source: trunk/doc/src/docbook/admindoc/plugin_installation.xml @ 3911

Last change on this file since 3911 was 3911, checked in by Nicklas Nordborg, 14 years ago

Fixes #811: Wildcard or regular expressions in raw data column mappings

To be consistent with exact name matching the first column found is always returned

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 46.3 KB
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1<?xml version="1.0" encoding="UTF-8"?>
2<!DOCTYPE chapter PUBLIC
3    "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
4    "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd">
5<!--
6  $Id: plugin_installation.xml 3911 2007-11-06 08:42:09Z nicklas $
7
8  Copyright (C) 2007 Johan Enell, Jari Hakkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 2
16  of the License, or (at your option) any later version.
17
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28
29<chapter id="plugins">
30  <?dbhtml dir="plugin_installation"?>
31  <title>Plug-ins</title>
32
33  <para>
34    BASE can get extended functionality by the use of plug-ins. In fact, most
35    of the hard work, such as data import/export and analysis is done with plug-ins.
36    BASE ships with a number of standard plug-ins, the core plug-ins, which gives
37    basic import/export and analysis functionality. See <xref linkend="resources" />
38    for more information about the core plug-ins and 3rd-party plug-ins.
39  </para>
40
41
42  <sect1 id="plugins.installation">
43    <title>Installing plug-ins</title>
44    <para>
45      The first step is to install the plug-in on the web server. To make
46      these instructions easier to read we assume the plug-in comes as
47      a single JAR file and that it does not depend on any other JAR files.
48    </para>
49   
50    <para>
51      We recommend that you install the plug-in JAR file outside the web
52      server's Classpath. Do not put the plug-in in the
53      <filename>&lt;base-dir&gt;/www/WEB-INF/lib</filename>
54      directory or any other directory where the web server keeps it's classes.
55      This makes BASE use it's own class loader that support unloading of classes
56      as well. This means that you can install new plug-ins and update
57      existing ones without restarting the web server.
58    </para>
59   
60    <para>
61      We recommend that you create a separate directory for plug-ins and
62      install all of them there. You may use a sub-directory for each plug-in
63      if you like, for example:
64      <filename>&lt;base-dir&gt;/plugins/&lt;name-of-plugin&gt;</filename>
65    </para>
66   
67    <note>
68      <title>Plug-ins that use other JAR files</title>
69      <para>
70        Some plug-ins may depend on other JAR files. Normally,
71        these JAR files should be put in the same directory as the
72        plug-in JAR file. This may, however, vary from plug-in to plug-in
73        so always check the plug-in documentation first.
74      </para>
75    </note>
76   
77    <para>
78      When the plug-in is installed on the server you must register it with BASE. To register
79      the plug-in with BASE go to
80      <menuchoice>
81        <guimenu>Administrate</guimenu>
82        <guisubmenu>Plugins</guisubmenu>
83        <guimenuitem>Definitions</guimenuitem>
84      </menuchoice>
85      and click on the &gbNew; button. The pop-up window that appears looks different
86      depending on if the <property>plugins.dir</property> property
87      in <filename>base.config</filename>
88      has been defined or not. If this has been defined you will first have to
89      choose between manual or automatic installation as described below. Otherwise
90      you will immediately be taken to the manual installation.
91    </para>
92   
93    <sect2 id="plugins.select.installtype">
94      <title>Select installation method</title>
95      <para>
96        This window appears, like described above, when automatic installation/registration
97        of plug-ins is available.
98        <figure id="plugins.figures.selectinstall">
99          <title>Select installation type</title>
100          <screenshot>
101            <mediaobject>
102              <imageobject>
103                <imagedata fileref="figures/select_install.png" format="PNG"
104                  scalefit="1" width="70%" />
105              </imageobject>
106            </mediaobject>
107          </screenshot>
108        </figure>
109      </para>
110      <helptext external_id="plugindefinition.installationtype"
111        title="Select installation type">
112        <variablelist>
113          <varlistentry>
114            <term><guilabel>Install</guilabel>
115            </term>
116            <listitem>
117              <para>
118              How to register the plug-in(s) with BASE.
119              <variablelist>
120              <varlistentry>
121                <term><emphasis>Automatically</emphasis></term>
122                <listitem>
123                  <para>
124                  BASE will scan the given path for JAR files containing
125                  plug-ins. If it finds any, you will have the option
126                  to select which ones to install from a list.
127                  <nohelp>The next step will be <xref linkend="plugins.autoinstall" /></nohelp>
128                  </para>
129                </listitem>
130              </varlistentry>
131              <varlistentry>
132                <term><emphasis>Manually</emphasis></term>
133                <listitem>
134                  <para>
135                  Class name and JAR path have to be entered manually by the
136                  administrator. Only one plug-in can be registered at
137                  a time in this way. Next step will be
138                  <nohelp><xref linkend="plugins.install.properties" /></nohelp>
139                  </para>
140                </listitem>
141              </varlistentry>
142              </variablelist>
143            </para>
144            </listitem>
145          </varlistentry>
146          <varlistentry>
147            <term><guilabel>Path</guilabel> (only when <emphasis>Automatically</emphasis> is selected)</term>
148            <listitem>
149              <para>
150                Where BASE will look for JAR files with plug-ins.
151              </para>
152            </listitem>
153          </varlistentry>
154        </variablelist>
155       
156        <note>
157          The automatic installation doesn't allow you to set all properties
158          that can be set in a manual installation. If you for example, need
159          to share the plug-ins to other users or assign them to job agents
160          this must be done after the auto-installation has been completed.
161        </note>
162       
163        <seeother>
164          <other external_id="plugindefinition.edit">Manual installation</other>
165          <other external_id="plugindefintion.autoinstaller">Automatic installation</other>
166        </seeother>
167       
168      </helptext>
169    </sect2>
170
171    <sect2 id="plugins.install.properties">
172      <title>Plug-in properties</title>
173   
174    <para>
175      This section describes the manual installation of a plug-in.
176    </para>
177   
178    <figure id="plugins.figures.install">
179      <title>Installing a plug-in</title>
180      <screenshot>
181        <mediaobject>
182          <imageobject><imagedata 
183            fileref="figures/install_plugin.png" format="PNG"
184            /></imageobject>
185        </mediaobject>
186      </screenshot>
187    </figure>
188   
189    <helptext external_id="plugindefinition.edit" 
190      title="Plug-in properties">
191     
192      <variablelist>
193      <varlistentry>
194        <term><guilabel>Name</guilabel></term>
195        <listitem>
196          <para>
197            The name of the plug-in. This name is set automatically by
198            the plug-in and cannot be changed.
199          </para>
200        </listitem>
201      </varlistentry>
202      <varlistentry>
203        <term><guilabel>Class</guilabel></term>
204        <listitem>
205          <para>
206            The Java class name of the plug-in.
207          </para>
208        </listitem>
209      </varlistentry>
210      <varlistentry>
211        <term><guilabel>Path</guilabel></term>
212        <listitem>
213          <para>
214            The path to the JAR file on the web server. If left empty
215            the plug-in must be on the web server's class path (not
216            recommended).
217          </para>
218        </listitem>
219      </varlistentry>
220      <varlistentry>
221        <term><guilabel>Max memory</guilabel></term>
222        <listitem>
223          <para>
224            The maximum amount of memory the plug-in may use. This setting
225            only applies when the plug-in is executed with a job agent. If
226            the internal job queue is used this setting has no effect and the
227            plug-in may use as much memory as it likes.
228            <nohelp>See <xref linkend="plugins.jobagents" /> later
229            in this chapter.</nohelp>
230          </para>
231        </listitem>
232      </varlistentry>
233      <varlistentry>
234        <term><guilabel>Trusted</guilabel></term>
235        <listitem>
236          <para>
237            If the plug-in is trusted enough to be executed in an
238            unprotected environment. This setting has currently no
239            effect since BASE cannot run in a protected environment.
240            When this becomes implemented in the future a
241            <guilabel>no</guilabel> value will apply security restrictions
242            to plug-ins similar to those a web browser put on applets.
243            For example, the plug-in is not allowed to access the file
244            system, open ports, shut down the server, and a lot of
245            other nasty things.
246          </para>
247        </listitem>
248      </varlistentry>
249      <varlistentry>
250        <term><guilabel>Allow immediate execution</guilabel></term>
251        <listitem>
252          <para>
253            If the plug-in is allowed to bypass the job queue
254            and be executed immediately.
255           
256            <itemizedlist>
257              <listitem>
258                <para>
259                <guilabel>No</guilabel>: The plug-in must always use
260                the job queue.
261                </para>
262              </listitem>
263              <listitem>
264                <para>
265                <guilabel>Yes</guilabel>: The plug-in is allowed to bypass
266                the job queue. This also means that the plug-in always
267                executes on the web server, job agents are not used.
268                This setting is mainly useful for export plug-ins that
269                needs to support immediate download of the exported data.
270                <nohelp>
271                See <xref linkend="import_export_data.export.immediatedownload" />.
272                </nohelp>
273                </para>
274               
275                <note>
276                  If a plug-in should be executed immediately or not
277                  is always decided by the plug-in. BASE will never give
278                  the users a choice.
279                </note>
280               
281              </listitem>
282              <listitem>
283                <para>
284                <guilabel>Auto</guilabel>: BASE will allow export plug-ins
285                to execute immediately, and deny all other types of plug-ins.
286                This alternative is only available when registering a new
287                plug-in.
288                </para>
289              </listitem>
290            </itemizedlist>
291           
292          </para>
293        </listitem>
294      </varlistentry>
295      </variablelist>
296     
297      <para>
298        Click on &gbSave; to finish the registration
299        or on &gbCancel; to abort.
300      </para>
301     
302      <seeother>
303        <other external_id="plugindefinition.edit.permissions">Plug-in permissions</other>
304        <other external_id="plugindefinition.jobagents">Job agents</other>
305        <other external_id="plugindefintion.autoinstaller">Automatic installation</other>
306      </seeother>   
307     
308    </helptext>
309    </sect2>
310   
311    <sect2 id="plugins.autoinstall">
312      <title>Automatic installation of plug-ins</title>
313     
314      <para>
315        This section describes the automatic installation of plug-ins
316        using a wizard.
317      </para>
318     
319      <figure id="plugins.figures.autoinstall">
320        <title>Auto install plug-ins</title>
321     
322        <screenshot>
323          <mediaobject>
324            <imageobject>
325              <imagedata 
326                fileref="figures/plugin_autoinstall.png" format="PNG"
327              />
328            </imageobject>
329          </mediaobject>
330        </screenshot>
331      </figure>
332     
333      <para>
334        This window lists all the plug-ins that were found in JAR files, located in the path defined in
335        <filename>base.config</filename>.
336        There is a few option to set for each plug-in before they can be registered.
337      </para>
338     
339      <helptext external_id="plugindefintion.autoinstaller" title="Auto install plugins">
340        <para>
341          The page has, for each plug-in, a row that is devided into four columns with
342          information or settings. These are explained more in details below. In front of
343          each row is an icon that displays summarized information about the plug-in when
344          the mouse pointer is held over it. Most of this information is from the plug-in's
345          <classname>About</classname>
346          property but some, like 'Works with', 'Class' and 'Jar' is from the installation
347          file included in the JAR file. A plug-in can also be distributed with one or many
348          configurations that can be selected for import together with plug-in
349          registration. The configurations are by default hidden but can easily be viewed by
350          expanding the configuration tree for a plug-in.
351          <variablelist>
352            <varlistentry>
353              <term>
354                <guilabel>Plugins</guilabel>
355              </term>
356              <listitem>
357                <para>
358                  The plug-in's name, from the plug-in class. Names of the
359                  configurations that comes with a plug-in are also displayed in
360                  this column but in a tree under the plug-in they belong to.
361                </para>
362              </listitem>
363            </varlistentry>
364            <varlistentry>
365              <term>
366                <guilabel>Install</guilabel>
367              </term>
368              <listitem>
369                <para>
370                  A select list for each plug-in that can be registered. There are
371                  at least two option for each plug-in in this drop-down list. The
372                  default option
373                  <emphasis>no</emphasis>
374                  will not register the plug-in to BASE while
375                  <emphasis>yes</emphasis>
376                  will register the plug-in when proceeding. If the plug-in
377                  also have configurations the <emphasis>yes</emphasis>
378                  option is replaced with <emphasis>plugin only</emphasis>
379                  and <emphasis>plugin + configurations</emphasis>.
380                  If the last option is selected all configurations for the
381                  specific plug-in will be imported.
382                </para>
383                <para>
384                  Each listed configuration can individually be defined if it
385                  should be imported or not. This is done by selecting
386                  <emphasis>yes</emphasis> or <emphasis>no</emphasis>.
387                </para>
388                <note>
389                  <para>
390                    Plug-ins that already are registered in BASE will not be displayed in the list,
391                    unless the plug-in in the list comes from a JAR file in a different path than the
392                    one registered in BASE. In this case the drop-down lists is enabled for
393                    selection but marked with a exclamation mark and the plug-in will be
394                    re-registered with the new JAR path if any of the two install options are
395                    selected.
396                  </para>
397                </note>
398                <note>
399                  <para>
400                    If a configuration in the list has an identical name as a configuration in BASE
401                    and the configurations are for the same plug-in, there will be a warning in the
402                    list beside the install-select box. The already existing configuration will not
403                    be overwritten if the new plug-in is set to be imported, but there will be two
404                    configurations with the same name and for the same plug-in.
405                  </para>
406                </note>
407              </listitem>
408            </varlistentry>
409            <varlistentry>
410              <term>
411                <guilabel>Trusted</guilabel>
412              </term>
413              <listitem>
414                <para>
415                  If the plug-in is trusted enough to be executed in an
416                  unprotected environment. See
417                  <nohelp>
418                    <xref linkend="plugins.install.properties" />
419                  </nohelp>
420                </para>
421              </listitem>
422            </varlistentry>
423            <varlistentry>
424              <term>
425                <guilabel>Immediate execution</guilabel>
426              </term>
427              <listitem>
428                <para>
429                  If the plug-in is allowed to bypass the job queue and be
430                  executed immediately. See
431                  <nohelp>
432                    <xref linkend="plugins.install.properties" />
433                  </nohelp>
434                </para>
435              </listitem>
436            </varlistentry>
437          </variablelist>
438        </para>       
439        <para>
440          Click on &gbSave; to finish the registration
441          or on &gbCancel; to abort.
442        </para>
443        <seeother>
444          <other external_id="plugindefinition.edit">Edit plugins</other>
445        </seeother>
446      </helptext>
447    </sect2>
448   
449    <sect2 id="plugins.installation.base1">
450      <title>BASE 1 plug-ins</title>
451      <para>
452        BASE 1 plug-ins are supported by BASE 2 through the use of
453        the <emphasis>BASE 1 plug-in executer</emphasis> plug-in. This
454        is itself a plug-in and BASE 1 plug-ins are added as configurations
455        to this plug-in. See <xref linkend="plugins.configuration" />. To
456        install a BASE 1 plug-in to BASE 2 follow these instructions:
457      </para>
458     
459      <orderedlist>
460        <listitem>
461        <para>
462          Install the BASE 1 plug-in executable and any
463          other files needed by it on the BASE server. Check the documentation
464          for the plug-in for information about what is needed.
465        </para>
466        </listitem>
467       
468        <listitem>
469        <para>
470          Upload the <filename>*.base</filename> file for the BASE 1 plug-in
471          to BASE 2. If you cannot find the file, you can let BASE 1 create one for you.
472          In your BASE 1 installation go to
473          <menuchoice>
474            <guimenu>Analyze data</guimenu>
475            <guimenuitem>Plug-ins</guimenuitem>
476          </menuchoice>
477          and use the <guilabel>Export</guilabel> function. This will create a
478          configuration file for your BASE 1 plug-in that you can upload to BASE 2.
479        </para>
480        </listitem>
481       
482        <listitem>
483          <para>
484            Create a new plug-in configuration in BASE 2 using, for example,
485            the <guibutton>New configuration</guibutton> button
486            in single-item view for the <emphasis>BASE 1 plug-in executer</emphasis>
487            plug-in.
488          </para>
489        </listitem>
490       
491        <listitem>
492          <para>
493            Start the configuration wizard and select the <filename>*.base</filename>
494            file describing the BASE 1 plug-in and enter the path and
495            file name to the location of the executable.
496          </para>
497        </listitem>
498       
499        <listitem>
500          <para>
501            To check that the new plug-in works correctly, you need
502            to have an experiment with some data. Go to the single-item
503            view for a bioassayset and click on the <guibutton>Run analysis</guibutton>
504            button. Select the <emphasis>Base1PluginExecuter</emphasis>
505            plug-in. The list of configurations should include the newly
506            installed plug-in. Select it and click on &gbNext;.
507          </para>
508        </listitem>
509       
510        <listitem>
511          <para>
512            This will enter regular plug-in execution wizard and you
513            will have to enter parameters needed by the plug-in.
514          </para>
515        </listitem>
516       
517      </orderedlist>
518     
519
520    </sect2>
521   
522  </sect1>
523
524  <sect1 id="plugins.permissions">
525    <title>Plug-in permissions</title>
526
527    <helptext external_id="plugindefinition.edit.permissions" 
528      title="Edit plug-in permissions">
529
530   
531      <para>
532        When a plug-in is executed the default is to give it the same
533        permissions as the user that started it. This can be seen as a
534        security risk if the plug-in is not trusted, or if someone manages
535        to replace the plug-in code with their own code. A malicious plugin can,
536        for example, delete the entire database if invoked by the root user.
537      </para>
538     
539      <para>
540        To limit this problem it is possible to tune the permissions for
541        a plug-in so that it only has permission to do things that it
542        is supposed to do. For example, a plug-in that import reporters
543        may only need permission to update and create new reporters and
544        nothing else.
545      </para>
546   
547      <nohelp>
548      <para>
549        To enable the permission system for a plug-in go the
550        edit view of the plug-in and select the <guilabel>Permissions</guilabel>
551        tab.
552      </para>
553     
554      <figure id="plugins.figures.permissions">
555        <title>Setting permissions on a plug-in</title>
556        <screenshot>
557          <mediaobject>
558            <imageobject><imagedata 
559              fileref="figures/plugin_permissions.png" format="PNG"
560              /></imageobject>
561          </mediaobject>
562        </screenshot>
563      </figure>
564      </nohelp>
565
566      <variablelist>
567      <varlistentry>
568        <term><guilabel>Use permissions</guilabel></term>
569        <listitem>
570          <para>
571            Select if the plug-in should use the permission system
572            or not. If <guilabel>no</guilabel> is selected, the rest
573            of the form is disabled.
574          </para>
575        </listitem>
576      </varlistentry>
577      <varlistentry>
578        <term><guilabel>Item types</guilabel></term>
579        <listitem>
580          <para>
581            The list contains all item types found in BASE that
582            can have permissions set on them. The list is more or less the
583            same as the permission list for roles.
584            <nohelp>
585              See <xref linkend="user_administration.roles.edit.permissions" />.
586            </nohelp>
587          </para>
588        </listitem>
589      </varlistentry>
590      <varlistentry>
591        <term><guilabel>Always grant</guilabel></term>
592        <listitem>
593          <para>
594            The selected permissions will always be granted
595            to the plug-in no matter if the logged in user had the
596            permission to begin with or not. This makes it possible to
597            develop a plugin that allows users to do things that they
598            are normally not allowed to do. The reporter importer is
599            for example allowed to create and use reporter types.
600          </para>
601        </listitem>
602      </varlistentry>
603      <varlistentry>
604        <term><guilabel>Always deny</guilabel></term>
605        <listitem>
606          <para>
607            The selected permissions will always be denied
608            to the plug-in no matter if the logged in user had the
609            permission to begin with or not. The default is to always
610            deny all permissions. Permissions that are not always
611            denied and not always granted uses permissions from
612            the logged in user.
613          </para>
614        </listitem>
615      </varlistentry>
616      <varlistentry>
617        <term><guilabel>Requested by plug-in</guilabel></term>
618        <listitem>
619          <para>
620            To make it easier for the server administrator
621            to assign permissions, the plug-in developer can
622            let the plug-in include a list of permissions that
623            are needed. Plug-in developers are advised to
624            only include the minimal set of permissions that are
625            required for the plug-in to function. Click on the
626            <guibutton>Use requested permissions</guibutton>
627            button to give the plug-in the requested permissions.
628          </para>
629        </listitem>
630      </varlistentry>
631      </variablelist>
632   
633      <seeother>
634        <other external_id="plugindefinition.edit">Plug-in properties</other>
635        <other external_id="plugindefinition.jobagents">Job agents</other>
636        <other external_id="role.edit.permissions">Role permissions</other>
637      </seeother>   
638    </helptext>
639   
640   
641  </sect1>
642
643
644  <sect1 id="plugins.jobagents">
645    <title>Job agents</title>
646    <para>
647      Job agents are used for executing plug-ins on external
648      computers. Using job agents will free up resources on the BASE
649      application server, and allow the server to concentrate on
650      serving web pages. Job agents are optional and must be installed
651      separately. See <xref linkend="installation_upgrade.jobagents"
652      /> for more information about setting up job agents. This
653      section assumes that at least one job agent is setup to serve
654      your BASE installation.
655    </para>
656   
657    <para>
658      A job agent will not execute a plug-in unless the administrator
659      has configured the job agent to do so. This can be done either
660      from the plug-in pages or from the job agent pages. To register
661      a plug-in with one or more job agents from the plug-in pages, go
662      to the edit view of the plug-in and select the <guilabel>Job
663      agents</guilabel> tab. To do the same from the job agent pages,
664      go to the edit view of the job agent and select
665      the <guilabel>Plugins</guilabel> tab. The registration dialogs
666      are very similar but only the plug-in side of registration is
667      described here, the job agent route is described in
668      <xref linkend="installation_upgrade.jobagents" />.
669    </para>
670   
671    <figure id="plugins.figures.jobagents">
672      <title>Select job agents for a plug-in</title>
673      <screenshot>
674        <mediaobject>
675          <imageobject><imagedata 
676            fileref="figures/plugin_jobagents.png" format="PNG"
677            /></imageobject>
678        </mediaobject>
679      </screenshot>
680    </figure>
681   
682    <helptext external_id="plugindefinition.jobagents" 
683      title="Job agents">
684     
685      <para>
686        Use this tab to specify which job agents the plug-in is
687        installed and allowed to be executed on.
688      </para>
689     
690      <variablelist>
691      <varlistentry>
692        <term><guilabel>Run this plugin on</guilabel></term>
693        <listitem>
694          <para>
695            You may select if the internal job queue should execute the
696            plug-in or not.
697          </para>
698        </listitem>
699      </varlistentry>
700      <varlistentry>
701        <term><guilabel>Job agents</guilabel></term>
702        <listitem>
703          <para>
704            A list with the job agents where the plug-in is installed and
705            allowed to be executed. Select a plug-in in this list to display
706            more configuration options for the plug-in.
707          </para>
708        </listitem>
709      </varlistentry>
710      <varlistentry>
711        <term><guilabel>Add job agents</guilabel></term>
712        <listitem>
713          <para>
714            Use this button to open a popup window for selecting
715            job agents.
716          </para>
717        </listitem>
718      </varlistentry>
719      <varlistentry>
720        <term><guilabel>Remove</guilabel></term>
721        <listitem>
722          <para>
723            Remove the selected plug-in from the list.
724          </para>
725        </listitem>
726      </varlistentry>
727      </variablelist>
728     
729      <para>
730        The following properties are only displayed when a
731        job agent has been selected in the list. Each job agent may have it's
732        own settings of these properties. If you leave the values unspecified
733        the job agent will use the default values specified on the
734        <guilabel>Plugin</guilabel> tab.
735      </para>
736     
737      <variablelist>
738      <varlistentry>
739        <term><guilabel>Jar path</guilabel></term>
740        <listitem>
741          <para>
742            The path on the external server to the JAR file containing the
743            plug-in code. If not specified the same path as on the web server
744            is used.
745          </para>
746        </listitem>
747      </varlistentry>
748      <varlistentry>
749        <term><guilabel>Max memory</guilabel></term>
750        <listitem>
751          <para>
752            The maximum amount of memory the plug-in is allowed to use.
753            Add around 40MB for the Java runtime environment and BASE.
754            If not specified Java will choose it's default value which is 64MB.
755          </para>
756        </listitem>
757      </varlistentry>
758      <varlistentry>
759        <term><guilabel>Trusted</guilabel></term>
760        <listitem>
761          <para>
762            If the plug-in should be executed in a protected or
763            unprotected environment. Currently, BASE only supports
764            running plug-ins in an unprotected environment.
765          </para>
766        </listitem>
767      </varlistentry>
768      <varlistentry>
769        <term><guilabel>Priority boost</guilabel></term>
770        <listitem>
771          <para>
772            Used to give a plug-in higher priority in the queue.
773            Values between 0 and 10 are allowed. A higher value will
774            give the plug-in higher priority. The priority boost is useful
775            if we, for example, want to use one server mainly for importing
776            data. By giving all import plugins a priority boost they will
777            be executed before all other jobs, which will have to wait
778            until there are no more waiting imports.
779          </para>
780        </listitem>
781      </varlistentry>
782      </variablelist>
783     
784      <seeother>
785        <other external_id="plugindefinition.edit">Plug-in properties</other>
786        <other external_id="plugindefinition.edit.permissions">Plug-in permissions</other>
787      </seeother>
788    </helptext>
789  </sect1>
790 
791  <sect1 id="plugins.configuration">
792    <title>Plug-in configurations</title>
793
794    <para>
795      While some plug-ins work right out of the box, some
796      may require configuration before they can be used. For example,
797      most of the core import plug-ins need configurations in the
798      form of regular expressions to be able to find headers and
799      data in the data files and the BASE 1 plug-in executer uses
800      configurations to store information about the BASE 1 plug-ins.
801    </para>
802
803    <para>
804      Configurations are managed from a plug-in's single-item view page
805      or from the
806      <menuchoice>
807        <guimenu>Administrate</guimenu>
808        <guisubmenu>Plugins</guisubmenu>
809        <guimenuitem>Configurations</guimenuitem>
810      </menuchoice>
811      page.
812    </para>
813   
814    <para>
815      Click on the &gbNew; button
816      to create a new configuration.
817    </para>
818   
819    <figure id="plugins.figures.configuration">
820      <title>Create plug-in configuration</title>
821      <screenshot>
822        <mediaobject>
823          <imageobject><imagedata 
824            fileref="figures/plugin_configuration.png" format="PNG"
825            /></imageobject>
826        </mediaobject>
827      </screenshot>
828    </figure>
829   
830    <helptext external_id="pluginconfiguration.edit" 
831      title="Edit plugin configuration">
832     
833      <variablelist>
834      <varlistentry>
835        <term><guilabel>Plugin</guilabel></term>
836        <listitem>
837          <para>
838            The plug-in this configuration belongs to. This cannot
839            be changed for existing configurations. Use the
840            <guibutton>Select&hellip;</guibutton> button
841            to open a popup window where you can select a plug-in.
842          </para>
843        </listitem>
844      </varlistentry>
845      <varlistentry>
846        <term><guilabel>Name</guilabel></term>
847        <listitem>
848          <para>
849            The name of the configuration.
850          </para>
851        </listitem>
852      </varlistentry>
853      <varlistentry>
854        <term><guilabel>Description</guilabel></term>
855        <listitem>
856          <para>
857            A description of the configuration (optional).
858          </para>
859        </listitem>
860      </varlistentry>
861      </variablelist>
862     
863      <note>
864        You cannot create configurations for plug-ins that
865        does not support being configured.
866      </note>
867   
868      <para>
869        Use the &gbSave; button to save the
870        configuration or the <guibutton>Save and configure</guibutton>
871        button to save and then start the configuration wizard.
872      </para>
873   
874    </helptext>
875   
876    <sect2 id="plugins.configuration.wizard">
877      <title>Configuring plug-in configurations</title>
878
879      <helptext external_id="runplugin.configure"
880        title="The plug-in configuration wizard">
881     
882      <para>
883        Configuring a plug-in is done with a wizard-like
884        interface. Since the configuration parameters may vary
885        from plug-in to plug-in BASE uses a generic interface
886        to enter parameter values. In short, it works like this:
887       
888        <orderedlist>
889          <listitem>
890            <para>
891              BASE asks the plug-in for information about
892              the parameters the plug-in needs. For example,
893              if the value is a string or number or should be
894              selected among a list of predefined values.
895            </para>
896          </listitem>
897         
898          <listitem>
899            <para>
900              BASE uses this information to create a generic form
901              for entering the values. The form consists of three
902              parts:
903             
904              <nohelp>
905              <figure id="plugins.figures.wizard">
906                <title>The plug-in configuration wizard</title>
907                <screenshot>
908                  <mediaobject>
909                    <imageobject><imagedata 
910                      fileref="figures/plugin_wizard.png" format="PNG"
911                      /></imageobject>
912                  </mediaobject>
913                </screenshot>
914              </figure>
915              </nohelp>
916             
917              <itemizedlist>
918              <listitem>
919                <para>
920                <emphasis>The top part</emphasis>: Displays
921                the name of the selected plug-in and configuration.
922                </para>
923              </listitem>
924             
925              <listitem>
926                <para>
927                <emphasis>The left part</emphasis>: Displays
928                a list of all parameters supported by the plug-in.
929                Parameters with an <guilabel>X</guilabel> in front
930                of their names already have a value. Parameters
931                marked with a blue rectangle are required and
932                must be given a value before it is possible to
933                proceed.
934                </para>
935              </listitem>
936             
937              <listitem>
938                <para>
939                <emphasis>The right part</emphasis>: Click on a parameter
940                in the list to display a form for entering values for
941                that parameter. The form may be a simple free text field,
942                a list of checkboxes or radiobuttons, or something else
943                depending on the kind of values supported by that
944                parameter.
945                </para>
946              </listitem>
947              </itemizedlist> 
948             
949            </para>
950          </listitem>
951
952          <listitem>
953            <para>
954              When the user clicks &gbNext;
955              the entered values are sent to the plug-in which
956              validate the correctness. The plug-in may return
957              three different replies:
958             
959              <itemizedlist>
960              <listitem>
961                <para>
962                <emphasis>ERROR</emphasis>:
963                There is an error in the input. BASE will redisplay
964                the same form with any additional error information that
965                the plug-in sends back.
966                </para>
967              </listitem>
968              <listitem>
969                <para>
970                <emphasis>DONE</emphasis>:
971                All parameter values are okay and no more values
972                are needed. BASE will save the values to the database
973                and finish the configuration wizard.
974                </para>
975              </listitem>
976              <listitem>
977                <para>
978                <emphasis>CONTINUE</emphasis>:
979                All parameter values are okay, but the plug-in
980                wants more parameters. The procedure is repeated from the
981                first step.
982                </para>
983              </listitem>
984              </itemizedlist>
985            </para>
986          </listitem>
987         
988        </orderedlist>
989      </para>
990
991      <note>
992        <title>Do not go back</title>
993        It is not possible to go backwards in the wizard.
994        If you try it will most likely result in an
995        unexpected error and the configuration must be restarted
996        from the beginning.
997      </note>
998     
999      <seeother>
1000        <other external_id="runplugin.configure.import">Common parameter for import plug-ins</other>
1001        <other external_id="runplugin.configure.export">Common parameter for export plug-ins</other>
1002        <other external_id="runplugin.configure.analysis">Common parameter for analysis plug-ins</other>
1003      </seeother>
1004      </helptext>
1005     
1006    </sect2>
1007
1008    <sect2 id="plugins.configuration.importexport">
1009      <title>Importing and exporting plug-in configurations</title>
1010      <para>
1011        BASE ships with one importer and one exporter that allows
1012        you to import and export plug-in configurations. This makes
1013        it easy to copy configurations between servers. The BASE website
1014        also has a <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"
1015        >page where you can download additional configurations</ulink>
1016        not included in the main distribution.
1017      </para>
1018     
1019      <para>
1020        Both the import and the export is started from the plug-in
1021        configuration list view:
1022        <menuchoice>
1023          <guimenu>Administrate</guimenu>
1024          <guisubmenu>Plugins</guisubmenu>
1025          <guimenuitem>Configurations</guimenuitem>
1026        </menuchoice>
1027      </para>
1028     
1029      <para>
1030        The importer supports auto detection. Simply upload and select the XML file with the
1031        configurations. No more parameters are needed.
1032      </para>
1033     
1034      <para>
1035        If you don't want to import all
1036        configurations that exist in the XML-file, there is an option that lets you select
1037        each configuration individually. When the option to import all configurations is set
1038        to FALSE in the first step of job-configuration, the following step after pressing
1039        <guibutton>Next</guibutton>
1040        will be to select those configurations that should be imported, otherwise this step
1041        is skipped.
1042      </para>
1043
1044
1045      <para>
1046        To use the exporter you must first select the configurations
1047        that should be exported in the list. Then, enter a path and file name
1048        if you wish to leave the XML file on the BASE server or leave it
1049        empty to download it immediately.
1050      </para>
1051     
1052      <note>
1053        The import and export only supports simple values, such as strings,
1054        numbers, etc. It does not support configuration values that reference
1055        other items. If the plug-in has such values they must be fixed
1056        manually after the import.
1057      </note>
1058     
1059    </sect2>
1060
1061    <sect2 id="plugins.configuration.testwithfile">
1062      <title>The <guilabel>Test with file</guilabel> function</title>
1063     
1064      <para>
1065        The <guilabel>Test with file</guilabel> function is a very useful
1066        function for specifying import file formats. It is supported by
1067        many of the import plug-ins that read data from a simple text
1068        file. This includes the raw data importer, the reporter importer,
1069        plate reporter, etc.
1070      </para>
1071
1072      <note>
1073        The <guilabel>Test with file</guilabel> function can only
1074        be used with simple (tab- or comma-separated) text files.
1075        It does not work with XML files or binary files. The text file
1076        may have headers in the beginning.
1077      </note>
1078     
1079      <para>
1080        As you can see in figure <xref linkend="plugins.figures.wizard"/>
1081        there is a <guibutton>Test with file</guibutton> button. This
1082        will appear in the file format setup step for all plug-ins that
1083        support the test with file function. For detailed technical
1084        information about this see <xref linkend="plugin_developer.import" />
1085        in <xref linkend="plugin_developer" />. Clicking on the
1086        <guibutton>Test with file</guibutton> button opens the following dialog:
1087      </para>
1088     
1089      <figure id="plugins.figures.testwithfile">
1090        <title>The test with file function</title>
1091        <screenshot>
1092          <mediaobject>
1093            <imageobject><imagedata 
1094              scalefit="1" width="100%"
1095              fileref="figures/test_with_file.png" format="PNG"
1096              /></imageobject>
1097          </mediaobject>
1098        </screenshot>
1099      </figure>
1100     
1101      <helptext external_id="runplugin.testwithfile" 
1102        title="Test with file">
1103       
1104      <para>
1105        The window consists of two parts, the upper part where the file
1106        to parse and the parameters used to parse it are entered, and
1107        the lower part that displays information about the parsing.
1108      </para>
1109       
1110      <variablelist>
1111      <varlistentry>
1112        <term><guilabel>File to test</guilabel></term>
1113        <listitem>
1114          <para>
1115            The path and file name of the file to use for testing.
1116            Use the &gbBrowse; button to
1117            select a file from the BASE file system or upload
1118            a new file. Click on the <guibutton>Parse the file</guibutton>
1119            button to start parsing. The lower part will update itself with
1120            information about the parsed file. The file must follow a few simple rules:
1121           
1122            <itemizedlist>
1123            <listitem>
1124              <para>Data must be organised into columns, with one record per line.</para>
1125            </listitem>
1126            <listitem>
1127              <para>
1128                Each data column must be separated by some special character or
1129                character sequence not occurring in the data, for example a tab or a comma.
1130                Data in fixed-size columns cannot be parsed.
1131              </para>
1132            </listitem>
1133            <listitem>
1134              <para>
1135                Data may optionally be preceded by a data header, for example,
1136                the names of the columns.
1137              </para>
1138            </listitem>
1139            <listitem>
1140              <para>
1141                The data header may optionally be preceded by file headers.
1142                A file header is something that can be split into a name-value pair.
1143              </para>
1144            </listitem>
1145            <listitem>
1146              <para>
1147                The file may contain comments, which are ignored by the parser.
1148              </para>
1149            </listitem>
1150            </itemizedlist>
1151          </para>
1152        </listitem>
1153      </varlistentry>
1154      <varlistentry>
1155        <term><guilabel>Lines to parse</guilabel></term>
1156        <listitem>
1157          <para>
1158            The number of lines to parse. The default is 100.
1159          </para>
1160        </listitem>
1161      </varlistentry>
1162      <varlistentry>
1163        <term><guilabel>Encoding</guilabel></term>
1164        <listitem>
1165          <para>
1166            The character encoding of the file. The default
1167            is ISO-8859-1 (same as Latin-1). This list contains all encodings
1168            supported by the underlying Java runtime and can be quite long.
1169          </para>
1170        </listitem>
1171      </varlistentry>
1172      <varlistentry>
1173        <term><guilabel>Header regexp</guilabel></term>
1174        <listitem>
1175          <para>
1176            A regular expression matching a header line. A header
1177            is a key-value pair with information about the
1178            data in the file. The regular expression must contain two capturing groups,
1179            the first should capture the name and the second the value of the header.
1180            For example, the file contains headers like:
1181<screen>
1182"Type=GenePix Results 3"
1183"DateTime=2006/05/16 13:17:59"
1184</screen>
1185            To match this we can use the following regular expression:
1186            <userinput>"(.*)=(.*)"</userinput>.
1187          </para>
1188         
1189          <para>
1190            Use the &gbPredefined; button to select from a
1191            list of common regular expressions.
1192          </para>
1193         
1194        </listitem>
1195      </varlistentry>
1196     
1197      <varlistentry>
1198        <term><guilabel>Data splitter regexp</guilabel></term>
1199        <listitem>
1200          <para>
1201            A regular expression used to split a data line into columns. For
1202            example, <userinput>\t</userinput> to split on tabs. Use
1203            &gbPredefined; button to select from a list of
1204            common regular expressions.
1205          </para>
1206        </listitem>
1207      </varlistentry>
1208     
1209      <varlistentry>
1210        <term><guilabel>Ignore regexp</guilabel></term>
1211        <listitem>
1212          <para>
1213            A regular expression that matches all lines that should be ignored.
1214            For example, <userinput>\#.*</userinput> to ignore all lines starting with
1215            a #. Use
1216            &gbPredefined; button to select from a list of
1217            common regular expressions.
1218          </para>
1219        </listitem>
1220      </varlistentry>
1221     
1222      <varlistentry>
1223        <term><guilabel>Data header regexp</guilabel></term>
1224        <listitem>
1225          <para>
1226            A regular expression that matches the line containing the data header.
1227            Usually the data header contains the column names separated with the
1228            same separator as the data. For example, the file contains a header
1229            like:
1230<screen>
1231"Block"{tab}"Column"{tab}"Row"{tab}"Name"{tab}"ID" ...and so on
1232</screen>
1233            To match this we can use the following regular expression:
1234            <userinput>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</userinput>.
1235          </para>
1236         
1237          <para>
1238            The easiest way to set this regular is expression is to leave it empty
1239            to start with, click on the <guibutton>Parse the file</guibutton> button.
1240            Then, in the <guilabel>File data</guilabel> tab, use the dropdown lists
1241            in the <guilabel>Use as</guilabel> column to select the line containing the
1242            data header. BASE will automatically generate a regular expression matching
1243            the line.
1244          </para>
1245        </listitem>
1246      </varlistentry>
1247
1248      <varlistentry>
1249        <term><guilabel>Date footer regexp</guilabel></term>
1250        <listitem>
1251          <para>
1252            A regular expression that matches the first line of non-data after
1253            all data lines. In most cases you can leave this empty.
1254          </para>
1255        </listitem>
1256      </varlistentry>
1257
1258      <varlistentry>
1259        <term><guilabel>Min and max data columns</guilabel></term>
1260        <listitem>
1261          <para>
1262            If you specify values a data line is ignored if the number of
1263            columns does not fall within the range. If your data file does not have
1264            a data header with column names you can use these settings to find the
1265            start of data.
1266          </para>
1267        </listitem>
1268      </varlistentry>
1269      <varlistentry>
1270        <term><guilabel>Remove quotes</guilabel></term>
1271        <listitem>
1272          <para>
1273            If enabled, the parser will remove quotes around data entries.
1274          </para>
1275        </listitem>
1276      </varlistentry>
1277 
1278      <varlistentry>
1279        <term><guilabel>File data</guilabel></term>
1280        <listitem>
1281          <para>
1282            Press the <guilabel>Parse the file</guilabel> button
1283            to start parsing the file. This tab will be updated with the data
1284            from the file, organised as a table. For each line the following information
1285            is displayed:
1286            <itemizedlist>
1287            <listitem>
1288              <para>
1289              <emphasis>Line</emphasis>: The line number in the file
1290              </para>
1291            </listitem>
1292
1293            <listitem>
1294              <para>
1295              <emphasis>Columns</emphasis>: The number of columns the line could be
1296              split into with the data splitter regular expression.
1297              </para>
1298            </listitem>
1299
1300            <listitem>
1301              <para>
1302              <emphasis>Type</emphasis>: The type of line as detected by the parser.
1303              It should be one of the following: <emphasis>Unknown</emphasis>,
1304              <emphasis>Header</emphasis>, <emphasis>Data header</emphasis>,
1305              <emphasis>Data</emphasis> or <emphasis>Data footer</emphasis>.
1306              </para>
1307            </listitem>
1308           
1309            <listitem>
1310              <para>
1311              <emphasis>Use as</emphasis>: Use the dropdown lists to use a
1312              line as either the data header or data footer. BASE will automatically
1313              generate a regular expression.
1314              </para>
1315            </listitem>
1316           
1317            <listitem>
1318              <para>
1319              <emphasis>File data</emphasis>: The contents of the file after
1320              splitting and, optionally, removal of quotes.
1321              </para>
1322            </listitem>
1323            </itemizedlist>
1324           
1325          </para>
1326        </listitem>
1327      </varlistentry>
1328      <varlistentry>
1329        <term><guilabel>Column mappings</guilabel></term>
1330        <listitem>
1331          <para>
1332            This tab is only displayed if data has been found in the file and a
1333            data header is present. It allows you to easily select the mapping
1334            between columns in the file and the properties in the database.
1335          </para>
1336          <nohelp>
1337          <figure id="plugins.figures.testwithfilemappings">
1338            <title>Mapping columns from a file</title>
1339            <screenshot>
1340              <mediaobject>
1341                <imageobject><imagedata 
1342                  fileref="figures/test_with_file_mappings.png" format="PNG"
1343                  /></imageobject>
1344              </mediaobject>
1345            </screenshot>
1346          </figure>
1347          </nohelp>
1348         
1349          <itemizedlist>
1350          <listitem>
1351            <para>
1352              <emphasis>Mapping style</emphasis>: The type
1353              of mapping to use when you pick a column from the
1354              <emphasis>File columns</emphasis> list boxes.
1355            </para>
1356          </listitem>
1357         
1358          <listitem>
1359            <para>
1360              <emphasis>Property</emphasis>: The database property.
1361            </para>
1362          </listitem>
1363
1364          <listitem>
1365            <para>
1366              <emphasis>Mapping expression</emphasis>: An expression that
1367              maps the data in the file columns to the property in the
1368              database. There are two types of mappings, simple and expressions.
1369              A simple mapping is a string template with placeholders for data
1370              from the file. An expression mapping starts with an equal sign and
1371              is evaluated dynamically for each line of data. The simple
1372              mapping has better performance and we recommend that you use
1373              it unless you have to recalculate any of the numerical values.
1374              In both cases, if no column matching the placeholder exactly is found
1375              the placeholder is interpreted as a regular expression that
1376              is matched against each column. The first one found is used.
1377              Here are a few mapping examples:
1378            </para>
1379           
1380<informalexample>
1381<literallayout>\Name\ --&gt; exact match is required
1382\1\ --&gt; column with index 1 (the second column)
1383[\row\, \column\] --&gt; combining row and column to a single coordinate
1384=2 * col('radius') --&gt; calculate the diameter dynamically
1385\F63(3|5) Median\ --&gt; use regular expression to match either F633 or F635
1386</literallayout>
1387</informalexample>
1388           
1389            <note>
1390              Column numbers are 0-based. We recommend that you use
1391              column names at all times if they are present in the
1392              file.
1393            </note>
1394          </listitem>
1395         
1396          <listitem>
1397            <para>
1398              <emphasis>File columns</emphasis>: Lists of column found in the file.
1399              Select a value from this list to let BASE automatically
1400              generate a mapping that picks the selected column.
1401            </para>
1402          </listitem>
1403          </itemizedlist>
1404        </listitem>
1405      </varlistentry>
1406      </variablelist>     
1407     
1408      </helptext>
1409     
1410     
1411    </sect2>
1412 
1413  </sect1>
1414 
1415
1416</chapter>
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