Ignore:
Timestamp:
May 16, 2007, 1:17:55 PM (14 years ago)
Author:
Martin Svensson
Message:

Fixes #548

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/src/docbook/admindoc/plugin_installation.xml

    r3339 r3345  
    4444    <para>
    4545      The first step is to install the plug-in on the web server. To make
    46       these instructions easier to read we assume the the plug-in comes as
     46      these instructions easier to read we assume the plug-in comes as
    4747      a single JAR file and that it doesn't depend on any other JAR files.
    4848    </para>
     
    139139            The maximum amount of memory the plug-in may use. This setting
    140140            only applies when the plug-in is executed with a job agent. If
    141             the inernal job queue is used this setting has no effect and the
     141            the internal job queue is used this setting has no effect and the
    142142            plug-in may use as much memory as it likes.
    143143            <nohelp>See <xref linkend="plugins.jobagents" /> later
     
    155155            When this becomes implemented in the future a
    156156            <guilabel>no</guilabel> value will apply security restrictions
    157             to plug-ins similiar to those a web browser put on applets.
    158             For example, the plug-in is not allowed to access the file
    159             system, open ports, shut down the server, and a lot of
    160             other nasty things.
    161           </para>
    162         </listitem>
    163       </varlistentry>
    164       <varlistentry>
    165         <term><guilabel>Trusted</guilabel></term>
    166         <listitem>
    167           <para>
    168             If the plug-in is trusted enough to be executed in an
    169             unprotected environment. This setting has currently no
    170             effect since BASE can't run in a protected environment.
    171             When this becomes implemented in the future a
    172             <guilabel>no</guilabel> value will apply security restrictions
    173             to plug-ins similiar to those a web browser put on applets.
     157            to plug-ins similar to those a web browser put on applets.
    174158            For example, the plug-in is not allowed to access the file
    175159            system, open ports, shut down the server, and a lot of
     
    261245        <para>
    262246          Upload the <filename>*.base</filename> file for the BASE 1 plug-in
    263           to BASE 2. If you can't the file, you can let BASE 1 create one for you.
     247          to BASE 2. If you can't find the file, you can let BASE 1 create one for you.
    264248          In your BASE 1 installation go to
    265249          <menuchoice>
     
    294278            to have an experiment with some data. Go to the single-item
    295279            view for a bioassayset and click on the <guibutton>Run analysis</guibutton>
    296             button. Select the <emphasis>Base1PluginExecutor</emphasis>
     280            button. Select the <emphasis>Base1PluginExecuter</emphasis>
    297281            plug-in. The list of configurations should include the newly
    298282            installed plug-in. Select it and click on <guibutton>Next</guibutton>.
     
    303287          <para>
    304288            This will enter regular plug-in execution wizard and you
    305             will have to enter paraters needed by the plug-in.
     289            will have to enter parameters needed by the plug-in.
    306290          </para>
    307291        </listitem>
     
    331315      <para>
    332316        To limit this problem it is possible to tune the permissions for
    333         a the plug-in so that it only has permission to do things that it
     317        a plug-in so that it only has permission to do things that it
    334318        is supposed to do. For example, a plug-in that import reporters
    335         may only need permission to update and create new reporter and
     319        may only need permission to update and create new reporters and
    336320        nothing else.
    337321      </para>
     
    447431    <para>
    448432      A job agent will not execute a plug-in unless the admin has configured
    449       told the job agent to do so. This can be done either from the plug-in
     433      the job agent to do so. This can be done either from the plug-in
    450434      side or from the job agent side. To register a plug-in with one or more
    451       job agents from the plug-in side go to the edit view the plug-in and
     435      job agents from the plug-in side go to the edit view of the plug-in and
    452436      select the <guilabel>Job agents</guilabel> tab. To do the same from
    453437      the job agent side go to the edit view of the job agent and select
     
    831815     
    832816      <para>
    833         The <guilabel>Test with file</guilabel> function is avery useful
     817        The <guilabel>Test with file</guilabel> function is a very useful
    834818        function for specifying import file formats. It is supported by
    835819        many of the import plug-ins that read data from a simple text
     
    871855      <para>
    872856        The window consists of two parts, the upper part where the file
    873         to parse and the parmeters used to parse it are entered, and
     857        to parse and the parameters used to parse it are entered, and
    874858        the lower part that displays information about the parsing.
    875859      </para>
     
    894878              <para>
    895879                Each data column must be separated by some special character or
    896                 character sequence not occuring in the data, for example a tab or a comma.
     880                character sequence not occurring in the data, for example a tab or a comma.
    897881                Data in fixed-size columns cannot be parsed.
    898882              </para>
     
    900884            <listitem>
    901885              <para>
    902                 Data may optionally be preceeded by a data header, for example,
     886                Data may optionally be preceded by a data header, for example,
    903887                the names of the columns.
    904888              </para>
     
    906890            <listitem>
    907891              <para>
    908                 The data header may optionally be preceeded by file headers.
     892                The data header may optionally be preceded by file headers.
    909893                A file header is something that can be split into a name-value pair.
    910894              </para>
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