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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE chapter PUBLIC |
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"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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<!-- |
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$Id$ |
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|
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Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Martin Svensson |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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--> |
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|
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<chapter id="jobs" chunked="0"> |
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<title>Jobs</title> |
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|
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<para> |
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A <emphasis>job</emphasis> is a task that is performed by a plug-in. |
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Some jobs can be configured to execute immediately (for a few plug-ins it is mandatory that |
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the job runs immediately), but normally jobs are placed in the job queue after they have |
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been configured. The jobs will then be picked out for execution depending on their priority |
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and waiting time in the queue. |
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</para> |
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<para> |
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Creating and configuring a job is made from a context, eg. a particular list page or singe-item page, |
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which is supported by the plug-in you want to use. If no context is needed, the job configuration is started from the |
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plug-in's single item view. Typically, there are three main types of jobs, <emphasis>import</emphasis>, |
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<emphasis>export</emphasis> and <emphasis>other</emphasis> jobs. They usually show up as <guilabel>Import</guilabel>, |
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<guilabel>Export</guilabel> and <guilabel>Run plug-in</guilabel> buttons in the gui. In the experiment analysis |
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section two more types of plug-ins are used, <emphasis>intensity</emphasis> and <emphasis>analysis</emphasis>. |
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</para> |
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|
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<para> |
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Click on |
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<menuchoice> |
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<guimenu>View</guimenu> |
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<guimenuitem>Jobs</guimenuitem> |
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</menuchoice> |
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to list your jobs. |
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Details of a single job is displayed in a pop-up window. This window opens either if you |
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click on a job's name from the list page of jobs or when a job configuration is |
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finished. The window contain two tabs, one with information about the job and another |
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with the parameters for the plug-in used in the job. |
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</para> |
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<helptext external_id="job.view.parameters" title="Job parameters"> |
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<para> |
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The values listed on the <guilabel>Parameters</guilabel> tab depends on |
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what the plug-in needs from the user. If a specific plug-in configuration was |
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used, those parameters are also listed here. |
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</para> |
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</helptext> |
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|
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<figure id="jobs.figures.properties"> |
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<title>Job properties</title> |
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<screenshot> |
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<mediaobject> |
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<imageobject> |
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<imagedata fileref="figures/job_properties.png" format="PNG" /> |
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</imageobject> |
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</mediaobject> |
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</screenshot> |
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</figure> |
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|
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<helptext external_id="job.view.properties" title="Job properties"> |
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<para> |
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The properties are set either when configuring the job or by the system. No |
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parameters can be edit after a job is created. |
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<variablelist> |
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<varlistentry> |
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<term> |
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<guilabel>Name</guilabel> |
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</term> |
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<listitem> |
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<para> |
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The name of the job is set in the last step of a job configuration. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Plugin</guilabel> |
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</term> |
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<listitem> |
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<para>The plug-in to use in the job.</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Configuration</guilabel> |
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</term> |
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<listitem> |
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<para>Name of the plug-in configuration that is used.</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>User</guilabel> |
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</term> |
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<listitem> |
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<para>The user who created/configured the job.</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Experiment</guilabel> |
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</term> |
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<listitem> |
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<para>Name of the experiment which the job was configured within.</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Description</guilabel> |
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</term> |
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<listitem> |
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<para> |
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A description of the job. Like the name-property it can be set in |
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the job configuration. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Priority</guilabel> |
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</term> |
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<listitem> |
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<para>Priority the job has in the job queue.</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Status</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Shows the status of the job. A job can have one of following status. |
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<itemizedlist> |
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<listitem> |
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<para> |
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<emphasis>Not configured</emphasis> |
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- The plug-in has not been configured properly and is not |
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placed in the job queue. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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<emphasis>Waiting</emphasis> |
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- The job is waiting in the job queue. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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<emphasis>Preparing</emphasis> |
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- The job queue is preparing to executed the job. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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<emphasis>Executing</emphasis> |
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- The job is being executed. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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<emphasis>Paused</emphasis> |
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- The job has been paused. The user may |
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restart or resume the job. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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<emphasis>Done</emphasis> |
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- Indicates that the job has finished successfully. |
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</para> |
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</listitem> |
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<listitem> |
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<para> |
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<emphasis>Error</emphasis> |
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- The job has finsished with an error. |
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</para> |
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</listitem> |
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c <listitem> |
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<para> |
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<emphasis>Aborting</emphasis> |
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- The job has received an abort signal from the user |
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and tries to abort the work. |
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</para> |
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</listitem> |
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</itemizedlist> |
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|
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This field will also display any messages from the plug-in while it |
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is running and the final message after it's completion. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Percent complete</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Progress of the job. How detailed this is depends on how often the |
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plug-in reports it's progress. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Created</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Date and time when the job was created and registered in the database. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Scheduled</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Date and time when the job was added to the job queue. This is usually the same |
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as the <emphasis>created</emphasis> date and time, but can be different if the |
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job has been restared after an error. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Started</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Date and time when execution of the job started. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Ended</guilabel> |
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</term> |
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<listitem> |
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<para> |
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Date and time when the job stopped running. Either because it was |
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finished, aborted or interrupted by an error. |
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</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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<guilabel>Running time</guilabel> |
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</term> |
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<listitem> |
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<para>Time the job has been running.</para> |
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</listitem> |
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</varlistentry> |
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<varlistentry> |
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<term> |
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273 |
<guilabel>Server</guilabel> |
4307 |
21 May 08 |
martin |
274 |
</term> |
4307 |
21 May 08 |
martin |
275 |
<listitem> |
4307 |
21 May 08 |
martin |
276 |
<para>Name of the server, where the job was performed.</para> |
4307 |
21 May 08 |
martin |
277 |
</listitem> |
4307 |
21 May 08 |
martin |
278 |
</varlistentry> |
4307 |
21 May 08 |
martin |
279 |
<varlistentry> |
4307 |
21 May 08 |
martin |
280 |
<term> |
4311 |
23 May 08 |
nicklas |
281 |
<guilabel>Job agent</guilabel> |
4311 |
23 May 08 |
nicklas |
282 |
</term> |
4311 |
23 May 08 |
nicklas |
283 |
<listitem> |
4311 |
23 May 08 |
nicklas |
284 |
<para> |
4311 |
23 May 08 |
nicklas |
285 |
The job agent the job is/was running on. It is also |
4311 |
23 May 08 |
nicklas |
286 |
possible to set this value before a job is executed. If that |
4311 |
23 May 08 |
nicklas |
287 |
has been done only the selected job agent will accept the job. |
4311 |
23 May 08 |
nicklas |
288 |
This options is normally only given to powers users and |
4311 |
23 May 08 |
nicklas |
289 |
needs the <emphasis>Select job agent</emphasis> permission. |
5738 |
15 Sep 11 |
nicklas |
290 |
See <xref linkend="accounts.roles.edit" />. |
4311 |
23 May 08 |
nicklas |
291 |
</para> |
4311 |
23 May 08 |
nicklas |
292 |
</listitem> |
4311 |
23 May 08 |
nicklas |
293 |
</varlistentry> |
4307 |
21 May 08 |
martin |
294 |
</variablelist> |
4307 |
21 May 08 |
martin |
295 |
</para> |
4324 |
03 Jun 08 |
nicklas |
296 |
|
4324 |
03 Jun 08 |
nicklas |
297 |
<para> |
4324 |
03 Jun 08 |
nicklas |
298 |
Depending on the status of the job, there may also be one or |
4324 |
03 Jun 08 |
nicklas |
299 |
more buttons on the form. |
4324 |
03 Jun 08 |
nicklas |
300 |
</para> |
4324 |
03 Jun 08 |
nicklas |
301 |
|
4324 |
03 Jun 08 |
nicklas |
302 |
<variablelist> |
7342 |
18 Apr 17 |
nicklas |
303 |
|
7342 |
18 Apr 17 |
nicklas |
304 |
<varlistentry> |
7342 |
18 Apr 17 |
nicklas |
305 |
<term><guibutton>Pause</guibutton></term> |
7342 |
18 Apr 17 |
nicklas |
306 |
<listitem> |
7342 |
18 Apr 17 |
nicklas |
307 |
<para> |
7342 |
18 Apr 17 |
nicklas |
308 |
Pauses a job that is running. This feature requires special |
7342 |
18 Apr 17 |
nicklas |
309 |
support by the plug-in and is not available for all types of jobs. |
7342 |
18 Apr 17 |
nicklas |
310 |
A paused job may be restarted from the beginning or resumed from |
7342 |
18 Apr 17 |
nicklas |
311 |
the latest checkpoint. |
7342 |
18 Apr 17 |
nicklas |
312 |
</para> |
7342 |
18 Apr 17 |
nicklas |
313 |
</listitem> |
7342 |
18 Apr 17 |
nicklas |
314 |
</varlistentry> |
4324 |
03 Jun 08 |
nicklas |
315 |
|
4324 |
03 Jun 08 |
nicklas |
316 |
<varlistentry> |
4324 |
03 Jun 08 |
nicklas |
317 |
<term><guibutton>Abort</guibutton></term> |
4324 |
03 Jun 08 |
nicklas |
318 |
<listitem> |
4324 |
03 Jun 08 |
nicklas |
319 |
<para> |
4324 |
03 Jun 08 |
nicklas |
320 |
Aborts a job that is running or hasn't started yet. Jobs that hasn't |
5705 |
22 Aug 11 |
nicklas |
321 |
started can always be aborted. Jobs that are already executing can only |
4324 |
03 Jun 08 |
nicklas |
322 |
be aborted if the plug-in supports it. The button will not be visible if |
4324 |
03 Jun 08 |
nicklas |
323 |
the plug-in doesn't supports being aborted. |
4324 |
03 Jun 08 |
nicklas |
324 |
</para> |
4324 |
03 Jun 08 |
nicklas |
325 |
</listitem> |
4324 |
03 Jun 08 |
nicklas |
326 |
</varlistentry> |
4324 |
03 Jun 08 |
nicklas |
327 |
|
4324 |
03 Jun 08 |
nicklas |
328 |
<varlistentry> |
5705 |
22 Aug 11 |
nicklas |
329 |
<term><guibutton>Restart job</guibutton></term> |
4324 |
03 Jun 08 |
nicklas |
330 |
<listitem> |
4324 |
03 Jun 08 |
nicklas |
331 |
<para> |
7342 |
18 Apr 17 |
nicklas |
332 |
Retry a failed or paused job with the same parameters. Sometimes |
7342 |
18 Apr 17 |
nicklas |
333 |
the reason that a job failed can be fixed. For |
7342 |
18 Apr 17 |
nicklas |
334 |
example, by changing the permissions on items the job needs to access. |
7342 |
18 Apr 17 |
nicklas |
335 |
A paused job can typically be restarted from the beginning or resumed |
7342 |
18 Apr 17 |
nicklas |
336 |
from the latest checkpoint. Use |
4324 |
03 Jun 08 |
nicklas |
337 |
this button to place the job in the job queue again. It is not possible to |
4324 |
03 Jun 08 |
nicklas |
338 |
change job parameters with one exception, if the job uses a plug-in configuration |
4324 |
03 Jun 08 |
nicklas |
339 |
and the configuration has been changed it is possible to select if |
4324 |
03 Jun 08 |
nicklas |
340 |
the old or new configuration values should be used. |
4324 |
03 Jun 08 |
nicklas |
341 |
</para> |
4324 |
03 Jun 08 |
nicklas |
342 |
</listitem> |
4324 |
03 Jun 08 |
nicklas |
343 |
</varlistentry> |
4324 |
03 Jun 08 |
nicklas |
344 |
|
4324 |
03 Jun 08 |
nicklas |
345 |
<varlistentry> |
5705 |
22 Aug 11 |
nicklas |
346 |
<term><guibutton>Re-configure job</guibutton></term> |
5705 |
22 Aug 11 |
nicklas |
347 |
<listitem> |
5705 |
22 Aug 11 |
nicklas |
348 |
<para> |
7342 |
18 Apr 17 |
nicklas |
349 |
Retry a failed or paused job with different parameters. This feature is |
7342 |
18 Apr 17 |
nicklas |
350 |
supported by most but not all plug-ins. It is very useful when the failure |
7342 |
18 Apr 17 |
nicklas |
351 |
is due to a misconfiguration and the job may succeed if it was configured |
7342 |
18 Apr 17 |
nicklas |
352 |
differently. A paused job can be restarted from the beginning or resumed |
7342 |
18 Apr 17 |
nicklas |
353 |
from the latest checkpoint, but note that changing the parameters may |
7342 |
18 Apr 17 |
nicklas |
354 |
cause the latest checkpoint to become invalid and requires a restart from |
7342 |
18 Apr 17 |
nicklas |
355 |
the beginning. |
5705 |
22 Aug 11 |
nicklas |
356 |
</para> |
5705 |
22 Aug 11 |
nicklas |
357 |
</listitem> |
5705 |
22 Aug 11 |
nicklas |
358 |
</varlistentry> |
5705 |
22 Aug 11 |
nicklas |
359 |
|
5705 |
22 Aug 11 |
nicklas |
360 |
<varlistentry> |
5705 |
22 Aug 11 |
nicklas |
361 |
<term><guibutton>Really run</guibutton></term> |
5705 |
22 Aug 11 |
nicklas |
362 |
<listitem> |
5705 |
22 Aug 11 |
nicklas |
363 |
<para> |
5705 |
22 Aug 11 |
nicklas |
364 |
Some plug-ins have support for a <emphasis>dry-run</emphasis> mode that executes |
5705 |
22 Aug 11 |
nicklas |
365 |
the job but doesn't save any changes to the database. If the dry run completes |
5705 |
22 Aug 11 |
nicklas |
366 |
successfully, this button can be used to run the job for real. |
5705 |
22 Aug 11 |
nicklas |
367 |
</para> |
5705 |
22 Aug 11 |
nicklas |
368 |
</listitem> |
5705 |
22 Aug 11 |
nicklas |
369 |
</varlistentry> |
5705 |
22 Aug 11 |
nicklas |
370 |
|
5705 |
22 Aug 11 |
nicklas |
371 |
<varlistentry> |
4324 |
03 Jun 08 |
nicklas |
372 |
<term><guibutton>Close</guibutton></term> |
4324 |
03 Jun 08 |
nicklas |
373 |
<listitem> |
4324 |
03 Jun 08 |
nicklas |
374 |
<para> |
4324 |
03 Jun 08 |
nicklas |
375 |
Close the window. |
4324 |
03 Jun 08 |
nicklas |
376 |
</para> |
4324 |
03 Jun 08 |
nicklas |
377 |
</listitem> |
4324 |
03 Jun 08 |
nicklas |
378 |
</varlistentry> |
4324 |
03 Jun 08 |
nicklas |
379 |
|
4324 |
03 Jun 08 |
nicklas |
380 |
</variablelist> |
4324 |
03 Jun 08 |
nicklas |
381 |
|
4307 |
21 May 08 |
martin |
382 |
</helptext> |
4309 |
22 May 08 |
martin |
383 |
</chapter> |