Re: [galaxy-dev] tool_type=data_source_async

2012-01-04 Thread Matt Vincent

Does this functionality exist? If so, how do we get it working?
Sorry to bump!

On 1/3/12 8:50 AM, Matt Vincent matt.vinc...@jax.org wrote:

ost recent version of Galaxy.
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Re: [galaxy-dev] tool_type=data_source_async

2012-01-04 Thread Daniel Blankenberg
Hi Matt,

The asynchronous protocol should be working fine. 

Can you confirm that your flow is similar to:
- User starts at Galaxy, gets sent to external resource with 'GALAXY_URL' 
parameter.
- User browses external site and selects options, sends data to Galaxy by using 
the GALAXY_URL parameter, providing with it a URL parameter that contains where 
Galaxy should inform the external site of the final GALAXY_URL
- Galaxy contacts 'URL', with a new GALAXY_URL (the page content of accessing 
'URL' should end with 'OK')
- When data is ready, the external site contacts the new GALAXY_URL, providing 
'URL' which contains final data and 'STATUS' which should be 'OK' (when 
successful)
- Data is loaded into the Galaxy history.


If your tool flow is following this template, but not working, or if there are 
some other problems, can you provide the log output of trying to use the tool 
and any other information that might be helpful? Please let us know if we can 
provide additional information.


Thanks for using Galaxy,

Dan


On Jan 3, 2012, at 8:50 AM, Matt Vincent wrote:

 Hello all,
 
 I am trying to configure an Asynchronous tool (I can get it to work 
 synchronously).
 
 My configuration looks something like this for the tool:
 
 ?xml version=1.0?
 tool name=mytoolname id=myunique_tool_id_1 tool_type=data_source_async
 descriptionmytool description/description
 command interpreter=pythondata_source.py $output 
 $__app__.config.output_size_limit/command
 inputs action=http://myurl; check_values=false method=post
 displayGo to MyTool $GALAXY_URL/display
 /inputs
 request_param_translation
 request_param galaxy_name=URL_method remote_name=URL_method 
 missing=post /
 request_param galaxy_name=URL remote_name=URL missing= /
 request_param galaxy_name=jobname remote_name=jobname 
 missing=N/A /
 /request_param_translation
 uihints minwidth=800/
 outputs
 data name=output format=zip /
 /outputs
 options sanitize=False refresh=True/
 /tool
 
 
 This works fine and downloads the data, but I was expecting Galaxy to post 
 another GALAXY_URL parameter for me to generate the data and than post back 
 to Galaxy once done.  This is described here...
 
 http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources
 
 However, I never receive “another” GALAXY_URL as descripbed in Step 1 of the 
 Asynchronous data depositing section.
 
 I am using the most recent version of Galaxy.
 
 Can someone please show an example?
 
 Matt
 
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[galaxy-dev] tool_type=data_source_async

2012-01-03 Thread Matt Vincent
Hello all,

I am trying to configure an Asynchronous tool (I can get it to work 
synchronously).

My configuration looks something like this for the tool:

?xml version=1.0?
tool name=mytoolname id=myunique_tool_id_1 tool_type=data_source_async
descriptionmytool description/description
command interpreter=pythondata_source.py $output 
$__app__.config.output_size_limit/command
inputs action=http://myurl; check_values=false method=post
displayGo to MyTool $GALAXY_URL/display
/inputs
request_param_translation
request_param galaxy_name=URL_method remote_name=URL_method 
missing=post /
request_param galaxy_name=URL remote_name=URL missing= /
request_param galaxy_name=jobname remote_name=jobname 
missing=N/A /
/request_param_translation
uihints minwidth=800/
outputs
data name=output format=zip /
/outputs
options sanitize=False refresh=True/
/tool


This works fine and downloads the data, but I was expecting Galaxy to post 
another GALAXY_URL parameter for me to generate the data and than post back to 
Galaxy once done.  This is described here...

http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources

However, I never receive “another” GALAXY_URL as descripbed in Step 1 of the 
Asynchronous data depositing section.

I am using the most recent version of Galaxy.

Can someone please show an example?

Matt
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