This seems to be a bug. Can you raise a JIRA on this as well? Sorry Shinyoung, you are bleeding with lot of issues but you are contributing to an open source project and helping fix all these issues. These can be fixed on a short order, but looks like you will have to work on a trunk instead of a release so as soon as the bug is fixed you can do a svn update and re-test.
Saminda, will you be able to address this? Suresh On Apr 10, 2013, at 1:27 AM, 안신영 <[email protected]> wrote: > Hi Suresh, > > Is it possible to use ForEach such like below? > threadCount, refIndexFile is String Type. > input_3, input_4 is StringArray Type. > > I want to ‘bwa_aln_fwd_p’ read same value from threadCount and refIndexFile, > and read other value via ForEach from input_3. > > <image001.png> > When I execute this workflow with input values like below > <image002.png> > > Airavat show unexpected behavior like below. Invoking service do not use > right value that I expected… > I expect the input parameters’ values of bwa_aln_fwd_p_invoke are same with > the parameter of WorkflowInvoked. > <image003.png> > > Is it a bug? Or do I have to compose workflow in other ways? > > Regards > Shinyoung. > From: Suresh Marru [mailto:[email protected]] > Sent: Wednesday, April 10, 2013 11:11 AM > To: [email protected] > Subject: Re: Question on ForEach > > Hi Shinyoung, > > Couple of things. You are using String and using Foreach, so it is assumed as > one string with comas in it. You should change the inputs bwdFqFile and > bwdSaiFile inputs to String Arrays. > > Suresh > > On Apr 9, 2013, at 4:38 AM, 안신영 <[email protected]> wrote: > > > Hi Suresh. > This is Another questions different from my previous emails. > > I am tring to use ForEach component. > I have register a service ‘bwa_aln_bwd’ which works well when I do not use > ForEach component. > The output type of bwa_aln_bwd is URI type. > > <image001.png> > > Next, I compose a new workflow using ForEach, EndForEach component. > <image002.png> > > When I executed as follows, I gave “/home/team/genome/Demo/sample_1.fq.00, > /home/team/genome/Demo/sample_1.fq.01” as input_3 > and “/home/team/genome/DemoOut/sample_1.fq.00.sai, > /home/team/genome/DemoOut/sample_1.fq.01.sai” as input_4 > > <image003.png> > But Airavata show ‘Error Invoking API’ > > Error messages are > > org.apache.airavata.client.api.AiravataAPIInvocationException: Error invoking > API > at > org.apache.airavata.client.impl.ExecutionManagerImpl.runExperimentGeneral(ExecutionManagerImpl.java:228) > at > org.apache.airavata.client.impl.ExecutionManagerImpl.runExperiment(ExecutionManagerImpl.java:80) > at > org.apache.airavata.xbaya.ui.experiment.WorkflowInterpreterLaunchWindow$3.run(WorkflowInterpreterLaunchWindow.java:322) > Caused by: org.apache.airavata.workflow.model.component.ComponentException: > could not find definition for type > {http://airavata.apache.org/xbaya/Workflow1/xsd/}URIParameterTypeArrayType in > {http://airavata.apache.org/xbaya/Workflow1/}Workflow1 > at > org.apache.airavata.workflow.model.component.ws.WSComponent.parseType(WSComponent.java:468) > at > org.apache.airavata.workflow.model.component.ws.WSComponent.parseMessage(WSComponent.java:398) > at > org.apache.airavata.workflow.model.component.ws.WSComponent.parseOperation(WSComponent.java:369) > at > org.apache.airavata.workflow.model.component.ws.WSComponent.parsePortType(WSComponent.java:353) > at > org.apache.airavata.workflow.model.component.ws.WSComponent.parse(WSComponent.java:345) > at > org.apache.airavata.workflow.model.component.ws.WSComponent.<init>(WSComponent.java:132) > at > org.apache.airavata.workflow.model.component.ws.WSComponentFactory.createComponent(WSComponentFactory.java:136) > at > org.apache.airavata.workflow.model.component.ws.WSComponentFactory.createComponent(WSComponentFactory.java:110) > at org.apache.airavata.workflow.model.wf.Workflow.getInputs(Workflow.java:484) > at > org.apache.airavata.client.impl.ExecutionManagerImpl.getWSComponentPortInputs(ExecutionManagerImpl.java:268) > at > org.apache.airavata.client.impl.ExecutionManagerImpl.runExperimentGeneral(ExecutionManagerImpl.java:185) > ... 2 more > > I expected that ForEach read StringArray, EndForEach wrote URIArray type. > I thought I don’t need to specify URIArray type as application parameter > because ForEach, EndForEach hand Array type. > > Any comment will be beneficial. > Thanks in advance. > > Shinyoung. > From: Suresh Marru [mailto:[email protected]] > Sent: Friday, April 05, 2013 9:19 PM > To: [email protected] > Subject: Re: Another Question on parallel execution! > > Hi Shinyoung, > > Just drop both the applications in parallel and do not connect them. There > can be multiple independent paths in the workflow and Airavata will execute > them in parallel. If you connect the edges (inputs/outputs) then it assumes > data dependency. You can connect the corners on the nodes which will be shown > as dotted lines that will create control dependencies -- that is even if you > do not have data dependency, execute one after another. But your case is > simple, just have them mutually independent. > > Suresh > > On Apr 5, 2013, at 5:00 AM, 안신영 <[email protected]> wrote: > > > > Hi guys! > > Let’s assume that a workflow contains several works(services). Some works are > independent with each other, some works are dependent some other works. > Dependency mean that a work should be executed after another dependent work’s > completion. > In this case, How can I configure some independent work to be executed > simultaneously? > I will run this workflow in HPC cluster. > > Regards, > Shinyoung. > >
