tool_type="data_source_async"
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"> <description>mytool description</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://myurl" check_values="false" method="post"> <display>Go 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
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"> <description>mytool description</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://myurl" check_values="false" method="post"> <display>Go 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
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.Vincent@jax.org> wrote: ost recent version of Galaxy.
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"> <description>mytool description</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> <inputs action="http://myurl" check_values="false" method="post"> <display>Go 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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participants (2)
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Daniel Blankenberg -
Matt Vincent