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