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From: <Lia...@cs...> - 2006-03-28 22:02:12
|
Hi Justin, Thanks heaps for the help, it worked a treat :). We're using the engine to enact pre-made workflows using a web interface. Cheers, Liam -----Original Message----- Hi Liam =3D20 The stack trace is useful. There's a slightly strange issue with using java.awt image libraries on Linux that may be the cause of the problem you have.=3D20 Try the following in the (bash) shell before restarting tomcat and re-running your test.=3D20 export JAVA_OPTS=3D3D-Djava.awt.headless=3D3Dtrue On Suse 9 I think you can restart tomcat as follows if you've installed Tomcat with Yast. /etc/init.d/tomcat restart If your test works, I'd suggest setting the JAVA_OPTS as above in $TOMCAT_HOME/bin/catalina.sh instead of setting in the shell each time before starting tomcat. By the way, the current freefluo release is lagging behind Taverna releases as we've been largely working on other areas recently, and Taverna 2.0 development is underway and this entails a complete rewrite, including the workflow engine. I just want to warn you that you may hit problems using freefluo 0.9 as it hasn't been tested with taverna 1.3.1. It's also intermittently supported at present due to other commitments. That said, we're very glad you're using the software and it would be interesting to know what you are doing. cheers Justin Ferris IT Innovation Centre 2 Venture Road Chilworth Science Park Southampton, SO16 7NP, UK tel: +44 23 8076 0834 fax: +44 23 8076 0833 mailto:jf...@it... http://www.it-innovation.soton.ac.uk > -----Original Message----- > From: fre...@li...=3D20 > [mailto:fre...@li...] On Behalf=3D20 > Of Lia...@cs... > Sent: 27 March 2006 06:26 > To: fre...@li... > Subject: [Freefluo-users] Re: Critical error compiling workflow >=3D20 > More info fresh in on the error. On the server side, the logs are > showing the following error: >=3D20 > java.lang.InternalError: Can't connect to X11 window server=3D20 > using ':0.0' > as the value of the DISPLAY variable. > at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) > at > sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment > .java:134) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at > java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(Graph > icsEnviron > ment.java:62) > at sun.awt.motif.MToolkit.<clinit>(MToolkit.java:81) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at java.awt.Toolkit$2.run(Toolkit.java:748) > at java.security.AccessController.doPrivileged(Native Method) > at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) > at javax.swing.ImageIcon.<init>(ImageIcon.java:119) > at javax.swing.ImageIcon.<init>(ImageIcon.java:138) > at > org.embl.ebi.escience.scuflworkers.ProcessorHelper.<clinit>(Pr > ocessorHel > per.java:85) > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(X > ScuflParse > r.java:438) >=3D20 > Liam Childs > Data Analyst > CSIRO Plant Industry > GPO Box 1600 > Canberra ACT 2601 >=3D20 > Tel: +61 (0) 262 464 924 > Mob: +61 (0) 423 394 921 >=3D20 >=3D20 > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking=3D20 > scripting language > that extends applications into web and mobile media. Attend=3D20 > the live webcast > and join the prime developer group breaking into this new=3D20 > coding territory! > = http://sel.as-us.falkag.net/sel?cmd=3D3Dk&kid=3D110944&bid$1720&dat=3D121= 642 > _______________________________________________ > Freefluo-users mailing list > Fre...@li... > https://lists.sourceforge.net/lists/listinfo/freefluo-users >=3D20 --__--__-- _______________________________________________ Freefluo-users mailing list Fre...@li... https://lists.sourceforge.net/lists/listinfo/freefluo-users End of Freefluo-users Digest |
|
From: Justin F. <jf...@it...> - 2006-03-27 09:20:06
|
Hi Liam =20 The stack trace is useful. There's a slightly strange issue with using java.awt image libraries on Linux that may be the cause of the problem you have.=20 Try the following in the (bash) shell before restarting tomcat and re-running your test.=20 export JAVA_OPTS=3D-Djava.awt.headless=3Dtrue On Suse 9 I think you can restart tomcat as follows if you've installed Tomcat with Yast. /etc/init.d/tomcat restart If your test works, I'd suggest setting the JAVA_OPTS as above in $TOMCAT_HOME/bin/catalina.sh instead of setting in the shell each time before starting tomcat. By the way, the current freefluo release is lagging behind Taverna releases as we've been largely working on other areas recently, and Taverna 2.0 development is underway and this entails a complete rewrite, including the workflow engine. I just want to warn you that you may hit problems using freefluo 0.9 as it hasn't been tested with taverna 1.3.1. It's also intermittently supported at present due to other commitments. That said, we're very glad you're using the software and it would be interesting to know what you are doing. cheers Justin Ferris IT Innovation Centre 2 Venture Road Chilworth Science Park Southampton, SO16 7NP, UK tel: +44 23 8076 0834 fax: +44 23 8076 0833 mailto:jf...@it... http://www.it-innovation.soton.ac.uk > -----Original Message----- > From: fre...@li...=20 > [mailto:fre...@li...] On Behalf=20 > Of Lia...@cs... > Sent: 27 March 2006 06:26 > To: fre...@li... > Subject: [Freefluo-users] Re: Critical error compiling workflow >=20 > More info fresh in on the error. On the server side, the logs are > showing the following error: >=20 > java.lang.InternalError: Can't connect to X11 window server=20 > using ':0.0' > as the value of the DISPLAY variable. > at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) > at > sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment > .java:134) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at > java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(Graph > icsEnviron > ment.java:62) > at sun.awt.motif.MToolkit.<clinit>(MToolkit.java:81) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:141) > at java.awt.Toolkit$2.run(Toolkit.java:748) > at java.security.AccessController.doPrivileged(Native Method) > at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739) > at javax.swing.ImageIcon.<init>(ImageIcon.java:119) > at javax.swing.ImageIcon.<init>(ImageIcon.java:138) > at > org.embl.ebi.escience.scuflworkers.ProcessorHelper.<clinit>(Pr > ocessorHel > per.java:85) > at > org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(X > ScuflParse > r.java:438) >=20 > Liam Childs > Data Analyst > CSIRO Plant Industry > GPO Box 1600 > Canberra ACT 2601 >=20 > Tel: +61 (0) 262 464 924 > Mob: +61 (0) 423 394 921 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking=20 > scripting language > that extends applications into web and mobile media. Attend=20 > the live webcast > and join the prime developer group breaking into this new=20 > coding territory! > http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642 > _______________________________________________ > Freefluo-users mailing list > Fre...@li... > https://lists.sourceforge.net/lists/listinfo/freefluo-users >=20 |
|
From: <Lia...@cs...> - 2006-03-27 05:26:41
|
More info fresh in on the error. On the server side, the logs are
showing the following error:
java.lang.InternalError: Can't connect to X11 window server using ':0.0'
as the value of the DISPLAY variable.
at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at
sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:134)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:141)
at
java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnviron
ment.java:62)
at sun.awt.motif.MToolkit.<clinit>(MToolkit.java:81)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:141)
at java.awt.Toolkit$2.run(Toolkit.java:748)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:739)
at javax.swing.ImageIcon.<init>(ImageIcon.java:119)
at javax.swing.ImageIcon.<init>(ImageIcon.java:138)
at
org.embl.ebi.escience.scuflworkers.ProcessorHelper.<clinit>(ProcessorHel
per.java:85)
at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run(XScuflParse
r.java:438)
Liam Childs
Data Analyst
CSIRO Plant Industry
GPO Box 1600
Canberra ACT 2601
Tel: +61 (0) 262 464 924
Mob: +61 (0) 423 394 921
|
|
From: <Lia...@cs...> - 2006-03-27 03:02:35
|
I'm having trouble trying to get freefluo to compile and run workflows. When using the Taverna or a custom client using the Taverna-1.3.1 API, I get the exception "Serious error compiling workflow". When I try to communicate with Freefluo using SOAP, I get the http response code 500 (server error).=20 Currently I have freefluo installed on two computers. One is a winxp box using Apache Tomcat/5.5.7 and the deployed freefluo.war file. The other is a Suse9 linux box using Apache Tomcat/5.0.19 and the deployed freefluo.war file. Both are configured identically. Taverna, custom clients and SOAP clients can communicate with the former one with no problem. The latter is the one I'm having trouble talking to. I can view the freefluo services using a html browser. I can also use a SOAP client to run the freefluo getVersion service (return value: 1.0). That is the extent to which I can talk to freefluo though. Beyond that I get "Serious error compiling workflow" or http response code 500. Liam Childs Data Analyst CSIRO Plant Industry GPO Box 1600 Canberra ACT 2601 Tel: +61 (0) 262 464 924 Mob: +61 (0) 423 394 921 |
|
From: Tim T. <tim...@ed...> - 2006-02-13 11:05:27
|
Hi,
I posted this to the taverna hackers mailing list a while ago with no
response. Apologies for cross-posting but I was hoping I may have
more luck here as from what I can tell the issue is more closely tied
to freefluo.
I am using Taverna to build and execute a workflow which uses
implicit iteration. In this workflow i specify an array of Strings as
input to a nested workflow which accepts a String as input. The array
is of size 200 so it should iterate 200 times. I have run this
workflow numerous times using the same services and data sets each
time. With each invocation it iterates a seemingly random number of
times before stating the workflow has completed successfully.
I run Taverna from the command line in linux. Just before the
workflow dies I see the following error written to the terminal (see
below). It seems as though the freefluo enactment engine is having
some issues with threading. Anyone else encounter this problem? Any
known work-arounds or fixes?
Thanks,
Tim
Exception in thread "Thread-1171"
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at java.util.ArrayList.toArray(ArrayList.java:305)
at org.embl.ebi.escience.scufl.ScuflModel.getProcessors
(ScuflModel.java:341)
at org.embl.ebi.escience.scufl.Processor.<init>
(Processor.java:492)
at
org.embl.ebi.escience.scuflworkers.beanshell.BeanshellProcessor.<init>
(BeanshellProcessor.java:38)
at
org.embl.ebi.escience.scuflworkers.beanshell.BeanshellXMLHandler.loadPro
cessorFromXML(BeanshellXMLHandler.java:91)
at
org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(
ProcessorHelper.java:416)
at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run
(XScuflParser.java:446)
Exception in thread "Thread-1175"
java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at java.util.ArrayList.toArray(ArrayList.java:305)
at org.embl.ebi.escience.scufl.ScuflModel.getProcessors
(ScuflModel.java:341)
at org.embl.ebi.escience.scufl.Processor.<init>
(Processor.java:492)
at
org.embl.ebi.escience.scuflworkers.java.LocalServiceProcessor.<init>
(LocalServiceProcessor.java:46)
at
org.embl.ebi.escience.scuflworkers.java.LocalServiceXMLHandler.loadProce
ssorFromXML(LocalServiceXMLHandler.java:60)
at
org.embl.ebi.escience.scuflworkers.ProcessorHelper.loadProcessorFromXML(
ProcessorHelper.java:416)
at
org.embl.ebi.escience.scufl.parser.ProcessorLoaderThread.run
(XScuflParser.java:446)
text/plain
text/plain
text/plain
ERROR 2006-01-25 14:46:24,897
(uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser:
82) - Serious error compiling workflow.
org.embl.ebi.escience.scufl.UnknownProcessorException: Unable to
locate processor with name 'FuzzPath1'
at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor
(ScuflModel.java:587)
at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate
(ScuflModel.java:561)
at org.embl.ebi.escience.scufl.DataConstraint.<init>
(DataConstraint.java:32)
at org.embl.ebi.escience.scufl.parser.XScuflParser.populate
(XScuflParser.java:369)
at org.embl.ebi.escience.scufl.parser.XScuflParser.populate
(XScuflParser.java:85)
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p
arse(TavernaScuflModelParser.java:78)
at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile
(EngineImpl.java:128)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:100)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:91)
at
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute
(WorkflowTask.java:97)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:462)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:407)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:329)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle
Iteration(ProcessorTask.java:878)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access
$000(ProcessorTask.java:88)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run
(ProcessorTask.java:690)
ERROR 2006-01-25 14:46:24,898
(uk.ac.soton.itinnovation.freefluo.main.EngineImpl:147) - Serio
us error compiling workflow.
java.lang.RuntimeException: Serious error compiling workflow.
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p
arse(TavernaScuflModelParser.java:83)
at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile
(EngineImpl.java:128)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:100)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:91)
at
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute
(WorkflowTask.java:97)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:462)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:407)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:329)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle
Iteration(ProcessorTask.java:878)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access
$000(ProcessorTask.java:88)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run
(ProcessorTask.java:690)
Caused by: org.embl.ebi.escience.scufl.UnknownProcessorException:
Unable to locate processor with name 'FuzzPath1'
at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor
(ScuflModel.java:587)
at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate
(ScuflModel.java:561)
at org.embl.ebi.escience.scufl.DataConstraint.<init>
(DataConstraint.java:32)
at org.embl.ebi.escience.scufl.parser.XScuflParser.populate
(XScuflParser.java:369)
at org.embl.ebi.escience.scufl.parser.XScuflParser.populate
(XScuflParser.java:85)
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p
arse(TavernaScuflModelParser.java:78)
... 10 more
java.lang.RuntimeException: Serious error compiling workflow.
at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile
(EngineImpl.java:148)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:100)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:91)
at
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute
(WorkflowTask.java:97)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:462)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:407)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:329)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle
Iteration(ProcessorTask.java:878)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access
$000(ProcessorTask.java:88)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run
(ProcessorTask.java:690)
Caused by: java.lang.RuntimeException: Serious error compiling workflow.
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p
arse(TavernaScuflModelParser.java:83)
at uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile
(EngineImpl.java:128)
... 9 more
Caused by: org.embl.ebi.escience.scufl.UnknownProcessorException:
Unable to locate processor with name 'FuzzPath1'
at org.embl.ebi.escience.scufl.ScuflModel.locateProcessor
(ScuflModel.java:587)
at org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate
(ScuflModel.java:561)
at org.embl.ebi.escience.scufl.DataConstraint.<init>
(DataConstraint.java:32)
at org.embl.ebi.escience.scufl.parser.XScuflParser.populate
(XScuflParser.java:369)
at org.embl.ebi.escience.scufl.parser.XScuflParser.populate
(XScuflParser.java:85)
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser.p
arse(TavernaScuflModelParser.java:78)
... 10 more
java.lang.IllegalStateException: Can't overwrite cause
at java.lang.Throwable.initCause(Throwable.java:320)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:116)
at
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy.
compileWorkflow(FreefluoEnactorProxy.java:91)
at
org.embl.ebi.escience.scuflworkers.workflow.WorkflowTask.execute
(WorkflowTask.java:97)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGe
nerateTemplates(ProcessorTask.java:462)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvoca
tionWithRetryLogic(ProcessorTask.java:407)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOn
ce(ProcessorTask.java:329)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doSingle
Iteration(ProcessorTask.java:878)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.access
$000(ProcessorTask.java:88)
at
uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask$1.run
(ProcessorTask.java:690)
Thread[Thread-326,6,main] completed
Getting results...
|
|
From: Alexis T. Martinez<ato...@ls...> - 2006-01-02 09:35:04
|
Hello, Hello Ismael, I have seen your mail about commandline freefluo. Maybe you need some more configuration steps for your freefluo. Look at this web-page : http://twiki.mygrid.org.uk/twiki/bin/view/Mygrid/FreefluoXScufl good luck. Alexis. -- ----------------------------------------------------- Alexis Torrano Martinez e-mail: ato...@ls... Nodo Computacional GNHC-2 UPC-CIRI (inb.lsi.upc.edu) Instituto Nacional de Bioinformatica (www.inab.org) Barcelona Supercomputing Center Node (www.bsc.es) c/. Jordi Girona 29 Edifici Nexus II, despatx 113 Tel: (+34) 93 413 4049 E-08034 Barcelona Fax: (+34) 93 Catalunya (Spain) Team info: http://www.inab.org/~malaga/MOWServ/services/HELP/MarcoBajo/team.html ----------------------------------------------------- |
|
From: Alexis T. Martinez<ato...@ls...> - 2006-01-02 09:30:22
|
Hello,
We have sent this mail asking for help. We are computer technicians from
UPC-BSC(Polytechnic University of Catalonia - Barcelona SuperComputing
Center)=20
providing computational resources and bioinformatic support to our
community of biologic scientist.=20
The matter is we are in need of using FreeFluo to launch webservices from=
=20
commandline. Although it was possible to launch most of our services, some=
=20
of them, which take advantage of features from Taverna 1.2 ( collections ),=
=20
gave error or simply returned void results.=20
Our first trial seemed to work, but the attached workflow (and its
input) did not ran as we expected. I would mention it contains
nested workflows.
There is a way to improve freefluo to match the capabilities of Taverna
1.2, or even further?
A lot of thanks.
Romina Royo & Alexis Torrano.=20
=09
pd : we also attach our migrid.properties which links our BioMoby
repositories.
pd2: yes, the first trial was with XScufl workflows compliant, and they
worked.
--
-----------------------------------------------------
Alexis Torrano Martinez
e-mail: ato...@ls...
Nodo Computacional GNHC-2 UPC-CIRI (inb.lsi.upc.edu)
Instituto Nacional de Bioinformatica (www.inab.org)
Barcelona Supercomputing Center Node (www.bsc.es)
c/. Jordi Girona 29
Edifici Nexus II, despatx 113 Tel: (+34) 93 413 4049
E-08034 Barcelona Fax: (+34) 93
Catalunya (Spain)
Team info:
http://www.inab.org/~malaga/MOWServ/services/HELP/MarcoBajo/team.html
-----------------------------------------------------
|
|
From: Ohler, N. T. <Nat...@hm...> - 2005-07-19 15:51:33
|
I have a web service returning multiple outputs. I can only get freefluo = to read the first one.=20 I have three files to work with: The workflow xml, the wsdl, and the web = service. I have the web service returning two parts, and the message looks like: -------------------------------------------------------------------------= -- <?xml version=3D"1.0" encoding=3D"UTF-8"?><SOAP-ENV:Envelope = xmlns:xsi=3D"http://www.w3.org/2001/XMLSchema-instance" = xmlns:SOAP-ENC=3D"http://schemas.xmlsoap.org/soap/encoding/" = xmlns:SOAP-ENV=3D"http://schemas.xmlsoap.org/soap/envelope/" = xmlns:xsd=3D"http://www.w3.org/2001/XMLSchema" = SOAP-ENV:encodingStyle=3D"http://schemas.xmlsoap.org/soap/encoding/"><SOA= P-ENV:Body><namesp1:getemmaResponse = xmlns:namesp1=3D"urn:getemma"><stderr xsi:type=3D"xsd:string">standard = error message</stderr><stdout xsi:type=3D"xsd:string">standard output = message</stdout></namesp1:getemmaResponse></SOAP-ENV:Body></SOAP-ENV:Enve= lope> -------------------------------------------------------------------------= -- If I set the wsdl to claim the web service only has one response (when = the web service really has two), and the workflow xml to only look for = one: -------------------------------------------------------------------------= -- <message name=3D"emmaResponse"> <part name=3D"stdout" type=3D"xsd:string"/> </message> -------------------------------------------------------------------------= -- <s:link source=3D"getemma:stdout" sink=3D"stdout" /> <s:sink name=3D"stdout" /> -------------------------------------------------------------------------= -- Then my output file saves only the first response, even if the names = don't match! (It saves the part named stderr as stdout, and discards the = part named stdout). If I set the wsdl and workflow for both outputs: -------------------------------------------------------------------------= -- <message name=3D"emmaResponse"> <part name=3D"stdout" type=3D"xsd:string"/> <part name=3D"stderr" type=3D"xsd:string"/> </message> -------------------------------------------------------------------------= -- <s:link source=3D"getemma:stdout" sink=3D"stdout" /> <s:link source=3D"getemma:stderr" sink=3D"stderr" /> <s:sink name=3D"stderr" /> <s:sink name=3D"stdout" /> -------------------------------------------------------------------------= -- Then the output file only gets this much written: -------------------------------------------------------------------------= -- <?xml version=3D"1.0" encoding=3D"UTF-8"?> <b:dataThingMap = xmlns:b=3D"http://org.embl.ebi.escience/baclava/0.1alpha" /> -------------------------------------------------------------------------= -- And the std.err.log reports: -------------------------------------------------------------------------= -- java.lang.RuntimeException: Attempt to create a null data object, = definitely not allowed! at org.embl.ebi.escience.baclava.DataThing.<init>(DataThing.java:231) at = org.embl.ebi.escience.scuflworkers.wsdl.WSDLInvocationTask.execute(WSDLIn= vocationTask.java:196) -------------------------------------------------------------------------= -- I would appreciate any ideas where I'm going wrong with these forms. I = can forward the whole xml files if desired, just wasn't certain how the = mailling list would handle them, and was trying to keep this somewhat = brief. Thanks for any help -Nathaniel |
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From: Nick D. <nic...@li...> - 2005-05-03 16:57:13
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Hi,
I've been trying out the standalone freefluo and I can get it to work
for example workflow files such as IterationStrategyExample and
AlternateExample, but I get errors when I try to run a workflow that
contains web services (such as BasicArithmeticWithDotNet). Is there
something else I need to do before I can use the web services? The
error message I got whilst trying to run the BasicArithmeticWithDotNet
workflow is below.
many thanks,
Nick
E:\freefluo-0.8.2>freefluo -s -o doc\examples\results2.txt
doc\examples\BasicAri
thmeticWithDotNet.xml
Exception in thread "main" java.lang.RuntimeException: Serious error
compiling w
orkflow.
at
uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile(EngineImpl.
java:121)
at
uk.ac.soton.itinnovation.freefluo.main.Console.runWorkflowAndWait(Con
sole.java:211)
at
uk.ac.soton.itinnovation.freefluo.main.Console.run(Console.java:152)
at
uk.ac.soton.itinnovation.freefluo.main.Console.main(Console.java:69)
Caused by: java.lang.RuntimeException: Serious error compiling workflow.
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParse
r.parse(TavernaScuflModelParser.java:82)
at
uk.ac.soton.itinnovation.freefluo.main.EngineImpl.compile(EngineImpl.
java:101)
... 3 more
Caused by: org.embl.ebi.escience.scufl.UnknownProcessorException: Unable
to loca
te processor with name 'add'
at
org.embl.ebi.escience.scufl.ScuflModel.locateProcessor(ScuflModel.jav
a:528)
at
org.embl.ebi.escience.scufl.ScuflModel.locatePortOrCreate(ScuflModel.
java:499)
at
org.embl.ebi.escience.scufl.DataConstraint.<init>(DataConstraint.java
:32)
at
org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser
.java:361)
at
org.embl.ebi.escience.scufl.parser.XScuflParser.populate(XScuflParser
.java:85)
at
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParse
r.parse(TavernaScuflModelParser.java:77)
... 4 more
---
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