b02m7962f04e81310421@mail.gmail.com> Hey Eddie, On Mon, Sep 8, 2008 at 8:46 PM, Edward Kawas wrote: > One of the problems that I have with soap lite and trying to perform doc/lit > requests/responses is the inability to use attributes in the request. OK. I've sent this off as a query to the SOAP-Lite dev list - I'll see what they have to say. Either there is an intended workaround or it needs to be implemented. Thanks. jas. From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 08:11:10 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 10 Sep 2008 14:11:10 +0200 Subject: [MOBY-dev] Problem with dashboard to list services Message-ID: <48C7B95E.4080903@avignon.inra.fr> Hi, We have a problem with dashboard. We unregistered and re-registred our services (with some changes), but after reloading the service list we don't see these services in the list and our authority is missing. We tried to delete manually our cache and to restart the dashboard several time. We tried to reload or update every thing without changes (which obviously make sense). Does it link in any way to experimental "big bang" this morning in Geneve ? Any other ideas ? Thanks, Regards, Dominique From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 08:23:31 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 10 Sep 2008 14:23:31 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7B95E.4080903@avignon.inra.fr> References: <48C7B95E.4080903@avignon.inra.fr> Message-ID: <48C7BC43.70008@avignon.inra.fr> Dominique Jeannin a ?crit : > Hi, > > We have a problem with dashboard. We unregistered and re-registred our > services (with some changes), but after reloading the service list we > don't see these services in the list and our authority is missing. > We tried to delete manually our cache and to restart the dashboard > several time. We tried to reload or update every thing without changes > (which obviously make sense). > > Does it link in any way to experimental "big bang" this morning in > Geneve ? > Any other ideas ? > Does anyone see our services named Solstis_getDatasetDescFromKeyword on avilin05.avignon.inra.fr ? From all our tests we cannot... Thanks, Regards, Dominique From groscurt at mpiz-koeln.mpg.de Wed Sep 10 08:47:29 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 10 Sep 2008 14:47:29 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7BC43.70008@avignon.inra.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7BC43.70008@avignon.inra.fr> Message-ID: <48C7C1E1.1030406@mpiz-koeln.mpg.de> Hi Dominique, i do find it in the dashboard on the test central and via a simple moby java test. I had the same issue some days ago that changes (like service (de)registration) could not be shown in dashboard, whatever i did to it... My solution was then to use someonelse moby checkout and this dashboard :( Hope someone knows about that and knows a general solution Andreas Dominique Jeannin wrote: > Dominique Jeannin a ?crit : >> Hi, >> >> We have a problem with dashboard. We unregistered and re-registred >> our services (with some changes), but after reloading the service >> list we don't see these services in the list and our authority is >> missing. >> We tried to delete manually our cache and to restart the dashboard >> several time. We tried to reload or update every thing without >> changes (which obviously make sense). >> >> Does it link in any way to experimental "big bang" this morning in >> Geneve ? >> Any other ideas ? >> > Does anyone see our services named Solstis_getDatasetDescFromKeyword > on avilin05.avignon.inra.fr ? > From all our tests we cannot... > > Thanks, > 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 Sep 10 08:49:19 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 10 Sep 2008 14:49:19 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7B95E.4080903@avignon.inra.fr> References: <48C7B95E.4080903@avignon.inra.fr> Message-ID: <48C7C24F.3050709@pingoured.fr> Dominique Jeannin wrote: > Hi, > > We have a problem with dashboard. We unregistered and re-registred our > services (with some changes), but after reloading the service list we > don't see these services in the list and our authority is missing. > We tried to delete manually our cache and to restart the dashboard > several time. We tried to reload or update every thing without changes > (which obviously make sense). > > Does it link in any way to experimental "big bang" this morning in Geneve ? > Any other ideas ? More informations on the problem: While doing an "Update" on all (Services, datatypes...) we have the following error: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== While on the other when doing a "Reload" all, we do not have any error but we still can't see our services nor authority. Regards, Pierre From edward.kawas at gmail.com Wed Sep 10 09:12:10 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 06:12:10 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7C24F.3050709@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> Message-ID: <48c7c7b5.26bc720a.7554.72fd@mx.google.com> Hi, I am trying to reproduce your problems, but I cannot. I am not seeing any SOAP exceptions and I don't see your service either. The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I tried to use non utf8 characters in my soap message. 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: September-10-08 5:49 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Dominique Jeannin wrote: > Hi, > > We have a problem with dashboard. We unregistered and re-registred our > services (with some changes), but after reloading the service list we > don't see these services in the list and our authority is missing. > We tried to delete manually our cache and to restart the dashboard > several time. We tried to reload or update every thing without changes > (which obviously make sense). > > Does it link in any way to experimental "big bang" this morning in Geneve ? > Any other ideas ? More informations on the problem: While doing an "Update" on all (Services, datatypes...) we have the following error: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== While on the other when doing a "Reload" all, we do not have any error but we still can't see our services nor authority. Regards, Pierre _______________________________________________ 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 Sep 10 09:31:33 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 10 Sep 2008 15:31:33 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> Message-ID: <48C7CC35.6090803@pingoured.fr> Edward Kawas wrote: > Hi, > > I am trying to reproduce your problems, but I cannot. I am not seeing any > SOAP exceptions and I don't see your service either. Strange since Andreas seems to see it as well as another person that contacted us off-list. > The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I > tried to use non utf8 characters in my soap message. > What surprise us the most is that two of our services that we did not change (Solstis_getProjet and dom_test2) are not shown either. The whole authority avilin05.avignon.inra.fr seems to have disappeared... We will try by deleting jMoby and re-downloading it from the CVS. Hope that fix the problem Thanks for your help, Regards, Pierre From edward.kawas at gmail.com Wed Sep 10 09:33:30 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 06:33:30 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7CC35.6090803@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> Message-ID: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> I also forgot to mention that I also tried looking for your services in the database that backs the registry and failed to find it! ??? 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: September-10-08 6:32 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Edward Kawas wrote: > Hi, > > I am trying to reproduce your problems, but I cannot. I am not seeing any > SOAP exceptions and I don't see your service either. Strange since Andreas seems to see it as well as another person that contacted us off-list. > The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I > tried to use non utf8 characters in my soap message. > What surprise us the most is that two of our services that we did not change (Solstis_getProjet and dom_test2) are not shown either. The whole authority avilin05.avignon.inra.fr seems to have disappeared... We will try by deleting jMoby and re-downloading it from the CVS. Hope that fix the problem Thanks for your help, Regards, Pierre _______________________________________________ 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 Sep 10 09:47:47 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 10 Sep 2008 15:47:47 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> Message-ID: <48C7D003.3070903@pingoured.fr> Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! This is weird because the registration seems to work (cf below) Could you check Solstis_getProject ? We did not change that one normally. Thanks for your help, Regards, Pierre ../jMoby/build/run/run-cmdline-client -e http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl -uri http://bioinfo.icapture.ubc.ca/MOBY/Central -call registerService ' moby Solstis_getDatasetDescFromKeyword getDataset avilin05.avignon.inra.fr http://avilin05/axis/services/Solstis_getDatasetDescFromKeyword jean-paul.bouchet at avignon.inra.fr 1 String OSE_dataset ' Calling method 'registerService' with the input from ' moby Solstis_getDatasetDescFromKeyword getDataset avilin05.avignon.inra.fr http://avilin05/axis/services/Solstis_getDatasetDescFromKeyword jean-paul.bouchet at avignon.inra.fr 1 String OSE_dataset ': moby Solstis_getDatasetDescFromKeyword getDataset avilin05.avignon.inra.fr http://avilin05/axis/services/Solstis_getDatasetDescFromKeyword jean-paul.bouchet at avignon.inra.fr 1 String OSE_dataset -------------- 0 From groscurt at mpiz-koeln.mpg.de Wed Sep 10 09:53:13 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 10 Sep 2008 15:53:13 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> Message-ID: <48C7D149.1020308@mpiz-koeln.mpg.de> So basically its not there anymore but i can see it in dashboard ? then my cache is old. My problem was not even based on the encoding problem. I set a different cache location and did reload/update and everything. I didnt get any SOAP error, but still the service i registered didnt show up. If i queried the central via the jmoby api and looked explictly for my service i found it... dont know if and how this error might be reproducable :( Best andreas Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > > ??? > > 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: September-10-08 6:32 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Problem with dashboard to list services > > Edward Kawas wrote: > >> Hi, >> >> I am trying to reproduce your problems, but I cannot. I am not seeing any >> SOAP exceptions and I don't see your service either. >> > > Strange since Andreas seems to see it as well as another person that > contacted us off-list. > > >> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I >> tried to use non utf8 characters in my soap message. >> >> > > What surprise us the most is that two of our services that we did not > change (Solstis_getProjet and dom_test2) are not shown either. > > The whole authority avilin05.avignon.inra.fr seems to have disappeared... > > > We will try by deleting jMoby and re-downloading it from the CVS. > Hope that fix the problem > > Thanks for your help, > Regards, > > Pierre > _______________________________________________ > 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 > -- ===================================================== 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 jason.e.stewart at gmail.com Wed Sep 10 10:28:16 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Wed, 10 Sep 2008 19:58:16 +0530 Subject: [MOBY-dev] More info on SOAP::Lite document/literal Message-ID: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> Hey Eddie, So I dug a bit on the server side and this is what I found. If your server class subclasses from SOAP::Server::Parameters, the method will get an extra parameter of type SOAP::SOM which gives access to all the request information. That object contains a lot of methods for searching the soap envelope - but it converts all the data it finds into a SOAP::Data instance - which throws away all attributes not located at the root of the data being returned. For example if the XML looked like this: Joe Blow Joe and we did a query like $root = $som->dataof('//Body'), then $root would be the soap:Body and we would see all of the sub-elements but not their attributes. Only if we do $gn = $som->dataof('//givenName') do we actually get the givenName element with the middlename attribute still intact. But the $som object has all the information in an internal hash table - both as a hash table representation of the entire message and the HTTP::Request object with the original XML. What I don't understand is why when the dataof() method traverses the internal hash table structure it throws away all the attributes not on the root element being returned. Also, I don't understand why there isn't a method that just returns the content of the soap:Body element as plain XML - this should be the default behavior for document/literal. I would like to see a call something like $xml = $som->document(); Any thoughts of how I could make this interface most useful for MOBY purposes? I will have to alter the internal SOAP::Lite code, and send the patches to the maintainers. Cheers, jas. From jmfernandez at cnio.es Wed Sep 10 11:06:50 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Wed, 10 Sep 2008 17:06:50 +0200 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> Message-ID: <48C7E28A.6020203@cnio.es> Hi Jason, when we were developing the Perl MOBY::Async libraries we had the same problem (we needed to access to the full input message), and we solved it using custom deserializers fom WSRF::Lite package. Next sentences set-up them: my $server = new SOAP::Transport::HTTP::CGI; $server->serializer(WSRF::Serializer->new); $server->deserializer(WSRF::Deserializer->new); WSRF::Serializer and WSRF::Deserializer are subclasses of SOAP::Serializer and SOAP::Deserializer, respectively. SOAP::Deserializer translates input SOAP message into a SOAP::SOM instance. WSRF::Deserializer translates input SOAP message into a WSRF::SOM instance, which is a SOAP::SOM instance plus a new method called 'raw_xml'. This method returns the raw input message, which can be parsed with XML::LibXML (for instance). Hope this helps, Jos? Mar?a Jason Stewart wrote: > Hey Eddie, > > So I dug a bit on the server side and this is what I found. > > If your server class subclasses from SOAP::Server::Parameters, the > method will get an extra parameter of type SOAP::SOM which gives > access to all the request information. That object contains a lot of > methods for searching the soap envelope - but it converts all the data > it finds into a SOAP::Data instance - which throws away all attributes > not located at the root of the data being returned. For example if the > XML looked like this: > > > > Joe Blow > Joe > > > > and we did a query like $root = $som->dataof('//Body'), then $root > would be the soap:Body and we would see all of the sub-elements but > not their attributes. Only if we do $gn = $som->dataof('//givenName') > do we actually get the givenName element with the middlename attribute > still intact. > > But the $som object has all the information in an internal hash table > - both as a hash table representation of the entire message and the > HTTP::Request object with the original XML. > > What I don't understand is why when the dataof() method traverses the > internal hash table structure it throws away all the attributes not on > the root element being returned. > > Also, I don't understand why there isn't a method that just returns > the content of the soap:Body element as plain XML - this should be the > default behavior for document/literal. I would like to see a call > something like $xml = $som->document(); > > Any thoughts of how I could make this interface most useful for MOBY > purposes? I will have to alter the internal SOAP::Lite code, and send > the patches to the maintainers. > > Cheers, jas. > _______________________________________________ > 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 martin.senger at gmail.com Wed Sep 10 14:28:06 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 11 Sep 2008 02:28:06 +0800 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7C24F.3050709@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> Message-ID: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> > Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 > sequence. This seems to be a re-occurrence of the same problem that we were solving couple of months ago with a service from Germany. In that case, the problem was caused by using non-ascii characters (such as German umlaut characters) in the service description. The problem was (and I guess still is, with your services) has two parts: First, jMoby (in Dashboard but also in any other usage og its libraries) may send a wrong Unicode characters. This is probably a bug in my libraries. I should fix it. Second, BioMoby central registry accepts wrong Unicode characters, stores them in its database and sends back them as an invalid XML. This should be fixed by Eddie or Mark I guess. If I am correct and your situation is indeed the one I am describing, it is a very dangerous situation because by registering a service with such description *all* jMoby users around the world will be affected (their Dashboards, for example, will not be able to reload or update anymore - until Eddie manually fixes the descriptions in the registry database; that's how he fixed it last time). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Wed Sep 10 14:41:24 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 11:41:24 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> Message-ID: <48c814e0.14b48c0a.2f35.ffff9d83@mx.google.com> So I haven't seen anything obvious in the description field for the services from avilin05.avignon.inra.fr. I am trying to track down the offending service and once it is found, I will fix it. Then I will update the registry to use the utf8 patch that I coded last month to solve this problem. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: September-10-08 11:28 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services > Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 > sequence. This seems to be a re-occurrence of the same problem that we were solving couple of months ago with a service from Germany. In that case, the problem was caused by using non-ascii characters (such as German umlaut characters) in the service description. The problem was (and I guess still is, with your services) has two parts: First, jMoby (in Dashboard but also in any other usage og its libraries) may send a wrong Unicode characters. This is probably a bug in my libraries. I should fix it. Second, BioMoby central registry accepts wrong Unicode characters, stores them in its database and sends back them as an invalid XML. This should be fixed by Eddie or Mark I guess. If I am correct and your situation is indeed the one I am describing, it is a very dangerous situation because by registering a service with such description *all* jMoby users around the world will be affected (their Dashboards, for example, will not be able to reload or update anymore - until Eddie manually fixes the descriptions in the registry database; that's how he fixed it last time). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Sep 10 15:20:59 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 12:20:59 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> Message-ID: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com> Okay, I found the culprit and I have fixed it. It was a the service simpleTest under the authority mpiz-koeln.mpg.de. I will also deploy patches to the test registry to see if we can trap these errors in the future. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: September-10-08 11:28 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services > Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 > sequence. This seems to be a re-occurrence of the same problem that we were solving couple of months ago with a service from Germany. In that case, the problem was caused by using non-ascii characters (such as German umlaut characters) in the service description. The problem was (and I guess still is, with your services) has two parts: First, jMoby (in Dashboard but also in any other usage og its libraries) may send a wrong Unicode characters. This is probably a bug in my libraries. I should fix it. Second, BioMoby central registry accepts wrong Unicode characters, stores them in its database and sends back them as an invalid XML. This should be fixed by Eddie or Mark I guess. If I am correct and your situation is indeed the one I am describing, it is a very dangerous situation because by registering a service with such description *all* jMoby users around the world will be affected (their Dashboards, for example, will not be able to reload or update anymore - until Eddie manually fixes the descriptions in the registry database; that's how he fixed it last time). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ 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 Sep 10 15:35:11 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 10 Sep 2008 13:35:11 -0600 Subject: [MOBY-dev] Problems calling a Moby service with secondary parameters In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de> References: <000001c90da5$eb498a40$c1dc9ec0$@de> Message-ID: <48C8216F.8090801@ucalgary.ca> Hi Michael, Sorry for not getting back to you earlier. The problem is in the way to create the secondary data instances. If you do a toString() on them, you;ll see that they have a blank name based on the constructor you used. The easiest way to use the default secondaries is with the one-arg constructor, e.g.: int i = 0; for (MobySecondaryData param: service.getSecondaryInputs()) { secParams[i++] = new MobyDataSecondaryInstance(param); //auto-populates the instance with the template's default value } I'll add a check to MobyRequest that'll complain if you give blank or duplicately named secondaries, which should make this mistake more obvious to others in the future. Regards, Paul P.S. I've also updated MobyDataComposite to handle put() for cases such as your where the data type is not in the registry yet, facilitating testing. Better yet though is to use the test registry in such cases. Michael Gerlich wrote: > Hi all, > > I'm working on a simple java app (client) that calls some Biomoby services I > wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist" > registered under authority "ipb-halle.de" takes additional 2 secondary > parameters that modify its query behavior and the resulting number of > outputs. > > Now when I try to add both secondary parameters to the input, the service > call fails with the following message: > > Exception in thread "main" org.biomoby.shared.MobyException: Service > get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but > takes 2 (query 1). Extra secondary parameters must have been specified > at > org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java > :928) > at > org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302) > at > org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282) > at > org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275) > at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86) > > > My code is like that: > > Central worker = new CentralImpl(); > templateService = new MobyService("get_DBLinks_From_Peaklist", authority); > // authority = "ipb-halle.de" > validServices = worker.findService(templateService); > > comp = new MobyDataComposite(new MobyDataType("MSPeakRel")); > comp.put("relInt", new MobyDataInt(999)); > comp.put("mz", new MobyDataFloat(273.069)); > > MobyDataSecondaryInstance[] secParams = new > MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length]; > for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) { > secParams[i] = new MobyDataSecondaryInstance(new > MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()), > validServices[0].getSecondaryInputs()[i].getDefaultValue()); } > > mr.setService(validServices[0]); > mr.setInput(comp); > mr.setSecondaryInput(secParams); > System.out.println(mr.invokeService().toString()); > > > > The setSecondaryInput() function takes an array that consists of all > parameters and applies them to all inputs. Now there are 2 parameters and an > array of length 2 - with the default values for both parameters (I defined > default values for both parameters). > > Some hints what I'm doing wrong? > > > Another question - my input is of type MSPeakRel and is defined as > collection. How do I manage to add multiple inputs - in this case, they > would represent a complete peaklist of (m/z value, relative intensity) for > querying a database? > > > > Best wishes, > > Michael > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,48be578210950321565264! > > > > From gordonp at ucalgary.ca Wed Sep 10 16:08:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 10 Sep 2008 14:08:52 -0600 Subject: [MOBY-dev] Java MobyRequest changes In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de> References: <000001c90da5$eb498a40$c1dc9ec0$@de> Message-ID: <48C82954.5030507@ucalgary.ca> Hi all, If you use MobyRequest in your code, please note that setSecondaries() now throws a MobyException in CVS. This is to help catch problems with invalid secondary parameter values. You will need to ensure any call to this method is now enclosed in a "try" block. Sorry for any inconvenience this API change may cause. Paul From jason.e.stewart at gmail.com Thu Sep 11 00:14:54 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Thu, 11 Sep 2008 09:44:54 +0530 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <48C7E28A.6020203@cnio.es> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> Message-ID: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com> Hey Jose, On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez wrote: > when we were developing the Perl MOBY::Async libraries we had the > same problem (we needed to access to the full input message), and we solved > it using custom deserializers fom WSRF::Lite package. Thanks, that's useful for MOBY users, definately. I still think that it should be a functionality that is built into the core of SOAP::Lite, though, especially since document/literal is the standard encoding now. I will get a response from Martin, the current maintainer of SOAP::Lite, and see what he thinks should be done. Likewise, on the client side it should be made trivial to attach a fragment of XML as the body of the soap message without any interference from SOAP::Lite. Any comments? Thanks, jas. From groscurt at mpiz-koeln.mpg.de Thu Sep 11 01:50:02 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 11 Sep 2008 07:50:02 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> <48c81e2a.16538c0a.5326.ffffb815@mx.google.com> Message-ID: <48C8B18A.7020401@mpiz-koeln.mpg.de> ohoh - that was my service... at least kind of - i tested the problem we discussed last time with the umlaut etc. I'm sorry - i totally forgot that service :( Andreas Edward Kawas wrote: > Okay, I found the culprit and I have fixed it. It was a the service > simpleTest under the authority mpiz-koeln.mpg.de. > > I will also deploy patches to the test registry to see if we can trap these > errors in the future. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: September-10-08 11:28 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Problem with dashboard to list services > > >> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte >> > UTF-8 > >> sequence. >> > > > This seems to be a re-occurrence of the same problem that we were solving > couple of months ago with a service from Germany. In that case, the problem > was caused by using non-ascii characters (such as German umlaut characters) > in the service description. The problem was (and I guess still is, with your > services) has two parts: > > First, jMoby (in Dashboard but also in any other usage og its libraries) may > send a wrong Unicode characters. This is probably a bug in my libraries. I > should fix it. > > Second, BioMoby central registry accepts wrong Unicode characters, stores > them in its database and sends back them as an invalid XML. This should be > fixed by Eddie or Mark I guess. > > If I am correct and your situation is indeed the one I am describing, it is > a very dangerous situation because by registering a service with such > description *all* jMoby users around the world will be affected (their > Dashboards, for example, will not be able to reload or update anymore - > until Eddie manually fixes the descriptions in the registry database; that's > how he fixed it last time). > > Martin > > -- ===================================================== 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 Thu Sep 11 03:45:30 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 11 Sep 2008 09:45:30 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> Message-ID: <48C8CC9A.7050808@pingoured.fr> Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > Few minutes after this email and after a couple of trials we have been able to see our services again. What we observed is: - avilin05.avignon.inra.fr appears in the second position in the /moses generator/ panel while it was easily at the fourth or fifth position before. - the list of services starting by the letter 's' (or S) seems to have decrease dramatically now compare to earlier. - when we try to reload or update our cache, or when we regenerate it after removal when ends with the following error: "rethrew: org.xml.sax.SAXParseException: XML document structures must start and end within the same entity." In the console I got the following error: dashboard: [Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] [Fatal Error] :-1:-1: Premature end of file. It does not stop us from work so that's more for the report. To us it would seems like something has gone wrong yesterday on the server and a file has been corrupted ? Thanks for your help, Best regards, Pierre From jason.e.stewart at gmail.com Thu Sep 11 04:54:10 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Thu, 11 Sep 2008 14:24:10 +0530 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <48C7E28A.6020203@cnio.es> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> Message-ID: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com> Hi Jose Maria, On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez wrote: > $server->serializer(WSRF::Serializer->new); This code dies with a class not found error from Perl, I presume you mean WSRF::WSRFSerializer->new? Cheers, jas. From edward.kawas at gmail.com Thu Sep 11 09:11:07 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Sep 2008 06:11:07 -0700 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com> Message-ID: <48c918f9.27b38c0a.385f.ffffdcea@mx.google.com> Hi Jason, I like your thinking. I don?t have much experience with doc/lit services, but I do feel that the additions that you have mentioned would probably be best (and similar to what we have now for rpc/encoded). 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 Jason Stewart Sent: September-10-08 9:15 PM To: Core developer announcements Subject: Re: [MOBY-dev] More info on SOAP::Lite document/literal Hey Jose, On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez wrote: > when we were developing the Perl MOBY::Async libraries we had the > same problem (we needed to access to the full input message), and we solved > it using custom deserializers fom WSRF::Lite package. Thanks, that's useful for MOBY users, definately. I still think that it should be a functionality that is built into the core of SOAP::Lite, though, especially since document/literal is the standard encoding now. I will get a response from Martin, the current maintainer of SOAP::Lite, and see what he thinks should be done. Likewise, on the client side it should be made trivial to attach a fragment of XML as the body of the soap message without any interference from SOAP::Lite. Any comments? Thanks, jas. _______________________________________________ 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 Sep 11 09:15:49 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Sep 2008 06:15:49 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C8CC9A.7050808@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> <48C8CC9A.7050808@pingoured.fr> Message-ID: <48c91a12.16538c0a.530a.ffffdd16@mx.google.com> Yes, for some reason the file is not being generated properly. I am not sure if this is a memory problem on the server or ...??? I noticed that yesterday, the RDF file is generated once properly and then truncated the following times. Hopefully I get this fixed soon, 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: September-11-08 12:46 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > Few minutes after this email and after a couple of trials we have been able to see our services again. What we observed is: - avilin05.avignon.inra.fr appears in the second position in the /moses generator/ panel while it was easily at the fourth or fifth position before. - the list of services starting by the letter 's' (or S) seems to have decrease dramatically now compare to earlier. - when we try to reload or update our cache, or when we regenerate it after removal when ends with the following error: "rethrew: org.xml.sax.SAXParseException: XML document structures must start and end within the same entity." In the console I got the following error: dashboard: [Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] [Fatal Error] :-1:-1: Premature end of file. It does not stop us from work so that's more for the report. To us it would seems like something has gone wrong yesterday on the server and a file has been corrupted ? Thanks 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 jerzyo at genesilico.pl Thu Sep 11 10:22:09 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 11 Sep 2008 16:22:09 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java Message-ID: <48C92991.2000407@genesilico.pl> Hi I have several hundreds of workflows made up of BioMoby Services and want to execute them all without opening any GUI. I was looking for some solution over the internet and the think I came across was using Taverna plugin and try to execute it programaticaly. I have a few questions: 1. Is it the only way? 2. I found several tutorial tutorials on running saved workflow saved in scufl language. http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html How do you one make a workflow step by step? like: workflow.addProcesor(...) workflow.addConnector(...) ... workflow.execute() and especially, how do one add BioMoby objects this way? Is there any tutorial or do I have go though the API? Best Jerzy Orlowski From edward.kawas at gmail.com Thu Sep 11 10:36:02 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Sep 2008 07:36:02 -0700 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C92991.2000407@genesilico.pl> References: <48C92991.2000407@genesilico.pl> Message-ID: <48c92ce0.28d7720a.65e4.0366@mx.google.com> Hi Jerzy, You can execute workflows from the command line too if you have your input file for the workflows handy. If you want to create workflows programmatically, you will need to look at the javadoc for the taverna source code. You should probably explore the taverna website[1] and its manual[2] for more information. Eddie [1] http://taverna.sourceforge.net/ [2] http://taverna.sourceforge.net/doc -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: September-11-08 7:22 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Executing Moby Workflow straight from java Hi I have several hundreds of workflows made up of BioMoby Services and want to execute them all without opening any GUI. I was looking for some solution over the internet and the think I came across was using Taverna plugin and try to execute it programaticaly. I have a few questions: 1. Is it the only way? 2. I found several tutorial tutorials on running saved workflow saved in scufl language. http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html How do you one make a workflow step by step? like: workflow.addProcesor(...) workflow.addConnector(...) ... workflow.execute() and especially, how do one add BioMoby objects this way? Is there any tutorial or do I have go though the API? Best Jerzy Orlowski _______________________________________________ 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 Sep 11 10:49:25 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 11 Sep 2008 16:49:25 +0200 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com> Message-ID: <48C92FF5.5040405@cnio.es> Hi Jason, yes, you are right, it should be WSRF::WSRFSerializer. We have some pending janitorial work on MOBY::Async, related to our usage of some namespace classes which we do not own (WSRF::Serializer is one of those cases). Best Regards, Jos? Mar?a Jason Stewart wrote: > Hi Jose Maria, > > On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez > wrote: > >> $server->serializer(WSRF::Serializer->new); > > This code dies with a class not found error from Perl, I presume you > mean WSRF::WSRFSerializer->new? > > Cheers, jas. > > _______________________________________________ > 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 serr at ac.uma.es Thu Sep 11 10:38:49 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Thu, 11 Sep 2008 16:38:49 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C92991.2000407@genesilico.pl> References: <48C92991.2000407@genesilico.pl> Message-ID: <48C92D79.9010706@ac.uma.es> Hello Jerzy I had the same problem that you. I have got it to work by browsing deep in the Taverna code. I cannot give you many sample code because I'm trying to organize all the code tries and examples that I have. But I can give you some comments: For build a workflow model the class is: org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new ScuflModel(); This class contains the methods that you mention addProcessor ... For run I'm using freeflow, because taverna classes and raven are a "little" tricky. The classes: uk.ac.soton.itinnovation.freefluo.main.Engine or org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy can help you. I hope this little details help you to begin. If you have more detailed questions I will be very happy of help you. Best regards, Sergio Jerzy Orlowski wrote: > Hi > > I have several hundreds of workflows made up of BioMoby Services and > want to execute them all without opening any GUI. > > I was looking for some solution over the internet and the think I came > across was using Taverna plugin and try to execute it programaticaly. > I have a few questions: > > 1. Is it the only way? > > 2. I found several tutorial tutorials on running saved workflow saved > in scufl language. > http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html > > How do you one make a workflow step by step? like: > > workflow.addProcesor(...) > workflow.addConnector(...) > ... > workflow.execute() > > and especially, how do one add BioMoby objects this way? Is there any > tutorial or do I have go though the API? > > Best > > Jerzy Orlowski > > _______________________________________________ > 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 gordonp at ucalgary.ca Thu Sep 11 11:10:13 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 11 Sep 2008 09:10:13 -0600 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C92D79.9010706@ac.uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> Message-ID: <48C934D5.50700@ucalgary.ca> I think whoever has a headless Taverna workflow creation and/or enactment working should put examples up in the Java developer's section of the Moby Web site...I believe the myExperiment people also have a headless workflow enactment engine working now...anyone from there on this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in the BioWEP software. So many people are doing this, but no good sample code is easily available, especially for Moby services... Sergio Ramirez Ramirez wrote: > Hello Jerzy > > I had the same problem that you. > > I have got it to work by browsing deep in the Taverna code. I cannot > give you many sample code because I'm trying to organize all the code > tries and examples that I have. > > But I can give you some comments: > > For build a workflow model the class is: > org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new > ScuflModel(); > This class contains the methods that you mention addProcessor ... > > For run I'm using freeflow, because taverna classes and raven are a > "little" tricky. The classes: > uk.ac.soton.itinnovation.freefluo.main.Engine or > org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy > can help you. > > I hope this little details help you to begin. If you have more > detailed questions I will be very happy of help you. > > Best regards, > Sergio > > Jerzy Orlowski wrote: >> Hi >> >> I have several hundreds of workflows made up of BioMoby Services and >> want to execute them all without opening any GUI. >> >> I was looking for some solution over the internet and the think I >> came across was using Taverna plugin and try to execute it >> programaticaly. >> I have a few questions: >> >> 1. Is it the only way? >> >> 2. I found several tutorial tutorials on running saved workflow >> saved in scufl language. >> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >> >> >> How do you one make a workflow step by step? like: >> >> workflow.addProcesor(...) >> workflow.addConnector(...) >> ... >> workflow.execute() >> >> and especially, how do one add BioMoby objects this way? Is there any >> tutorial or do I have go though the API? >> >> Best >> >> Jerzy Orlowski >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From serr at ac.uma.es Thu Sep 11 11:23:30 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Thu, 11 Sep 2008 17:23:30 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C934D5.50700@ucalgary.ca> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> Message-ID: <48C937F2.3030708@ac.uma.es> Here there is my small contribution, just the two methods that I use for run a workflow. Hope it can help to someone Paul Gordon wrote: > I think whoever has a headless Taverna workflow creation and/or > enactment working should put examples up in the Java developer's > section of the Moby Web site...I believe the myExperiment people also > have a headless workflow enactment engine working now...anyone from > there on this list? Also, Paolo Romano in Italy has a headless SCUFL > enactor in the BioWEP software. So many people are doing this, but no > good sample code is easily available, especially for Moby services... > > Sergio Ramirez Ramirez wrote: >> Hello Jerzy >> >> I had the same problem that you. >> >> I have got it to work by browsing deep in the Taverna code. I cannot >> give you many sample code because I'm trying to organize all the code >> tries and examples that I have. >> >> But I can give you some comments: >> >> For build a workflow model the class is: >> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >> new ScuflModel(); >> This class contains the methods that you mention addProcessor ... >> >> For run I'm using freeflow, because taverna classes and raven are a >> "little" tricky. The classes: >> uk.ac.soton.itinnovation.freefluo.main.Engine or >> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >> can help you. >> >> I hope this little details help you to begin. If you have more >> detailed questions I will be very happy of help you. >> >> Best regards, >> Sergio >> >> Jerzy Orlowski wrote: >>> Hi >>> >>> I have several hundreds of workflows made up of BioMoby Services and >>> want to execute them all without opening any GUI. >>> >>> I was looking for some solution over the internet and the think I >>> came across was using Taverna plugin and try to execute it >>> programaticaly. >>> I have a few questions: >>> >>> 1. Is it the only way? >>> >>> 2. I found several tutorial tutorials on running saved workflow >>> saved in scufl language. >>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>> >>> >>> How do you one make a workflow step by step? like: >>> >>> workflow.addProcesor(...) >>> workflow.addConnector(...) >>> ... >>> workflow.execute() >>> >>> and especially, how do one add BioMoby objects this way? Is there >>> any tutorial or do I have go though the API? >>> >>> Best >>> >>> Jerzy Orlowski >>> >>> _______________________________________________ >>> 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 > -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: runWF.java Type: text/java Size: 2093 bytes Desc: not available URL: From jmfernandez at cnio.es Thu Sep 11 11:49:29 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 11 Sep 2008 17:49:29 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C937F2.3030708@ac.uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> Message-ID: <48C93E09.3030107@cnio.es> Hi everybody, as Sergio *should* know, we have at INB IWWE&M, which means 'Interactive Web Workflow Enactor and Manager'. It is able to host workflows, workflow examples with documentation, do web workflow enactions, and take and store workflow enaction snapshots. Next days we are going to have a Trac server with is going to host the source code and development of IWWE&M. Best Regards, Jos? Mar?a Sergio Ramirez Ramirez wrote: > Here there is my small contribution, just the two methods that I use for > run a workflow. > Hope it can help to someone > > Paul Gordon wrote: >> I think whoever has a headless Taverna workflow creation and/or >> enactment working should put examples up in the Java developer's >> section of the Moby Web site...I believe the myExperiment people also >> have a headless workflow enactment engine working now...anyone from >> there on this list? Also, Paolo Romano in Italy has a headless SCUFL >> enactor in the BioWEP software. So many people are doing this, but no >> good sample code is easily available, especially for Moby services... >> >> Sergio Ramirez Ramirez wrote: >>> Hello Jerzy >>> >>> I had the same problem that you. >>> >>> I have got it to work by browsing deep in the Taverna code. I cannot >>> give you many sample code because I'm trying to organize all the code >>> tries and examples that I have. >>> >>> But I can give you some comments: >>> >>> For build a workflow model the class is: >>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>> new ScuflModel(); >>> This class contains the methods that you mention addProcessor ... >>> >>> For run I'm using freeflow, because taverna classes and raven are a >>> "little" tricky. The classes: >>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>> can help you. >>> >>> I hope this little details help you to begin. If you have more >>> detailed questions I will be very happy of help you. >>> >>> Best regards, >>> Sergio >>> >>> Jerzy Orlowski wrote: >>>> Hi >>>> >>>> I have several hundreds of workflows made up of BioMoby Services and >>>> want to execute them all without opening any GUI. >>>> >>>> I was looking for some solution over the internet and the think I >>>> came across was using Taverna plugin and try to execute it >>>> programaticaly. >>>> I have a few questions: >>>> >>>> 1. Is it the only way? >>>> >>>> 2. I found several tutorial tutorials on running saved workflow >>>> saved in scufl language. >>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>> >>>> >>>> How do you one make a workflow step by step? like: >>>> >>>> workflow.addProcesor(...) >>>> workflow.addConnector(...) >>>> ... >>>> workflow.execute() >>>> >>>> and especially, how do one add BioMoby objects this way? Is there >>>> any tutorial or do I have go though the API? >>>> >>>> Best >>>> >>>> Jerzy Orlowski >>>> >>>> _______________________________________________ >>>> 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 -- "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 alanrw at cs.man.ac.uk Thu Sep 11 11:25:18 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Thu, 11 Sep 2008 16:25:18 +0100 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C934D5.50700@ucalgary.ca> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> Message-ID: <48C9385E.8060209@cs.man.ac.uk> Paul Gordon wrote: > I think whoever has a headless Taverna workflow creation and/or > enactment working should put examples up in the Java developer's section > of the Moby Web site...I believe the myExperiment people also have a > headless workflow enactment engine working now...anyone from there on > this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in > the BioWEP software. So many people are doing this, but no good sample > code is easily available, especially for Moby services... If by headless you mean without the UI, then there is a WorkflowLauncher that enacts a Taverna workflow. The source code (written by the myGrid team) can be downloaded from http://prdownloads.sourceforge.net/taverna/workflowlauncher-0.1.2.zip?download It may not what you need as it reads in a pre-existing Taverna workflow - it does not create one programmatically. You can also execute a Taverna workflow on a remote machine see myExperiment can run the workflow you are looking at on a Taverna remote execution engine. (You will, of course, need to have the right authorization to get at a given remote enactor.) I'm rather confused as to what people are trying to do. Could someone give a use case? I'll probably have to get Katy Wolstencroft to explain the biology for me :-) Alan R Williams (currently the support hat wearer for Taverna) From jason at bioteam.net Thu Sep 11 21:54:46 2008 From: jason at bioteam.net (jason) Date: Fri, 12 Sep 2008 09:54:46 +0800 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> Message-ID: <48C9CBE6.7010808@bioteam.net> Hi, all Edward Kawas wrote: > Hi, > > I am trying to reproduce your problems, but I cannot. I am not seeing any > SOAP exceptions and I don't see your service either. > > The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I > tried to use non utf8 characters in my soap message. > Part of the Moby code use String manipulation to parse and generate Xml message instead of using a standard of XML parsing/writing. The invalid byte could be related to this. I saw this error in another project. Xml message generated by String concatenation could cause many unexpected XML parsing error. > Eddie > > > From soiland-reyes at cs.manchester.ac.uk Fri Sep 12 04:46:03 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 12 Sep 2008 09:46:03 +0100 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBBFAD.7060401@ac.uma.es> References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es> Message-ID: On Mon, Sep 1, 2008 at 11:10, Sergio Ramirez Ramirez wrote: > Unfortunately, moby can not handle workflows by itself for now. Normally you > use taverna for building workflows. > I'm trying to learn how to use Taverna libraries to run workflows. There is > a taverna class (workflowlauncher or similar) available in the web page for > taverna, but I couldn't make it work. Hi, also check out http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram.html If you can't make it work - do please send us an email about what kind of error message you get or what doesn't work - so we can improve it. Note that if you run this within a container like Tomcat (instead of standalone, which should work) you might run into issues recently uncovered, there's a workaround described here: http://markmail.org/search/?q=taverna-hackers+globus#query:taverna-hackers%20globus+page:1+mid:leq2tlx3adyekssq+state:results I recommend signing up to the taverna-hackers mailing list for any further questions and issues you might run into - we're happy to help! http://taverna.sourceforge.net/lists -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From edward.kawas at gmail.com Fri Sep 12 09:41:51 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 12 Sep 2008 06:41:51 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C8CC9A.7050808@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> <48C8CC9A.7050808@pingoured.fr> Message-ID: <48ca71b0.2a528c0a.282c.ffffba33@mx.google.com> Hi All, The problem now should be all fixed. I recently created a patch to avoid this non utf8 mess and deployed it on the test registry; moreover, the RDF shouldn't cause problems with Dashboard. Let me know how things work out, 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: September-11-08 12:46 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > Few minutes after this email and after a couple of trials we have been able to see our services again. What we observed is: - avilin05.avignon.inra.fr appears in the second position in the /moses generator/ panel while it was easily at the fourth or fifth position before. - the list of services starting by the letter 's' (or S) seems to have decrease dramatically now compare to earlier. - when we try to reload or update our cache, or when we regenerate it after removal when ends with the following error: "rethrew: org.xml.sax.SAXParseException: XML document structures must start and end within the same entity." In the console I got the following error: dashboard: [Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] [Fatal Error] :-1:-1: Premature end of file. It does not stop us from work so that's more for the report. To us it would seems like something has gone wrong yesterday on the server and a file has been corrupted ? Thanks 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 Sep 18 13:08:21 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 18 Sep 2008 10:08:21 -0700 Subject: [MOBY-dev] FWD: Making SOAP::Lite painlessly support document-literal encoding In-Reply-To: <146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry> References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com><48d26bbb.27b38c0a.32a5.ffff9576@mx.google.com> <146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry> Message-ID: <48d28b06.1cbd720a.50af.ffff83bc@mx.google.com> Just to keep everyone on the list in the know ... Eddie -------------------- From: "Ed Kawas" Date: Thu, 18 Sep 2008 07:54:49 To: 'Jason Stewart'; 'Mark'; 'Martin Kutter'; Subject: RE: Making SOAP::Lite painlessly support document-literal encoding Hi Jason, I like the fact that you hand off the XML document to the server service developer. Also the ability of the client to just attach a document looks good too. I wonder how other toolkits do it? I am pretty sure that if the soap envelope was compatible with other toolkits and all I could do was get/set the XML document, I would definitely start using S::L for doc/lit services. Eddie -----Original Message----- From: Jason Stewart [mailto:jason.e.stewart at gmail.com] Sent: September-18-08 1:40 AM To: Mark; Martin Kutter; soaplite-devel at lists.sf.net; Ed Kawas Subject: Making SOAP::Lite painlessly support document-literal encoding Hey All, So I've been doing a lot of digging through the codebase understanding how doc/lit could be used at the moment, and I find that the ease of use that S::L provides for rpc/enc is not matched in it's doc/lit support. I don't think it would take very much effort to enable simple support for doc/lit on both the client and the server - but very likely there would be issues with compatibility with Java and .NET implementations that would have to be worked out. For me the major difference is that a client wanting to use a doc/lit service wants to simply attach a pre-produced XML payload to the soap message - and the server wants to retrieve that message - WITHOUT ANY INTERFERENCE FROM SOAP::LIT. so we have: -- begin of client.pl 8< -- use SOAP::Lite; my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); my $xml =< Kutter Martin Hello Martin Kutter! XML $soap->on_action( sub { "urn:HelloWorld#sayHello" }); $soap->autotype(0); $soap->default_ns('urn:HelloWorld'); my $som = $soap->document($xml)->call("sayHello"); die $som->fault->{ faultstring } if ($som->fault); print $som->result, "\n"; -- end of client.pl -- -- begin server.pl 8< -- package HelloWorld; use SOAP::Lite; use base qw(SOAP::Server::Document); sub sayHello { my $self = shift; my $doc = shift; my $som = shift; my $ret_val = some_processing_method($doc); return $ret_val; } -- end of server.pl -- The client builds an XML document inserts it into the request using the document() method on the SOAP object. The client subclasses from SOAP::Server::Document so it gets the XML payload as the second argument on the stack, processes it somehow, and returns an XML payload back to the client. feedback? Cheers, jas. From jason.e.stewart at gmail.com Fri Sep 19 04:02:49 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Fri, 19 Sep 2008 13:32:49 +0530 Subject: [MOBY-dev] Making SOAP::Lite painlessly support document-literal encoding In-Reply-To: <1221760547.9975.19.camel@cyclops> References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com> <1221760547.9975.19.camel@cyclops> Message-ID: <41c1ade50809190102n16ee2f2fh94dd0da1d7dc9e@mail.gmail.com> Hey All, I like your suggestions Martin. I think the namespace SOAP::Lite::Server::Document is definitely the way to go. I support the idea of using a SOAP::Data object in addition to an XML scalar as the value for either the client or the server. I will make a patch and some test cases and send them to the list. Cheers, jas. On Thu, Sep 18, 2008 at 11:25 PM, Martin Kutter wrote: > Hi Jason, > > forcing the server developer to create XML may or may not be a good > idea, depending on it's complexity. > > How about making the proposed SOAP::Server::Document a bit more DWIM by > accepting either a scalar (which is supposed to be plain XML) or a > SOAP::Data object? > > This would ease migration for existing web services which want to move > to SOAP::Server::Document > > Maybe SOAP::Lite::Server::Document would be the more appropriate name - > the use of the SOAP namespace has provoked numerous errors on CPAN, so > SOAP::Lite is a better namespace for new modules. > > Thanks for your ideas, > > Martin > > Am Donnerstag, den 18.09.2008, 14:10 +0530 schrieb Jason Stewart: >> Hey All, >> >> So I've been doing a lot of digging through the codebase understanding >> how doc/lit could be used at the moment, and I find that the ease of >> use that S::L provides for rpc/enc is not matched in it's doc/lit >> support. I don't think it would take very much effort to enable simple >> support for doc/lit on both the client and the server - but very >> likely there would be issues with compatibility with Java and .NET >> implementations that would have to be worked out. >> >> For me the major difference is that a client wanting to use a doc/lit >> service wants to simply attach a pre-produced XML payload to the soap >> message - and the server wants to retrieve that message - WITHOUT ANY >> INTERFERENCE FROM SOAP::LIT. >> >> so we have: >> >> -- begin of client.pl 8< -- >> >> use SOAP::Lite; >> my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); >> >> my $xml =<> >> Kutter >> Martin >> >> >> >> Hello Martin Kutter! >> >> XML >> >> $soap->on_action( sub { "urn:HelloWorld#sayHello" }); >> $soap->autotype(0); >> $soap->default_ns('urn:HelloWorld'); >> >> my $som = $soap->document($xml)->call("sayHello"); >> >> die $som->fault->{ faultstring } if ($som->fault); >> print $som->result, "\n"; >> >> -- end of client.pl -- >> >> -- begin server.pl 8< -- >> >> package HelloWorld; >> use SOAP::Lite; >> >> use base qw(SOAP::Server::Document); >> >> sub sayHello { >> my $self = shift; >> my $doc = shift; >> my $som = shift; >> >> my $ret_val = some_processing_method($doc); >> return $ret_val; >> } >> >> -- end of server.pl -- >> >> The client builds an XML document inserts it into the request using >> the document() method on the SOAP object. >> >> The client subclasses from SOAP::Server::Document so it gets the XML >> payload as the second argument on the stack, processes it somehow, and >> returns an XML payload back to the client. >> >> feedback? >> >> Cheers, jas. >> > > From jason.e.stewart at gmail.com Fri Sep 19 05:29:46 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Fri, 19 Sep 2008 14:59:46 +0530 Subject: [MOBY-dev] moby doc-lit services. In-Reply-To: <48D411EB.2080606@bsc.es> References: <48D32B1C.3050304@bsc.es> <41c1ade50809190044l124fcf63h52e728402f4a4de3@mail.gmail.com> <48D411EB.2080606@bsc.es> Message-ID: <41c1ade50809190229me6e597arb728754a03ab9eb7@mail.gmail.com> Hey Dmitry, I agree with your suggestion as to the "right" way to do it. I am less concerned with the WSDL, from my current understanding of MOBY (which is very weak I am afraid) the WSDL is almost useless, MOBY-enabled clients will have to be aware of how to deserialize data types that they handle using their own libraries or libraries bundled with MOBY. Originally I thought MOBY would rely heavily on XML Schemas to define their data types, and that would be the core - but since that isn't how things are done, I don't see much use in the WSDL. I'd like to know if I am understanding this incorrectly. Cheers, jas. On Sat, Sep 20, 2008 at 2:26 AM, Dmitry Repchevsky wrote: > Hi Jason, > >> Mark has asked me to modify SOAP::Lite in order to better support doc/lit >> services in general... > > This is a good news, because my concern was that you are going to do a sort > of hack - make a common schema for all services, > something like a "" and pass a Moby message inside... > > What I suggested to do (and this is the "right" way to do in java) is to > pass all the MobyMessage inside a soap message: > Something like: > > > > > > > > > > ns1:id="" > ns1:namespace="">AGHFJHGDKHGJKADGHJGDJH > > > > > > > > > This way there is no problem as it is a STANDARD Moby XML inside a SOAP > . > > The problem is that you need to attach a XML Schema to your WSDL (if you > wish a "real" web-service") > Such a schema could be divided in two parts: > > 1. Static (common for all moby doc/lit services) that contains Moby specific > schema (MobySimple, MobyContent....): > > ****************************************************************************************************************************** > > version="1.0" > targetNamespace="http://www.biomoby.org/moby" > > xmlns:xs="http://www.w3.org/2001/XMLSchema" > > xmlns="http://www.biomoby.org/moby" > > > > > > > > > > > > > > > > > > > > > > > > > > > > > maxOccurs="unbounded"/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ****************************************************************************************************************************** > > 2. Moby Datatypes specific one - that one depends of the ontology types used > by service... > In extreme case you can put the same scheme representing ALL the ontology > (not generate it for every service, but generate it once for the ontology > and use for every service). > You can even put an EXTERNAL reference to it (for example make a servlet > that dynamically generates it from the ontology). This way it will be always > updated. > > Cheers, > > Dmitry > > > > > Jason Stewart wrote: >> >> Hi Dmitry, >> >> On Fri, Sep 19, 2008 at 10:01 AM, Dmitry Repchevsky >> wrote: >> >> >>> >>> My name is Dmitry and I am a developer in Spanish National Institute of >>> Bioinformatics. >>> We just have finished an informal meeting with Mark Wilkinson and he >>> suggested to contact you about moby document/literal services... >>> >>> I have my own implementation of it based on XML Schema and I would like >>> to >>> know the way you are implementing it. >>> >> >> Mark has asked me to modify SOAP::Lite in order to better support >> doc/lit services in general, not just for MOBY. >> >> I'd love to hear more about how you do things. >> >> Currently, I'm in discussion with the SOAP::Lite developer group how >> to modify the core of S::L in order to better handle doc/lit. >> >> Cheers, jas. >> >> > > From jerzyo at genesilico.pl Wed Sep 24 11:55:58 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 24 Sep 2008 17:55:58 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C937F2.3030708@ac.uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> Message-ID: <48DA630E.6050901@genesilico.pl> Hi 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). Where can I find source code or javadoc for uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes? I cannot find in anywhere on the web.... Jerzy Sergio Ramirez Ramirez wrote: > Here there is my small contribution, just the two methods that I use for > run a workflow. > Hope it can help to someone > > Paul Gordon wrote: >> I think whoever has a headless Taverna workflow creation and/or >> enactment working should put examples up in the Java developer's >> section of the Moby Web site...I believe the myExperiment people also >> have a headless workflow enactment engine working now...anyone from >> there on this list? Also, Paolo Romano in Italy has a headless SCUFL >> enactor in the BioWEP software. So many people are doing this, but no >> good sample code is easily available, especially for Moby services... >> >> Sergio Ramirez Ramirez wrote: >>> Hello Jerzy >>> >>> I had the same problem that you. >>> >>> I have got it to work by browsing deep in the Taverna code. I cannot >>> give you many sample code because I'm trying to organize all the code >>> tries and examples that I have. >>> >>> But I can give you some comments: >>> >>> For build a workflow model the class is: >>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>> new ScuflModel(); >>> This class contains the methods that you mention addProcessor ... >>> >>> For run I'm using freeflow, because taverna classes and raven are a >>> "little" tricky. The classes: >>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>> can help you. >>> >>> I hope this little details help you to begin. If you have more >>> detailed questions I will be very happy of help you. >>> >>> Best regards, >>> Sergio >>> >>> Jerzy Orlowski wrote: >>>> Hi >>>> >>>> I have several hundreds of workflows made up of BioMoby Services and >>>> want to execute them all without opening any GUI. >>>> >>>> I was looking for some solution over the internet and the think I >>>> came across was using Taverna plugin and try to execute it >>>> programaticaly. >>>> I have a few questions: >>>> >>>> 1. Is it the only way? >>>> >>>> 2. I found several tutorial tutorials on running saved workflow >>>> saved in scufl language. >>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>> >>>> >>>> How do you one make a workflow step by step? like: >>>> >>>> workflow.addProcesor(...) >>>> workflow.addConnector(...) >>>> ... >>>> workflow.execute() >>>> >>>> and especially, how do one add BioMoby objects this way? Is there >>>> any tutorial or do I have go though the API? >>>> >>>> Best >>>> >>>> Jerzy Orlowski >>>> >>>> _______________________________________________ >>>> 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 groscurt at mpiz-koeln.mpg.de Wed Sep 24 12:31:14 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Wed, 24 Sep 2008 18:31:14 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DA630E.6050901@genesilico.pl> Message-ID: Hi, i would really encourage you to use the taverna mailing list for issues concerning taverna. As some people here have strong experience with it, i think its way better to ask the people working with it and developing it directly. Cheers Andreas ----------------original message----------------- From: "Jerzy Orlowski" jerzyo at genesilico.pl To: moby-dev at lists.open-bio.org Date: Wed, 24 Sep 2008 17:55:58 +0200 ------------------------------------------------- > Hi > > 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). > > Where can I find source code or javadoc for > uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes? > > I cannot find in anywhere on the web.... > > Jerzy > > > Sergio Ramirez Ramirez wrote: >> Here there is my small contribution, just the two methods that I use for >> run a workflow. >> Hope it can help to someone >> >> Paul Gordon wrote: >>> I think whoever has a headless Taverna workflow creation and/or >>> enactment working should put examples up in the Java developer's >>> section of the Moby Web site...I believe the myExperiment people also >>> have a headless workflow enactment engine working now...anyone from >>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL >>> enactor in the BioWEP software. So many people are doing this, but no >>> good sample code is easily available, especially for Moby services... >>> >>> Sergio Ramirez Ramirez wrote: >>>> Hello Jerzy >>>> >>>> I had the same problem that you. >>>> >>>> I have got it to work by browsing deep in the Taverna code. I cannot >>>> give you many sample code because I'm trying to organize all the code >>>> tries and examples that I have. >>>> >>>> But I can give you some comments: >>>> >>>> For build a workflow model the class is: >>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>>> new ScuflModel(); >>>> This class contains the methods that you mention addProcessor ... >>>> >>>> For run I'm using freeflow, because taverna classes and raven are a >>>> "little" tricky. The classes: >>>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>>> can help you. >>>> >>>> I hope this little details help you to begin. If you have more >>>> detailed questions I will be very happy of help you. >>>> >>>> Best regards, >>>> Sergio >>>> >>>> Jerzy Orlowski wrote: >>>>> Hi >>>>> >>>>> I have several hundreds of workflows made up of BioMoby Services and >>>>> want to execute them all without opening any GUI. >>>>> >>>>> I was looking for some solution over the internet and the think I >>>>> came across was using Taverna plugin and try to execute it >>>>> programaticaly. >>>>> I have a few questions: >>>>> >>>>> 1. Is it the only way? >>>>> >>>>> 2. I found several tutorial tutorials on running saved workflow >>>>> saved in scufl language. >>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>>> >>>>> >>>>> >>>>> How do you one make a workflow step by step? like: >>>>> >>>>> workflow.addProcesor(...) >>>>> workflow.addConnector(...) >>>>> ... >>>>> workflow.execute() >>>>> >>>>> and especially, how do one add BioMoby objects this way? Is there >>>>> any tutorial or do I have go though the API? >>>>> >>>>> Best >>>>> >>>>> Jerzy Orlowski >>>>> >>>>> _______________________________________________ >>>>> 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 soiland-reyes at cs.manchester.ac.uk Thu Sep 25 05:54:47 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Thu, 25 Sep 2008 10:54:47 +0100 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DA630E.6050901@genesilico.pl> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> Message-ID: 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. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From jerzyo at genesilico.pl Thu Sep 25 06:22:02 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 25 Sep 2008 12:22:02 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DA6624.7040806@uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es> Message-ID: <48DB664A.6030305@genesilico.pl> I keep trying, but I cannot find anywhere a jar with uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser I have an impression that freefluo is outdated ---------------------------------------------------------------------- uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error with configuration named tavernaClassNotFound for WorkflowParser implementation: uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser at uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108) at uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64) at org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84) at org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11) Caused by: java.lang.ClassNotFoundException: uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102) ... 3 more ------------------------------------------------------------------------ Jerzyo Sergio Ramirez Ramirez wrote: > Hi Jerzy > > I see you cannot got to resolve the problem. > > Try to use this class: org.embl.ebi.escience.scufl.ScuflModel; > > Maybe is what you need. to built your own workflow. > > Keep me informed ;) and good luck. > > Jerzy Orlowski wrote: >> Hi >> >> 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). >> >> Where can I find source code or javadoc for >> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other >> classes? >> >> I cannot find in anywhere on the web.... >> >> Jerzy >> >> >> Sergio Ramirez Ramirez wrote: >>> Here there is my small contribution, just the two methods that I use >>> for run a workflow. >>> Hope it can help to someone >>> >>> Paul Gordon wrote: >>>> I think whoever has a headless Taverna workflow creation and/or >>>> enactment working should put examples up in the Java developer's >>>> section of the Moby Web site...I believe the myExperiment people >>>> also have a headless workflow enactment engine working now...anyone >>>> from there on this list? Also, Paolo Romano in Italy has a headless >>>> SCUFL enactor in the BioWEP software. So many people are doing this, >>>> but no good sample code is easily available, especially for Moby >>>> services... >>>> >>>> Sergio Ramirez Ramirez wrote: >>>>> Hello Jerzy >>>>> >>>>> I had the same problem that you. >>>>> >>>>> I have got it to work by browsing deep in the Taverna code. I >>>>> cannot give you many sample code because I'm trying to organize all >>>>> the code tries and examples that I have. >>>>> >>>>> But I can give you some comments: >>>>> >>>>> For build a workflow model the class is: >>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>>>> new ScuflModel(); >>>>> This class contains the methods that you mention addProcessor ... >>>>> >>>>> For run I'm using freeflow, because taverna classes and raven are a >>>>> "little" tricky. The classes: >>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>>>> can help you. >>>>> >>>>> I hope this little details help you to begin. If you have more >>>>> detailed questions I will be very happy of help you. >>>>> >>>>> Best regards, >>>>> Sergio >>>>> >>>>> Jerzy Orlowski wrote: >>>>>> Hi >>>>>> >>>>>> I have several hundreds of workflows made up of BioMoby Services >>>>>> and want to execute them all without opening any GUI. >>>>>> >>>>>> I was looking for some solution over the internet and the think I >>>>>> came across was using Taverna plugin and try to execute it >>>>>> programaticaly. >>>>>> I have a few questions: >>>>>> >>>>>> 1. Is it the only way? >>>>>> >>>>>> 2. I found several tutorial tutorials on running saved workflow >>>>>> saved in scufl language. >>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>>>> >>>>>> >>>>>> How do you one make a workflow step by step? like: >>>>>> >>>>>> workflow.addProcesor(...) >>>>>> workflow.addConnector(...) >>>>>> ... >>>>>> workflow.execute() >>>>>> >>>>>> and especially, how do one add BioMoby objects this way? Is there >>>>>> any tutorial or do I have go though the API? >>>>>> >>>>>> Best >>>>>> >>>>>> Jerzy Orlowski >>>>>> >>>>>> _______________________________________________ >>>>>> 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 jerzyo at genesilico.pl Fri Sep 26 04:28:48 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Fri, 26 Sep 2008 10:28:48 +0200 Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna Message-ID: <48DC9D40.5030604@genesilico.pl> Hi I think there is one important option missing in BioMoby plugins in Taverna. Suppose I have a MobyService that returns an AminoAcidSequence. I want to extract the sequence on my AminAcidSequence (it is a String object) and use it as input for another MobyServices that eats String as its input. The only way I can do it now is to use a Parser which decomposes AminoAcidSequence to basic types and then construct my String from these basic elements (namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns,aminoacid_'SequenceString',aminoacid_'SequenceString'_id and aminoacid_'SequenceString'_ns). This is not very difficult in this case, but imagine what would happen if I parse an object which is composed of for example WieghtedAminoSequences and try to get AminoAcidSequence out of it... In fact current BioMobyObjectProcessors are processors for constructing MobyObjects (with basic types as input ports and composite types as output ports). There should be another type of BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects (with composite types as input ports and basic types as output ports). Please inform me if such option already exists somewhere and I missed it. Jerzy Orlowski From edward.kawas at gmail.com Fri Sep 26 08:16:20 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Sep 2008 05:16:20 -0700 Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna In-Reply-To: <48DC9D40.5030604@genesilico.pl> References: <48DC9D40.5030604@genesilico.pl> Message-ID: <48dcd299.1bbc720a.76c6.ffffb9d8@mx.google.com> Hi Jerzy, That option is indeed unavailable. It can be something that we add in the future. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: September-26-08 1:29 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna Hi I think there is one important option missing in BioMoby plugins in Taverna. Suppose I have a MobyService that returns an AminoAcidSequence. I want to extract the sequence on my AminAcidSequence (it is a String object) and use it as input for another MobyServices that eats String as its input. The only way I can do it now is to use a Parser which decomposes AminoAcidSequence to basic types and then construct my String from these basic elements (namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns ,aminoacid_'SequenceString',aminoacid_'SequenceString'_id and aminoacid_'SequenceString'_ns). This is not very difficult in this case, but imagine what would happen if I parse an object which is composed of for example WieghtedAminoSequences and try to get AminoAcidSequence out of it... In fact current BioMobyObjectProcessors are processors for constructing MobyObjects (with basic types as input ports and composite types as output ports). There should be another type of BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects (with composite types as input ports and basic types as output ports). Please inform me if such option already exists somewhere and I missed it. Jerzy Orlowski _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From soiland-reyes at cs.manchester.ac.uk Fri Sep 26 09:39:14 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 26 Sep 2008 14:39:14 +0100 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DB664A.6030305@genesilico.pl> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es> <48DB664A.6030305@genesilico.pl> Message-ID: On Thu, Sep 25, 2008 at 11:22, Jerzy Orlowski wrote: > I keep trying, but I cannot find anywhere a jar with > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser : stain at mira ~/.m2/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1;unzip -t freefluo-taverna-exts-1.7.1.jar Archive: freefluo-taverna-exts-1.7.1.jar testing: META-INF/ OK testing: META-INF/MANIFEST.MF OK testing: uk/ OK testing: uk/ac/ OK testing: uk/ac/soton/ OK testing: uk/ac/soton/itinnovation/ OK testing: uk/ac/soton/itinnovation/freefluo/ OK testing: uk/ac/soton/itinnovation/freefluo/exts/ OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/ OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaDataHandler.class OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaScuflModelParser.class OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaWorkflowInstance.class OK No errors detected in compressed data of freefluo-taverna-exts-1.7.1.jar. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From srramirez at uma.es Thu Sep 25 06:29:18 2008 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Thu, 25 Sep 2008 12:29:18 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DB664A.6030305@genesilico.pl> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es> <48DB664A.6030305@genesilico.pl> Message-ID: <48DB67FE.4000507@uma.es> Yes, you are right but taverna still using it in the core. If you download the entire src of taverna you will find a jar file: taverna-workbench with that class If you couldn't find it, just tell me and I will sent it to you Best regards, Sergio Jerzy Orlowski wrote: > I keep trying, but I cannot find anywhere a jar with > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser > > I have an impression that freefluo is outdated > > ---------------------------------------------------------------------- > uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error > with configuration named tavernaClassNotFound for WorkflowParser > implementation: > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser > at > uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108) > > at > uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64) > > at > org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84) > at > org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11) > Caused by: java.lang.ClassNotFoundException: > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser > at java.net.URLClassLoader$1.run(URLClassLoader.java:200) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:188) > at java.lang.ClassLoader.loadClass(ClassLoader.java:306) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276) > at java.lang.ClassLoader.loadClass(ClassLoader.java:251) > at > uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102) > > ... 3 more > ------------------------------------------------------------------------ > > Jerzyo > > > > Sergio Ramirez Ramirez wrote: >> Hi Jerzy >> >> I see you cannot got to resolve the problem. >> >> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel; >> >> Maybe is what you need. to built your own workflow. >> >> Keep me informed ;) and good luck. >> >> Jerzy Orlowski wrote: >>> Hi >>> >>> 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). >>> >>> Where can I find source code or javadoc for >>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other >>> classes? >>> >>> I cannot find in anywhere on the web.... >>> >>> Jerzy >>> >>> >>> Sergio Ramirez Ramirez wrote: >>>> Here there is my small contribution, just the two methods that I >>>> use for run a workflow. >>>> Hope it can help to someone >>>> >>>> Paul Gordon wrote: >>>>> I think whoever has a headless Taverna workflow creation and/or >>>>> enactment working should put examples up in the Java developer's >>>>> section of the Moby Web site...I believe the myExperiment people >>>>> also have a headless workflow enactment engine working >>>>> now...anyone from there on this list? Also, Paolo Romano in Italy >>>>> has a headless SCUFL enactor in the BioWEP software. So many >>>>> people are doing this, but no good sample code is easily >>>>> available, especially for Moby services... >>>>> >>>>> Sergio Ramirez Ramirez wrote: >>>>>> Hello Jerzy >>>>>> >>>>>> I had the same problem that you. >>>>>> >>>>>> I have got it to work by browsing deep in the Taverna code. I >>>>>> cannot give you many sample code because I'm trying to organize >>>>>> all the code tries and examples that I have. >>>>>> >>>>>> But I can give you some comments: >>>>>> >>>>>> For build a workflow model the class is: >>>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model >>>>>> = new ScuflModel(); >>>>>> This class contains the methods that you mention addProcessor ... >>>>>> >>>>>> For run I'm using freeflow, because taverna classes and raven are >>>>>> a "little" tricky. The classes: >>>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>>>>> can help you. >>>>>> >>>>>> I hope this little details help you to begin. If you have more >>>>>> detailed questions I will be very happy of help you. >>>>>> >>>>>> Best regards, >>>>>> Sergio >>>>>> >>>>>> Jerzy Orlowski wrote: >>>>>>> Hi >>>>>>> >>>>>>> I have several hundreds of workflows made up of BioMoby Services >>>>>>> and want to execute them all without opening any GUI. >>>>>>> >>>>>>> I was looking for some solution over the internet and the think >>>>>>> I came across was using Taverna plugin and try to execute it >>>>>>> programaticaly. >>>>>>> I have a few questions: >>>>>>> >>>>>>> 1. Is it the only way? >>>>>>> >>>>>>> 2. I found several tutorial tutorials on running saved workflow >>>>>>> saved in scufl language. >>>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>>>>> >>>>>>> >>>>>>> How do you one make a workflow step by step? like: >>>>>>> >>>>>>> workflow.addProcesor(...) >>>>>>> workflow.addConnector(...) >>>>>>> ... >>>>>>> workflow.execute() >>>>>>> >>>>>>> and especially, how do one add BioMoby objects this way? Is >>>>>>> there any tutorial or do I have go though the API? >>>>>>> >>>>>>> Best >>>>>>> >>>>>>> Jerzy Orlowski >>>>>>> >>>>>>> _______________________________________________ >>>>>>> MOBY-dev mailing list >>>>>>> MOBY-dev at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- 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 jerzyo at genesilico.pl Mon Sep 1 10:01:45 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Mon, 01 Sep 2008 12:01:45 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? Message-ID: <48BBBD89.6020803@genesilico.pl> Hello I am searchng for a java class representing a BioMoby workflow: I found some classes that represent connections: datatype -> service service -> datatype datatype -> datatype in org.biomoby.client. (There is even a class for drawing graphs using graphviz, but unfortunately without datatype -> datatype connections.) I do not find find any class that these connections gathers them together as a workflow and enables execution of this workflow given some inputs. Does such class exist in jMoby? Or should I run my workflows using Taverna libraries (How should I do it)? If it does not exist I will probably write it but maybe somebody is already doing it. Jerzy Orlowski From serr at ac.uma.es Mon Sep 1 10:10:53 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Mon, 01 Sep 2008 12:10:53 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBBD89.6020803@genesilico.pl> References: <48BBBD89.6020803@genesilico.pl> Message-ID: <48BBBFAD.7060401@ac.uma.es> Hello Jerzy Unfortunately, moby can not handle workflows by itself for now. Normally you use taverna for building workflows. I'm trying to learn how to use Taverna libraries to run workflows. There is a taverna class (workflowlauncher or similar) available in the web page for taverna, but I couldn't make it work. I'm also very interesting in this topic. Greetings, Sergio Jerzy Orlowski wrote: > Hello > > I am searchng for a java class representing a BioMoby workflow: > > I found some classes that represent connections: > datatype -> service > service -> datatype > datatype -> datatype > in org.biomoby.client. > (There is even a class for drawing graphs using graphviz, but > unfortunately without datatype -> datatype connections.) > > I do not find find any class that these connections gathers them > together as a workflow and enables execution of this workflow given > some inputs. > > Does such class exist in jMoby? Or should I run my workflows using > Taverna libraries (How should I do it)? > If it does not exist I will probably write it but maybe somebody is > already doing it. > > Jerzy Orlowski > > _______________________________________________ > 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 groscurt at mpiz-koeln.mpg.de Mon Sep 1 10:44:58 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 01 Sep 2008 12:44:58 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBBFAD.7060401@ac.uma.es> References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es> Message-ID: <48BBC7AA.2060002@mpiz-koeln.mpg.de> Hi Sergio, if you follow the mail list correspondance of the taverna list http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results you will find the same question with answer and links to your problem. best andreas Sergio Ramirez Ramirez wrote: > Hello Jerzy > > Unfortunately, moby can not handle workflows by itself for now. > Normally you use taverna for building workflows. > I'm trying to learn how to use Taverna libraries to run workflows. > There is a taverna class (workflowlauncher or similar) available in > the web page for taverna, but I couldn't make it work. > > I'm also very interesting in this topic. > Greetings, Sergio > > Jerzy Orlowski wrote: >> Hello >> >> I am searchng for a java class representing a BioMoby workflow: >> >> I found some classes that represent connections: >> datatype -> service >> service -> datatype >> datatype -> datatype >> in org.biomoby.client. >> (There is even a class for drawing graphs using graphviz, but >> unfortunately without datatype -> datatype connections.) >> >> I do not find find any class that these connections gathers them >> together as a workflow and enables execution of this workflow given >> some inputs. >> >> Does such class exist in jMoby? Or should I run my workflows using >> Taverna libraries (How should I do it)? >> If it does not exist I will probably write it but maybe somebody is >> already doing it. >> >> Jerzy Orlowski >> >> _______________________________________________ >> 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 serr at ac.uma.es Mon Sep 1 11:15:17 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Mon, 01 Sep 2008 13:15:17 +0200 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBC7AA.2060002@mpiz-koeln.mpg.de> References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es> <48BBC7AA.2060002@mpiz-koeln.mpg.de> Message-ID: <48BBCEC5.1070505@ac.uma.es> Thank you very much Best Sergio. Andreas Groscurth wrote: > Hi Sergio, > > if you follow the mail list correspondance of the taverna list > > http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results > > > you will find the same question with answer and links to your problem. > > best > andreas > > Sergio Ramirez Ramirez wrote: >> Hello Jerzy >> >> Unfortunately, moby can not handle workflows by itself for now. >> Normally you use taverna for building workflows. >> I'm trying to learn how to use Taverna libraries to run workflows. >> There is a taverna class (workflowlauncher or similar) available in >> the web page for taverna, but I couldn't make it work. >> >> I'm also very interesting in this topic. >> Greetings, Sergio >> >> Jerzy Orlowski wrote: >>> Hello >>> >>> I am searchng for a java class representing a BioMoby workflow: >>> >>> I found some classes that represent connections: >>> datatype -> service >>> service -> datatype >>> datatype -> datatype >>> in org.biomoby.client. >>> (There is even a class for drawing graphs using graphviz, but >>> unfortunately without datatype -> datatype connections.) >>> >>> I do not find find any class that these connections gathers them >>> together as a workflow and enables execution of this workflow given >>> some inputs. >>> >>> Does such class exist in jMoby? Or should I run my workflows using >>> Taverna libraries (How should I do it)? >>> If it does not exist I will probably write it but maybe somebody is >>> already doing it. >>> >>> Jerzy Orlowski >>> >>> _______________________________________________ >>> 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 MichaelGerlich at gmx.de Wed Sep 3 09:17:42 2008 From: MichaelGerlich at gmx.de (Michael Gerlich) Date: Wed, 3 Sep 2008 11:17:42 +0200 Subject: [MOBY-dev] Problems calling a Moby service with secondary parameters Message-ID: <000001c90da5$eb498a40$c1dc9ec0$@de> Hi all, I'm working on a simple java app (client) that calls some Biomoby services I wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist" registered under authority "ipb-halle.de" takes additional 2 secondary parameters that modify its query behavior and the resulting number of outputs. Now when I try to add both secondary parameters to the input, the service call fails with the following message: Exception in thread "main" org.biomoby.shared.MobyException: Service get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but takes 2 (query 1). Extra secondary parameters must have been specified at org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java :928) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282) at org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275) at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86) My code is like that: Central worker = new CentralImpl(); templateService = new MobyService("get_DBLinks_From_Peaklist", authority); // authority = "ipb-halle.de" validServices = worker.findService(templateService); comp = new MobyDataComposite(new MobyDataType("MSPeakRel")); comp.put("relInt", new MobyDataInt(999)); comp.put("mz", new MobyDataFloat(273.069)); MobyDataSecondaryInstance[] secParams = new MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length]; for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) { secParams[i] = new MobyDataSecondaryInstance(new MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()), validServices[0].getSecondaryInputs()[i].getDefaultValue()); } mr.setService(validServices[0]); mr.setInput(comp); mr.setSecondaryInput(secParams); System.out.println(mr.invokeService().toString()); The setSecondaryInput() function takes an array that consists of all parameters and applies them to all inputs. Now there are 2 parameters and an array of length 2 - with the default values for both parameters (I defined default values for both parameters). Some hints what I'm doing wrong? Another question - my input is of type MSPeakRel and is defined as collection. How do I manage to add multiple inputs - in this case, they would represent a complete peaklist of (m/z value, relative intensity) for querying a database? Best wishes, Michael From jason.e.stewart at gmail.com Mon Sep 8 11:06:59 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Mon, 8 Sep 2008 16:36:59 +0530 Subject: [MOBY-dev] SOAP::Lite claims support for document/literal Message-ID: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> Hey Moby-devs, The version of SOAP::Lite in CVS claims to support Document/literal encoding - I need help determing if this support is sufficient. Can you look this over? =head3 DOCUMENT/LITERAL SOAP web services using the document/literal message encoding are usually described by some Web Service Definition. Our web service has the following WSDL description: The XML message (inside the SOAP Envelope) look like this: Kutter Martin Hello Martin Kutter! You can call this web service with the following client code: use SOAP::Lite; my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); $soap->on_action( sub { "urn:HelloWorld#sayHello" }); $soap->autotype(0); $soap->default_ns('urn:HelloWorld'); my $som = $soap->call("sayHello", SOAP::Data->name('name')->value( 'Kutter' ), SOAP::Data->name('givenName')->value('Martin'), ); die $som->fault->{ faultstring } if ($som->fault); print $som->result, "\n"; =head2 Differences between the implementations You may have noticed that there's no between the rpc/literal and the document/literal example's implementation. In fact, from SOAP::Lite's point of view, the only differences between rpc/literal and document/literal that parameters are always named. In our example, the rpc/literal variant already used named parameters (by using a single complexType only as positional parameter), so there's no difference at all. The differences would have been bigger if the rpc/literal example had used more than one positional parameter, but this is quite unlikely to happen in the future: Current interoperability standards (like the WS-I basic profile) mandate the use of a single complexType as only parameter in rpc/literal calls. -- snip -- Help me on this one - is this valid? Is it sufficient for what MOBY and the rest of the Perl world needs? I suggest that I test this claim against: * perl SOAP::Lite client = axis Java server * java client = perl SOAP::Lite server I could use some suggestions for how to make these tests useful. Cheers, jas. From edward.kawas at gmail.com Mon Sep 8 15:16:08 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 8 Sep 2008 08:16:08 -0700 Subject: [MOBY-dev] SOAP::Lite claims support for document/literal In-Reply-To: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> Message-ID: <48c541bc.2a528c0a.2895.3efe@mx.google.com> Hi Jason, One of the problems that I have with soap lite and trying to perform doc/lit requests/responses is the inability to use attributes in the request. Since that statement doesn't make too much sense (to some it might have ;-), I will provide an example: I modified the wsdl that you sent to include an attribute in the givenName element, so that a request now looks like: Joe Blow Joe The server side code is simply: sub sayHello { SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) ); } So all that I am doing is dumping whatever is sent to the server. The response is $VAR1 = [ 'HelloWorld', 'Joe Blow', 'Joe' ]; I do believe that this is one of the biggest stumbling blocks so far. Because numerous Moby api calls use attributes. One such example is the retrieveService call. My dispatcher code is below! Eddie ------ CODE START ----- #!/usr/bin/perl -w # _________________________________________________________________ use SOAP::Transport::HTTP; if ($ENV{REQUEST_METHOD} eq "GET") { if (lc($ENV{QUERY_STRING} || "") eq "wsdl") { require CGI; my $q = CGI->new(); my $wsdl = HelloWorld::wsdl(); my $c = length($wsdl); print $q->header(-type=>'application/xml',-Content-length=>$c); print "$wsdl"; } } else { my $x = new SOAP::Transport::HTTP::CGI; $x->dispatch_to('/var/www/cgi-bin', 'HelloWorld'); $x->handle; } package HelloWorld; use Data::Dumper; sub sayHello { SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) ); } sub wsdl { return < EOF } 1; ------ CODE END ------ -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jason Stewart Sent: September-08-08 4:07 AM To: Core developer announcements Subject: [MOBY-dev] SOAP::Lite claims support for document/literal Hey Moby-devs, The version of SOAP::Lite in CVS claims to support Document/literal encoding - I need help determing if this support is sufficient. Can you look this over? =head3 DOCUMENT/LITERAL SOAP web services using the document/literal message encoding are usually described by some Web Service Definition. Our web service has the following WSDL description: The XML message (inside the SOAP Envelope) look like this: Kutter Martin Hello Martin Kutter! You can call this web service with the following client code: use SOAP::Lite; my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); $soap->on_action( sub { "urn:HelloWorld#sayHello" }); $soap->autotype(0); $soap->default_ns('urn:HelloWorld'); my $som = $soap->call("sayHello", SOAP::Data->name('name')->value( 'Kutter' ), SOAP::Data->name('givenName')->value('Martin'), ); die $som->fault->{ faultstring } if ($som->fault); print $som->result, "\n"; =head2 Differences between the implementations You may have noticed that there's no between the rpc/literal and the document/literal example's implementation. In fact, from SOAP::Lite's point of view, the only differences between rpc/literal and document/literal that parameters are always named. In our example, the rpc/literal variant already used named parameters (by using a single complexType only as positional parameter), so there's no difference at all. The differences would have been bigger if the rpc/literal example had used more than one positional parameter, but this is quite unlikely to happen in the future: Current interoperability standards (like the WS-I basic profile) mandate the use of a single complexType as only parameter in rpc/literal calls. -- snip -- Help me on this one - is this valid? Is it sufficient for what MOBY and the rest of the Perl world needs? I suggest that I test this claim against: * perl SOAP::Lite client = axis Java server * java client = perl SOAP::Lite server I could use some suggestions for how to make these tests useful. Cheers, jas. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jason.e.stewart at gmail.com Mon Sep 8 16:00:18 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Mon, 8 Sep 2008 21:30:18 +0530 Subject: [MOBY-dev] SOAP::Lite claims support for document/literal In-Reply-To: <48c541bc.2a528c0a.2895.3efe@mx.google.com> References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com> <48c541bc.2a528c0a.2895.3efe@mx.google.com> Message-ID: <41c1ade50809080900l4d681b02m7962f04e81310421@mail.gmail.com> Hey Eddie, On Mon, Sep 8, 2008 at 8:46 PM, Edward Kawas wrote: > One of the problems that I have with soap lite and trying to perform doc/lit > requests/responses is the inability to use attributes in the request. OK. I've sent this off as a query to the SOAP-Lite dev list - I'll see what they have to say. Either there is an intended workaround or it needs to be implemented. Thanks. jas. From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 12:11:10 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 10 Sep 2008 14:11:10 +0200 Subject: [MOBY-dev] Problem with dashboard to list services Message-ID: <48C7B95E.4080903@avignon.inra.fr> Hi, We have a problem with dashboard. We unregistered and re-registred our services (with some changes), but after reloading the service list we don't see these services in the list and our authority is missing. We tried to delete manually our cache and to restart the dashboard several time. We tried to reload or update every thing without changes (which obviously make sense). Does it link in any way to experimental "big bang" this morning in Geneve ? Any other ideas ? Thanks, Regards, Dominique From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 12:23:31 2008 From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin) Date: Wed, 10 Sep 2008 14:23:31 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7B95E.4080903@avignon.inra.fr> References: <48C7B95E.4080903@avignon.inra.fr> Message-ID: <48C7BC43.70008@avignon.inra.fr> Dominique Jeannin a ?crit : > Hi, > > We have a problem with dashboard. We unregistered and re-registred our > services (with some changes), but after reloading the service list we > don't see these services in the list and our authority is missing. > We tried to delete manually our cache and to restart the dashboard > several time. We tried to reload or update every thing without changes > (which obviously make sense). > > Does it link in any way to experimental "big bang" this morning in > Geneve ? > Any other ideas ? > Does anyone see our services named Solstis_getDatasetDescFromKeyword on avilin05.avignon.inra.fr ? From all our tests we cannot... Thanks, Regards, Dominique From groscurt at mpiz-koeln.mpg.de Wed Sep 10 12:47:29 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 10 Sep 2008 14:47:29 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7BC43.70008@avignon.inra.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7BC43.70008@avignon.inra.fr> Message-ID: <48C7C1E1.1030406@mpiz-koeln.mpg.de> Hi Dominique, i do find it in the dashboard on the test central and via a simple moby java test. I had the same issue some days ago that changes (like service (de)registration) could not be shown in dashboard, whatever i did to it... My solution was then to use someonelse moby checkout and this dashboard :( Hope someone knows about that and knows a general solution Andreas Dominique Jeannin wrote: > Dominique Jeannin a ?crit : >> Hi, >> >> We have a problem with dashboard. We unregistered and re-registred >> our services (with some changes), but after reloading the service >> list we don't see these services in the list and our authority is >> missing. >> We tried to delete manually our cache and to restart the dashboard >> several time. We tried to reload or update every thing without >> changes (which obviously make sense). >> >> Does it link in any way to experimental "big bang" this morning in >> Geneve ? >> Any other ideas ? >> > Does anyone see our services named Solstis_getDatasetDescFromKeyword > on avilin05.avignon.inra.fr ? > From all our tests we cannot... > > Thanks, > 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 Sep 10 12:49:19 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 10 Sep 2008 14:49:19 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7B95E.4080903@avignon.inra.fr> References: <48C7B95E.4080903@avignon.inra.fr> Message-ID: <48C7C24F.3050709@pingoured.fr> Dominique Jeannin wrote: > Hi, > > We have a problem with dashboard. We unregistered and re-registred our > services (with some changes), but after reloading the service list we > don't see these services in the list and our authority is missing. > We tried to delete manually our cache and to restart the dashboard > several time. We tried to reload or update every thing without changes > (which obviously make sense). > > Does it link in any way to experimental "big bang" this morning in Geneve ? > Any other ideas ? More informations on the problem: While doing an "Update" on all (Services, datatypes...) we have the following error: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== While on the other when doing a "Reload" all, we do not have any error but we still can't see our services nor authority. Regards, Pierre From edward.kawas at gmail.com Wed Sep 10 13:12:10 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 06:12:10 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7C24F.3050709@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> Message-ID: <48c7c7b5.26bc720a.7554.72fd@mx.google.com> Hi, I am trying to reproduce your problems, but I cannot. I am not seeing any SOAP exceptions and I don't see your service either. The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I tried to use non utf8 characters in my soap message. 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: September-10-08 5:49 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Dominique Jeannin wrote: > Hi, > > We have a problem with dashboard. We unregistered and re-registred our > services (with some changes), but after reloading the service list we > don't see these services in the list and our authority is missing. > We tried to delete manually our cache and to restart the dashboard > several time. We tried to reload or update every thing without changes > (which obviously make sense). > > Does it link in any way to experimental "big bang" this morning in Geneve ? > Any other ideas ? More informations on the problem: While doing an "Update" on all (Services, datatypes...) we have the following error: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 sequence. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException Fault actor: null When calling: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl =========== While on the other when doing a "Reload" all, we do not have any error but we still can't see our services nor authority. Regards, Pierre _______________________________________________ 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 Sep 10 13:31:33 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 10 Sep 2008 15:31:33 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> Message-ID: <48C7CC35.6090803@pingoured.fr> Edward Kawas wrote: > Hi, > > I am trying to reproduce your problems, but I cannot. I am not seeing any > SOAP exceptions and I don't see your service either. Strange since Andreas seems to see it as well as another person that contacted us off-list. > The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I > tried to use non utf8 characters in my soap message. > What surprise us the most is that two of our services that we did not change (Solstis_getProjet and dom_test2) are not shown either. The whole authority avilin05.avignon.inra.fr seems to have disappeared... We will try by deleting jMoby and re-downloading it from the CVS. Hope that fix the problem Thanks for your help, Regards, Pierre From edward.kawas at gmail.com Wed Sep 10 13:33:30 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 06:33:30 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7CC35.6090803@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> Message-ID: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> I also forgot to mention that I also tried looking for your services in the database that backs the registry and failed to find it! ??? 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: September-10-08 6:32 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Edward Kawas wrote: > Hi, > > I am trying to reproduce your problems, but I cannot. I am not seeing any > SOAP exceptions and I don't see your service either. Strange since Andreas seems to see it as well as another person that contacted us off-list. > The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I > tried to use non utf8 characters in my soap message. > What surprise us the most is that two of our services that we did not change (Solstis_getProjet and dom_test2) are not shown either. The whole authority avilin05.avignon.inra.fr seems to have disappeared... We will try by deleting jMoby and re-downloading it from the CVS. Hope that fix the problem Thanks for your help, Regards, Pierre _______________________________________________ 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 Sep 10 13:47:47 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 10 Sep 2008 15:47:47 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> Message-ID: <48C7D003.3070903@pingoured.fr> Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! This is weird because the registration seems to work (cf below) Could you check Solstis_getProject ? We did not change that one normally. Thanks for your help, Regards, Pierre ../jMoby/build/run/run-cmdline-client -e http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl -uri http://bioinfo.icapture.ubc.ca/MOBY/Central -call registerService ' moby Solstis_getDatasetDescFromKeyword getDataset avilin05.avignon.inra.fr http://avilin05/axis/services/Solstis_getDatasetDescFromKeyword jean-paul.bouchet at avignon.inra.fr 1 String OSE_dataset ' Calling method 'registerService' with the input from ' moby Solstis_getDatasetDescFromKeyword getDataset avilin05.avignon.inra.fr http://avilin05/axis/services/Solstis_getDatasetDescFromKeyword jean-paul.bouchet at avignon.inra.fr 1 String OSE_dataset ': moby Solstis_getDatasetDescFromKeyword getDataset avilin05.avignon.inra.fr http://avilin05/axis/services/Solstis_getDatasetDescFromKeyword jean-paul.bouchet at avignon.inra.fr 1 String OSE_dataset -------------- 0 From groscurt at mpiz-koeln.mpg.de Wed Sep 10 13:53:13 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 10 Sep 2008 15:53:13 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> Message-ID: <48C7D149.1020308@mpiz-koeln.mpg.de> So basically its not there anymore but i can see it in dashboard ? then my cache is old. My problem was not even based on the encoding problem. I set a different cache location and did reload/update and everything. I didnt get any SOAP error, but still the service i registered didnt show up. If i queried the central via the jmoby api and looked explictly for my service i found it... dont know if and how this error might be reproducable :( Best andreas Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > > ??? > > 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: September-10-08 6:32 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Problem with dashboard to list services > > Edward Kawas wrote: > >> Hi, >> >> I am trying to reproduce your problems, but I cannot. I am not seeing any >> SOAP exceptions and I don't see your service either. >> > > Strange since Andreas seems to see it as well as another person that > contacted us off-list. > > >> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I >> tried to use non utf8 characters in my soap message. >> >> > > What surprise us the most is that two of our services that we did not > change (Solstis_getProjet and dom_test2) are not shown either. > > The whole authority avilin05.avignon.inra.fr seems to have disappeared... > > > We will try by deleting jMoby and re-downloading it from the CVS. > Hope that fix the problem > > Thanks for your help, > Regards, > > Pierre > _______________________________________________ > 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 > -- ===================================================== 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 jason.e.stewart at gmail.com Wed Sep 10 14:28:16 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Wed, 10 Sep 2008 19:58:16 +0530 Subject: [MOBY-dev] More info on SOAP::Lite document/literal Message-ID: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> Hey Eddie, So I dug a bit on the server side and this is what I found. If your server class subclasses from SOAP::Server::Parameters, the method will get an extra parameter of type SOAP::SOM which gives access to all the request information. That object contains a lot of methods for searching the soap envelope - but it converts all the data it finds into a SOAP::Data instance - which throws away all attributes not located at the root of the data being returned. For example if the XML looked like this: Joe Blow Joe and we did a query like $root = $som->dataof('//Body'), then $root would be the soap:Body and we would see all of the sub-elements but not their attributes. Only if we do $gn = $som->dataof('//givenName') do we actually get the givenName element with the middlename attribute still intact. But the $som object has all the information in an internal hash table - both as a hash table representation of the entire message and the HTTP::Request object with the original XML. What I don't understand is why when the dataof() method traverses the internal hash table structure it throws away all the attributes not on the root element being returned. Also, I don't understand why there isn't a method that just returns the content of the soap:Body element as plain XML - this should be the default behavior for document/literal. I would like to see a call something like $xml = $som->document(); Any thoughts of how I could make this interface most useful for MOBY purposes? I will have to alter the internal SOAP::Lite code, and send the patches to the maintainers. Cheers, jas. From jmfernandez at cnio.es Wed Sep 10 15:06:50 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Wed, 10 Sep 2008 17:06:50 +0200 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> Message-ID: <48C7E28A.6020203@cnio.es> Hi Jason, when we were developing the Perl MOBY::Async libraries we had the same problem (we needed to access to the full input message), and we solved it using custom deserializers fom WSRF::Lite package. Next sentences set-up them: my $server = new SOAP::Transport::HTTP::CGI; $server->serializer(WSRF::Serializer->new); $server->deserializer(WSRF::Deserializer->new); WSRF::Serializer and WSRF::Deserializer are subclasses of SOAP::Serializer and SOAP::Deserializer, respectively. SOAP::Deserializer translates input SOAP message into a SOAP::SOM instance. WSRF::Deserializer translates input SOAP message into a WSRF::SOM instance, which is a SOAP::SOM instance plus a new method called 'raw_xml'. This method returns the raw input message, which can be parsed with XML::LibXML (for instance). Hope this helps, Jos? Mar?a Jason Stewart wrote: > Hey Eddie, > > So I dug a bit on the server side and this is what I found. > > If your server class subclasses from SOAP::Server::Parameters, the > method will get an extra parameter of type SOAP::SOM which gives > access to all the request information. That object contains a lot of > methods for searching the soap envelope - but it converts all the data > it finds into a SOAP::Data instance - which throws away all attributes > not located at the root of the data being returned. For example if the > XML looked like this: > > > > Joe Blow > Joe > > > > and we did a query like $root = $som->dataof('//Body'), then $root > would be the soap:Body and we would see all of the sub-elements but > not their attributes. Only if we do $gn = $som->dataof('//givenName') > do we actually get the givenName element with the middlename attribute > still intact. > > But the $som object has all the information in an internal hash table > - both as a hash table representation of the entire message and the > HTTP::Request object with the original XML. > > What I don't understand is why when the dataof() method traverses the > internal hash table structure it throws away all the attributes not on > the root element being returned. > > Also, I don't understand why there isn't a method that just returns > the content of the soap:Body element as plain XML - this should be the > default behavior for document/literal. I would like to see a call > something like $xml = $som->document(); > > Any thoughts of how I could make this interface most useful for MOBY > purposes? I will have to alter the internal SOAP::Lite code, and send > the patches to the maintainers. > > Cheers, jas. > _______________________________________________ > 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 martin.senger at gmail.com Wed Sep 10 18:28:06 2008 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 11 Sep 2008 02:28:06 +0800 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C7C24F.3050709@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> Message-ID: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> > Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 > sequence. This seems to be a re-occurrence of the same problem that we were solving couple of months ago with a service from Germany. In that case, the problem was caused by using non-ascii characters (such as German umlaut characters) in the service description. The problem was (and I guess still is, with your services) has two parts: First, jMoby (in Dashboard but also in any other usage og its libraries) may send a wrong Unicode characters. This is probably a bug in my libraries. I should fix it. Second, BioMoby central registry accepts wrong Unicode characters, stores them in its database and sends back them as an invalid XML. This should be fixed by Eddie or Mark I guess. If I am correct and your situation is indeed the one I am describing, it is a very dangerous situation because by registering a service with such description *all* jMoby users around the world will be affected (their Dashboards, for example, will not be able to reload or update anymore - until Eddie manually fixes the descriptions in the registry database; that's how he fixed it last time). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From edward.kawas at gmail.com Wed Sep 10 18:41:24 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 11:41:24 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> Message-ID: <48c814e0.14b48c0a.2f35.ffff9d83@mx.google.com> So I haven't seen anything obvious in the description field for the services from avilin05.avignon.inra.fr. I am trying to track down the offending service and once it is found, I will fix it. Then I will update the registry to use the utf8 patch that I coded last month to solve this problem. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: September-10-08 11:28 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services > Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 > sequence. This seems to be a re-occurrence of the same problem that we were solving couple of months ago with a service from Germany. In that case, the problem was caused by using non-ascii characters (such as German umlaut characters) in the service description. The problem was (and I guess still is, with your services) has two parts: First, jMoby (in Dashboard but also in any other usage og its libraries) may send a wrong Unicode characters. This is probably a bug in my libraries. I should fix it. Second, BioMoby central registry accepts wrong Unicode characters, stores them in its database and sends back them as an invalid XML. This should be fixed by Eddie or Mark I guess. If I am correct and your situation is indeed the one I am describing, it is a very dangerous situation because by registering a service with such description *all* jMoby users around the world will be affected (their Dashboards, for example, will not be able to reload or update anymore - until Eddie manually fixes the descriptions in the registry database; that's how he fixed it last time). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Sep 10 19:20:59 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 10 Sep 2008 12:20:59 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> Message-ID: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com> Okay, I found the culprit and I have fixed it. It was a the service simpleTest under the authority mpiz-koeln.mpg.de. I will also deploy patches to the test registry to see if we can trap these errors in the future. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: September-10-08 11:28 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services > Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8 > sequence. This seems to be a re-occurrence of the same problem that we were solving couple of months ago with a service from Germany. In that case, the problem was caused by using non-ascii characters (such as German umlaut characters) in the service description. The problem was (and I guess still is, with your services) has two parts: First, jMoby (in Dashboard but also in any other usage og its libraries) may send a wrong Unicode characters. This is probably a bug in my libraries. I should fix it. Second, BioMoby central registry accepts wrong Unicode characters, stores them in its database and sends back them as an invalid XML. This should be fixed by Eddie or Mark I guess. If I am correct and your situation is indeed the one I am describing, it is a very dangerous situation because by registering a service with such description *all* jMoby users around the world will be affected (their Dashboards, for example, will not be able to reload or update anymore - until Eddie manually fixes the descriptions in the registry database; that's how he fixed it last time). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger _______________________________________________ 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 Sep 10 19:35:11 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 10 Sep 2008 13:35:11 -0600 Subject: [MOBY-dev] Problems calling a Moby service with secondary parameters In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de> References: <000001c90da5$eb498a40$c1dc9ec0$@de> Message-ID: <48C8216F.8090801@ucalgary.ca> Hi Michael, Sorry for not getting back to you earlier. The problem is in the way to create the secondary data instances. If you do a toString() on them, you;ll see that they have a blank name based on the constructor you used. The easiest way to use the default secondaries is with the one-arg constructor, e.g.: int i = 0; for (MobySecondaryData param: service.getSecondaryInputs()) { secParams[i++] = new MobyDataSecondaryInstance(param); //auto-populates the instance with the template's default value } I'll add a check to MobyRequest that'll complain if you give blank or duplicately named secondaries, which should make this mistake more obvious to others in the future. Regards, Paul P.S. I've also updated MobyDataComposite to handle put() for cases such as your where the data type is not in the registry yet, facilitating testing. Better yet though is to use the test registry in such cases. Michael Gerlich wrote: > Hi all, > > I'm working on a simple java app (client) that calls some Biomoby services I > wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist" > registered under authority "ipb-halle.de" takes additional 2 secondary > parameters that modify its query behavior and the resulting number of > outputs. > > Now when I try to add both secondary parameters to the input, the service > call fails with the following message: > > Exception in thread "main" org.biomoby.shared.MobyException: Service > get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but > takes 2 (query 1). Extra secondary parameters must have been specified > at > org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java > :928) > at > org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302) > at > org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282) > at > org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275) > at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86) > > > My code is like that: > > Central worker = new CentralImpl(); > templateService = new MobyService("get_DBLinks_From_Peaklist", authority); > // authority = "ipb-halle.de" > validServices = worker.findService(templateService); > > comp = new MobyDataComposite(new MobyDataType("MSPeakRel")); > comp.put("relInt", new MobyDataInt(999)); > comp.put("mz", new MobyDataFloat(273.069)); > > MobyDataSecondaryInstance[] secParams = new > MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length]; > for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) { > secParams[i] = new MobyDataSecondaryInstance(new > MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()), > validServices[0].getSecondaryInputs()[i].getDefaultValue()); } > > mr.setService(validServices[0]); > mr.setInput(comp); > mr.setSecondaryInput(secParams); > System.out.println(mr.invokeService().toString()); > > > > The setSecondaryInput() function takes an array that consists of all > parameters and applies them to all inputs. Now there are 2 parameters and an > array of length 2 - with the default values for both parameters (I defined > default values for both parameters). > > Some hints what I'm doing wrong? > > > Another question - my input is of type MSPeakRel and is defined as > collection. How do I manage to add multiple inputs - in this case, they > would represent a complete peaklist of (m/z value, relative intensity) for > querying a database? > > > > Best wishes, > > Michael > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,48be578210950321565264! > > > > From gordonp at ucalgary.ca Wed Sep 10 20:08:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 10 Sep 2008 14:08:52 -0600 Subject: [MOBY-dev] Java MobyRequest changes In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de> References: <000001c90da5$eb498a40$c1dc9ec0$@de> Message-ID: <48C82954.5030507@ucalgary.ca> Hi all, If you use MobyRequest in your code, please note that setSecondaries() now throws a MobyException in CVS. This is to help catch problems with invalid secondary parameter values. You will need to ensure any call to this method is now enclosed in a "try" block. Sorry for any inconvenience this API change may cause. Paul From jason.e.stewart at gmail.com Thu Sep 11 04:14:54 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Thu, 11 Sep 2008 09:44:54 +0530 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <48C7E28A.6020203@cnio.es> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> Message-ID: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com> Hey Jose, On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez wrote: > when we were developing the Perl MOBY::Async libraries we had the > same problem (we needed to access to the full input message), and we solved > it using custom deserializers fom WSRF::Lite package. Thanks, that's useful for MOBY users, definately. I still think that it should be a functionality that is built into the core of SOAP::Lite, though, especially since document/literal is the standard encoding now. I will get a response from Martin, the current maintainer of SOAP::Lite, and see what he thinks should be done. Likewise, on the client side it should be made trivial to attach a fragment of XML as the body of the soap message without any interference from SOAP::Lite. Any comments? Thanks, jas. From groscurt at mpiz-koeln.mpg.de Thu Sep 11 05:50:02 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 11 Sep 2008 07:50:02 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com> <48c81e2a.16538c0a.5326.ffffb815@mx.google.com> Message-ID: <48C8B18A.7020401@mpiz-koeln.mpg.de> ohoh - that was my service... at least kind of - i tested the problem we discussed last time with the umlaut etc. I'm sorry - i totally forgot that service :( Andreas Edward Kawas wrote: > Okay, I found the culprit and I have fixed it. It was a the service > simpleTest under the authority mpiz-koeln.mpg.de. > > I will also deploy patches to the test registry to see if we can trap these > errors in the future. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: September-10-08 11:28 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Problem with dashboard to list services > > >> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte >> > UTF-8 > >> sequence. >> > > > This seems to be a re-occurrence of the same problem that we were solving > couple of months ago with a service from Germany. In that case, the problem > was caused by using non-ascii characters (such as German umlaut characters) > in the service description. The problem was (and I guess still is, with your > services) has two parts: > > First, jMoby (in Dashboard but also in any other usage og its libraries) may > send a wrong Unicode characters. This is probably a bug in my libraries. I > should fix it. > > Second, BioMoby central registry accepts wrong Unicode characters, stores > them in its database and sends back them as an invalid XML. This should be > fixed by Eddie or Mark I guess. > > If I am correct and your situation is indeed the one I am describing, it is > a very dangerous situation because by registering a service with such > description *all* jMoby users around the world will be affected (their > Dashboards, for example, will not be able to reload or update anymore - > until Eddie manually fixes the descriptions in the registry database; that's > how he fixed it last time). > > Martin > > -- ===================================================== 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 Thu Sep 11 07:45:30 2008 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Thu, 11 Sep 2008 09:45:30 +0200 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> Message-ID: <48C8CC9A.7050808@pingoured.fr> Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > Few minutes after this email and after a couple of trials we have been able to see our services again. What we observed is: - avilin05.avignon.inra.fr appears in the second position in the /moses generator/ panel while it was easily at the fourth or fifth position before. - the list of services starting by the letter 's' (or S) seems to have decrease dramatically now compare to earlier. - when we try to reload or update our cache, or when we regenerate it after removal when ends with the following error: "rethrew: org.xml.sax.SAXParseException: XML document structures must start and end within the same entity." In the console I got the following error: dashboard: [Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] [Fatal Error] :-1:-1: Premature end of file. It does not stop us from work so that's more for the report. To us it would seems like something has gone wrong yesterday on the server and a file has been corrupted ? Thanks for your help, Best regards, Pierre From jason.e.stewart at gmail.com Thu Sep 11 08:54:10 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Thu, 11 Sep 2008 14:24:10 +0530 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <48C7E28A.6020203@cnio.es> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> Message-ID: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com> Hi Jose Maria, On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez wrote: > $server->serializer(WSRF::Serializer->new); This code dies with a class not found error from Perl, I presume you mean WSRF::WSRFSerializer->new? Cheers, jas. From edward.kawas at gmail.com Thu Sep 11 13:11:07 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Sep 2008 06:11:07 -0700 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com> Message-ID: <48c918f9.27b38c0a.385f.ffffdcea@mx.google.com> Hi Jason, I like your thinking. I don?t have much experience with doc/lit services, but I do feel that the additions that you have mentioned would probably be best (and similar to what we have now for rpc/encoded). 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 Jason Stewart Sent: September-10-08 9:15 PM To: Core developer announcements Subject: Re: [MOBY-dev] More info on SOAP::Lite document/literal Hey Jose, On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez wrote: > when we were developing the Perl MOBY::Async libraries we had the > same problem (we needed to access to the full input message), and we solved > it using custom deserializers fom WSRF::Lite package. Thanks, that's useful for MOBY users, definately. I still think that it should be a functionality that is built into the core of SOAP::Lite, though, especially since document/literal is the standard encoding now. I will get a response from Martin, the current maintainer of SOAP::Lite, and see what he thinks should be done. Likewise, on the client side it should be made trivial to attach a fragment of XML as the body of the soap message without any interference from SOAP::Lite. Any comments? Thanks, jas. _______________________________________________ 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 Sep 11 13:15:49 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Sep 2008 06:15:49 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C8CC9A.7050808@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> <48C8CC9A.7050808@pingoured.fr> Message-ID: <48c91a12.16538c0a.530a.ffffdd16@mx.google.com> Yes, for some reason the file is not being generated properly. I am not sure if this is a memory problem on the server or ...??? I noticed that yesterday, the RDF file is generated once properly and then truncated the following times. Hopefully I get this fixed soon, 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: September-11-08 12:46 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > Few minutes after this email and after a couple of trials we have been able to see our services again. What we observed is: - avilin05.avignon.inra.fr appears in the second position in the /moses generator/ panel while it was easily at the fourth or fifth position before. - the list of services starting by the letter 's' (or S) seems to have decrease dramatically now compare to earlier. - when we try to reload or update our cache, or when we regenerate it after removal when ends with the following error: "rethrew: org.xml.sax.SAXParseException: XML document structures must start and end within the same entity." In the console I got the following error: dashboard: [Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] [Fatal Error] :-1:-1: Premature end of file. It does not stop us from work so that's more for the report. To us it would seems like something has gone wrong yesterday on the server and a file has been corrupted ? Thanks 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 jerzyo at genesilico.pl Thu Sep 11 14:22:09 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 11 Sep 2008 16:22:09 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java Message-ID: <48C92991.2000407@genesilico.pl> Hi I have several hundreds of workflows made up of BioMoby Services and want to execute them all without opening any GUI. I was looking for some solution over the internet and the think I came across was using Taverna plugin and try to execute it programaticaly. I have a few questions: 1. Is it the only way? 2. I found several tutorial tutorials on running saved workflow saved in scufl language. http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html How do you one make a workflow step by step? like: workflow.addProcesor(...) workflow.addConnector(...) ... workflow.execute() and especially, how do one add BioMoby objects this way? Is there any tutorial or do I have go though the API? Best Jerzy Orlowski From edward.kawas at gmail.com Thu Sep 11 14:36:02 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 11 Sep 2008 07:36:02 -0700 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C92991.2000407@genesilico.pl> References: <48C92991.2000407@genesilico.pl> Message-ID: <48c92ce0.28d7720a.65e4.0366@mx.google.com> Hi Jerzy, You can execute workflows from the command line too if you have your input file for the workflows handy. If you want to create workflows programmatically, you will need to look at the javadoc for the taverna source code. You should probably explore the taverna website[1] and its manual[2] for more information. Eddie [1] http://taverna.sourceforge.net/ [2] http://taverna.sourceforge.net/doc -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: September-11-08 7:22 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Executing Moby Workflow straight from java Hi I have several hundreds of workflows made up of BioMoby Services and want to execute them all without opening any GUI. I was looking for some solution over the internet and the think I came across was using Taverna plugin and try to execute it programaticaly. I have a few questions: 1. Is it the only way? 2. I found several tutorial tutorials on running saved workflow saved in scufl language. http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html How do you one make a workflow step by step? like: workflow.addProcesor(...) workflow.addConnector(...) ... workflow.execute() and especially, how do one add BioMoby objects this way? Is there any tutorial or do I have go though the API? Best Jerzy Orlowski _______________________________________________ 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 Sep 11 14:49:25 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 11 Sep 2008 16:49:25 +0200 Subject: [MOBY-dev] More info on SOAP::Lite document/literal In-Reply-To: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com> References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es> <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com> Message-ID: <48C92FF5.5040405@cnio.es> Hi Jason, yes, you are right, it should be WSRF::WSRFSerializer. We have some pending janitorial work on MOBY::Async, related to our usage of some namespace classes which we do not own (WSRF::Serializer is one of those cases). Best Regards, Jos? Mar?a Jason Stewart wrote: > Hi Jose Maria, > > On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez > wrote: > >> $server->serializer(WSRF::Serializer->new); > > This code dies with a class not found error from Perl, I presume you > mean WSRF::WSRFSerializer->new? > > Cheers, jas. > > _______________________________________________ > 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 serr at ac.uma.es Thu Sep 11 14:38:49 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Thu, 11 Sep 2008 16:38:49 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C92991.2000407@genesilico.pl> References: <48C92991.2000407@genesilico.pl> Message-ID: <48C92D79.9010706@ac.uma.es> Hello Jerzy I had the same problem that you. I have got it to work by browsing deep in the Taverna code. I cannot give you many sample code because I'm trying to organize all the code tries and examples that I have. But I can give you some comments: For build a workflow model the class is: org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new ScuflModel(); This class contains the methods that you mention addProcessor ... For run I'm using freeflow, because taverna classes and raven are a "little" tricky. The classes: uk.ac.soton.itinnovation.freefluo.main.Engine or org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy can help you. I hope this little details help you to begin. If you have more detailed questions I will be very happy of help you. Best regards, Sergio Jerzy Orlowski wrote: > Hi > > I have several hundreds of workflows made up of BioMoby Services and > want to execute them all without opening any GUI. > > I was looking for some solution over the internet and the think I came > across was using Taverna plugin and try to execute it programaticaly. > I have a few questions: > > 1. Is it the only way? > > 2. I found several tutorial tutorials on running saved workflow saved > in scufl language. > http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html > > How do you one make a workflow step by step? like: > > workflow.addProcesor(...) > workflow.addConnector(...) > ... > workflow.execute() > > and especially, how do one add BioMoby objects this way? Is there any > tutorial or do I have go though the API? > > Best > > Jerzy Orlowski > > _______________________________________________ > 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 gordonp at ucalgary.ca Thu Sep 11 15:10:13 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 11 Sep 2008 09:10:13 -0600 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C92D79.9010706@ac.uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> Message-ID: <48C934D5.50700@ucalgary.ca> I think whoever has a headless Taverna workflow creation and/or enactment working should put examples up in the Java developer's section of the Moby Web site...I believe the myExperiment people also have a headless workflow enactment engine working now...anyone from there on this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in the BioWEP software. So many people are doing this, but no good sample code is easily available, especially for Moby services... Sergio Ramirez Ramirez wrote: > Hello Jerzy > > I had the same problem that you. > > I have got it to work by browsing deep in the Taverna code. I cannot > give you many sample code because I'm trying to organize all the code > tries and examples that I have. > > But I can give you some comments: > > For build a workflow model the class is: > org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new > ScuflModel(); > This class contains the methods that you mention addProcessor ... > > For run I'm using freeflow, because taverna classes and raven are a > "little" tricky. The classes: > uk.ac.soton.itinnovation.freefluo.main.Engine or > org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy > can help you. > > I hope this little details help you to begin. If you have more > detailed questions I will be very happy of help you. > > Best regards, > Sergio > > Jerzy Orlowski wrote: >> Hi >> >> I have several hundreds of workflows made up of BioMoby Services and >> want to execute them all without opening any GUI. >> >> I was looking for some solution over the internet and the think I >> came across was using Taverna plugin and try to execute it >> programaticaly. >> I have a few questions: >> >> 1. Is it the only way? >> >> 2. I found several tutorial tutorials on running saved workflow >> saved in scufl language. >> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >> >> >> How do you one make a workflow step by step? like: >> >> workflow.addProcesor(...) >> workflow.addConnector(...) >> ... >> workflow.execute() >> >> and especially, how do one add BioMoby objects this way? Is there any >> tutorial or do I have go though the API? >> >> Best >> >> Jerzy Orlowski >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From serr at ac.uma.es Thu Sep 11 15:23:30 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Thu, 11 Sep 2008 17:23:30 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C934D5.50700@ucalgary.ca> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> Message-ID: <48C937F2.3030708@ac.uma.es> Here there is my small contribution, just the two methods that I use for run a workflow. Hope it can help to someone Paul Gordon wrote: > I think whoever has a headless Taverna workflow creation and/or > enactment working should put examples up in the Java developer's > section of the Moby Web site...I believe the myExperiment people also > have a headless workflow enactment engine working now...anyone from > there on this list? Also, Paolo Romano in Italy has a headless SCUFL > enactor in the BioWEP software. So many people are doing this, but no > good sample code is easily available, especially for Moby services... > > Sergio Ramirez Ramirez wrote: >> Hello Jerzy >> >> I had the same problem that you. >> >> I have got it to work by browsing deep in the Taverna code. I cannot >> give you many sample code because I'm trying to organize all the code >> tries and examples that I have. >> >> But I can give you some comments: >> >> For build a workflow model the class is: >> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >> new ScuflModel(); >> This class contains the methods that you mention addProcessor ... >> >> For run I'm using freeflow, because taverna classes and raven are a >> "little" tricky. The classes: >> uk.ac.soton.itinnovation.freefluo.main.Engine or >> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >> can help you. >> >> I hope this little details help you to begin. If you have more >> detailed questions I will be very happy of help you. >> >> Best regards, >> Sergio >> >> Jerzy Orlowski wrote: >>> Hi >>> >>> I have several hundreds of workflows made up of BioMoby Services and >>> want to execute them all without opening any GUI. >>> >>> I was looking for some solution over the internet and the think I >>> came across was using Taverna plugin and try to execute it >>> programaticaly. >>> I have a few questions: >>> >>> 1. Is it the only way? >>> >>> 2. I found several tutorial tutorials on running saved workflow >>> saved in scufl language. >>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>> >>> >>> How do you one make a workflow step by step? like: >>> >>> workflow.addProcesor(...) >>> workflow.addConnector(...) >>> ... >>> workflow.execute() >>> >>> and especially, how do one add BioMoby objects this way? Is there >>> any tutorial or do I have go though the API? >>> >>> Best >>> >>> Jerzy Orlowski >>> >>> _______________________________________________ >>> 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 > -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: runWF.java Type: text/java Size: 2093 bytes Desc: not available URL: From jmfernandez at cnio.es Thu Sep 11 15:49:29 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 11 Sep 2008 17:49:29 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C937F2.3030708@ac.uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> Message-ID: <48C93E09.3030107@cnio.es> Hi everybody, as Sergio *should* know, we have at INB IWWE&M, which means 'Interactive Web Workflow Enactor and Manager'. It is able to host workflows, workflow examples with documentation, do web workflow enactions, and take and store workflow enaction snapshots. Next days we are going to have a Trac server with is going to host the source code and development of IWWE&M. Best Regards, Jos? Mar?a Sergio Ramirez Ramirez wrote: > Here there is my small contribution, just the two methods that I use for > run a workflow. > Hope it can help to someone > > Paul Gordon wrote: >> I think whoever has a headless Taverna workflow creation and/or >> enactment working should put examples up in the Java developer's >> section of the Moby Web site...I believe the myExperiment people also >> have a headless workflow enactment engine working now...anyone from >> there on this list? Also, Paolo Romano in Italy has a headless SCUFL >> enactor in the BioWEP software. So many people are doing this, but no >> good sample code is easily available, especially for Moby services... >> >> Sergio Ramirez Ramirez wrote: >>> Hello Jerzy >>> >>> I had the same problem that you. >>> >>> I have got it to work by browsing deep in the Taverna code. I cannot >>> give you many sample code because I'm trying to organize all the code >>> tries and examples that I have. >>> >>> But I can give you some comments: >>> >>> For build a workflow model the class is: >>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>> new ScuflModel(); >>> This class contains the methods that you mention addProcessor ... >>> >>> For run I'm using freeflow, because taverna classes and raven are a >>> "little" tricky. The classes: >>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>> can help you. >>> >>> I hope this little details help you to begin. If you have more >>> detailed questions I will be very happy of help you. >>> >>> Best regards, >>> Sergio >>> >>> Jerzy Orlowski wrote: >>>> Hi >>>> >>>> I have several hundreds of workflows made up of BioMoby Services and >>>> want to execute them all without opening any GUI. >>>> >>>> I was looking for some solution over the internet and the think I >>>> came across was using Taverna plugin and try to execute it >>>> programaticaly. >>>> I have a few questions: >>>> >>>> 1. Is it the only way? >>>> >>>> 2. I found several tutorial tutorials on running saved workflow >>>> saved in scufl language. >>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>> >>>> >>>> How do you one make a workflow step by step? like: >>>> >>>> workflow.addProcesor(...) >>>> workflow.addConnector(...) >>>> ... >>>> workflow.execute() >>>> >>>> and especially, how do one add BioMoby objects this way? Is there >>>> any tutorial or do I have go though the API? >>>> >>>> Best >>>> >>>> Jerzy Orlowski >>>> >>>> _______________________________________________ >>>> 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 -- "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 alanrw at cs.man.ac.uk Thu Sep 11 15:25:18 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Thu, 11 Sep 2008 16:25:18 +0100 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C934D5.50700@ucalgary.ca> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> Message-ID: <48C9385E.8060209@cs.man.ac.uk> Paul Gordon wrote: > I think whoever has a headless Taverna workflow creation and/or > enactment working should put examples up in the Java developer's section > of the Moby Web site...I believe the myExperiment people also have a > headless workflow enactment engine working now...anyone from there on > this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in > the BioWEP software. So many people are doing this, but no good sample > code is easily available, especially for Moby services... If by headless you mean without the UI, then there is a WorkflowLauncher that enacts a Taverna workflow. The source code (written by the myGrid team) can be downloaded from http://prdownloads.sourceforge.net/taverna/workflowlauncher-0.1.2.zip?download It may not what you need as it reads in a pre-existing Taverna workflow - it does not create one programmatically. You can also execute a Taverna workflow on a remote machine see myExperiment can run the workflow you are looking at on a Taverna remote execution engine. (You will, of course, need to have the right authorization to get at a given remote enactor.) I'm rather confused as to what people are trying to do. Could someone give a use case? I'll probably have to get Katy Wolstencroft to explain the biology for me :-) Alan R Williams (currently the support hat wearer for Taverna) From jason at bioteam.net Fri Sep 12 01:54:46 2008 From: jason at bioteam.net (jason) Date: Fri, 12 Sep 2008 09:54:46 +0800 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> Message-ID: <48C9CBE6.7010808@bioteam.net> Hi, all Edward Kawas wrote: > Hi, > > I am trying to reproduce your problems, but I cannot. I am not seeing any > SOAP exceptions and I don't see your service either. > > The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I > tried to use non utf8 characters in my soap message. > Part of the Moby code use String manipulation to parse and generate Xml message instead of using a standard of XML parsing/writing. The invalid byte could be related to this. I saw this error in another project. Xml message generated by String concatenation could cause many unexpected XML parsing error. > Eddie > > > From soiland-reyes at cs.manchester.ac.uk Fri Sep 12 08:46:03 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 12 Sep 2008 09:46:03 +0100 Subject: [MOBY-dev] jmoby class for workflow. Does it exist? In-Reply-To: <48BBBFAD.7060401@ac.uma.es> References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es> Message-ID: On Mon, Sep 1, 2008 at 11:10, Sergio Ramirez Ramirez wrote: > Unfortunately, moby can not handle workflows by itself for now. Normally you > use taverna for building workflows. > I'm trying to learn how to use Taverna libraries to run workflows. There is > a taverna class (workflowlauncher or similar) available in the web page for > taverna, but I couldn't make it work. Hi, also check out http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram.html If you can't make it work - do please send us an email about what kind of error message you get or what doesn't work - so we can improve it. Note that if you run this within a container like Tomcat (instead of standalone, which should work) you might run into issues recently uncovered, there's a workaround described here: http://markmail.org/search/?q=taverna-hackers+globus#query:taverna-hackers%20globus+page:1+mid:leq2tlx3adyekssq+state:results I recommend signing up to the taverna-hackers mailing list for any further questions and issues you might run into - we're happy to help! http://taverna.sourceforge.net/lists -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From edward.kawas at gmail.com Fri Sep 12 13:41:51 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 12 Sep 2008 06:41:51 -0700 Subject: [MOBY-dev] Problem with dashboard to list services In-Reply-To: <48C8CC9A.7050808@pingoured.fr> References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com> <48C8CC9A.7050808@pingoured.fr> Message-ID: <48ca71b0.2a528c0a.282c.ffffba33@mx.google.com> Hi All, The problem now should be all fixed. I recently created a patch to avoid this non utf8 mess and deployed it on the test registry; moreover, the RDF shouldn't cause problems with Dashboard. Let me know how things work out, 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: September-11-08 12:46 AM To: Core developer announcements Subject: Re: [MOBY-dev] Problem with dashboard to list services Edward Kawas wrote: > I also forgot to mention that I also tried looking for your services in the > database that backs the registry and failed to find it! > Few minutes after this email and after a couple of trials we have been able to see our services again. What we observed is: - avilin05.avignon.inra.fr appears in the second position in the /moses generator/ panel while it was easily at the fourth or fifth position before. - the list of services starting by the letter 's' (or S) seems to have decrease dramatically now compare to earlier. - when we try to reload or update our cache, or when we regenerate it after removal when ends with the following error: "rethrew: org.xml.sax.SAXParseException: XML document structures must start and end within the same entity." In the console I got the following error: dashboard: [Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line 46041 column 103): XML document structures must start and end within the same entity. [Dashboard] [Fatal Error] :-1:-1: Premature end of file. It does not stop us from work so that's more for the report. To us it would seems like something has gone wrong yesterday on the server and a file has been corrupted ? Thanks 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 Sep 18 17:08:21 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 18 Sep 2008 10:08:21 -0700 Subject: [MOBY-dev] FWD: Making SOAP::Lite painlessly support document-literal encoding In-Reply-To: <146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry> References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com><48d26bbb.27b38c0a.32a5.ffff9576@mx.google.com> <146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry> Message-ID: <48d28b06.1cbd720a.50af.ffff83bc@mx.google.com> Just to keep everyone on the list in the know ... Eddie -------------------- From: "Ed Kawas" Date: Thu, 18 Sep 2008 07:54:49 To: 'Jason Stewart'; 'Mark'; 'Martin Kutter'; Subject: RE: Making SOAP::Lite painlessly support document-literal encoding Hi Jason, I like the fact that you hand off the XML document to the server service developer. Also the ability of the client to just attach a document looks good too. I wonder how other toolkits do it? I am pretty sure that if the soap envelope was compatible with other toolkits and all I could do was get/set the XML document, I would definitely start using S::L for doc/lit services. Eddie -----Original Message----- From: Jason Stewart [mailto:jason.e.stewart at gmail.com] Sent: September-18-08 1:40 AM To: Mark; Martin Kutter; soaplite-devel at lists.sf.net; Ed Kawas Subject: Making SOAP::Lite painlessly support document-literal encoding Hey All, So I've been doing a lot of digging through the codebase understanding how doc/lit could be used at the moment, and I find that the ease of use that S::L provides for rpc/enc is not matched in it's doc/lit support. I don't think it would take very much effort to enable simple support for doc/lit on both the client and the server - but very likely there would be issues with compatibility with Java and .NET implementations that would have to be worked out. For me the major difference is that a client wanting to use a doc/lit service wants to simply attach a pre-produced XML payload to the soap message - and the server wants to retrieve that message - WITHOUT ANY INTERFERENCE FROM SOAP::LIT. so we have: -- begin of client.pl 8< -- use SOAP::Lite; my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); my $xml =< Kutter Martin Hello Martin Kutter! XML $soap->on_action( sub { "urn:HelloWorld#sayHello" }); $soap->autotype(0); $soap->default_ns('urn:HelloWorld'); my $som = $soap->document($xml)->call("sayHello"); die $som->fault->{ faultstring } if ($som->fault); print $som->result, "\n"; -- end of client.pl -- -- begin server.pl 8< -- package HelloWorld; use SOAP::Lite; use base qw(SOAP::Server::Document); sub sayHello { my $self = shift; my $doc = shift; my $som = shift; my $ret_val = some_processing_method($doc); return $ret_val; } -- end of server.pl -- The client builds an XML document inserts it into the request using the document() method on the SOAP object. The client subclasses from SOAP::Server::Document so it gets the XML payload as the second argument on the stack, processes it somehow, and returns an XML payload back to the client. feedback? Cheers, jas. From jason.e.stewart at gmail.com Fri Sep 19 08:02:49 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Fri, 19 Sep 2008 13:32:49 +0530 Subject: [MOBY-dev] Making SOAP::Lite painlessly support document-literal encoding In-Reply-To: <1221760547.9975.19.camel@cyclops> References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com> <1221760547.9975.19.camel@cyclops> Message-ID: <41c1ade50809190102n16ee2f2fh94dd0da1d7dc9e@mail.gmail.com> Hey All, I like your suggestions Martin. I think the namespace SOAP::Lite::Server::Document is definitely the way to go. I support the idea of using a SOAP::Data object in addition to an XML scalar as the value for either the client or the server. I will make a patch and some test cases and send them to the list. Cheers, jas. On Thu, Sep 18, 2008 at 11:25 PM, Martin Kutter wrote: > Hi Jason, > > forcing the server developer to create XML may or may not be a good > idea, depending on it's complexity. > > How about making the proposed SOAP::Server::Document a bit more DWIM by > accepting either a scalar (which is supposed to be plain XML) or a > SOAP::Data object? > > This would ease migration for existing web services which want to move > to SOAP::Server::Document > > Maybe SOAP::Lite::Server::Document would be the more appropriate name - > the use of the SOAP namespace has provoked numerous errors on CPAN, so > SOAP::Lite is a better namespace for new modules. > > Thanks for your ideas, > > Martin > > Am Donnerstag, den 18.09.2008, 14:10 +0530 schrieb Jason Stewart: >> Hey All, >> >> So I've been doing a lot of digging through the codebase understanding >> how doc/lit could be used at the moment, and I find that the ease of >> use that S::L provides for rpc/enc is not matched in it's doc/lit >> support. I don't think it would take very much effort to enable simple >> support for doc/lit on both the client and the server - but very >> likely there would be issues with compatibility with Java and .NET >> implementations that would have to be worked out. >> >> For me the major difference is that a client wanting to use a doc/lit >> service wants to simply attach a pre-produced XML payload to the soap >> message - and the server wants to retrieve that message - WITHOUT ANY >> INTERFERENCE FROM SOAP::LIT. >> >> so we have: >> >> -- begin of client.pl 8< -- >> >> use SOAP::Lite; >> my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl'); >> >> my $xml =<> >> Kutter >> Martin >> >> >> >> Hello Martin Kutter! >> >> XML >> >> $soap->on_action( sub { "urn:HelloWorld#sayHello" }); >> $soap->autotype(0); >> $soap->default_ns('urn:HelloWorld'); >> >> my $som = $soap->document($xml)->call("sayHello"); >> >> die $som->fault->{ faultstring } if ($som->fault); >> print $som->result, "\n"; >> >> -- end of client.pl -- >> >> -- begin server.pl 8< -- >> >> package HelloWorld; >> use SOAP::Lite; >> >> use base qw(SOAP::Server::Document); >> >> sub sayHello { >> my $self = shift; >> my $doc = shift; >> my $som = shift; >> >> my $ret_val = some_processing_method($doc); >> return $ret_val; >> } >> >> -- end of server.pl -- >> >> The client builds an XML document inserts it into the request using >> the document() method on the SOAP object. >> >> The client subclasses from SOAP::Server::Document so it gets the XML >> payload as the second argument on the stack, processes it somehow, and >> returns an XML payload back to the client. >> >> feedback? >> >> Cheers, jas. >> > > From jason.e.stewart at gmail.com Fri Sep 19 09:29:46 2008 From: jason.e.stewart at gmail.com (Jason Stewart) Date: Fri, 19 Sep 2008 14:59:46 +0530 Subject: [MOBY-dev] moby doc-lit services. In-Reply-To: <48D411EB.2080606@bsc.es> References: <48D32B1C.3050304@bsc.es> <41c1ade50809190044l124fcf63h52e728402f4a4de3@mail.gmail.com> <48D411EB.2080606@bsc.es> Message-ID: <41c1ade50809190229me6e597arb728754a03ab9eb7@mail.gmail.com> Hey Dmitry, I agree with your suggestion as to the "right" way to do it. I am less concerned with the WSDL, from my current understanding of MOBY (which is very weak I am afraid) the WSDL is almost useless, MOBY-enabled clients will have to be aware of how to deserialize data types that they handle using their own libraries or libraries bundled with MOBY. Originally I thought MOBY would rely heavily on XML Schemas to define their data types, and that would be the core - but since that isn't how things are done, I don't see much use in the WSDL. I'd like to know if I am understanding this incorrectly. Cheers, jas. On Sat, Sep 20, 2008 at 2:26 AM, Dmitry Repchevsky wrote: > Hi Jason, > >> Mark has asked me to modify SOAP::Lite in order to better support doc/lit >> services in general... > > This is a good news, because my concern was that you are going to do a sort > of hack - make a common schema for all services, > something like a "" and pass a Moby message inside... > > What I suggested to do (and this is the "right" way to do in java) is to > pass all the MobyMessage inside a soap message: > Something like: > > > > > > > > > > ns1:id="" > ns1:namespace="">AGHFJHGDKHGJKADGHJGDJH > > > > > > > > > This way there is no problem as it is a STANDARD Moby XML inside a SOAP > . > > The problem is that you need to attach a XML Schema to your WSDL (if you > wish a "real" web-service") > Such a schema could be divided in two parts: > > 1. Static (common for all moby doc/lit services) that contains Moby specific > schema (MobySimple, MobyContent....): > > ****************************************************************************************************************************** > > version="1.0" > targetNamespace="http://www.biomoby.org/moby" > > xmlns:xs="http://www.w3.org/2001/XMLSchema" > > xmlns="http://www.biomoby.org/moby" > > > > > > > > > > > > > > > > > > > > > > > > > > > > > maxOccurs="unbounded"/> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ****************************************************************************************************************************** > > 2. Moby Datatypes specific one - that one depends of the ontology types used > by service... > In extreme case you can put the same scheme representing ALL the ontology > (not generate it for every service, but generate it once for the ontology > and use for every service). > You can even put an EXTERNAL reference to it (for example make a servlet > that dynamically generates it from the ontology). This way it will be always > updated. > > Cheers, > > Dmitry > > > > > Jason Stewart wrote: >> >> Hi Dmitry, >> >> On Fri, Sep 19, 2008 at 10:01 AM, Dmitry Repchevsky >> wrote: >> >> >>> >>> My name is Dmitry and I am a developer in Spanish National Institute of >>> Bioinformatics. >>> We just have finished an informal meeting with Mark Wilkinson and he >>> suggested to contact you about moby document/literal services... >>> >>> I have my own implementation of it based on XML Schema and I would like >>> to >>> know the way you are implementing it. >>> >> >> Mark has asked me to modify SOAP::Lite in order to better support >> doc/lit services in general, not just for MOBY. >> >> I'd love to hear more about how you do things. >> >> Currently, I'm in discussion with the SOAP::Lite developer group how >> to modify the core of S::L in order to better handle doc/lit. >> >> Cheers, jas. >> >> > > From jerzyo at genesilico.pl Wed Sep 24 15:55:58 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Wed, 24 Sep 2008 17:55:58 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48C937F2.3030708@ac.uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> Message-ID: <48DA630E.6050901@genesilico.pl> Hi 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). Where can I find source code or javadoc for uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes? I cannot find in anywhere on the web.... Jerzy Sergio Ramirez Ramirez wrote: > Here there is my small contribution, just the two methods that I use for > run a workflow. > Hope it can help to someone > > Paul Gordon wrote: >> I think whoever has a headless Taverna workflow creation and/or >> enactment working should put examples up in the Java developer's >> section of the Moby Web site...I believe the myExperiment people also >> have a headless workflow enactment engine working now...anyone from >> there on this list? Also, Paolo Romano in Italy has a headless SCUFL >> enactor in the BioWEP software. So many people are doing this, but no >> good sample code is easily available, especially for Moby services... >> >> Sergio Ramirez Ramirez wrote: >>> Hello Jerzy >>> >>> I had the same problem that you. >>> >>> I have got it to work by browsing deep in the Taverna code. I cannot >>> give you many sample code because I'm trying to organize all the code >>> tries and examples that I have. >>> >>> But I can give you some comments: >>> >>> For build a workflow model the class is: >>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>> new ScuflModel(); >>> This class contains the methods that you mention addProcessor ... >>> >>> For run I'm using freeflow, because taverna classes and raven are a >>> "little" tricky. The classes: >>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>> can help you. >>> >>> I hope this little details help you to begin. If you have more >>> detailed questions I will be very happy of help you. >>> >>> Best regards, >>> Sergio >>> >>> Jerzy Orlowski wrote: >>>> Hi >>>> >>>> I have several hundreds of workflows made up of BioMoby Services and >>>> want to execute them all without opening any GUI. >>>> >>>> I was looking for some solution over the internet and the think I >>>> came across was using Taverna plugin and try to execute it >>>> programaticaly. >>>> I have a few questions: >>>> >>>> 1. Is it the only way? >>>> >>>> 2. I found several tutorial tutorials on running saved workflow >>>> saved in scufl language. >>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>> >>>> >>>> How do you one make a workflow step by step? like: >>>> >>>> workflow.addProcesor(...) >>>> workflow.addConnector(...) >>>> ... >>>> workflow.execute() >>>> >>>> and especially, how do one add BioMoby objects this way? Is there >>>> any tutorial or do I have go though the API? >>>> >>>> Best >>>> >>>> Jerzy Orlowski >>>> >>>> _______________________________________________ >>>> 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 groscurt at mpiz-koeln.mpg.de Wed Sep 24 16:31:14 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Wed, 24 Sep 2008 18:31:14 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DA630E.6050901@genesilico.pl> Message-ID: Hi, i would really encourage you to use the taverna mailing list for issues concerning taverna. As some people here have strong experience with it, i think its way better to ask the people working with it and developing it directly. Cheers Andreas ----------------original message----------------- From: "Jerzy Orlowski" jerzyo at genesilico.pl To: moby-dev at lists.open-bio.org Date: Wed, 24 Sep 2008 17:55:58 +0200 ------------------------------------------------- > Hi > > 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). > > Where can I find source code or javadoc for > uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes? > > I cannot find in anywhere on the web.... > > Jerzy > > > Sergio Ramirez Ramirez wrote: >> Here there is my small contribution, just the two methods that I use for >> run a workflow. >> Hope it can help to someone >> >> Paul Gordon wrote: >>> I think whoever has a headless Taverna workflow creation and/or >>> enactment working should put examples up in the Java developer's >>> section of the Moby Web site...I believe the myExperiment people also >>> have a headless workflow enactment engine working now...anyone from >>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL >>> enactor in the BioWEP software. So many people are doing this, but no >>> good sample code is easily available, especially for Moby services... >>> >>> Sergio Ramirez Ramirez wrote: >>>> Hello Jerzy >>>> >>>> I had the same problem that you. >>>> >>>> I have got it to work by browsing deep in the Taverna code. I cannot >>>> give you many sample code because I'm trying to organize all the code >>>> tries and examples that I have. >>>> >>>> But I can give you some comments: >>>> >>>> For build a workflow model the class is: >>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>>> new ScuflModel(); >>>> This class contains the methods that you mention addProcessor ... >>>> >>>> For run I'm using freeflow, because taverna classes and raven are a >>>> "little" tricky. The classes: >>>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>>> can help you. >>>> >>>> I hope this little details help you to begin. If you have more >>>> detailed questions I will be very happy of help you. >>>> >>>> Best regards, >>>> Sergio >>>> >>>> Jerzy Orlowski wrote: >>>>> Hi >>>>> >>>>> I have several hundreds of workflows made up of BioMoby Services and >>>>> want to execute them all without opening any GUI. >>>>> >>>>> I was looking for some solution over the internet and the think I >>>>> came across was using Taverna plugin and try to execute it >>>>> programaticaly. >>>>> I have a few questions: >>>>> >>>>> 1. Is it the only way? >>>>> >>>>> 2. I found several tutorial tutorials on running saved workflow >>>>> saved in scufl language. >>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>>> >>>>> >>>>> >>>>> How do you one make a workflow step by step? like: >>>>> >>>>> workflow.addProcesor(...) >>>>> workflow.addConnector(...) >>>>> ... >>>>> workflow.execute() >>>>> >>>>> and especially, how do one add BioMoby objects this way? Is there >>>>> any tutorial or do I have go though the API? >>>>> >>>>> Best >>>>> >>>>> Jerzy Orlowski >>>>> >>>>> _______________________________________________ >>>>> 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 soiland-reyes at cs.manchester.ac.uk Thu Sep 25 09:54:47 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Thu, 25 Sep 2008 10:54:47 +0100 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DA630E.6050901@genesilico.pl> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> Message-ID: 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. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From jerzyo at genesilico.pl Thu Sep 25 10:22:02 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Thu, 25 Sep 2008 12:22:02 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DA6624.7040806@uma.es> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es> Message-ID: <48DB664A.6030305@genesilico.pl> I keep trying, but I cannot find anywhere a jar with uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser I have an impression that freefluo is outdated ---------------------------------------------------------------------- uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error with configuration named tavernaClassNotFound for WorkflowParser implementation: uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser at uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108) at uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64) at org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84) at org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11) Caused by: java.lang.ClassNotFoundException: uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser at java.net.URLClassLoader$1.run(URLClassLoader.java:200) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102) ... 3 more ------------------------------------------------------------------------ Jerzyo Sergio Ramirez Ramirez wrote: > Hi Jerzy > > I see you cannot got to resolve the problem. > > Try to use this class: org.embl.ebi.escience.scufl.ScuflModel; > > Maybe is what you need. to built your own workflow. > > Keep me informed ;) and good luck. > > Jerzy Orlowski wrote: >> Hi >> >> 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). >> >> Where can I find source code or javadoc for >> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other >> classes? >> >> I cannot find in anywhere on the web.... >> >> Jerzy >> >> >> Sergio Ramirez Ramirez wrote: >>> Here there is my small contribution, just the two methods that I use >>> for run a workflow. >>> Hope it can help to someone >>> >>> Paul Gordon wrote: >>>> I think whoever has a headless Taverna workflow creation and/or >>>> enactment working should put examples up in the Java developer's >>>> section of the Moby Web site...I believe the myExperiment people >>>> also have a headless workflow enactment engine working now...anyone >>>> from there on this list? Also, Paolo Romano in Italy has a headless >>>> SCUFL enactor in the BioWEP software. So many people are doing this, >>>> but no good sample code is easily available, especially for Moby >>>> services... >>>> >>>> Sergio Ramirez Ramirez wrote: >>>>> Hello Jerzy >>>>> >>>>> I had the same problem that you. >>>>> >>>>> I have got it to work by browsing deep in the Taverna code. I >>>>> cannot give you many sample code because I'm trying to organize all >>>>> the code tries and examples that I have. >>>>> >>>>> But I can give you some comments: >>>>> >>>>> For build a workflow model the class is: >>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = >>>>> new ScuflModel(); >>>>> This class contains the methods that you mention addProcessor ... >>>>> >>>>> For run I'm using freeflow, because taverna classes and raven are a >>>>> "little" tricky. The classes: >>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>>>> can help you. >>>>> >>>>> I hope this little details help you to begin. If you have more >>>>> detailed questions I will be very happy of help you. >>>>> >>>>> Best regards, >>>>> Sergio >>>>> >>>>> Jerzy Orlowski wrote: >>>>>> Hi >>>>>> >>>>>> I have several hundreds of workflows made up of BioMoby Services >>>>>> and want to execute them all without opening any GUI. >>>>>> >>>>>> I was looking for some solution over the internet and the think I >>>>>> came across was using Taverna plugin and try to execute it >>>>>> programaticaly. >>>>>> I have a few questions: >>>>>> >>>>>> 1. Is it the only way? >>>>>> >>>>>> 2. I found several tutorial tutorials on running saved workflow >>>>>> saved in scufl language. >>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>>>> >>>>>> >>>>>> How do you one make a workflow step by step? like: >>>>>> >>>>>> workflow.addProcesor(...) >>>>>> workflow.addConnector(...) >>>>>> ... >>>>>> workflow.execute() >>>>>> >>>>>> and especially, how do one add BioMoby objects this way? Is there >>>>>> any tutorial or do I have go though the API? >>>>>> >>>>>> Best >>>>>> >>>>>> Jerzy Orlowski >>>>>> >>>>>> _______________________________________________ >>>>>> 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 jerzyo at genesilico.pl Fri Sep 26 08:28:48 2008 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Fri, 26 Sep 2008 10:28:48 +0200 Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna Message-ID: <48DC9D40.5030604@genesilico.pl> Hi I think there is one important option missing in BioMoby plugins in Taverna. Suppose I have a MobyService that returns an AminoAcidSequence. I want to extract the sequence on my AminAcidSequence (it is a String object) and use it as input for another MobyServices that eats String as its input. The only way I can do it now is to use a Parser which decomposes AminoAcidSequence to basic types and then construct my String from these basic elements (namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns,aminoacid_'SequenceString',aminoacid_'SequenceString'_id and aminoacid_'SequenceString'_ns). This is not very difficult in this case, but imagine what would happen if I parse an object which is composed of for example WieghtedAminoSequences and try to get AminoAcidSequence out of it... In fact current BioMobyObjectProcessors are processors for constructing MobyObjects (with basic types as input ports and composite types as output ports). There should be another type of BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects (with composite types as input ports and basic types as output ports). Please inform me if such option already exists somewhere and I missed it. Jerzy Orlowski From edward.kawas at gmail.com Fri Sep 26 12:16:20 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Sep 2008 05:16:20 -0700 Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna In-Reply-To: <48DC9D40.5030604@genesilico.pl> References: <48DC9D40.5030604@genesilico.pl> Message-ID: <48dcd299.1bbc720a.76c6.ffffb9d8@mx.google.com> Hi Jerzy, That option is indeed unavailable. It can be something that we add in the future. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski Sent: September-26-08 1:29 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna Hi I think there is one important option missing in BioMoby plugins in Taverna. Suppose I have a MobyService that returns an AminoAcidSequence. I want to extract the sequence on my AminAcidSequence (it is a String object) and use it as input for another MobyServices that eats String as its input. The only way I can do it now is to use a Parser which decomposes AminoAcidSequence to basic types and then construct my String from these basic elements (namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns ,aminoacid_'SequenceString',aminoacid_'SequenceString'_id and aminoacid_'SequenceString'_ns). This is not very difficult in this case, but imagine what would happen if I parse an object which is composed of for example WieghtedAminoSequences and try to get AminoAcidSequence out of it... In fact current BioMobyObjectProcessors are processors for constructing MobyObjects (with basic types as input ports and composite types as output ports). There should be another type of BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects (with composite types as input ports and basic types as output ports). Please inform me if such option already exists somewhere and I missed it. Jerzy Orlowski _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From soiland-reyes at cs.manchester.ac.uk Fri Sep 26 13:39:14 2008 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 26 Sep 2008 14:39:14 +0100 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DB664A.6030305@genesilico.pl> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es> <48DB664A.6030305@genesilico.pl> Message-ID: On Thu, Sep 25, 2008 at 11:22, Jerzy Orlowski wrote: > I keep trying, but I cannot find anywhere a jar with > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser : stain at mira ~/.m2/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1;unzip -t freefluo-taverna-exts-1.7.1.jar Archive: freefluo-taverna-exts-1.7.1.jar testing: META-INF/ OK testing: META-INF/MANIFEST.MF OK testing: uk/ OK testing: uk/ac/ OK testing: uk/ac/soton/ OK testing: uk/ac/soton/itinnovation/ OK testing: uk/ac/soton/itinnovation/freefluo/ OK testing: uk/ac/soton/itinnovation/freefluo/exts/ OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/ OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaDataHandler.class OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaScuflModelParser.class OK testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaWorkflowInstance.class OK No errors detected in compressed data of freefluo-taverna-exts-1.7.1.jar. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From srramirez at uma.es Thu Sep 25 10:29:18 2008 From: srramirez at uma.es (Sergio Ramirez Ramirez) Date: Thu, 25 Sep 2008 12:29:18 +0200 Subject: [MOBY-dev] Executing Moby Workflow straight from java In-Reply-To: <48DB664A.6030305@genesilico.pl> References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es> <48DB664A.6030305@genesilico.pl> Message-ID: <48DB67FE.4000507@uma.es> Yes, you are right but taverna still using it in the core. If you download the entire src of taverna you will find a jar file: taverna-workbench with that class If you couldn't find it, just tell me and I will sent it to you Best regards, Sergio Jerzy Orlowski wrote: > I keep trying, but I cannot find anywhere a jar with > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser > > I have an impression that freefluo is outdated > > ---------------------------------------------------------------------- > uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error > with configuration named tavernaClassNotFound for WorkflowParser > implementation: > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser > at > uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108) > > at > uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64) > > at > org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84) > at > org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11) > Caused by: java.lang.ClassNotFoundException: > uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser > at java.net.URLClassLoader$1.run(URLClassLoader.java:200) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:188) > at java.lang.ClassLoader.loadClass(ClassLoader.java:306) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276) > at java.lang.ClassLoader.loadClass(ClassLoader.java:251) > at > uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102) > > ... 3 more > ------------------------------------------------------------------------ > > Jerzyo > > > > Sergio Ramirez Ramirez wrote: >> Hi Jerzy >> >> I see you cannot got to resolve the problem. >> >> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel; >> >> Maybe is what you need. to built your own workflow. >> >> Keep me informed ;) and good luck. >> >> Jerzy Orlowski wrote: >>> Hi >>> >>> 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). >>> >>> Where can I find source code or javadoc for >>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other >>> classes? >>> >>> I cannot find in anywhere on the web.... >>> >>> Jerzy >>> >>> >>> Sergio Ramirez Ramirez wrote: >>>> Here there is my small contribution, just the two methods that I >>>> use for run a workflow. >>>> Hope it can help to someone >>>> >>>> Paul Gordon wrote: >>>>> I think whoever has a headless Taverna workflow creation and/or >>>>> enactment working should put examples up in the Java developer's >>>>> section of the Moby Web site...I believe the myExperiment people >>>>> also have a headless workflow enactment engine working >>>>> now...anyone from there on this list? Also, Paolo Romano in Italy >>>>> has a headless SCUFL enactor in the BioWEP software. So many >>>>> people are doing this, but no good sample code is easily >>>>> available, especially for Moby services... >>>>> >>>>> Sergio Ramirez Ramirez wrote: >>>>>> Hello Jerzy >>>>>> >>>>>> I had the same problem that you. >>>>>> >>>>>> I have got it to work by browsing deep in the Taverna code. I >>>>>> cannot give you many sample code because I'm trying to organize >>>>>> all the code tries and examples that I have. >>>>>> >>>>>> But I can give you some comments: >>>>>> >>>>>> For build a workflow model the class is: >>>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model >>>>>> = new ScuflModel(); >>>>>> This class contains the methods that you mention addProcessor ... >>>>>> >>>>>> For run I'm using freeflow, because taverna classes and raven are >>>>>> a "little" tricky. The classes: >>>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or >>>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy >>>>>> can help you. >>>>>> >>>>>> I hope this little details help you to begin. If you have more >>>>>> detailed questions I will be very happy of help you. >>>>>> >>>>>> Best regards, >>>>>> Sergio >>>>>> >>>>>> Jerzy Orlowski wrote: >>>>>>> Hi >>>>>>> >>>>>>> I have several hundreds of workflows made up of BioMoby Services >>>>>>> and want to execute them all without opening any GUI. >>>>>>> >>>>>>> I was looking for some solution over the internet and the think >>>>>>> I came across was using Taverna plugin and try to execute it >>>>>>> programaticaly. >>>>>>> I have a few questions: >>>>>>> >>>>>>> 1. Is it the only way? >>>>>>> >>>>>>> 2. I found several tutorial tutorials on running saved workflow >>>>>>> saved in scufl language. >>>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html >>>>>>> >>>>>>> >>>>>>> How do you one make a workflow step by step? like: >>>>>>> >>>>>>> workflow.addProcesor(...) >>>>>>> workflow.addConnector(...) >>>>>>> ... >>>>>>> workflow.execute() >>>>>>> >>>>>>> and especially, how do one add BioMoby objects this way? Is >>>>>>> there any tutorial or do I have go though the API? >>>>>>> >>>>>>> Best >>>>>>> >>>>>>> Jerzy Orlowski >>>>>>> >>>>>>> _______________________________________________ >>>>>>> MOBY-dev mailing list >>>>>>> MOBY-dev at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> MOBY-dev mailing list >>>>> MOBY-dev at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>>> >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- 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