Mercurial > repos > geco-team > gmql_queries_monitor
annotate 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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4bfc6a2c4855
planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
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1 <tool id="gmql_queries_monitor" name="GMLQ Jobs Monitor" version="0.1.1"> |
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2 <description>List the user's jobs and their status</description> |
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3 <macros> |
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4 <import>gmql_rest_macros.xml</import> |
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5 </macros> |
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6 <command><![CDATA[ |
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7 python $__tool_directory__/gmql_rest_queries.py |
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8 -user=$authToken |
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9 #if $control.operation == 'list' |
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10 -cmd=jobs |
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11 -log=$jobs_list |
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12 #else : |
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13 -cmd=stop |
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14 -log=$stop_output |
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15 -job=$control.job |
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16 #end if |
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17 ]]></command> |
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planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
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18 <code file="dynamic_utils.py"> |
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19 <hook validate_input="validate" /> |
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20 </code> |
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21 <inputs> |
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22 <param format="gmql_user" name="authToken" type="data" label="Select user" /> |
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23 <conditional name="control"> |
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24 <param name="operation" type="select" display="radio" multiple="false" label="Select the desired action" > |
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25 <option value="list">View Active Queries</option> |
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26 <option value="stop">Stop a running query</option> |
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27 </param> |
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28 <when value="list"> |
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29 <!-- do nothing --> |
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planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
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30 </when> |
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31 <when value="stop"> |
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planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
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32 <param name="user_jobs" type="data" format="tabular" label="Select User's jobs list" /> |
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33 <param name="job" type="select" label="Select running job to stop"> |
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34 <options from_dataset="user_jobs"> |
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35 <column name="value" index="0" /> |
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36 <filter column="1" type="static_value" value="RUNNING" /> |
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37 </options> |
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38 </param> |
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39 </when> |
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40 </conditional> |
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41 </inputs> |
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42 <outputs> |
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43 <data format="tabular" name="jobs_list" label="${authToken.name.split()[0].rstrip('')} Jobs" > |
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44 <filter>control['operation'] == 'list'</filter> |
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45 <actions> |
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46 <action name="column_names" type="metadata" default="Job ID, Status, Message, Datasets name, Elapsed time" /> |
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47 </actions> |
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48 </data> |
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49 <data format="txt" name="stop_output" label="Stopping Outcome (Job ${control.job})" > |
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50 <filter>control['operation'] == 'stop'</filter> |
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51 </data> |
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52 </outputs> |
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53 <tests> |
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54 <test> |
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55 <param name="authToken" value="guest.gmql_user" /> |
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56 <conditional name="control"> |
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57 <param name="operation" value="list" /> |
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58 </conditional> |
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59 <output name="jobs_list" ftype="tabular" > |
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60 <assert_contents> |
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61 <has_n_columns n="5" /> |
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62 </assert_contents> |
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63 </output> |
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64 </test> |
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65 </tests> |
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66 <help> |
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67 Once GMQL queries have been created and sent to execution, this tool helps the user to monitor the current jobs and their status. |
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68 |
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69 ---- |
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70 |
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71 **What it does** |
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72 |
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73 - **View Active Queries**: returns a list of active queries and their status |
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74 - **Stop Active Query**: stop the execution of a pending query (provide a list of active queries) |
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75 |
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76 .. class:: warningmark |
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77 |
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78 A gmql_user authentication token is required for every action. |
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79 |
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80 </help> |
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81 <expand macro="citations" /> |
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82 </tool> |