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Fixes #548
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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 3345 2007-05-16 11:17:55Z martin $
7
8	Copyright (C) Authors contributing to this file.
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 doesn't 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><base-dir>/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 classloader 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><base-dir>/plugins/<name-of-plugin></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
79	with BASE. BASE lacks functionality for discovering plug-ins automatically
80	so you have to enter information about the JAR file and plug-in manually.
81	This can be hard to get right. To register the plug-in with BASE go to
82	<menuchoice>
83	<guimenu>Administrate</guimenu>
84	<guisubmenu>Plugins</guisubmenu>
85	<guimenuitem>Definitions</guimenuitem>
86	</menuchoice> and click on the <guibutton>New…</guibutton>
87	button.
88	</para>
89
90	<sect2 id="plugins.install.properties">
91	<title>Plug-in properties</title>
92
93	<figure id="plugins.figures.install">
94	<title>Installing a plug-in</title>
95	<screenshot>
96	<mediaobject>
97	<imageobject><imagedata
98	fileref="figures/install_plugin.png" format="PNG"
99	/></imageobject>
100	</mediaobject>
101	</screenshot>
102	</figure>
103
104	<helptext external_id="plugindefinition.edit"
105	title="Plug-in properties">
106
107	<variablelist>
108	<varlistentry>
109	<term><guilabel>Name</guilabel></term>
110	<listitem>
111	<para>
112	The name of the plug-in. This name is set automatically by
113	the plug-in and can't be changed.
114	</para>
115	</listitem>
116	</varlistentry>
117	<varlistentry>
118	<term><guilabel>Class</guilabel></term>
119	<listitem>
120	<para>
121	The Java class name of the plug-in.
122	</para>
123	</listitem>
124	</varlistentry>
125	<varlistentry>
126	<term><guilabel>Path</guilabel></term>
127	<listitem>
128	<para>
129	The path to the JAR file on the web server. If left empty
130	the plug-in must be on the web server's class path (not
131	recommended).
132	</para>
133	</listitem>
134	</varlistentry>
135	<varlistentry>
136	<term><guilabel>Max memory</guilabel></term>
137	<listitem>
138	<para>
139	The maximum amount of memory the plug-in may use. This setting
140	only applies when the plug-in is executed with a job agent. If
141	the internal job queue is used this setting has no effect and the
142	plug-in may use as much memory as it likes.
143	<nohelp>See <xref linkend="plugins.jobagents" /> later
144	in this chapter.</nohelp>
145	</para>
146	</listitem>
147	</varlistentry>
148	<varlistentry>
149	<term><guilabel>Trusted</guilabel></term>
150	<listitem>
151	<para>
152	If the plug-in is trusted enough to be executed in an
153	unprotected environment. This setting has currently no
154	effect since BASE can't run in a protected environment.
155	When this becomes implemented in the future a
156	<guilabel>no</guilabel> value will apply security restrictions
157	to plug-ins similar 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>Allow immediate execution</guilabel></term>
166	<listitem>
167	<para>
168	If the plug-in is allowed to bypass the job queue
169	and be executed immediately.
170
171	<itemizedlist>
172	<listitem>
173	<para>
174	<guilabel>No</guilabel>: The plug-in must always use
175	the job queue.
176	</para>
177	</listitem>
178	<listitem>
179	<para>
180	<guilabel>Yes</guilabel>: The plug-in is allowed to bypass
181	the job queue. This also means that the plug-in always
182	executes on the web server, job agents are not used.
183	This setting is mainly useful for export plug-ins that
184	needs to support immediate download of the exported data.
185	<nohelp>
186	See <xref linkend="import_export_data.export.immediatedownload" />.
187	</nohelp>
188	</para>
189
190	<note>
191	If a plug-in should be executed immediately or not
192	is always decided by the plug-in. BASE will never give
193	the users a choice.
194	</note>
195
196	</listitem>
197	<listitem>
198	<para>
199	<guilabel>Auto</guilabel>: BASE will allow export plug-ins
200	to execute immediately, and deny all other types of plug-ins.
201	This alternative is only available when registering a new
202	plug-in.
203	</para>
204	</listitem>
205	</itemizedlist>
206
207	</para>
208	</listitem>
209	</varlistentry>
210	</variablelist>
211
212	<para>
213	Click on <guibutton>Save</guibutton> to finish the registration
214	or on <guibutton>Cancel</guibutton> to abort.
215	</para>
216
217	<seeother>
218	<other external_id="plugindefinition.edit.permissions">Plug-in permissions</other>
219	<other external_id="plugindefinition.jobagents">Job agents</other>
220	</seeother>
221
222	</helptext>
223	</sect2>
224
225	<sect2 id="plugins.installation.base1">
226	<title>BASE 1 plug-ins</title>
227	<para>
228	BASE 1 plug-ins are supported by BASE 2 through the use of
229	the <emphasis>BASE 1 plug-in executer</emphasis> plug-in. This
230	is itself a plug-in and BASE 1 plug-ins are added as configurations
231	to this plug-in. See <xref linkend="plugins.configuration" />. To
232	install a BASE 1 plug-in to BASE 2 follow these instructions:
233	</para>
234
235	<orderedlist>
236	<listitem>
237	<para>
238	Install the BASE 1 plug-in executable and any
239	other files needed by it on the BASE server. Check the documentation
240	for the plug-in for information about what is needed.
241	</para>
242	</listitem>
243
244	<listitem>
245	<para>
246	Upload the <filename>*.base</filename> file for the BASE 1 plug-in
247	to BASE 2. If you can't find the file, you can let BASE 1 create one for you.
248	In your BASE 1 installation go to
249	<menuchoice>
250	<guimenu>Analyze data</guimenu>
251	<guimenuitem>Plug-ins</guimenuitem>
252	</menuchoice>
253	and use the <guilabel>Export</guilabel> function. This will create a
254	configuration file for your BASE 1 plug-in that you can upload to BASE 2.
255	</para>
256	</listitem>
257
258	<listitem>
259	<para>
260	Create a new plug-in configuration in BASE 2 using, for example,
261	the <guibutton>New configuration</guibutton> button
262	in single-item view for the <emphasis>BASE 1 plug-in executer</emphasis>
263	plug-in.
264	</para>
265	</listitem>
266
267	<listitem>
268	<para>
269	Start the configuration wizard and select the <filename>*.base</filename>
270	file describing the BASE 1 plug-in and enter the path and
271	filename to the location of the executable.
272	</para>
273	</listitem>
274
275	<listitem>
276	<para>
277	To check that the new plug-in works correctly, you need
278	to have an experiment with some data. Go to the single-item
279	view for a bioassayset and click on the <guibutton>Run analysis</guibutton>
280	button. Select the <emphasis>Base1PluginExecuter</emphasis>
281	plug-in. The list of configurations should include the newly
282	installed plug-in. Select it and click on <guibutton>Next</guibutton>.
283	</para>
284	</listitem>
285
286	<listitem>
287	<para>
288	This will enter regular plug-in execution wizard and you
289	will have to enter parameters needed by the plug-in.
290	</para>
291	</listitem>
292
293	</orderedlist>
294
295
296	</sect2>
297
298	</sect1>
299
300	<sect1 id="plugins.permissions">
301	<title>Plug-in permissions</title>
302
303	<helptext external_id="plugindefinition.edit.permissions"
304	title="Edit plug-in permissions">
305
306
307	<para>
308	When a plug-in is executed the default is to give it the same
309	permissions as the user that started it. This can be seen as a
310	security risk if the plug-in is not trusted, or if someone manages
311	to replace the plug-in code with their own code. A malicious plugin can,
312	for example, delete the entire database if invoked by the root user.
313	</para>
314
315	<para>
316	To limit this problem it is possible to tune the permissions for
317	a plug-in so that it only has permission to do things that it
318	is supposed to do. For example, a plug-in that import reporters
319	may only need permission to update and create new reporters and
320	nothing else.
321	</para>
322
323	<nohelp>
324	<para>
325	To enable the permission system for a plug-in go the
326	edit view of the plug-in and select the <guilabel>Permissions</guilabel>
327	tab.
328	</para>
329
330	<figure id="plugins.figures.permissions">
331	<title>Setting permissions on a plug-in</title>
332	<screenshot>
333	<mediaobject>
334	<imageobject><imagedata
335	fileref="figures/plugin_permissions.png" format="PNG"
336	/></imageobject>
337	</mediaobject>
338	</screenshot>
339	</figure>
340	</nohelp>
341
342	<variablelist>
343	<varlistentry>
344	<term><guilabel>Use permissions</guilabel></term>
345	<listitem>
346	<para>
347	Select if the plug-in should use the permission system
348	or not. If <guilabel>no</guilabel> is selected, the rest
349	of the form is disabled.
350	</para>
351	</listitem>
352	</varlistentry>
353	<varlistentry>
354	<term><guilabel>Item types</guilabel></term>
355	<listitem>
356	<para>
357	The list contains all item types found in BASE that
358	can have permissions set on them. The list is more or less the
359	same as the permission list for roles.
360	<nohelp>
361	See <xref linkend="user_administration.roles.edit.permissions" />.
362	</nohelp>
363	</para>
364	</listitem>
365	</varlistentry>
366	<varlistentry>
367	<term><guilabel>Always grant</guilabel></term>
368	<listitem>
369	<para>
370	The selected permissions will always be granted
371	to the plug-in no matter if the logged in user had the
372	permission to begin with or not. This makes it possible to
373	develop a plugin that allows users to do things that they
374	are normally not allowed to do. The reporter importer is
375	for example allowed to create and use reporter types.
376	</para>
377	</listitem>
378	</varlistentry>
379	<varlistentry>
380	<term><guilabel>Always deny</guilabel></term>
381	<listitem>
382	<para>
383	The selected permissions will always be denied
384	to the plug-in no matter if the logged in user had the
385	permission to begin with or not. The default is to always
386	deny all permissions. Permissions that are not always
387	denied and not always granted uses permissions from
388	the logged in user.
389	</para>
390	</listitem>
391	</varlistentry>
392	<varlistentry>
393	<term><guilabel>Requested by plug-in</guilabel></term>
394	<listitem>
395	<para>
396	To make it easier for the server administrator
397	to assign permissions, the plug-in developer can
398	let the plug-in include a list of permissions that
399	are needed. Plug-in developers are advised to
400	only include the minimal set of permissions that are
401	required for the plug-in to function. Click on the
402	<guibutton>Use requested permissions</guibutton>
403	button to give the plug-in the requested permissions.
404	</para>
405	</listitem>
406	</varlistentry>
407	</variablelist>
408
409	<seeother>
410	<other external_id="plugindefinition.edit">Plug-in properties</other>
411	<other external_id="plugindefinition.jobagents">Job agents</other>
412	<other external_id="role.edit.permissions">Role permissions</other>
413	</seeother>
414	</helptext>
415
416
417	</sect1>
418
419
420	<sect1 id="plugins.jobagents">
421	<title>Job agents</title>
422	<para>
423	Job agents are used for executing plug-ins on external servers. This is a good
424	way to free up the web server so that it can concentrate on serving web pages.
425	Job agents are optional and must be installed separately. See
426	<xref linkend="installation_upgrade.jobagents" /> for more information about this.
427	The standard BASE installation doesn't include any job agents.
428	The rest of this section assumes that you have installed at least one job agent.
429	</para>
430
431	<para>
432	A job agent will not execute a plug-in unless the admin has configured
433	the job agent to do so. This can be done either from the plug-in
434	side or from the job agent side. To register a plug-in with one or more
435	job agents from the plug-in side go to the edit view of the plug-in and
436	select the <guilabel>Job agents</guilabel> tab. To do the same from
437	the job agent side go to the edit view of the job agent and select
438	the <guilabel>Plugins</guilabel> tab. The two dialogs are very similar.
439	Here is the plug-in side of the registration, the job agent side is described
440	in <xref linkend="installation_upgrade.jobagents" />.
441	</para>
442
443	<figure id="plugins.figures.jobagents">
444	<title>Select job agents for a plug-in</title>
445	<screenshot>
446	<mediaobject>
447	<imageobject><imagedata
448	fileref="figures/plugin_jobagents.png" format="PNG"
449	/></imageobject>
450	</mediaobject>
451	</screenshot>
452	</figure>
453
454	<helptext external_id="plugindefinition.jobagents"
455	title="Job agents">
456
457	<para>
458	Use this tab to specify which job agents the plug-in is
459	installed and allowed to be executed on.
460	</para>
461
462	<variablelist>
463	<varlistentry>
464	<term><guilabel>Run this plugin on</guilabel></term>
465	<listitem>
466	<para>
467	A list with the job agents where the plug-in is installed and
468	allowed to be executed. Select a plug-in in this list to display
469	more configuration options for the plug-in.
470	</para>
471	</listitem>
472	</varlistentry>
473	<varlistentry>
474	<term><guilabel>Add job agents</guilabel></term>
475	<listitem>
476	<para>
477	Use this button to open a popup window for selecting
478	job agents.
479	</para>
480	</listitem>
481	</varlistentry>
482	<varlistentry>
483	<term><guilabel>Remove</guilabel></term>
484	<listitem>
485	<para>
486	Remove the selected plug-in from the list.
487	</para>
488	</listitem>
489	</varlistentry>
490	</variablelist>
491
492	<para>
493	The following properties are only displayed when a
494	job agent has been selected in the list. Each job agent may have it's
495	own settings of these properties. If you leave the values unspecified
496	the job agent will use the default values specified on the
497	<guilabel>Plugin</guilabel> tab.
498	</para>
499
500	<variablelist>
501	<varlistentry>
502	<term><guilabel>Jar path</guilabel></term>
503	<listitem>
504	<para>
505	The path on the external server to the JAR file containing the
506	plug-in code. If not specified the same path as on the web server
507	is used.
508	</para>
509	</listitem>
510	</varlistentry>
511	<varlistentry>
512	<term><guilabel>Max memory</guilabel></term>
513	<listitem>
514	<para>
515	The maximum amount of memory the plug-in is allowed to use.
516	Add around 40MB for the Java runtime environment and BASE.
517	If not specified Java will choose it's default value which is 64MB.
518	</para>
519	</listitem>
520	</varlistentry>
521	<varlistentry>
522	<term><guilabel>Trusted</guilabel></term>
523	<listitem>
524	<para>
525	If the plug-in should be executed in a protected or
526	unprotected environment. Currently, BASE only supports
527	running plug-ins in an unprotected environment.
528	</para>
529	</listitem>
530	</varlistentry>
531	<varlistentry>
532	<term><guilabel>Priority boost</guilabel></term>
533	<listitem>
534	<para>
535	Used to give a plug-in higher priority in the queue.
536	Values between 0 and 10 are allowed. A higher value will
537	give the plug-in higher priority. The priority boost is useful
538	if we, for example, want to use one server mainly for importing
539	data. By giving all import plugins a priority boost they will
540	be executed before all other jobs, which will have to wait
541	until there are no more waiting imports.
542	</para>
543	</listitem>
544	</varlistentry>
545	</variablelist>
546
547	<seeother>
548	<other external_id="plugindefinition.edit">Plug-in properties</other>
549	<other external_id="plugindefinition.edit.permissions">Plug-in permissions</other>
550	</seeother>
551	</helptext>
552	</sect1>
553
554	<sect1 id="plugins.configuration">
555	<title>Plug-in configurations</title>
556
557	<para>
558	While some plug-ins work right out of the box, some
559	may require configuration before they can be used. For example,
560	most of the core import plug-ins need configurations in the
561	form of regular expressions to be able to find headers and
562	data in the data files and the BASE 1 plug-in executer uses
563	configurations to store information about the BASE 1 plug-ins.
564	</para>
565
566	<para>
567	Configurations are managed from a plug-in's single-item view page
568	or from the
569	<menuchoice>
570	<guimenu>Administrate</guimenu>
571	<guisubmenu>Plugins</guisubmenu>
572	<guimenuitem>Configurations</guimenuitem>
573	</menuchoice>
574	page.
575	</para>
576
577	<para>
578	Click on the <guibutton>New…</guibutton> button
579	to create a new configuration.
580	</para>
581
582	<figure id="plugins.figures.configuration">
583	<title>Create plug-in configuration</title>
584	<screenshot>
585	<mediaobject>
586	<imageobject><imagedata
587	fileref="figures/plugin_configuration.png" format="PNG"
588	/></imageobject>
589	</mediaobject>
590	</screenshot>
591	</figure>
592
593	<helptext external_id="pluginconfiguration.edit"
594	title="Edit plugin configuration">
595
596	<variablelist>
597	<varlistentry>
598	<term><guilabel>Plugin</guilabel></term>
599	<listitem>
600	<para>
601	The plug-in this configuration belongs to. This can't
602	be changed for existing configurations. Use the
603	<guibutton>Select…</guibutton> button
604	to open a popup window where you can select a plug-in.
605	</para>
606	</listitem>
607	</varlistentry>
608	<varlistentry>
609	<term><guilabel>Name</guilabel></term>
610	<listitem>
611	<para>
612	The name of the configuration.
613	</para>
614	</listitem>
615	</varlistentry>
616	<varlistentry>
617	<term><guilabel>Description</guilabel></term>
618	<listitem>
619	<para>
620	A description of the configuration (optional).
621	</para>
622	</listitem>
623	</varlistentry>
624	</variablelist>
625
626	<note>
627	You can't create configurations for plug-ins that
628	doesn't support being configured.
629	</note>
630
631	<para>
632	Use the <guibutton>Save</guibutton> button to save the
633	configuration or the <guibutton>Save and configure</guibutton>
634	button to save and then start the configuration wizard.
635	</para>
636
637	</helptext>
638
639	<sect2 id="plugins.configuration.wizard">
640	<title>Configuring plug-in configurations</title>
641
642	<helptext external_id="runplugin.configure"
643	title="The plug-in configuration wizard">
644
645	<para>
646	Configuring a plug-in is done with a wizard-like
647	interface. Since the configuration parameters may vary
648	from plug-in to plug-in BASE uses a generic interface
649	to enter parameter values. In short, it works like this:
650
651	<orderedlist>
652	<listitem>
653	<para>
654	BASE asks the plug-in for information about
655	the parameters the plug-in needs. For example,
656	if the value is a string or number or should be
657	selected among a list of predefined values.
658	</para>
659	</listitem>
660
661	<listitem>
662	<para>
663	BASE uses this information to create a generic form
664	for entering the values. The form consists of three
665	parts:
666
667	<nohelp>
668	<figure id="plugins.figures.wizard">
669	<title>The plug-in configuration wizard</title>
670	<screenshot>
671	<mediaobject>
672	<imageobject><imagedata
673	fileref="figures/plugin_wizard.png" format="PNG"
674	/></imageobject>
675	</mediaobject>
676	</screenshot>
677	</figure>
678	</nohelp>
679
680	<itemizedlist>
681	<listitem>
682	<para>
683	<emphasis>The top part</emphasis>: Displays
684	the name of the selected plug-in and configuration.
685	</para>
686	</listitem>
687
688	<listitem>
689	<para>
690	<emphasis>The left part</emphasis>: Displays
691	a list of all parameters supported by the plug-in.
692	Parameters with an <guilabel>X</guilabel> in front
693	of their names already have a value. Parameters
694	marked with a blue rectangle are required and
695	must be given a value before it is possible to
696	proceed.
697	</para>
698	</listitem>
699
700	<listitem>
701	<para>
702	<emphasis>The right part</emphasis>: Click on a parameter
703	in the list to display a form for entering values for
704	that parameter. The form may be a simple free text field,
705	a list of checkboxes or radiobuttons, or something else
706	depending on the kind of values supported by that
707	parameter.
708	</para>
709	</listitem>
710	</itemizedlist>
711
712	</para>
713	</listitem>
714
715	<listitem>
716	<para>
717	When the user clicks <guibutton>Next</guibutton>
718	the entered values are sent to the plug-in which
719	validate the correctness. The plug-in may return
720	three different replies:
721
722	<itemizedlist>
723	<listitem>
724	<para>
725	<emphasis>ERROR</emphasis>:
726	There is an error in the input. BASE will redisplay
727	the same form with any additional error information that
728	the plug-in sends back.
729	</para>
730	</listitem>
731	<listitem>
732	<para>
733	<emphasis>DONE</emphasis>:
734	All parameter values are ok and no more values
735	are needed. BASE will save the values to the database
736	and finish the configuration wizard.
737	</para>
738	</listitem>
739	<listitem>
740	<para>
741	<emphasis>CONTINUE</emphasis>:
742	All parameter values are ok, but the plug-in
743	wants more parameters. The procedure is repeated from the
744	first step.
745	</para>
746	</listitem>
747	</itemizedlist>
748	</para>
749	</listitem>
750
751	</orderedlist>
752	</para>
753
754	<note>
755	<title>Don't go back</title>
756	It is not possible to go backwards in the wizard.
757	If you try it will most likely result in an
758	unexpected error and the configuration must be restarted
759	from the beginning.
760	</note>
761
762	<seeother>
763	<other external_id="runplugin.configure.import">Common parameter for import plug-ins</other>
764	<other external_id="runplugin.configure.export">Common parameter for export plug-ins</other>
765	<other external_id="runplugin.configure.analysis">Common parameter for analysis plug-ins</other>
766	</seeother>
767	</helptext>
768
769	</sect2>
770
771	<sect2 id="plugins.configuration.importexport">
772	<title>Importing and exporting plug-in configurations</title>
773	<para>
774	BASE ships with one importer and one exporter that allows
775	you to import and export plug-in configurations. This makes
776	it easy to copy configurations between servers. The BASE website
777	also has a <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html"
778	>page where you can download additional configurations</ulink>
779	not included in the main distribution.
780	</para>
781
782	<para>
783	Both the import and the export is started from the plug-in
784	configuration list view:
785	<menuchoice>
786	<guimenu>Administrate</guimenu>
787	<guisubmenu>Plugins</guisubmenu>
788	<guimenuitem>Configurations</guimenuitem>
789	</menuchoice>
790	</para>
791
792	<para>
793	The importer supports auto detection. Simply upload and select the
794	XML file with the configurations. No more parameters are needed.
795	</para>
796
797	<para>
798	To use the exporter you must first select the configurations
799	that should be exported in the list. Then, enter a path and filename
800	if you wish to leave the XML file on the BASE server or leave it
801	empty to download it immediately.
802	</para>
803
804	<note>
805	The import and export only supports simple values, such as strings,
806	numbers, etc. It doesn't support configuration values that reference
807	other items. If the plug-in has such values they must be fixed by
808	hand after the import.
809	</note>
810
811	</sect2>
812
813	<sect2 id="plugins.configuration.testwithfile">
814	<title>The <guilabel>Test with file</guilabel> function</title>
815
816	<para>
817	The <guilabel>Test with file</guilabel> function is a very useful
818	function for specifying import file formats. It is supported by
819	many of the import plug-ins that read data from a simple text
820	file. This includes the raw data importer, the reporter importer,
821	plate reporter, etc.
822	</para>
823
824	<note>
825	The <guilabel>Test with file</guilabel> function can only
826	be used with simple (tab- or comma-separated) text files.
827	It doesn't work with XML files or binary files. The text file
828	may have headers in the beginning.
829	</note>
830
831	<para>
832	As you can see in figure <xref linkend="plugins.figures.wizard"/>
833	there is a <guibutton>Test with file</guibutton> button. This
834	will appear in the file format setup step for all plug-ins that
835	support the test with file function. For detailed technical
836	information about this see <xref linkend="plugin_developer.import" />
837	in <xref linkend="plugin_developer" />. Clicking on the
838	<guibutton>Test with file</guibutton> button opens the following dialog:
839	</para>
840
841	<figure id="plugins.figures.testwithfile">
842	<title>The test with file function</title>
843	<screenshot>
844	<mediaobject>
845	<imageobject><imagedata
846	fileref="figures/test_with_file.png" format="PNG"
847	/></imageobject>
848	</mediaobject>
849	</screenshot>
850	</figure>
851
852	<helptext external_id="runplugin.testwithfile"
853	title="Test with file">
854
855	<para>
856	The window consists of two parts, the upper part where the file
857	to parse and the parameters used to parse it are entered, and
858	the lower part that displays information about the parsing.
859	</para>
860
861	<variablelist>
862	<varlistentry>
863	<term><guilabel>File to test</guilabel></term>
864	<listitem>
865	<para>
866	The path and filename of the file to use for testing.
867	Use the <guibutton>Browse</guibutton> button to
868	select a file from the BASE file system or upload
869	a new file. Click on the <guibutton>Parse the file</guibutton>
870	button to start parsing. The lower part will update itself with
871	information about the parsed file. The file must follow a few simple rules:
872
873	<itemizedlist>
874	<listitem>
875	<para>Data must be organised into columns, with one record per line.</para>
876	</listitem>
877	<listitem>
878	<para>
879	Each data column must be separated by some special character or
880	character sequence not occurring in the data, for example a tab or a comma.
881	Data in fixed-size columns cannot be parsed.
882	</para>
883	</listitem>
884	<listitem>
885	<para>
886	Data may optionally be preceded by a data header, for example,
887	the names of the columns.
888	</para>
889	</listitem>
890	<listitem>
891	<para>
892	The data header may optionally be preceded by file headers.
893	A file header is something that can be split into a name-value pair.
894	</para>
895	</listitem>
896	<listitem>
897	<para>
898	The file may contain comments, which are ignored by the parser.
899	</para>
900	</listitem>
901	</itemizedlist>
902	</para>
903	</listitem>
904	</varlistentry>
905	<varlistentry>
906	<term><guilabel>Lines to parse</guilabel></term>
907	<listitem>
908	<para>
909	The number of lines to parse. The default is 100.
910	</para>
911	</listitem>
912	</varlistentry>
913	<varlistentry>
914	<term><guilabel>Encoding</guilabel></term>
915	<listitem>
916	<para>
917	The character encoding of the file. The default
918	is ISO-8859-1 (same as Latin-1). This list contains all encodings
919	supported by the underlying Java runtime and can be quite long.
920	</para>
921	</listitem>
922	</varlistentry>
923	<varlistentry>
924	<term><guilabel>Header regexp</guilabel></term>
925	<listitem>
926	<para>
927	A regular expression matching a header line. A header
928	is a key-value pair with information about the
929	data in the file. The regular expression must contain two capturing groups,
930	the first should capture the name and the second the value of the header.
931	For example, the file contains headers like:
932	<screen>
933	"Type=GenePix Results 3"
934	"DateTime=2006/05/16 13:17:59"
935	</screen>
936	To match this we can use the following regular expression:
937	<userinput>"(.)=(.)"</userinput>.
938	</para>
939
940	<para>
941	Use the <guibutton>Predefined</guibutton> button to select from a
942	list of common regular expressions.
943	</para>
944
945	</listitem>
946	</varlistentry>
947
948	<varlistentry>
949	<term><guilabel>Data splitter regexp</guilabel></term>
950	<listitem>
951	<para>
952	A regular expression used to split a data line into columns. For
953	example, <userinput>\t</userinput> to split on tabs. Use
954	<guibutton>Predefined</guibutton> button to select from a list of
955	common regular expressions.
956	</para>
957	</listitem>
958	</varlistentry>
959
960	<varlistentry>
961	<term><guilabel>Ignore regexp</guilabel></term>
962	<listitem>
963	<para>
964	A regular expression that matches all lines that should be ignored.
965	For example, <userinput>\#.*</userinput> to ignore all lines starting with
966	a #. Use
967	<guibutton>Predefined</guibutton> button to select from a list of
968	common regular expressions.
969	</para>
970	</listitem>
971	</varlistentry>
972
973	<varlistentry>
974	<term><guilabel>Data header regexp</guilabel></term>
975	<listitem>
976	<para>
977	A regular expression that matches the line containing the data header.
978	Usually the data header contains the column names separated with the
979	same separator as the data. For example, the file contains a header
980	like:
981	<screen>
982	"Block"{tab}"Column"{tab}"Row"{tab}"Name"{tab}"ID" ...and so on
983	</screen>
984	To match this we can use the following regular expression:
985	<userinput>"Block"\t"Column"\t"Row"\t"Name"\t"ID".*</userinput>.
986	</para>
987
988	<para>
989	The easiest way to set this regular is expression is to leave it empty
990	to start with, click on the <guibutton>Parse the file</guibutton> button.
991	Then, in the <guilabel>File data</guilabel> tab, use the dropdown lists
992	in the <guilabel>Use as</guilabel> column to select the line containing the
993	data header. BASE will automatically generate a regular expression matching
994	the line.
995	</para>
996	</listitem>
997	</varlistentry>
998
999	<varlistentry>
1000	<term><guilabel>Date footer regexp</guilabel></term>
1001	<listitem>
1002	<para>
1003	A regular expression that matches the first line of non-data after
1004	all data lines. In most cases you can leave this empty.
1005	</para>
1006	</listitem>
1007	</varlistentry>
1008
1009	<varlistentry>
1010	<term><guilabel>Min and max data columns</guilabel></term>
1011	<listitem>
1012	<para>
1013	If you specify values a data line is ignored if the number of
1014	columns doesn't fall within the range. If your data file doesn't have
1015	a data header with column names you can use these settings to find the
1016	start of data.
1017	</para>
1018	</listitem>
1019	</varlistentry>
1020	<varlistentry>
1021	<term><guilabel>Remove quotes</guilabel></term>
1022	<listitem>
1023	<para>
1024	If enabled, the parser will remove quotes around data entries.
1025	</para>
1026	</listitem>
1027	</varlistentry>
1028
1029	<varlistentry>
1030	<term><guilabel>File data</guilabel></term>
1031	<listitem>
1032	<para>
1033	Press the <guilabel>Parse the file</guilabel> button
1034	to start parsing the file. This tab will be updated with the data
1035	from the file, organised as a table. For each line the following information
1036	is displayed:
1037	<itemizedlist>
1038	<listitem>
1039	<para>
1040	<emphasis>Line</emphasis>: The line number in the file
1041	</para>
1042	</listitem>
1043
1044	<listitem>
1045	<para>
1046	<emphasis>Columns</emphasis>: The number of columns the line could be
1047	split into with the data splitter regular expression.
1048	</para>
1049	</listitem>
1050
1051	<listitem>
1052	<para>
1053	<emphasis>Type</emphasis>: The type of line as detected by the parser.
1054	It should be one of the following: <emphasis>Unknown</emphasis>,
1055	<emphasis>Header</emphasis>, <emphasis>Data header</emphasis>,
1056	<emphasis>Data</emphasis> or <emphasis>Data footer</emphasis>.
1057	</para>
1058	</listitem>
1059
1060	<listitem>
1061	<para>
1062	<emphasis>Use as</emphasis>: Use the dropdown lists to use a
1063	line as either the data header or data footer. BASE will automatically
1064	generate a regular expression.
1065	</para>
1066	</listitem>
1067
1068	<listitem>
1069	<para>
1070	<emphasis>File data</emphasis>: The contents of the file after
1071	splitting and, optionally, removal of quotes.
1072	</para>
1073	</listitem>
1074	</itemizedlist>
1075
1076	</para>
1077	</listitem>
1078	</varlistentry>
1079	<varlistentry>
1080	<term><guilabel>Column mappings</guilabel></term>
1081	<listitem>
1082	<para>
1083	This tab is only displayed if data has been found in the file and a
1084	data header is present. It allows you to easily select the mapping
1085	between columns in the file and the properties in the database.
1086	</para>
1087	<nohelp>
1088	<figure id="plugins.figures.testwithfilemappings">
1089	<title>Mapping columns from a file</title>
1090	<screenshot>
1091	<mediaobject>
1092	<imageobject><imagedata
1093	fileref="figures/test_with_file_mappings.png" format="PNG"
1094	/></imageobject>
1095	</mediaobject>
1096	</screenshot>
1097	</figure>
1098	</nohelp>
1099
1100	<itemizedlist>
1101	<listitem>
1102	<para>
1103	<emphasis>Mapping style</emphasis>: The type
1104	of mapping to use when you pick a column from the
1105	<emphasis>File columns</emphasis> list boxes.
1106	</para>
1107	</listitem>
1108
1109	<listitem>
1110	<para>
1111	<emphasis>Property</emphasis>: The database property.
1112	</para>
1113	</listitem>
1114
1115	<listitem>
1116	<para>
1117	<emphasis>Mapping expression</emphasis>: An expression that
1118	maps the data in the file columns to the property in the
1119	database. There are two types of mappings, simple and expressions.
1120	A simple mapping is a string template with placeholders for data
1121	from the file. An expression mapping starts with an equal sign and
1122	is evaluated dynamically for each line of data. The simple
1123	mapping has better performance and we recommend that you use
1124	it unless you have to recalculate any of the numerical values.
1125	Here are a few mapping examples:
1126	</para>
1127
1128	<informalexample>
1129	<literallayout>\Name\
1130	\1\
1131	[\row\, \column\]
1132	=2 * col('radius')
1133	</literallayout>
1134	</informalexample>
1135
1136	<note>
1137	Column numbers are 0-based. We recommend that you use
1138	column names at all times if they are present in the
1139	file.
1140	</note>
1141	</listitem>
1142
1143	<listitem>
1144	<para>
1145	<emphasis>File columns</emphasis>: Lists of column found in the file.
1146	Select a value from this list to let BASE automatically
1147	generate a mapping that picks the selected column.
1148	</para>
1149	</listitem>
1150	</itemizedlist>
1151	</listitem>
1152	</varlistentry>
1153	</variablelist>
1154
1155	</helptext>
1156
1157
1158	</sect2>
1159
1160	</sect1>
1161
1162
1163	</chapter>

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