Mercurial > repos > geco-team > gmql_queries_monitor
diff gmql_rest_queries_monitor.xml @ 0:4bfc6a2c4855 draft default tip
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
author | geco-team |
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date | Tue, 26 Jun 2018 08:58:28 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gmql_rest_queries_monitor.xml Tue Jun 26 08:58:28 2018 -0400 @@ -0,0 +1,82 @@ +<tool id="gmql_queries_monitor" name="GMLQ Jobs Monitor" version="0.1.1"> + <description>List the user's jobs and their status</description> + <macros> + <import>gmql_rest_macros.xml</import> + </macros> + <command><![CDATA[ + python $__tool_directory__/gmql_rest_queries.py + -user=$authToken + #if $control.operation == 'list' + -cmd=jobs + -log=$jobs_list + #else : + -cmd=stop + -log=$stop_output + -job=$control.job + #end if + ]]></command> + <code file="dynamic_utils.py"> + <hook validate_input="validate" /> + </code> + <inputs> + <param format="gmql_user" name="authToken" type="data" label="Select user" /> + <conditional name="control"> + <param name="operation" type="select" display="radio" multiple="false" label="Select the desired action" > + <option value="list">View Active Queries</option> + <option value="stop">Stop a running query</option> + </param> + <when value="list"> + <!-- do nothing --> + </when> + <when value="stop"> + <param name="user_jobs" type="data" format="tabular" label="Select User's jobs list" /> + <param name="job" type="select" label="Select running job to stop"> + <options from_dataset="user_jobs"> + <column name="value" index="0" /> + <filter column="1" type="static_value" value="RUNNING" /> + </options> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="jobs_list" label="${authToken.name.split()[0].rstrip('')} Jobs" > + <filter>control['operation'] == 'list'</filter> + <actions> + <action name="column_names" type="metadata" default="Job ID, Status, Message, Datasets name, Elapsed time" /> + </actions> + </data> + <data format="txt" name="stop_output" label="Stopping Outcome (Job ${control.job})" > + <filter>control['operation'] == 'stop'</filter> + </data> + </outputs> + <tests> + <test> + <param name="authToken" value="guest.gmql_user" /> + <conditional name="control"> + <param name="operation" value="list" /> + </conditional> + <output name="jobs_list" ftype="tabular" > + <assert_contents> + <has_n_columns n="5" /> + </assert_contents> + </output> + </test> + </tests> + <help> +Once GMQL queries have been created and sent to execution, this tool helps the user to monitor the current jobs and their status. + +---- + +**What it does** + +- **View Active Queries**: returns a list of active queries and their status +- **Stop Active Query**: stop the execution of a pending query (provide a list of active queries) + +.. class:: warningmark + +A gmql_user authentication token is required for every action. + + </help> + <expand macro="citations" /> +</tool> \ No newline at end of file