Changeset 5705


Ignore:
Timestamp:
Aug 22, 2011, 2:21:49 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1590: Documentation cleanup

User documentation chapters 7, 8 and 9 except for screenshots.

Re-ordered some properties in the View job dialog.

Location:
trunk
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/userdoc/file_system.xml

    r5362 r5705  
    340340                <para>
    341341                  This is the file-type that the uploaded file should get.
    342                   <nohelp>The
    343                   file-types to choose between from the drop-down list are
    344                   described in
    345                   <xref linkend="file_system.filetypes" />.</nohelp>
    346                   Select
    347                   <userinput>- none -</userinput>
     342                  Select <userinput>- none -</userinput>
    348343                  if the file should not be associated with any file type.
    349344                </para>
     
    487482            <listitem>
    488483              <para>
    489                 The full URL to the referenced file. Currently, BASE
    490                 only supports <emphasis>http</emphasis> or
    491                 <emphasis>https</emphasis> URLs.
     484                The full URL to the referenced file. BASE
     485                ships with support <emphasis>http</emphasis> and
     486                <emphasis>https</emphasis> URLs, but the administrator may have
     487                installed support for other protocols.
    492488              </para>
    493489            </listitem>
     
    541537              <para>
    542538                The name of the file server.
     539              </para>
     540            </listitem>
     541          </varlistentry>
     542          <varlistentry>
     543            <term>
     544              <guilabel>Host</guilabel>
     545            </term>
     546            <listitem>
     547              <para>
     548                If specified, overrides the host (and/or port) part of the file URL with the
     549                value in this field. This is useful, if for example, a file can be
     550                accessed using a "public" path that is entered as the URL for the file and
     551                an "internal" path that is used from the BASE server.
    543552              </para>
    544553            </listitem>
     
    636645            <listitem>
    637646              <para>
    638                 See <emphasis>External files</emphasis> below.
     647                See <emphasis>External files</emphasis> above.
    639648              </para>
    640649            </listitem>
     
    984993              <varlistentry>
    985994                <term>
    986                   <guilabel>Compress files</guilabel>
     995                  <guilabel>Compress new files</guilabel>
    987996                </term>
    988997                <listitem>
     
    10621071      </sect3>
    10631072    </sect2>
    1064 
    10651073  </sect1>
    10661074
    1067   <sect1 id="file_system.filetypes">
    1068     <title>File types</title>
    1069     <para>
    1070       A file can be associated with one of the file types that exists in BASE. File types
    1071       make it possible to filter the files depending of what kind of file it is. Here
    1072       is a list of file types that are defined in BASE.
    1073       <menuchoice>
    1074         <guimenu>Administrate</guimenu>
    1075         <guisubmenu>Types</guisubmenu>
    1076         <guimenuitem>File types</guimenuitem>
    1077       </menuchoice>
    1078     </para>
    1079     <variablelist>
    1080       <title>File types</title>
    1081       <varlistentry>
    1082         <term>Image</term>
    1083         <listitem>
    1084           <para>Indicates that the file is an image file.</para>
    1085         </listitem>
    1086       </varlistentry>
    1087       <varlistentry>
    1088         <term>Plate</term>
    1089         <listitem>
    1090           <para>The associated file is a file with information about plate/plates.</para>
    1091         </listitem>
    1092       </varlistentry>
    1093       <varlistentry>
    1094         <term>Plate mapping</term>
    1095         <listitem>
    1096           <para>Files with information about plate mapping.</para>
    1097         </listitem>
    1098       </varlistentry>
    1099       <varlistentry>
    1100         <term>Print map</term>
    1101         <listitem>
    1102           <para>Print map files</para>
    1103         </listitem>
    1104       </varlistentry>
    1105       <varlistentry>
    1106         <term>Protocol</term>
    1107         <listitem>
    1108           <para>Files with protocol information</para>
    1109         </listitem>
    1110       </varlistentry>
    1111       <varlistentry>
    1112         <term>Raw data</term>
    1113         <listitem>
    1114           <para>Raw data files</para>
    1115         </listitem>
    1116       </varlistentry>
    1117       <varlistentry>
    1118         <term>Reporter</term>
    1119         <listitem>
    1120           <para>Files with information about reporters</para>
    1121         </listitem>
    1122       </varlistentry>
    1123       <varlistentry>
    1124         <term>Reporter map</term>
    1125         <listitem>
    1126           <para>
    1127             Files of this type contain information about how the reporters are mapped.
    1128           </para>
    1129         </listitem>
    1130       </varlistentry>
    1131       <varlistentry>
    1132         <term>Spot images</term>
    1133         <listitem>
    1134           <para>A zip-file containing generated spot images in JPEG format.</para>
    1135         </listitem>
    1136       </varlistentry>
    1137     </variablelist>
    1138   </sect1>
    11391075</chapter>
  • trunk/doc/src/docbook/userdoc/jobs.xml

    r4889 r5705  
    2525-->
    2626
    27 <chapter id="jobs">
     27<chapter id="jobs" chunked="0">
    2828  <?dbhtml dir="jobs"?>
    2929  <title>Jobs</title>
    30   <para>Job is a configured task performed by a plug-in.</para>
     30 
    3131  <para>
    32     Creating/configuring a job is made from a context, which is supported by the plug-in you want
    33     to use. If no particularly context is needed, the job configuration is started from the
    34     plug-in's single item view.
    35   </para>
    36   <para>
     32    A <emphasis>job</emphasis> is a task that is performed by a plug-in.
    3733    Some jobs can be configured to execute immediately (for a few plug-ins it is mandatory that
    3834    the job runs immediately), but normally jobs are placed in the job queue after they have
    3935    been configured. The jobs will then be picked out for execution depending on their priority
    40     and estimated execution time.
     36    and waiting time in the queue.
     37  </para>
     38  <para>
     39    Creating and configuring a job is made from a context, eg. a particular list page or singe-item page,
     40    which is supported by the plug-in  you want to use. If no context is needed, the job configuration is started from the
     41    plug-in's single item view. Typically, there are three main types of jobs, <emphasis>import</emphasis>,
     42    <emphasis>export</emphasis> and <emphasis>other</emphasis> jobs. They usually show up as <guilabel>Import</guilabel>,
     43    <guilabel>Export</guilabel> and <guilabel>Run plug-in</guilabel> buttons in the gui. In the experiment analysis
     44    section two more types of plug-ins are used, <emphasis>intensity</emphasis> and <emphasis>analysis</emphasis>.
    4145  </para>
    4246
     
    6064        The values listed on the <guilabel>Parameters</guilabel> tab depends on
    6165        what the plug-in needs from the user. If a specific plug-in configuration was
    62         use, those parameters are also listed here.
     66        used, those parameters are also listed here.
    6367      </para>
    6468    </helptext>
     
    7680                The name of the job is set in the last step of a job configuration.
    7781              </para>
     82            </listitem>
     83          </varlistentry>
     84          <varlistentry>
     85            <term>
     86              <guilabel>Plugin</guilabel>
     87            </term>
     88            <listitem>
     89              <para>The plug-in to use in the job.</para>
     90            </listitem>
     91          </varlistentry>
     92          <varlistentry>
     93            <term>
     94              <guilabel>Configuration</guilabel>
     95            </term>
     96            <listitem>
     97              <para>Name of the plug-in configuration that is used.</para>
     98            </listitem>
     99          </varlistentry>
     100          <varlistentry>
     101            <term>
     102              <guilabel>User</guilabel>
     103            </term>
     104            <listitem>
     105              <para>The user who created/configured the job.</para>
     106            </listitem>
     107          </varlistentry>
     108          <varlistentry>
     109            <term>
     110              <guilabel>Experiment</guilabel>
     111            </term>
     112            <listitem>
     113              <para>Name of the experiment which the job was configured within.</para>
    78114            </listitem>
    79115          </varlistentry>
     
    135171                    <para>
    136172                      <emphasis>Waiting</emphasis>
    137                       - Job is waiting in the job queue.
     173                      - The job is waiting in the job queue.
    138174                    </para>
    139175                  </listitem>
     
    141177                    <para>
    142178                      <emphasis>Executing</emphasis>
    143                       - Job is being executed.
     179                      - The job is being executed.
    144180                    </para>
    145181                  </listitem>
     
    147183                    <para>
    148184                      <emphasis>Done</emphasis>
    149                       - Indicates that the job is finished.
     185                      - Indicates that the job has finished successfully.
    150186                    </para>
    151187                  </listitem>
     
    153189                    <para>
    154190                      <emphasis>Error</emphasis>
    155                       - The job was aborted cause of some error.
     191                      - The job has finsished with an error.
    156192                    </para>
    157193                  </listitem>
     
    159195                    <para>
    160196                      <emphasis>Preparing</emphasis>
    161                       - Doing some preparing tasks befor executing the job.
     197                      - The job queue is preparing to executed the job.
    162198                    </para>
    163199                  </listitem>
     
    165201                    <para>
    166202                      <emphasis>Aborting</emphasis>
    167                       - Job has received an abort signal and tries to abort the
    168                       work.
     203                      - The job has received an abort signal from the user
     204                      and tries to abort the work.
    169205                    </para>
    170206                  </listitem>
     
    201237            <listitem>
    202238              <para>
    203                 Date and time when the job was created and registerd in the database.
     239                Date and time when the job was created and registered in the database.
     240              </para>
     241            </listitem>
     242          </varlistentry>
     243          <varlistentry>
     244            <term>
     245              <guilabel>Scheduled</guilabel>
     246            </term>
     247            <listitem>
     248              <para>
     249                Date and time when the job was added to the job queue. This is usually the same
     250                as the <emphasis>created</emphasis> date and time, but can be different if the
     251                job has been restared after an error.
    204252              </para>
    205253            </listitem>
     
    221269            <listitem>
    222270              <para>
    223                 Date and time when the job stopped running. Either cause of it was
     271                Date and time when the job stopped running. Either because it was
    224272                finished, aborted or interrupted by an error.
    225273              </para>
     
    257305            </listitem>
    258306          </varlistentry>
    259           <varlistentry>
    260             <term>
    261               <guilabel>User/Owner</guilabel>
    262             </term>
    263             <listitem>
    264               <para>The user who created/configured the job.</para>
    265             </listitem>
    266           </varlistentry>
    267           <varlistentry>
    268             <term>
    269               <guilabel>Experiment</guilabel>
    270             </term>
    271             <listitem>
    272               <para>Name of the experiment which the job was configured within.</para>
    273             </listitem>
    274           </varlistentry>
    275           <varlistentry>
    276             <term>
    277               <guilabel>Plugin</guilabel>
    278             </term>
    279             <listitem>
    280               <para>The plug-in to use in the job.</para>
    281             </listitem>
    282           </varlistentry>
    283           <varlistentry>
    284             <term>
    285               <guilabel>Configuration</guilabel>
    286             </term>
    287             <listitem>
    288               <para>Name of the plug-in configuration that is used.</para>
    289             </listitem>
    290           </varlistentry>
    291307        </variablelist>
    292308      </para>
     
    298314     
    299315      <variablelist>
    300       <varlistentry>
    301         <term><guibutton>Refresh</guibutton></term>
    302         <listitem>
    303           <para>
    304           Update the page with the information. This button is available as long
    305           as the job has not finished. This button is only for the impatient since
    306           the page will automatically refresh every ten seconds anyway.
    307           </para>
    308         </listitem>
    309       </varlistentry>
    310316     
    311317      <varlistentry>
     
    314320          <para>
    315321          Aborts a job that is running or hasn't started yet. Jobs that hasn't
    316           started can always be aborted. Jobs that are already eecuting can only
     322          started can always be aborted. Jobs that are already executing can only
    317323          be aborted if the plug-in supports it. The button will not be visible if
    318324          the plug-in doesn't supports being aborted.
     
    322328     
    323329      <varlistentry>
    324         <term><guibutton>Restart</guibutton></term>
    325         <listitem>
    326           <para>
    327           Retry a failed job. Sometimes the reason that a job failed can be fixed. For
     330        <term><guibutton>Restart job</guibutton></term>
     331        <listitem>
     332          <para>
     333          Retry a failed job with the same parameters. Sometimes the reason that a job failed can be fixed. For
    328334          example, by changing the permissions on items the job needs to access. Use
    329335          this button to place the job in the job queue again. It is not possible to
     
    336342     
    337343      <varlistentry>
     344        <term><guibutton>Re-configure job</guibutton></term>
     345        <listitem>
     346          <para>
     347          Retry a failed job with different. This feeture is supported by most but not
     348          all plug-ins. It is very useful when the failure is due to a misconfiguration
     349          and the job may succeed if it was configured differently.
     350          </para>
     351        </listitem>
     352      </varlistentry>
     353
     354      <varlistentry>
     355        <term><guibutton>Really run</guibutton></term>
     356        <listitem>
     357          <para>
     358          Some plug-ins have support for a <emphasis>dry-run</emphasis> mode that executes
     359          the job but doesn't save any changes to the database. If the dry run completes
     360          successfully, this button can be used to run the job for real.
     361          </para>
     362        </listitem>
     363      </varlistentry>
     364     
     365      <varlistentry>
    338366        <term><guibutton>Close</guibutton></term>
    339367        <listitem>
  • trunk/doc/src/docbook/userdoc/project_permission.xml

    r5370 r5705  
    106106              <para>
    107107                Permission to change the owner of an item. This is implemented as a
    108                 <synopsis>Set owner</synopsis> function in the web client
     108                <guilabel>Set owner</guilabel> function in the web client
    109109                (<xref linkend="webclient.items.changeowner" />), where you can
    110110                change the owner of items that you have permission to do so on.
     
    143143        </variablelist>
    144144        <note>
    145           An user's permissions need to be reloaded for the permissions that have been
     145          A user's permissions need to be reloaded for the permissions that have been
    146146          changed should take effect. This is done either manually with the menu choice
    147147          <menuchoice>
     
    177177            generic item types and is valid for all items of that type.
    178178            The role-based permissions also include a special deny permission
    179             that can prevents an user from accessing any item. In that case,
     179            that can prevents a user from accessing any item. In that case,
    180180            the permission check stops here.
    181181            </para>
     
    410410              </para>
    411411              <para>
    412                 The drop-down menu can display a maximum of 25 projects. If you are a
    413                 member of more projects, the last menu entry will take you to the
    414                 complete list of projects.
     412                The most recently used projects are listed first, then the list is filled with the
     413                rest of your projects up to a maximum of 15. If you have more projects an option to
     414                display the remaining projects is activated.
    415415              </para>
    416416              <tip>
    417417                <para>
    418                 The sort order in the menu is the same as the sort order on the
     418                The sort order of the non-recent projects is the same as the sort order on the
    419419                projects list page. If you, for example, want to sort the newest
    420420                project first, select to sort by the <guilabel>Registered</guilabel>
     
    476476            settings for the project. Simply open the edit-view page for the project
    477477            and select the permissions you want and save. From now on, all new
    478             items will be shared with the specified permissions.
     478            items will be shared with the specified permissions. Items that are
     479            already in the project are not affected by the change.
    479480          </para>
    480481        </sect3>
     
    681682          <listitem>
    682683            <para>
    683               It support only a limited set of columns (name, description and
     684              It support only a limited set of columns (id, name, description and
    684685              owner) since these are the only properties that are common
    685686              among all items.
     
    689690          <listitem>
    690691            <para>
    691               The list cannot be filtered (except by item type)
    692               or sorted. This is due to a limitation in the query system
    693               used to generate the list.
     692              The list cannot be sorted. This is due to a limitation in the
     693              query system used to generate the list.
    694694            </para>
    695695          </listitem>
  • trunk/www/views/jobs/view_job.jsp

    r5556 r5705  
    318318        <td><%=HTML.encodeTags(job.getName())%></td>
    319319      </tr>
     320      <tr valign="top">
     321        <td class="prompt">Plugin</td>
     322        <td>
     323          <base:propertyvalue item="<%=job%>" property="pluginDefinition.name" />
     324          <%=job.getPluginVersion() == null ?
     325            "" : "(version " + HTML.encodeTags(job.getPluginVersion()) + ")"%>
     326        </td>
     327      </tr>
     328      <%
     329      if (currentConfig != null)
     330      {
     331        %>
     332        <tr valign="top">
     333          <td class="subprompt">-configuration</td>
     334          <td>
     335            <base:propertyvalue item="<%=job%>" property="pluginConfiguration.name" />
     336          </td>
     337        </tr>
     338        <%
     339      }
     340      %>
     341      <tr valign="top">
     342        <td class="prompt">User</td>
     343        <td>
     344          <base:propertyvalue item="<%=job%>" property="owner.name" />
     345        </td>
     346      </tr>
     347      <tr valign="top">
     348        <td class="prompt">Experiment</td>
     349        <td>
     350          <base:propertyvalue item="<%=job%>" property="experiment.name" />
     351        </td>
     352      </tr>
    320353      <tr>
    321354        <td class="prompt">Description</td>
     
    423456        <td class="prompt">Job agent</td>
    424457        <td><%=Base.getEncodedName(agent, !readAgent)%></td>
    425       </tr>
    426       <tr valign="top">
    427         <td class="prompt">User</td>
    428         <td>
    429           <base:propertyvalue item="<%=job%>" property="owner.name" />
    430         </td>
    431       </tr>
    432       <tr valign="top">
    433         <td class="prompt">Experiment</td>
    434         <td>
    435           <base:propertyvalue item="<%=job%>" property="experiment.name" />
    436         </td>
    437       </tr>
    438       <tr valign="top">
    439         <td class="prompt">Plugin</td>
    440         <td>
    441           <base:propertyvalue item="<%=job%>" property="pluginDefinition.name" />
    442           <%=job.getPluginVersion() == null ?
    443             "" : "(version " + HTML.encodeTags(job.getPluginVersion()) + ")"%>
    444         </td>
    445       </tr>
    446       <tr valign="top">
    447         <td class="prompt">Configuration</td>
    448         <td>
    449           <base:propertyvalue item="<%=job%>" property="pluginConfiguration.name" />
    450         </td>
    451458      </tr>
    452459      </table>
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