Re: [Opaltoolkit-users] How to use the simple form to pass an uploaded file to the app?

[Sam H. <sh...@nc...>]

Thanks, Conrad, that was it! For the record, here's a functional simple form file-upload deploy XML, since I had trouble finding any 
examples in the docs:

<appConfig xmlns="http://nbcr.sdsc.edu/opal/types"
            xmlns:xsd="http://www.w3.org/2001/XMLSchema">
   <metadata appName="meme">
     <usage><![CDATA[meme fasta-file]]></usage>
     <types>
         <untaggedParams>
             <param>
                 <id>fasta-file</id>
                 <paramType>FILE</paramType>
                 <ioType>INPUT</ioType>
                 <required>true</required>
                 <textDesc><![CDATA[Input FASTA file.]]></textDesc>
             </param>
         </untaggedParams>
     </types>
   </metadata>
   <binaryLocation>/home/shokin/meme/bin/meme</binaryLocation>
   <defaultArgs></defaultArgs>
   <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
   <parallel>false</parallel>
</appConfig>

On 08/29/2016 07:36 PM, Conrad Huang wrote:
> I think you need to wrap your "untaggedParams" inside a "types" tag. Here's a sample config file that works for me:
>
>> <appConfig xmlns="http://nbcr.sdsc.edu/opal/types"
>>            xmlns:xsd="http://www.w3.org/2001/XMLSchema">
>>   <metadata appName="CCD">
>>     <usage><![CDATA[ccd_cat returns the wwPDB Chemical Component Dictionary for
>> the requested residue type]]></usage>
>>     <types>
>>         <untaggedParams>
>>             <param>
>>                 <id>residue</id>
>>                 <paramType>STRING</paramType>
>>                 <ioType>INPUT</ioType>
>>                 <textDesc>The name of the residue of interest</textDesc>
>>             </param>
>>         </untaggedParams>
>>     </types>
>>   </metadata>
>>   <binaryLocation>/usr/local/opal-local/bin/ccd_cat.py</binaryLocation>
>>   <defaultArgs></defaultArgs>
>>   <parallel>false</parallel>
>> </appConfig>
>
> Good luck.
>
> Conrad
>
> On 8/29/2016 5:18 PM, Sam Hokin wrote:
>> Hiya, Opal users. I've just installed Opal, it's running fine, but I'm mystified as to how I can get my uploaded file placed on the
>> command line of my command-line app using the stock webapp simple form. I see that the file is called inputFile[0] on the form, but
>> I've tried everything I can think of, and my app always errors as if it has no input.
>>
>> Here's my deploy XML. I've tried with and without the untaggedParams block.
>>
>> <appConfig xmlns="http://nbcr.sdsc.edu/opal/types"
>>             xmlns:xsd="http://www.w3.org/2001/XMLSchema">
>>    <metadata appName="meme">
>>      <usage><![CDATA[meme fasta-file]]></usage>
>>
>>          <untaggedParams>
>>              <param>
>>                  <id>inputFile[0]</id>
>>                  <paramType>FILE</paramType>
>>                  <ioType>INPUT</ioType>
>>                  <required>true</required>
>>                  <textDesc><![CDATA[Input FASTA file.]]></textDesc>
>>              </param>
>>          </untaggedParams>
>>
>>    </metadata>
>>    <binaryLocation>/home/shokin/meme/bin/meme</binaryLocation>
>>    <defaultArgs></defaultArgs>
>>    <jobManagerFQCN>edu.sdsc.nbcr.opal.manager.ForkJobManager</jobManagerFQCN>
>>    <parallel>false</parallel>
>> </appConfig>
>>
>> The file is successfully uploaded to webapps/ROOT/appmeme#/
>>
>> stdout.txt is always empty; stderr.txt has the help output from meme when you run it without any parameters.
>>
>> Thanks for the help! I'm planning to use Opal to wrap meme so I can access it via Java calls from my InterMine instances.
>>
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