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Last change on this file since 7681 was 7681, checked in by Nicklas Nordborg, 4 years ago

References #2137: Remove some of the deprecated code

Added a note in the documentation.

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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: installation.xml 7681 2019-04-04 07:47:05Z nicklas $
7
8	Copyright (C) 2007 Jari Häkkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
9	Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
10	Copyright (C) 2009 Jari Häkkinen, Nicklas Nordborg
11	Copyright (C) 2010, 2011, 2012 Nicklas Nordborg
12	Copyright (C) 2013 Jari Häkkinen, Nicklas Nordborg
13
14	This file is part of BASE - BioArray Software Environment.
15	Available at http://base.thep.lu.se/
16
17	BASE is free software; you can redistribute it and/or
18	modify it under the terms of the GNU General Public License
19	as published by the Free Software Foundation; either version 3
20	of the License, or (at your option) any later version.
21
22	BASE is distributed in the hope that it will be useful,
23	but WITHOUT ANY WARRANTY; without even the implied warranty of
24	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25	GNU General Public License for more details.
26
27	You should have received a copy of the GNU General Public License
28	along with BASE. If not, see <http://www.gnu.org/licenses/>.
29	-->
30
31	<chapter id="installation">
32
33	<title>Installation and upgrade instructions</title>
34
35	<note>
36	<para>
37	These instructions apply only to the BASE release which this
38	document is a part of. The instructions here assume
39	that <ulink url="http://tomcat.apache.org/">Apache Tomcat 9 (or 8)</ulink> is used
40	on the server side. Other servlet engines may work but we only
41	test with Tomcat.
42	</para>
43	</note>
44
45	<sect1 id="installation.upgrade">
46	<title>Upgrade instructions</title>
47
48	<important id="installation.upgrade.important">
49	<title>Important information for upgrading to BASE 3.15</title>
50	<para>
51	This section list some important information that may or may not
52	apply when upgrading from the <emphasis>previous</emphasis> BASE
53	release to the current release (eg. 3.14 to 3.15). If you are
54	upgrading from a BASE installation that is older (3.0-3.13)
55	you should also read <xref linkend="appendix.update_warnings" />.
56	</para>
57
58	<bridgehead>Consider upgrading to Java 11 (OpenJDK)</bridgehead>
59	<para>
60	The next BASE release, BASE 3.16, will only support Java 11 or later. BASE 3.15 is
61	the last BASE version that supports Java 8. Our recommendation is to upgrade to
62	Java 11 as soon as possible. Note that Oracle no longer provide a free JDK or JRE.
63	Instead, OpenJDK has to be used, which can be downloaded from
64	<ulink url="https://openjdk.java.net/" />
65	</para>
66
67	<para>
68	If you experience any problems with BASE 3.15 and Java 8
69	you could try removing the listed files from the <filename>www/WEB-INF/lib</filename>
70	directory and then restart Tomcat. The listed JAR files contains functionality that
71	is included in core Java 8 but has been removed from Java 11.
72	</para>
73
74	<itemizedlist>
75	<listitem><filename>java.activation-api-1.2.0.jar</filename></listitem>
76	<listitem><filename>jaxb-api-2.3.1.jar</filename></listitem>
77	<listitem><filename>jaxb-core-2.3.0.1.jar</filename></listitem>
78	<listitem><filename>jaxb-impl-2.3.1.jar</filename></listitem>
79	</itemizedlist>
80
81	<bridgehead>Consider upgrading to Tomcat 9 and PostgreSQL 11</bridgehead>
82	<para>
83	We have started to test BASE with Tomcat 9 and PostgreSQL 11 and we have
84	not found any problems so far. For new installations we recommend that Tomcat 9
85	and PostgreSQL 11 is used. Official support for Tomcat 8 and PostgreSQL 9 will be
86	dropped in a future BASE version. For existing installations our recommendation
87	is to start planning for an upgrade to Tomcat 9 and PostgreSQL 11.
88	</para>
89
90	<bridgehead>Secondary storage support has been removed</bridgehead>
91	<para>
92	The <guilabel>Secondary storage</guilabel> feature has been removed.
93	Files that are located in the secondary storage will be marked as offline
94	by the upgrade script. The recommendation is to replace this feature with
95	an external files solution instead.
96	</para>
97
98	<bridgehead>Spot images support has been removed</bridgehead>
99	<para>
100	It is no longer possible to create new spot images or view existing
101	spot images via the BASE web client. Existing source image files and
102	zip archives with generated spot images have not been removed.
103	</para>
104
105	<bridgehead>Customizations made in Tomcat's global web.xml file</bridgehead>
106	<para>
107	In the configuration directory for Tomcat there is a <filename>web.xml</filename>
108	file that define global options for all web applications. The settings in this file
109	can be overridden per web application in the <filename>WEB-INF/classes/web.xml</filename>.
110	BASE 3.15 re-defines the <code>jsp</code> <sgmltag class="starttag">servlet</sgmltag>
111	definition to make sure that JSP files are compiled with proper settings. Changes that
112	have been made to the global <filename>web.xml</filename> file for the <code>jsp</code>
113	<sgmltag class="starttag">servlet</sgmltag> must be moved or copied to the
114	<filename>web.xml</filename> file for the BASE web application.
115	</para>
116
117	</important>
118
119	<para>
120	As always, backup your database before attempting an
121	upgrade. The BASE team performs extensive testing before
122	releasing a new version of BASE but there are always a
123	possibility for unexpected events during upgrades. In upgrades
124	requiring a change in the underlying database there is no
125	(supported) way to revert to a previous version of BASE using
126	BASE tools, you need to use your backup for this use case.
127	</para>
128
129	<para>
130	The strategy here is to install the new BASE release to another
131	directory than the one in use. This requires transfer of
132	configuration settings to the new install but more on that
133	below.
134	</para>
135
136	<variablelist>
137	<varlistentry>
138	<term>Shut down the Tomcat server</term>
139	<listitem>
140	<para>
141	If the BASE application is not shut down already, it is
142	time to do it now. Do something like <command>sudo
143	/etc/init.d/tomcat9.0 stop</command>
144	</para>
145
146	<tip>
147	<title>Notify logged in users!</title>
148	<para>
149	If there are users logged in to your BASE server, it may
150	be nice of you to notify them a few minutes prior to shutting
151	down the BASE server. See <xref linkend="installation.broadcast" />.
152	</para>
153	</tip>
154	</listitem>
155	</varlistentry>
156
157	<varlistentry>
158	<term>Rename your current server</term>
159	<listitem>
160	<para>
161	Rename your current BASE installation <command>mv
162	/path/to/base /path/to/base_old</command>.
163	</para>
164	</listitem>
165	</varlistentry>
166
167	<varlistentry>
168	<term>Download and unpack BASE</term>
169	<listitem>
170	<para>
171	There are several ways to download BASE. Please refer to
172	section <xref linkend="resources.home_page.download"/> for
173	information on downloading BASE, and select the item
174	matching your download option:
175	</para>
176
177	<variablelist>
178	<varlistentry>
179	<term><emphasis>Pre-compiled package</emphasis></term>
180	<listitem>
181	<para>
182	If you selected to download a pre-compiled package,
183	unpack the downloaded file with <command>tar zxpf
184	base-...tar.gz</command>.
185	</para>
186	</listitem>
187	</varlistentry>
188
189	<varlistentry>
190	<term><emphasis>Source package</emphasis></term>
191	<listitem>
192	<para>
193	If you selected to download a source package, unpack
194	the downloaded file with <command>tar zxpf
195	base-...src.tar.gz</command>. Change to the new
196	directory, and issue <command>ant
197	package.bin</command>. This will create a binary
198	package in the current directory. Unpack this new
199	package (outside of the source file hierarchy).
200	</para>
201	</listitem>
202	</varlistentry>
203
204	<varlistentry>
205	<term><emphasis>Subversion checkout</emphasis></term>
206	<listitem>
207	<para>
208	This option is for advanced users only and is not
209	covered here. Please refer to
210	<ulink url="http://base.thep.lu.se/wiki/BuildingBase" /> for information on
211	this download option.
212	</para>
213	</listitem>
214	</varlistentry>
215
216	</variablelist>
217	</listitem>
218
219	</varlistentry>
220
221	<varlistentry>
222	<term>Transfer files and settings</term>
223	<listitem>
224	<para>
225	Settings from the previous installation must be
226	transferred to the new installation. This is most easily
227	done by comparing the configuration files from the
228	previous install with the new files. Do not just copy the
229	old files to the new install since new options may have
230	appeared.
231	</para>
232	<para>
233	In the main BASE configuration file,
234	<filename><base-dir>/www/WEB-INF/classes/base.config</filename>,
235	fields that needs to be transferred are usually
236	<emphasis>db.username</emphasis>,
237	<emphasis>db.password</emphasis>,
238	and <emphasis>userfiles</emphasis>.
239	</para>
240	<para>
241	Local settings in the raw data
242	tables, <filename><base-dir>/www/WEB-INF/classes/raw-data-types.xml</filename>,
243	may need to be transferred. This also includes all files in
244	the <filename><base-dir>/www/WEB-INF/classes/raw-data-types</filename> and
245	<filename><base-dir>/www/WEB-INF/classes/extended-properties</filename>
246	directories.
247	</para>
248	</listitem>
249	</varlistentry>
250
251	<varlistentry>
252	<term>Updating database schema</term>
253	<listitem>
254	<para>
255	It is recommended that you also perform an update of your
256	database schema. Running the update scripts are not
257	always necessary when upgrading BASE, but the running the
258	update scripts are safe even in cases when there is no
259	need to run them. Change directory
260	to <filename
261	class="directory"><base-dir>/bin/</filename> and issue
262	<programlisting>
263	sh ./updatedb.sh [base_root_login] <emphasis>base_root_password</emphasis>
264	</programlisting>
265	where <emphasis>base_root_login</emphasis> is the login
266	for the root user and <emphasis>base_root_password</emphasis> is the
267	password. The login is optional. If not specified,
268	<constant>root</constant> is used as the login.
269	</para>
270	</listitem>
271	</varlistentry>
272
273	<varlistentry>
274	<term>Start Tomcat</term>
275	<listitem>
276	<para>
277	Start the Tomcat server: <command>sudo
278	/etc/init.d/tomcat9.0 start</command>
279	</para>
280	</listitem>
281	</varlistentry>
282
283	</variablelist>
284
285	<para>
286	Done! Upgrade of BASE is finished.
287	</para>
288
289	</sect1> <!-- Upgrade instructions -->
290
291	<sect1 id="installation.main">
292	<title>Installation instructions</title>
293
294	<variablelist>
295
296	<varlistentry>
297	<term>Java</term>
298	<listitem>
299	<para>
300	Download and install OpenJDK 11 (or later), available from
301	<ulink url="https://openjdk.java.net/" />.
302	</para>
303
304	<note>
305	<title>What about Java 8?</title>
306	<para>
307	BASE 3.15 is the last BASE version that supports Java 8. Starting
308	with BASE 3.16, Java 11 (or later) will be the only supported Java
309	version. Note that Oracle no longer provide a free JDK or JRE.
310	Instead, OpenJDK has to be used
311	</para>
312	</note>
313
314	</listitem>
315	</varlistentry>
316
317	<varlistentry>
318	<term>Set up an SQL database</term>
319	<listitem>
320	<para>
321	BASE
322	utilise <ulink
323	url="http://www.hibernate.org/">Hibernate</ulink> for
324	object persistence to a relational database. Hibernate
325	supports many database engines, but so far we only work
326	with <ulink url="http://www.postgresql.org/">PostgreSQL</ulink> (recommended)
327	and <ulink url="http://www.mysql.com">MySQL</ulink>.
328	</para>
329
330	<variablelist>
331	<varlistentry>
332	<term>PostgreSQL</term>
333	<listitem>
334	<para>
335	PostgreSQL 11 and 9 seems to be working very well with
336	BASE and Hibernate. We hve not tested with PostgreSQL 10
337	but don't have any reason to believe that it should not work.
338	Download and install PostgreSQL, available from
339	<ulink url="http://www.postgresql.org/" />. BASE comes
340	pre-configured for PostgreSQL so there is no need to change database
341	settings in the BASE configuration files.
342	</para>
343	</listitem>
344	</varlistentry>
345	<varlistentry>
346	<term>MySQL</term>
347	<listitem>
348	<para>
349	Download and install MySQL (tested with version
350	5.5), available from
351	<ulink url="http://www.mysql.com/" />. You need to
352	be able to connect to the server over TCP, so
353	the <emphasis>skip-networking</emphasis> option
354	must <command>not</command> be used. The InnoDB
355	table engine is also needed, so do not disable them
356	(not that you would) but you may want to tune the
357	InnoDB behaviour before creating BASE
358	databases.
359
360	You must edit your <filename><base-dir>/www/WEB-INF/classes/base.config</filename>
361	file. Uncomment the settings for MySQL and
362	comment out the settings for PostgreSQL.
363	</para>
364	</listitem>
365	</varlistentry>
366	</variablelist>
367
368	</listitem>
369	</varlistentry>
370
371	<varlistentry id="installation.main.database">
372	<term>BASE (database engine)</term>
373	<listitem>
374	<para>
375	The database names (base2 and base2dynamic are used here),
376	the <emphasis>db_user</emphasis>, and the
377	<emphasis>db_password</emphasis> can be changed during the
378	creation of the databases. It is recommended to change the
379	<emphasis>db_password</emphasis>, the other changes are
380	optional and can be made if desired. The database names,
381	the <emphasis>db_user</emphasis>, and the
382	<emphasis>db_password</emphasis> are needed below when
383	configuring BASE.
384	</para>
385	<note>
386	Note that the <emphasis>db_user</emphasis> name and
387	<emphasis>db_password</emphasis> set here is used
388	internally by BASE in communication with the database and
389	is never used to log on to the BASE application.
390	</note>
391	<important>
392	<title>The database must use the UTF-8 character set</title>
393	<para>
394	Otherwise there will be a problem with storing values
395	that uses characters outside the normal Latin1 range,
396	for example unit-related such as µ (micro) and Ω (ohm).
397	</para>
398	</important>
399	<variablelist>
400	<varlistentry>
401	<term>PostgreSQL</term>
402	<listitem>
403	<para>
404	Create a new database for BASE, and add a
405	<emphasis>db_user</emphasis> with the proper
406	privileges. To do this, log in as your PostgreSQL
407	user and issue these lines (omit comments):
408	<programlisting>createuser db_user -P
409	# this will prompt for an password for the new user, and issue two
410	# more question that should be answered with character 'n' for no.
411	createdb --owner db_user --encoding UTF8 base2
412	psql base2
413	# this will start the psql command line tool. Issue the next line
414	# within the tool and quit with a '\q'.
415	CREATE SCHEMA "dynamic" AUTHORIZATION "db_user";</programlisting>
416
417	If you download BASE (instructions below) you find a file
418	<filename><base-dir>/misc/sql/createdb.postgresql.sql</filename>
419	that contains the above statements and can be used
420	by the <filename>psql</filename> command-line tool:
421	<command>psql -f
422	<base-dir>/misc/sql/createdb.posgres.sql
423	template1</command> The header in the script file
424	contains further information about the script.
425	</para>
426	</listitem>
427	</varlistentry>
428	<varlistentry>
429	<term>MySQL</term>
430	<listitem>
431	<para>
432	Create a new database for BASE, and add a
433	<emphasis>db_user</emphasis> with at least
434	<emphasis>SELECT</emphasis>, <emphasis>INSERT</emphasis>,
435	<emphasis>UPDATE</emphasis>, <emphasis>DELETE</emphasis>,
436	<emphasis>CREATE</emphasis>, <emphasis>DROP</emphasis>,
437	<emphasis>INDEX</emphasis>,
438	and <emphasis>ALTER</emphasis> permission for the
439	new database. To do this, connect to your MySQL
440	server and issue the next lines:
441	<programlisting>CREATE DATABASE base2 DEFAULT CHARACTER SET utf8;
442	CREATE DATABASE base2dynamic DEFAULT CHARACTER SET utf8;
443	GRANT ALL ON base2.* TO db_user@localhost IDENTIFIED BY 'db_password';
444	GRANT ALL ON base2dynamic.* TO db_user@localhost;</programlisting>
445	</para>
446	<para>
447	If you download BASE (instructions below) you find a file
448	<filename><base-dir>/misc/sql/createdb.mysql.sql</filename>
449	that contains the above statements and can be used
450	by the <filename>mysql</filename> command-line tool
451	(remember to edit the <emphasis>db_user</emphasis>,
452	<emphasis>db_password</emphasis>, and the database
453	names in the script file before executing the
454	command): <command>mysql -uroot -p <
455	<base-dir>/misc/sql/createdb.mysql.sql</command>. The
456	header in the script file contains further
457	information about the script.
458	</para>
459	</listitem>
460	</varlistentry>
461	</variablelist>
462	</listitem>
463	</varlistentry>
464
465	<varlistentry>
466	<term>BASE (download and unpacking)</term>
467	<listitem>
468	<para>
469	<ulink
470	url="http://base.thep.lu.se/wiki/DownloadPage">Download
471	BASE</ulink> and unpack the downloaded file,
472	i.e. <command>tar zxpf base-...tar.gz</command>. If you
473	prefer to have the bleeding edge version of BASE, perform
474	a checkout of the source from the subversion repository
475	(subversion checkout instructions at
476	<ulink url="http://base.thep.lu.se/wiki/DownloadPage">BASE
477	trac site</ulink>).
478	</para>
479	<para>
480	If you choose to download the binary package, skip to the
481	next item. The rest of us, read on and compile BASE. If
482	you downloaded a source distribution, unpack the
483	downloaded file <command>tar zxpf
484	base-...src.tar.gz</command>, or you may have performed a
485	subversion checkout. Change to the 'root' base2
486	directory, and issue <command>ant
487	package.bin</command>. This will create a binary package
488	in the base2 'root' directory. Unpack this new package
489	(outside of the source file hierarchy), and from now on
490	the instructions are the same irrespective where you got
491	the binary package.
492	</para>
493	<para>
494	<emphasis>This section is intended for advanced users and
495	programmers only. In cases when you want to change the
496	BASE code and try out personalised features it may be
497	advantageous to run the tweaked BASE server against the
498	development tree. Instructions on how to accomplish this
499	is available in the
500	<ulink
501	url="http://base.thep.lu.se/wiki/BuildingBase">building
502	BASE document</ulink>. When you return back after
503	compiling in the subversion tree you can follow the
504	instruction here (with obvious changes to
505	paths).</emphasis>
506	</para>
507	</listitem>
508	</varlistentry>
509
510	<varlistentry>
511	<term>BASE (file storage setup)</term>
512	<listitem>
513	<para>
514	An area for file storage must be setup. Create an empty
515	directory in a proper location in your file system. Set
516	the owner of the created directory to the user the Tomcat
517	server will be running as. Tomcat server set up
518	instructions will follow below. Remember this location for
519	later use. The default location is <filename>/usr/local/base2/files</filename>.
520	</para>
521	</listitem>
522	</varlistentry>
523
524	<varlistentry>
525	<term>BASE (plug-in setup)</term>
526	<listitem>
527	<para>
528	An area for plug-in and extensions installation must be setup.
529	Create an empty directory in a proper location in your file system,
530	and make sure that the user that the Tomcat
531	server will be running as has read permission in this
532	directory. Tomcat server set up instructions will follow
533	below. Remember this location for
534	later use. The default location is <filename>/usr/local/base2/plugins</filename>.
535	</para>
536	</listitem>
537	</varlistentry>
538
539	<varlistentry id="installation.main.configuration">
540	<term>BASE (configuration)</term>
541	<listitem>
542	<para>
543	Basic BASE configuration is done in
544	<filename><base-dir>/www/WEB-INF/classes/base.config</filename>:
545	<itemizedlist>
546	<listitem>
547	Uncomment the database engine section that match your setup.
548	</listitem>
549	<listitem>
550	Modify the <emphasis>db.url</emphasis>,
551	<emphasis>db.dynamic.catalog</emphasis>,
552	<emphasis>db.username</emphasis>,
553	and <emphasis>db.password</emphasis> settings to match
554	your choice above. (<emphasis>database host and
555	database name (e.g. base2)</emphasis>,
556	<emphasis>e.g. base2dynamic</emphasis>,
557	<emphasis>db_user</emphasis>, and
558	<emphasis>db_password</emphasis>, respectively.)
559	</listitem>
560	<listitem>
561	Modify the <emphasis>userfiles</emphasis> setting to
562	match your choice in file storage setup above.
563	</listitem>
564	<listitem>
565	Modify the <emphasis>plugins.dir</emphasis> setting to
566	match your choice in plug-in setup above.
567	</listitem>
568	</itemizedlist>
569	See the <xref linkend="appendix.base.config"/> for more
570	information about the settings in
571	the <filename>base.config</filename> file.
572	</para>
573	<para>
574	<emphasis>Optional but recommended.</emphasis> You may want
575	to modify extended properties to fit your needs. Extended
576	properties are defined in
577	<filename><base-dir>/www/WEB-INF/classes/extended-properties.xml</filename>.
578	There is an
579	administrator <ulink
580	url="http://base.thep.lu.se/chrome/site/doc/historical/admin/extended-properties.html">document
581	discussing extended properties</ulink> available. If you
582	plan to perform a migration of a BASE version 1.2 database you
583	should probably not remove any extended properties
584	columns (this is not tested so the outcome is currently
585	undefined). However, adding columns does not affect
586	migration.
587	</para>
588	</listitem>
589	</varlistentry>
590
591	<varlistentry>
592	<term>BASE (database initialisation)</term>
593	<listitem>
594	<para>
595	Change directory to
596	<filename class="directory"><base-dir>/bin</filename>
597	and execute the following commands:
598	<programlisting>
599	sudo ./initdb.sh [base_root_login] base_root_password
600	</programlisting>
601	</para>
602
603	<para>
604	In the first command sudo is required because a file will
605	be created in the directory defined by
606	<emphasis>userfiles</emphasis> above. If the directory is
607	writable by you then sudo is not needed.
608	</para>
609
610	<important>
611	<para>
612	The <emphasis>base_root_login</emphasis> and
613	<emphasis>base_root_password</emphasis> you use here
614	is given to the BASE web application root user account.
615	The <emphasis>base_root_login</emphasis> is optional. If
616	not specified, <constant>root</constant> is used for
617	the login.
618	</para>
619	</important>
620
621	<para>
622	If the initialisation script fails, it is probably a
623	problem related to the underlying database. Make sure that
624	the database accepts network connection and make sure that
625	<emphasis>db_user</emphasis> has proper credentials. You
626	may also get a <emphasis>Permission denied</emphasis> on
627	file <filename>extension-settings.xml</filename> if you do
628	not have write permission to the directory defined by
629	variable <emphasis>userfiles</emphasis> in file
630	<filename>base.config</filename>. If the initialisation
631	fails on <filename>extension-settings.xml</filename> you
632	must drop the database and recreate the database as
633	described in <xref linkend="installation.main.database"/>.
634	</para>
635	</listitem>
636	</varlistentry>
637
638	<varlistentry>
639	<term>Tomcat</term>
640	<listitem>
641	<para>
642	Download and install Apache Tomcat 9
643	available from <ulink url="http://tomcat.apache.org" />.
644	</para>
645
646	<important>
647	<para>
648	As of BASE 3.15 we are recommending that Tomcat 9 is used for new
649	installations. BASE still supports Tomcat 8, but this will (officially)
650	be dropped in a future release.
651	</para>
652	</important>
653
654	<para>
655	There are a few configuration options that are needed to
656	make Tomcat work properly with BASE. The options are set in the
657	<code>CATALINA_OPTS</code> environment variable.
658	</para>
659
660	<itemizedlist>
661	<listitem>
662	<para>
663	Increase the amount of memory that Tomcat is allowed to use. The default setting is
664	usually not enough. To give Tomcat 1 gigabyte, use <code>-Xmx1G</code>.
665	</para>
666	</listitem>
667	<listitem>
668	<para>
669	Unless you have manually downloaded and installed JAI (Java Advanced
670	Imaging) native acceleration libraries (see <ulink
671	url="http://java.sun.com/javase/technologies/desktop/media/jai/" />)
672	it is a good idea to disable the native acceleration of JAI.
673	<code>-Dcom.sun.media.jai.disableMediaLib=true</code>
674	</para>
675	</listitem>
676	<listitem>
677	<para>
678	Enable headless mode if your are setting up a server which doesn't have
679	a display device connected to it. <code>-Djava.awt.headless=true</code>.
680	</para>
681	</listitem>
682	</itemizedlist>
683
684	<para>
685	Depending on your system there are probably several ways to set the
686	the <code>CATALINA_OPTS</code> variable. One suggestion is to add the following
687	line (as a single line) close to the top of the <filename>catalina.sh</filename>
688	script that comes with Tomcat (directory <filename
689	class="directory">bin</filename>):
690	<programlisting>CATALINA_OPTS="-Xmx1G
691	-Dcom.sun.media.jai.disableMediaLib=true
692	-Djava.awt.headless=true"</programlisting>
693	</para>
694	<para>
695	For more information about Tomcat options see
696	<ulink url="https://tomcat.apache.org/tomcat-9.0-doc/index.html" />.
697	</para>
698	</listitem>
699	</varlistentry>
700
701	<varlistentry>
702	<term>BASE and Tomcat</term>
703	<listitem>
704	<para>
705	Do the following:
706	<itemizedlist>
707	<listitem>
708	<para>
709	Either move the <filename
710	class="directory"><base-dir>/www</filename>
711	directory to the Tomcat <filename
712	class="directory">webapps</filename> directory or
713	create a symbolic link from the Tomcat <filename
714	class="directory">webapps</filename> directory to
715	the <filename
716	class="directory"><base-dir>/www</filename>
717	directory
718	<programlisting>cd /path/to/tomcat/webapps
719	ln -s /path_to_base/www base2</programlisting>
720	</para>
721	</listitem>
722	<listitem>
723	<para>
724	Make sure that user Tomcat is running as can read
725	all objects in the directory defined by
726	<emphasis>plugins.dir</emphasis> in file
727	<filename>base.config</filename>.
728	</para>
729	</listitem>
730	<listitem>
731	<para>
732	Make sure that user Tomcat is running as owns (i.e.,
733	can read, write, delete and create) all objects in
734	the directory, as well as the directory itself,
735	defined by <emphasis>userfiles</emphasis> in file
736	<filename>base.config</filename>.
737	</para>
738	</listitem>
739	<listitem>
740	<para>
741	If you plan to install extensions you should make
742	sure that the <filename
743	class="directory"><base-dir>/www/extensions</filename>
744	directory is writable by the user account Tomcat is
745	running as.
746	</para>
747	</listitem>
748	</itemizedlist>
749	</para>
750	<para>
751	and finalise with start, or restart, Tomcat, and try
752	http://hostname:8080/base2 (change
753	<emphasis>hostname</emphasis> to your hostname and
754	<emphasis>base2</emphasis> if you selected another name
755	for the BASE Tomcat application) in your favourite
756	browser. The BASE log-in page should appear after a few
757	seconds.
758	</para>
759	</listitem>
760	</varlistentry>
761
762	<varlistentry>
763	<term>BASE, Apache, and Apache/Tomcat connector</term>
764	<listitem>
765	<para>
766	<emphasis>This step is optional</emphasis>.
767	</para>
768	<para>
769	If you want run the Tomcat server through the Apache web
770	server, you need to install the Apache version 2 web
771	server, available
772	from <ulink url="http://httpd.apache.org/" />,
773	and a apache-tomcat connector, available
774	from <ulink
775	url="http://tomcat.apache.org/connectors-doc/index.html" />
776	</para>
777	</listitem>
778	</varlistentry>
779
780	<varlistentry>
781	<term>Setup done!</term>
782	<listitem>
783	<para>
784	Happy BASEing. Now you can log on to your BASE server as
785	user <emphasis>root</emphasis> (use
786	the <emphasis>base_root_password</emphasis> from the
787	database initialisation step above). You should begin with
788	creating a couple user accounts, for more information on
789	how to create user accounts please refer to
790	<xref linkend="accounts"/>.
791	</para>
792	</listitem>
793	</varlistentry>
794
795	</variablelist>
796
797	</sect1> <!-- Installation instructions -->
798
799	<sect1 id="installation.jobagents">
800	<title>Installing job agents</title>
801
802	<para>
803	It is important to understand that the BASE application can be
804	spread on to several computers. The main BASE application is
805	serving HTTP requests, the underlying database engine is
806	providing storage and persistence of data, and job agents can be
807	installed on computers that will serve the BASE installation
808	with computing power and perform analysis and run plug-ins. In a
809	straight forward setup one computer provides all services needed
810	for running BASE. From this starting point it is easy to add
811	computers to shares load from the BASE server by installing job
812	agents on these additional computers.
813	</para>
814
815	<para>
816	A job agent is a program running on a computer regularly
817	checking the BASE job queue for jobs awaiting execution. When
818	the job agent finds a job that it is enabled to execute, it
819	loads the plug-in and executes it. Job agents will in this way
820	free up resources on the BASE application server, and thus allow
821	the BASE server to concentrate on serving web pages. Job agents
822	are optional and must be installed and setup
823	separately. However, BASE is prepared for job agent setup and to
824	utilise the agents, but the agent are not required.
825	</para>
826
827	<para>
828	A job agent supports many configuration options that are not
829	supported by the internal job queue. For example, you can
830	<itemizedlist>
831	<listitem>
832	<para>
833	Specify exactly which plug-ins each job agent should be
834	able to execute.
835	</para>
836	</listitem>
837	<listitem>
838	<para>
839	Give some plug-ins higher priority than other plug-ins.
840	</para>
841	</listitem>
842	<listitem>
843	<para>
844	Specify which users/groups/projects should be able to use
845	a specific job agent.
846	</para>
847	</listitem>
848	<listitem>
849	<para>
850	Override memory settings and more for each plug-in.
851	</para>
852	</listitem>
853	<listitem>
854	<para>
855	Execute plug-ins in separate processes. Thus, a misbehaving
856	plug-in cannot bring the main application server down.
857	</para>
858	</listitem>
859	<listitem>
860	<para>
861	Add more computers with job agents as needed.
862	</para>
863	</listitem>
864	</itemizedlist>
865	All these options make it possible to create a very flexible
866	setup. For example one job agent can be assigned for importing
867	data only, another job agent can be assigned for running
868	analysis plug-ins for specific project only, and a third may be a
869	catch-all job agent that performs all low-priority jobs.
870	</para>
871
872	<sect2 id="installation.jobagents.serverside">
873	<title>BASE application server side setup</title>
874	<para>
875	<variablelist>
876	<varlistentry>
877	<term>Make sure the internal job queue doesn't execute all plug-ins</term>
878	<listitem>
879	<para>
880	The setting <command>jobqueue.internal.runallplugins</command>
881	should be set to <command>false</command> for the
882	BASE server. This setting is found in
883	the <filename><base-dir>/www/WEB-INF/classes/base.config</filename>
884	file. The changes will not take effect until the
885	application server is restarted.
886	</para>
887
888	</listitem>
889	</varlistentry>
890	<varlistentry id="installation.jobagent.user_account">
891	<term>Enable the job agent user account</term>
892	<listitem>
893	<para>
894	During installation of BASE a user account is created
895	for the job agent. This account is used by the job
896	agents to log on to BASE. The account is disabled by
897	default and must be enabled. Enable the account and
898	set a password using the BASE web interface.
899	The same password must also be set in the
900	<filename>jobagent.properties</filename> file, see
901	item
902	<xref linkend="installation.jobagent.client.properties"/>
903	below.
904	</para>
905	</listitem>
906	</varlistentry>
907	</variablelist>
908	</para>
909	</sect2>
910
911	<sect2 id="installation.jobagents.database">
912	<title>Database server setup</title>
913	<para>
914	<variablelist>
915	<varlistentry id="installation.jobagent.database">
916	<term>Create a user account on the database</term>
917	<listitem>
918	<para>
919	This is the similar to granting database access for
920	the BASE server user in the in the regular BASE
921	installation, cf.
922	<xref
923	linkend="installation.main.database"/>.
924	You must create an account in the database that is
925	allowed to connect from the job agent server. MySQL
926	example:
927	<programlisting>GRANT ALL ON base2.* TO db_user@job.agent.host IDENTIFIED BY 'db_password';
928	GRANT ALL ON base2dynamic.* TO db_user@job.agent.host;</programlisting>
929
930	Replace <command>job.agent.host</command> with the
931	host name of the server that is going to run the job
932	agent. You should also set password. This password is
933	used in item
934	<xref linkend="installation.jobagent.client.config"/>
935	below in job agent server setup. You can use the same
936	database user and password as in the regular database
937	setup.
938	</para>
939	</listitem>
940	</varlistentry>
941	</variablelist>
942	</para>
943	</sect2>
944
945	<sect2 id="installation.jobagents.client">
946	<title>Job agent client setup</title>
947	<para>
948	<variablelist>
949	<varlistentry>
950	<term>Download and unpack a regular BASE distribution</term>
951	<listitem>
952	<para>
953	You <emphasis>must</emphasis> use the same version on
954	the web server and all job agents. You find the
955	downloads at
956	<ulink
957	url="http://base.thep.lu.se/wiki/DownloadPage">http://base.thep.lu.se/wiki/DownloadPage</ulink>
958	</para>
959	</listitem>
960	</varlistentry>
961	<varlistentry id="installation.jobagent.client.config">
962	<term>Edit the <filename>base.config</filename> file</term>
963	<listitem>
964	<para>
965	The <filename><base-dir>/www/WEB-INF/classes/base.config</filename>
966	file must be configured as in regular BASE
967	installation, cf.
968	<xref
969	linkend="installation.main.configuration"/>,
970	to use the same database as the web server
971	application. The most important settings are
972	<itemizedlist>
973	<listitem>
974	<para>
975	<command>db.username</command>: The database
976	user you created in item
977	<xref
978	linkend="installation.jobagent.database"/>
979	above.
980	</para>
981	</listitem>
982	<listitem>
983	<para>
984	<command>db.password</command>: The password for
985	the user.
986	</para>
987	</listitem>
988	<listitem>
989	<para>
990	<command>db.url</command>: The connection url to
991	the database.
992	</para>
993	</listitem>
994	<listitem>
995	<para>
996	<command>userfiles</command>: The path to the
997	directory where user files are located. This
998	directory must be accessible from all job
999	agents, i.e., by nfs or other file system
1000	sharing method.
1001	</para>
1002	</listitem>
1003	<listitem>
1004	<para>
1005	<command>plugins.dir</command>: The path to the
1006	directory where plug-ins are located. This
1007	directory must be accessible from all job
1008	agents, i.e., by nfs or other file system
1009	sharing method.
1010	</para>
1011	</listitem>
1012	</itemizedlist>
1013	See the <xref linkend="appendix.base.config"/> for
1014	more information about the settings in
1015	the <filename>base.config</filename> file.
1016	</para>
1017	</listitem>
1018	</varlistentry>
1019	<varlistentry id="installation.jobagent.client.properties">
1020	<term>Edit
1021	the <filename>jobagent.properties</filename> file</term>
1022	<listitem>
1023	<para>
1024	The <filename><base-dir>/www/WEB-INF/classes/jobagent.properties</filename>
1025	file contains settings for the job agent. The most
1026	important ones to specify value for are
1027	<itemizedlist>
1028	<listitem>
1029	<para>
1030	<command>agent.password</command>: The password
1031	you set for the job agent user account in item
1032	<xref
1033	linkend="installation.jobagent.user_account"/>
1034	above.
1035	</para>
1036	</listitem>
1037	<listitem>
1038	<para>
1039	<command>agent.id</command>: An ID that must be
1040	unique for each job agent accessing the BASE application.
1041	</para>
1042	</listitem>
1043	<listitem>
1044	<para>
1045	<command>agent.remotecontrol</command>: The
1046	name or ip address of the web server if you want it
1047	to be able to display info about running
1048	jobs. The job agent will only allow connections
1049	from computers specified in this setting.
1050	</para>
1051	</listitem>
1052	</itemizedlist>
1053	</para>
1054	<para>
1055	The <filename>jobagent.properties</filename> file
1056	contains many more configuration options. See
1057	the <xref linkend="appendix.jobagent.properties"/> for
1058	more information.
1059	</para>
1060	</listitem>
1061	</varlistentry>
1062	<varlistentry>
1063	<term>Register the job agent</term>
1064	<listitem>
1065	<para>
1066	From the <filename>bin</filename> directory, register
1067	the job agent with
1068	<programlisting>./jobagent.sh register</programlisting>
1069	</para>
1070	</listitem>
1071	</varlistentry>
1072	<varlistentry>
1073	<term>Start the job agent</term>
1074	<listitem>
1075	<para>
1076	From the <filename>bin</filename> directory, start the
1077	job agent with
1078	<programlisting>./jobagent.sh start &</programlisting>
1079	</para>
1080	<para>
1081	See the <xref linkend="appendix.jobagent.sh"/>
1082	for more information about what you can do
1083	with the job agent command line interface.
1084	</para>
1085	</listitem>
1086	</varlistentry>
1087	</variablelist>
1088	</para>
1089	</sect2>
1090
1091
1092	<sect2 id="installation.jobagents.configuration">
1093	<title>Configuring the job agent</title>
1094
1095	<para>
1096	A job agent will not execute a plug-in unless the administrator
1097	has configured the job agent to do so. There are two things that
1098	must be done:
1099	</para>
1100
1101	<itemizedlist>
1102	<listitem>
1103	<para>
1104	Share the job agent to the users, groups and project that should be
1105	able to use it. If the job agent is not shared, only the owner of
1106	job agent is allowed to use it. Use the regular <guilabel>Share</guilabel>
1107	functionality to specify which users/groups/projects
1108	should be able to use the job agent. You must give
1109	them at least <command>USE</command> permission.
1110	To give all users permission to the job agent share it
1111	to the <command>EVERYONE</command> group.
1112	</para>
1113	</listitem>
1114
1115	<listitem>
1116	<para>
1117	Selecting plug-ins that the job agent should handle. This can be
1118	done either from the plug-in pages or from the job agent pages. To register
1119	a plug-in with one or more job agents from the plug-in pages, go
1120	to the edit view of the plug-in and select the <guilabel>Job
1121	agents</guilabel> tab. To do the same from the job agent pages,
1122	go to the edit view of the job agent and select
1123	the <guilabel>Plugins</guilabel> tab. The registration dialogues
1124	are very similar but only the plug-in side of registration is
1125	described here. The major difference is that it is not possible
1126	to enable/disable the internal job queue for plug-in when using
1127	the jobagent side of the registration.
1128	</para>
1129	</listitem>
1130	</itemizedlist>
1131
1132	<figure id="plugins.figures.jobagents">
1133	<title>Select job agents for a plug-in</title>
1134	<screenshot>
1135	<mediaobject>
1136	<imageobject><imagedata
1137	scalefit="1" width="100%"
1138	fileref="figures/plugin_jobagents.png" format="PNG"
1139	/></imageobject>
1140	</mediaobject>
1141	</screenshot>
1142	</figure>
1143
1144	<helptext external_id="plugindefinition.jobagents"
1145	title="Job agents">
1146
1147	<para>
1148	Use this tab to specify which job agents the plug-in is
1149	installed and allowed to be executed on.
1150	</para>
1151
1152	<variablelist>
1153	<varlistentry>
1154	<term><guilabel>Run this plugin on</guilabel></term>
1155	<listitem>
1156	<para>
1157	You may select if the internal job queue should execute the
1158	plug-in or not.
1159	</para>
1160	</listitem>
1161	</varlistentry>
1162	<varlistentry>
1163	<term><guilabel>Job agents</guilabel></term>
1164	<listitem>
1165	<para>
1166	A list with the job agents where the plug-in is installed and
1167	allowed to be executed. Select a job agent in this list to display
1168	more configuration options for the plug-in.
1169	</para>
1170	</listitem>
1171	</varlistentry>
1172	<varlistentry>
1173	<term><guilabel>Add job agents</guilabel></term>
1174	<listitem>
1175	<para>
1176	Use this button to open a pop-up window for selecting
1177	job agents.
1178	</para>
1179	</listitem>
1180	</varlistentry>
1181	<varlistentry>
1182	<term><guilabel>Remove</guilabel></term>
1183	<listitem>
1184	<para>
1185	Remove the selected plug-in from the list.
1186	</para>
1187	</listitem>
1188	</varlistentry>
1189	</variablelist>
1190
1191	<para>
1192	The following properties are only displayed when a
1193	job agent has been selected in the list. Each job agent may have it's
1194	own settings of these properties. If you leave the values unspecified
1195	the job agent will use the default values specified on the
1196	<guilabel>Plugin</guilabel> tab.
1197	</para>
1198
1199	<variablelist>
1200	<varlistentry>
1201	<term><guilabel>Max memory</guilabel></term>
1202	<listitem>
1203	<para>
1204	The maximum amount of memory the plug-in is allowed to use.
1205	Add around 40MB for the Java run-time environment and BASE.
1206	If not specified Java will choose it's default value which is 64MB.
1207	</para>
1208	</listitem>
1209	</varlistentry>
1210	<varlistentry>
1211	<term><guilabel>Trusted</guilabel></term>
1212	<listitem>
1213	<para>
1214	If the plug-in should be executed in a protected or
1215	unprotected environment. Currently, BASE only supports
1216	running plug-ins in an unprotected environment.
1217	</para>
1218	</listitem>
1219	</varlistentry>
1220	<varlistentry>
1221	<term><guilabel>Priority boost</guilabel></term>
1222	<listitem>
1223	<para>
1224	Used to give a plug-in higher priority in the job queue.
1225	Values between 0 and 10 are allowed. A higher value will
1226	give the plug-in higher priority. The priority boost is useful
1227	if we, for example, want to use one server mainly for importing
1228	data. By giving all import plugins a priority boost they will
1229	be executed before all other jobs, which will have to wait
1230	until there are no more waiting imports.
1231	</para>
1232	</listitem>
1233	</varlistentry>
1234	</variablelist>
1235
1236	<seeother>
1237	<other external_id="plugindefinition.edit">Plug-in properties</other>
1238	<other external_id="plugindefinition.edit.permissions">Plug-in permissions</other>
1239	</seeother>
1240	</helptext>
1241	</sect2>
1242
1243	</sect1> <!-- job agent setup -->
1244
1245	<sect1 id="installation.serverconfigurations">
1246	<title>Server configurations</title>
1247	<para>
1248	Some server configurations can be done when the installation process is finished and
1249	BASE is up and running. Log into BASE with administration rights and then
1250	open the configuration dialog from menu
1251	<menuchoice>
1252	<guimenu>Administrate</guimenu>
1253	<guimenuitem>Server settings</guimenuitem>
1254	</menuchoice>.
1255	Each tab in the configuration dialog-window is described below.
1256	</para>
1257
1258	<figure id="installation.figures.serverconfiguration">
1259	<title>Server configuration</title>
1260	<screenshot>
1261	<mediaobject>
1262	<imageobject><imagedata
1263	fileref="figures/server_configuration.png" format="PNG"
1264	/></imageobject>
1265	</mediaobject>
1266	</screenshot>
1267	</figure>
1268
1269	<variablelist>
1270	<varlistentry>
1271	<term>
1272	<guilabel>File transfer</guilabel>
1273	</term>
1274	<listitem>
1275	<helptext external_id="serverconfig.filetransfer" title="File transfer rate">
1276	<variablelist>
1277	<varlistentry>
1278	<term><guilabel>Max upload rate</guilabel></term>
1279	<listitem>
1280	<para>
1281	This is a limit of how many bytes of data that should be
1282	transferred per second when uploading files to BASE. Prefixes
1283	like k, M or G can be used for larger values, just like
1284	described in the tab. The limit is per ongoing upload
1285	and the default value is 100MB/s.
1286	</para>
1287	</listitem>
1288	</varlistentry>
1289	<varlistentry>
1290	<term><guilabel>Max download rate</guilabel></term>
1291	<listitem>
1292	<para>
1293	This is a limit of how many bytes of data that should be
1294	transferred per second when downloading files from BASE. Prefixes
1295	like k, M or G can be used for larger values. The limit is per ongoing
1296	download and the default value is unlimited.
1297	</para>
1298	</listitem>
1299	</varlistentry>
1300	<varlistentry>
1301	<term><guilabel>Unlimited</guilabel></term>
1302	<listitem>
1303	<para>
1304	Check one or both to not limit the upload/download transfer rate.
1305	In this case, the Internet connection of the server is the limit.
1306	</para>
1307	</listitem>
1308	</varlistentry>
1309	</variablelist>
1310	</helptext>
1311	</listitem>
1312	</varlistentry>
1313	<varlistentry>
1314	<term>
1315	<guilabel>About</guilabel>
1316	</term>
1317	<listitem>
1318	<helptext external_id="serverconfig.about"
1319	title="Information about the server">
1320	<variablelist>
1321	<varlistentry>
1322	<term><guilabel>Administrator name</guilabel></term>
1323	<listitem>
1324	<para>
1325	Name of the responsible administrator. The name is displayed
1326	at the bottom of each page in BASE and in the about-dialog.
1327	</para>
1328	</listitem>
1329	</varlistentry>
1330	<varlistentry>
1331	<term><guilabel>Administrator email</guilabel></term>
1332	<listitem>
1333	<para>
1334	An email which the administrator can be contacted on. The
1335	administrator name, visible at the bottom of each page, will
1336	be linked to this email address.
1337	</para>
1338	</listitem>
1339	</varlistentry>
1340	<varlistentry>
1341	<term><guilabel>About</guilabel></term>
1342	<listitem>
1343	<para>
1344	Text written in this field is displayed in the
1345	<guilabel>About this server</guilabel> section on the login
1346	page and in the about-dialog window. We recommend changing the
1347	default Latin text to something meaningful, or remove it
1348	to hide the section completely.
1349	</para>
1350	</listitem>
1351	</varlistentry>
1352	</variablelist>
1353	</helptext>
1354	</listitem>
1355	</varlistentry>
1356	<varlistentry>
1357	<term>
1358	<guilabel>Get account</guilabel>
1359	</term>
1360	<listitem>
1361	<helptext external_id="serverconfig.getaccount"
1362	title="Instructions to get an account">
1363	<para>
1364	A description what a user should do to get
1365	an account on the particular BASE server. This text is linked
1366	to the <guilabel>Get an account!</guilabel> link on the login
1367	page. We recommend that the Latin text is replaced with some useful
1368	information, or that it is removed to hide the link.
1369	</para>
1370	</helptext>
1371	</listitem>
1372	</varlistentry>
1373	<varlistentry>
1374	<term>
1375	<guilabel>Forgotten password</guilabel>
1376	</term>
1377	<listitem>
1378	<helptext external_id="serverconfig.password"
1379	title="Instructions when password is forgotten.">
1380	<para>
1381	A description what a user should do if the password is forgotten.
1382	This text is linked
1383	to the <guilabel>Forgot your password?</guilabel> link on the login
1384	page. We recommend that the Latin text is replaced with some useful
1385	information, or that it is removed to hide the link.
1386	</para>
1387	</helptext>
1388	</listitem>
1389	</varlistentry>
1390	<varlistentry>
1391	<term>
1392	<guilabel>Links</guilabel>
1393	</term>
1394	<listitem>
1395	<helptext external_id="serverconfig.links" title="Configurable links">
1396	<para>
1397	External configurable link-types inside BASE.
1398	<note>
1399	<para>
1400	Only link-types that have been set will be visible in the web
1401	client.
1402	</para>
1403	</note>
1404	</para>
1405	<variablelist>
1406	<varlistentry>
1407	<term><guilabel>Help</guilabel></term>
1408	<listitem>
1409	<para>
1410	Links to where the help text is located. By default
1411	this is set to the documentation for the latest released
1412	BASE version on the BASE web site,
1413	<ulink
1414	url="http://base.thep.lu.se/chrome/site/doc/html/index.html">
1415	http://base.thep.lu.se/chrome/site/doc/html/index.html</ulink>.
1416
1417	If you want the documentation for a specific version you will
1418	have to setup a site for that yourself and then change the link
1419	to that site. The documentation is included in the downloaded package
1420	in the directory <filename><basedir>/doc/html</filename>.
1421	</para>
1422	</listitem>
1423	</varlistentry>
1424	<varlistentry>
1425	<term>
1426	<guilabel>FAQ</guilabel>
1427	</term>
1428	<listitem>
1429	<para>Where frequently asked questions can be found. Empty by default.</para>
1430	</listitem>
1431	</varlistentry>
1432	<varlistentry>
1433	<term>
1434	<guilabel>Report a bug</guilabel>
1435	</term>
1436	<listitem>
1437	<para>
1438	Where the user could report bugs, feature request or
1439	perhaps other feedback that concerns the program. As default
1440	this is set to the feedback section on BASE web site,
1441	<ulink url="http://base.thep.lu.se/#Feedback">http://base.thep.lu.se/#Feedback</ulink>.
1442	Note that users must login in order to submit information.
1443	</para>
1444	</listitem>
1445	</varlistentry>
1446	</variablelist>
1447	</helptext>
1448	</listitem>
1449	</varlistentry>
1450	</variablelist>
1451
1452	<sect2 id="installation.broadcast">
1453	<title>Sending a broadcast message to logged in users</title>
1454
1455	<para>
1456	It is possible to send a message to all logged in user.
1457	Open the
1458	<menuchoice>
1459	<guimenu>Administrate</guimenu>
1460	<guimenuitem>Broadcast message</guimenuitem>
1461	</menuchoice> dialog box.
1462	</para>
1463
1464	<figure id="installation.figures.broadcast">
1465	<title>Broadcast message</title>
1466	<screenshot>
1467	<mediaobject>
1468	<imageobject><imagedata
1469	fileref="figures/broadcast_message.png" format="PNG"
1470	/></imageobject>
1471	</mediaobject>
1472	</screenshot>
1473	</figure>
1474
1475	<helptext external_id="broadcast.message" title="Broadcast message">
1476	<para>
1477	This dialog allows you to specify a message that is sent to all
1478	logged in users as well as on the login form. It is also possible
1479	to "disable" login.
1480	</para>
1481	<variablelist>
1482	<varlistentry>
1483	<term><guilabel>Title</guilabel></term>
1484	<listitem>
1485	<para>
1486	The title of the message. It should be a short and concise to
1487	avoid confusion. The title will be displayed on a lot of places
1488	and a user may have to click on it to read the more detailed
1489	message.
1490	</para>
1491	</listitem>
1492	</varlistentry>
1493	<varlistentry>
1494	<term><guilabel>Disable login</guilabel></term>
1495	<listitem>
1496	<para>
1497	Mark this check-box to try to prevent new users from logging in. To
1498	avoid problems that can be caused by blocking the server admin out,
1499	the login is not completely disabled. Any user can still login but
1500	only after by-passing several warnings.
1501	</para>
1502	</listitem>
1503	</varlistentry>
1504	<varlistentry>
1505	<term><guilabel>Message</guilabel></term>
1506	<listitem>
1507	<para>
1508	If needed, a longer message giving more information. Users may
1509	have to click on a link to be able to see the complete message.
1510	</para>
1511	</listitem>
1512	</varlistentry>
1513	</variablelist>
1514
1515	<note>
1516	The message will be enabled until it is manually removed by saving
1517	an empty form, or until the Tomcat server is restarted. Since the
1518	message is only kept in memory, a restart will always remove it.
1519	</note>
1520
1521	</helptext>
1522
1523	</sect2>
1524
1525	</sect1>
1526
1527	<sect1 id="installation.migrate">
1528	<title>Migrating from MySQL to PostgreSQL</title>
1529
1530	<para>
1531	It is possible to migrate a BASE installation on a MySQL database to a
1532	PostgreSQL database. In a real-world scenario a migration is probably coupled
1533	with a hardware upgrade, i.e. the MySQL installation is on one (the old) server
1534	and the PostgreSQL installation is on another (the new) server. While
1535	this is not any problem per se, it requires a few extra steps to ensure that
1536	everything has been moved to the new server. There are three main steps involved:
1537	</para>
1538
1539	<variablelist>
1540	<varlistentry>
1541	<term>Export</term>
1542	<listitem>
1543	<para>
1544	The first step is to export all data in the existing database. Use
1545	the following procedure:
1546	</para>
1547
1548	<orderedlist>
1549	<listitem>
1550	<para>
1551	Upgrade to the latest BASE release. This is recommended since
1552	it probably has fewer bugs.
1553	</para>
1554	</listitem>
1555
1556	<listitem>
1557	<para>
1558	Make sure that no other processes are writing to the database
1559	when the export is running. Shut down Tomcat and all job agents.
1560	It may also be a good idea to ensure that no backup scripts or
1561	other external programs are reading from the database at the same
1562	time. If the database is large, this may affect performance due to
1563	increased disk I/O.
1564	</para>
1565	</listitem>
1566
1567	<listitem>
1568	<para>
1569	Create a temporary working directory in a suitable
1570	location. This directory will be used for storing the
1571	exported data. Disk I/O performance may be better if
1572	this directory is on a different disk than what the
1573	database is using. Ensure that the location has enough
1574	free space to hold all data from the BASE database. The dump
1575	typically uses less than 10% of the disk space used by the
1576	MySQL tables.
1577	</para>
1578	</listitem>
1579
1580	<listitem>
1581	<para>
1582	Make sure that you have configured migration-specific settings
1583	in the <filename>base.config</filename> file. In most cases the
1584	default settings should be good, but if you are experiencing
1585	performance problems it may be necessary to change some settings.
1586	See <xref linkend="appendix.base.config.migrate" /> for more
1587	information.
1588	</para>
1589	</listitem>
1590
1591	<listitem>
1592	<para>
1593	Start the export by changing to the <filename
1594	class="directory"><base-dir>/bin/</filename>
1595	directory and execute:
1596	</para>
1597	<programlisting>
1598	./migrate.sh export <replaceable>/path/to/migration/dir</replaceable>
1599	</programlisting>
1600	<para>
1601	where <replaceable>/path/to/migration/dir</replaceable>
1602	is replaced with the path to the working directory created above.
1603	Depending on the size of the BASE installation the export may
1604	take a long time.
1605	</para>
1606	</listitem>
1607	</orderedlist>
1608
1609	<note>
1610	<para>
1611	Make sure that the migration working directory is empty to perform
1612	a full export. Existing files in the directory causes the corresponding
1613	tables to be skipped. This can be useful when debugging and after a
1614	server crash, since the export will resume where it stopped. Just make
1615	sure that the database hasn't been modified in the meantime.
1616	</para>
1617	</note>
1618	<warning>
1619	<para>
1620	When exporting, make sure that no other process is updating the
1621	database since that may create an inconsistent snapshot. The
1622	export process does not lock the database or take any other means
1623	to protect it against concurrent modifications.
1624	</para>
1625	</warning>
1626	</listitem>
1627	</varlistentry>
1628
1629	<varlistentry>
1630	<term>Moving data</term>
1631	<listitem>
1632	<para>
1633	This step is about moving the data from the old BASE server to the
1634	new BASE server. If the migration is taking place on a single server,
1635	this step can probably be skipped.
1636	</para>
1637
1638	<orderedlist>
1639	<listitem>
1640	<para>
1641	Download and unpack the BASE software on the new server. Make sure that you are
1642	using the same version as on the old server. It is also important that
1643	the database is identically configured. Pay special attention
1644	to the <filename>extended-properties.xml</filename> and
1645	<filename>raw-data-types.xml</filename> files and any files
1646	in the <filename
1647	class="directory"><base-dir>/WEB-INF/classes/extended-properties</filename>
1648	and <filename
1649	class="directory"><base-dir>/WEB-INF/classes/raw-data-types</filename>
1650	directories.
1651	The import program protects against some mistakes by comparing
1652	the column names from the export with the column names in the new
1653	database, but it will, for example, not check that data types match.
1654	</para>
1655
1656	<tip>
1657	The easiest way to do this is to simply copy the BASE installation
1658	from the old server to the new server. Then, go through the
1659	configuration files and make sure that paths are correct.
1660	</tip>
1661
1662	</listitem>
1663
1664	<listitem>
1665	<para>
1666	Move user files from the old server to the new server. Make sure that
1667	the <property>userfiles</property> setting in <filename>base.config</filename>
1668	is correct.
1669	</para>
1670	</listitem>
1671
1672	<listitem>
1673	<para>
1674	Move plug-ins from the old server to the new server. Make sure that
1675	the <property>plugins.dir</property> setting in <filename>base.config</filename>
1676	is correct.
1677	</para>
1678	</listitem>
1679
1680	<listitem>
1681	<para>
1682	Check other settings in <filename>base.config</filename> and
1683	other configuration files for settings that may be affected by
1684	the move.
1685	</para>
1686	</listitem>
1687
1688	</orderedlist>
1689
1690	</listitem>
1691	</varlistentry>
1692
1693	<varlistentry>
1694	<term>Import</term>
1695	<listitem>
1696	<para>
1697	When everything has been moved and is properly configured it is
1698	time to start with the import.
1699	</para>
1700
1701	<orderedlist>
1702	<listitem>
1703	<para>
1704	Create a new empty database following the
1705	instructions in <xref linkend="installation.main.database" />.
1706	Make the corresponding changes in <filename>base.config</filename>
1707	so that the BASE installation points to the new database.
1708	Also, make sure that you have configured migration-specific settings
1709	in the <filename>base.config</filename> file. In most cases the
1710	default settings should be good, but if you are experiencing
1711	performance problems it may be necessary to change some settings.
1712	See <xref linkend="appendix.base.config.migrate" /> for more
1713	information.
1714	</para>
1715	</listitem>
1716
1717	<listitem>
1718	<para>
1719	Read the
1720	<ulink url="https://www.postgresql.org/docs/11/populate.html">https://www.postgresql.org/docs/11/populate.html</ulink>
1721	document from the PostgreSQL documentation and consider implementing some
1722	of the tips. The migration script makes sure that no indexes or foreign
1723	key constraints are active during the data import, but the tips about memory,
1724	checkpoint intervals, WAL archiving, etc. (section 14.4.5 and on) can be useful.
1725	It may also be a good idea to turn off the auto-vacuum daemon during the import.
1726	</para>
1727	</listitem>
1728
1729	<listitem>
1730	<para>
1731	Start the import by changing to the <filename
1732	class="directory"><base-dir>/bin/</filename>
1733	directory and execute:
1734	</para>
1735	<programlisting>
1736	./migrate.sh import <replaceable>/path/to/migration/dir</replaceable>
1737	</programlisting>
1738	<para>
1739	where <replaceable>/path/to/migration/dir</replaceable>
1740	is replaced with the path to the directory where
1741	the exported data is stored. Depending on
1742	the size of the BASE installation this may take a long time.
1743	</para>
1744
1745	<note>
1746	<title>Installations with separate web and database servers</title>
1747	<para>
1748	Both export and import may be executed against remote MySQL/PostgreSQL
1749	servers without limitation. The migration working directory need only
1750	to be accessible by the BASE migration program.
1751	</para>
1752	</note>
1753
1754	</listitem>
1755
1756	<listitem>
1757	<para>
1758	Restart Tomcat and verify that the migration was successful. Eg.
1759	check that you can log in to BASE, that you can access files,
1760	that plug-ins are working, etc. Then, shut everything down again.
1761	</para>
1762	</listitem>
1763
1764	<listitem>
1765	<para>
1766	Setup backup procedures for the new server. Verify that the
1767	backup is working before starting up Tomcat again.
1768	Restart any job agents (make sure that the are configured to use
1769	the new server). When everything is up and running again, the
1770	<replaceable>/path/to/migration/dir</replaceable> directory
1771	and all files can be deleted.
1772	</para>
1773	</listitem>
1774	</orderedlist>
1775
1776	</listitem>
1777	</varlistentry>
1778	</variablelist>
1779
1780	</sect1>
1781
1782	</chapter>

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