Mercurial > repos > geco-team > gmql_queries_monitor
comparison 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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-1:000000000000 | 0:4bfc6a2c4855 |
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1 <tool id="gmql_queries_monitor" name="GMLQ Jobs Monitor" version="0.1.1"> | |
2 <description>List the user's jobs and their status</description> | |
3 <macros> | |
4 <import>gmql_rest_macros.xml</import> | |
5 </macros> | |
6 <command><![CDATA[ | |
7 python $__tool_directory__/gmql_rest_queries.py | |
8 -user=$authToken | |
9 #if $control.operation == 'list' | |
10 -cmd=jobs | |
11 -log=$jobs_list | |
12 #else : | |
13 -cmd=stop | |
14 -log=$stop_output | |
15 -job=$control.job | |
16 #end if | |
17 ]]></command> | |
18 <code file="dynamic_utils.py"> | |
19 <hook validate_input="validate" /> | |
20 </code> | |
21 <inputs> | |
22 <param format="gmql_user" name="authToken" type="data" label="Select user" /> | |
23 <conditional name="control"> | |
24 <param name="operation" type="select" display="radio" multiple="false" label="Select the desired action" > | |
25 <option value="list">View Active Queries</option> | |
26 <option value="stop">Stop a running query</option> | |
27 </param> | |
28 <when value="list"> | |
29 <!-- do nothing --> | |
30 </when> | |
31 <when value="stop"> | |
32 <param name="user_jobs" type="data" format="tabular" label="Select User's jobs list" /> | |
33 <param name="job" type="select" label="Select running job to stop"> | |
34 <options from_dataset="user_jobs"> | |
35 <column name="value" index="0" /> | |
36 <filter column="1" type="static_value" value="RUNNING" /> | |
37 </options> | |
38 </param> | |
39 </when> | |
40 </conditional> | |
41 </inputs> | |
42 <outputs> | |
43 <data format="tabular" name="jobs_list" label="${authToken.name.split()[0].rstrip('')} Jobs" > | |
44 <filter>control['operation'] == 'list'</filter> | |
45 <actions> | |
46 <action name="column_names" type="metadata" default="Job ID, Status, Message, Datasets name, Elapsed time" /> | |
47 </actions> | |
48 </data> | |
49 <data format="txt" name="stop_output" label="Stopping Outcome (Job ${control.job})" > | |
50 <filter>control['operation'] == 'stop'</filter> | |
51 </data> | |
52 </outputs> | |
53 <tests> | |
54 <test> | |
55 <param name="authToken" value="guest.gmql_user" /> | |
56 <conditional name="control"> | |
57 <param name="operation" value="list" /> | |
58 </conditional> | |
59 <output name="jobs_list" ftype="tabular" > | |
60 <assert_contents> | |
61 <has_n_columns n="5" /> | |
62 </assert_contents> | |
63 </output> | |
64 </test> | |
65 </tests> | |
66 <help> | |
67 Once GMQL queries have been created and sent to execution, this tool helps the user to monitor the current jobs and their status. | |
68 | |
69 ---- | |
70 | |
71 **What it does** | |
72 | |
73 - **View Active Queries**: returns a list of active queries and their status | |
74 - **Stop Active Query**: stop the execution of a pending query (provide a list of active queries) | |
75 | |
76 .. class:: warningmark | |
77 | |
78 A gmql_user authentication token is required for every action. | |
79 | |
80 </help> | |
81 <expand macro="citations" /> | |
82 </tool> |