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From "Shinyoung Ahn (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (AIRAVATA-820) Parameter mismatching when using ForEach
Date Fri, 16 Aug 2013 06:06:49 GMT

    [ https://issues.apache.org/jira/browse/AIRAVATA-820?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13741959#comment-13741959
] 

Shinyoung Ahn commented on AIRAVATA-820:
----------------------------------------

Thanks. Wijeratne

Today, I checked out trunk, and Built Apache Airavata from Source under JDK jdk1.7.0_25, Maven
3.0.5

Current version(0.9) works well for simple ForEach workflow like
	<intput>-<ForEach>-<echo_invoke>-<EndForEach>-<Output>

But it fails to satisfy my case
The workflow that I want is

	<input1>-----------\
	<input2>------------<registered_application_invoke>-<EndForEach>-<Output>
	<input3>-<ForEach>-/

In the upper workflow which I want to draw <input1> and <input2> is constant value
and <input3>  is string array
In other words, registered_application have a few input parameter,  a parameter should be
fed to registered_application iteratively using ForEach component while the other parameters
are fed to registered_application with same value.

For example, when <input1> value is "4" and <input2> value is "/home/team/genome/bwaindex/hg19.fa"
<input2> value is "/home/team/genome/Demo/sample_1.fq.00,/home/team/genome/Demo/sample_2.fq.00"
I want <registered_application_invoke> to be executed two times such like
	<input1> = "4", <input2> = "/home/team/genome/bwaindex/hg19.fa" <input3>
= "/home/team/genome/Demo/sample_1.fq.00"
	<input1> = "4", <input2> = "/home/team/genome/bwaindex/hg19.fa" <input3>
= "/home/team/genome/Demo/sample_2.fq.00"

However, Current version(0.9) does not work as I expected.
next is notification message form xbaya. 
----------------------------------------------------------------
<ns:workflowInvoked infoModelVersion="2.6"
  xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
  <ns:notificationSource ns:serviceID="Workflow1_729b7813_c42d_461f_bcf3_3a7c829e2fb5"
ns:experimentID="Workflow1_729b7813-c42d-461f-bcf3-3a7c829e2fb5" />
  <ns:timestamp>2013-08-16T14:28:42.557+09:00</ns:timestamp>
  <ns:description>input1=4, input2=/home/team/genome/bwaindex/hg19.fa, Input3=/home/team/genome/Demo/sample_1.fq.00,/home/team/genome/Demo/sample_2.fq.00</ns:description>
  <ns:annotation />
  <ns:initiator ns:serviceID="Workflow1_729b7813_c42d_461f_bcf3_3a7c829e2fb5" />
</ns:workflowInvoked>

<ns:invokingService infoModelVersion="2.6"
  xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
  <ns:notificationSource ns:serviceID="Workflow1_729b7813_c42d_461f_bcf3_3a7c829e2fb5"
ns:experimentID="Workflow1_729b7813-c42d-461f-bcf3-3a7c829e2fb5" />
  <ns:timestamp>2013-08-16T14:28:42.617+09:00</ns:timestamp>
  <ns:description>input1=/home/team/genome/Demo/sample_1.fq.00, input2=/home/team/genome/Demo/sample_1.fq.00,
input3=/home/team/genome/Demo/sample_1.fq.00</ns:description>
  <ns:annotation />
  <ns:request>
    <ns:body>
      <invoke_InputParams>
        <threadCount>/home/team/genome/Demo/sample_1.fq.00</threadCount>
        <refIndexFile>/home/team/genome/Demo/sample_1.fq.00</refIndexFile>
        <fqFile>/home/team/genome/Demo/sample_1.fq.00</fqFile>
      </invoke_InputParams>
    </ns:body>
  </ns:request>
  <ns:receiver ns:serviceID="bwa_aln_invoke" ns:workflowID="Workflow1_729b7813_c42d_461f_bcf3_3a7c829e2fb5"
ns:workflowTimestep="0" ns:workflowNodeID="bwa_aln_invoke" />
</ns:invokingService>
----------------------------------------------------------------
It might not be the use-case that you had designed.

Would you check again for my case?

Thanks.


                
> Parameter mismatching when using ForEach 
> -----------------------------------------
>
>                 Key: AIRAVATA-820
>                 URL: https://issues.apache.org/jira/browse/AIRAVATA-820
>             Project: Airavata
>          Issue Type: Bug
>            Reporter: Shinyoung Ahn
>
> When an application have three parameters, fir and second parameter's type is String
type and
> the third parameter is StringArray type.
> Third parameter is connected to ForEach.
> When I execute the applications
> 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'.
> The Notification Message as follows
> -----------------------------------------------------------------------------------------------------------------
> Status'workflowInvoked' 
> <ns:workflowInvoked infoModelVersion="2.6"
>   xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
>   <ns:notificationSource ns:serviceID="Workflow1_b8721d2f_d131_4ec3_bbb3_6fe12f528ed8"
ns:experimentID="Workflow1_b8721d2f-d131-4ec3-bbb3-6fe12f528ed8" />
>   <ns:timestamp>2013-04-11T09:15:41.988+09:00</ns:timestamp>
>   <ns:description>thread=4, refIndexFile=/home/team/genome/bwaindex/chr22.fa, Input=/home/team/genome/Demo/sample_1.fq.00,/home/team/genome/Demo/sample_1.fq.01,
Input=/home/team/genome/Demo/sample_1.fq.00,/home/team/genome/Demo/sample_1.fq.01</ns:description>
>   <ns:annotation />
>   <ns:initiator ns:serviceID="Workflow1_b8721d2f_d131_4ec3_bbb3_6fe12f528ed8" />
> </ns:workflowInvoked>
> -------------------------------------------------------------------------------------------------------------------
> Status: invokingService
> <ns:invokingService infoModelVersion="2.6"
>   xmlns:ns="http://airavata.apache.org/schemas/wft/2011/08">
>   <ns:notificationSource ns:serviceID="Workflow1_b8721d2f_d131_4ec3_bbb3_6fe12f528ed8"
ns:experimentID="Workflow1_b8721d2f-d131-4ec3-bbb3-6fe12f528ed8" />
>   <ns:timestamp>2013-04-11T09:15:42.240+09:00</ns:timestamp>
>   <ns:description>thread=/home/team/genome/Demo/sample_1.fq.00, refIndexFile=/home/team/genome/Demo/sample_1.fq.00,
bwdFqFile=/home/team/genome/Demo/sample_1.fq.00</ns:description>
>   <ns:annotation />
>   <ns:request>
>     <ns:body>
>       <n1:invoke_InputParams
>         xmlns:n1="http://airavata.apache.org/schemas/gfac/2012/12/bwa_aln_bwd/xsd">
>         <thread>/home/team/genome/Demo/sample_1.fq.00</thread>
>         <refIndexFile>/home/team/genome/Demo/sample_1.fq.00</refIndexFile>
>         <bwdFqFile>/home/team/genome/Demo/sample_1.fq.00</bwdFqFile>
>       </n1:invoke_InputParams>
>     </ns:body>
>   </ns:request>
>   <ns:receiver ns:serviceID="bwa_aln_bwd_invoke" ns:workflowID="Workflow1_b8721d2f_d131_4ec3_bbb3_6fe12f528ed8"
ns:workflowTimestep="0" ns:workflowNodeID="bwa_aln_bwd_invoke" />
> </ns:invokingService>
> -------------------------------------------------------------------------------------------------------------------------

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