source: trunk/doc/src/docbook/admindoc/installation_upgrade.xml @ 3992

Last change on this file since 3992 was 3992, checked in by Nicklas Nordborg, 15 years ago

Fixes #728: jobagent.sh should accept command status

Also made the jobagent log into it's own file (jobagent.log) instead of stdout

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 43.7 KB
Line 
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_upgrade.xml 3992 2007-11-22 13:19:37Z nicklas $
7
8  Copyright (C) 2007 Jari Hakkinen, Peter Johansson, Nicklas Nordborg, Martin Svensson
9
10  This file is part of BASE - BioArray Software Environment.
11  Available at http://base.thep.lu.se/
12
13  BASE is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License
15  as published by the Free Software Foundation; either version 2
16  of the License, or (at your option) any later version.
17
18  BASE is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21  GNU General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330,
26  Boston, MA  02111-1307, USA.
27-->
28
29<chapter id="installation_upgrade">
30  <?dbhtml dir="installation_upgrade"?>
31
32  <title>Installation, setup, migration, and upgrade instructions</title>
33
34  <note>
35    These instructions apply only to the BASE release which this
36    document is a part of.
37  </note>
38
39  <para>
40    This chapter is divided into four parts. First, the process of
41    upgrading a BASE 2 server is described. Followed by set up of job
42    agents. (For these two first parts it is assumed that there is a
43    running server.) Then, the first time installation instructions
44    follows, and the chapter is concluded with information on how to
45    migrate data from a BASE 1.2.17 server to a BASE 2 server.
46  </para>
47
48  <para>
49    The first time installation is only to be performed once,
50    optionally followed by a migration. The migration can only be done
51    to a pristine (empty) BASE 2 server with one exception; The
52    migration can be restarted if it fails during the RawBioAssaysData
53    transfer, for all other failure points the migration has to be
54    restarted with an empty database. Migration from several BASE 1
55    installations to one BASE 2 server is not supported.
56  </para>
57
58  <para>
59    The instructions here assume
60    that <ulink url="http://tomcat.apache.org/">tomcat</ulink> is used
61    on the server side. Other servlet engines may work but we only
62    test tomcat.
63  </para>
64
65
66  <sect1 id="installation_upgrade.upgrade">
67    <title>Upgrade instructions</title>
68
69    <important id="dropindexes">
70      <title>Upgrading from BASE 2.4.3 or lower to 2.4.4 or higher</title>
71      <para>
72        Older releases of BASE 2 used to create indexes for many columns
73        in the dynamic database. The same columns are part of the primary
74        key for the tables so the indexes are not really needed. The
75        result is very bad performance since the database engine sometimes
76        get stuck in "index update" mode making the entire server
77        very slow. BASE 2.4.4 no longer creates the indexes. Indexes on
78        existing tables should be dropped to increase the performance.
79        Tests have shown a 50-90% decrease in execution time for some
80        plug-ins
81        (<ulink url="http://base.thep.lu.se/ticket/294">http://base.thep.lu.se/ticket/294</ulink>).
82      </para>
83      <para>
84        Removing the indexes is very simple. <emphasis>After the server
85        has been upgraded</emphasis> following the usual instructions below, issue the
86        the following commands:
87      </para>
88   
89      <programlisting>
90cd &lt;basedir&gt;/bin
91./dynamicdb.sh -v -dropindexes
92</programlisting>
93
94      <para>
95        Skip the <option>-dropindexes</option> option to do a dry
96        run without actually deleting the indexes.
97      </para>
98    </important>
99
100    <para>
101      As always, backup your database before attempting an
102      upgrade. The BASE team performs extensive testing before
103      releasing a new version of BASE but there are always a
104      possibility for unexpected events during upgrades. In upgrades
105      requiring a change in the underlying database there is no
106      (supported) way to revert to a previous version of BASE using
107      BASE tools, you need to use your backup for this use case.
108    </para>
109
110    <para>
111      The strategy here is to install the new BASE release to another
112      directory than the one in use. This requires transfer of
113      configuration settings to the new install but more on that
114      below.
115    </para>
116
117    <variablelist>
118      <varlistentry>
119        <term>Shut down the tomcat server</term>
120        <listitem>
121          <para>
122            If the BASE application is not shut down already, it is
123            time to do it now. Do something like <command>sudo
124            /etc/init.d/tomcat5.5 stop</command>
125          </para>
126        </listitem>
127      </varlistentry>
128
129      <varlistentry>
130        <term>Rename your current server</term>
131        <listitem>
132          <para>
133            Rename your current BASE 2 installation <command>mv
134              /path/to/base /path/to/base_old</command>.
135          </para>
136        </listitem>
137      </varlistentry>
138
139      <varlistentry>
140        <term>Download and unpack BASE</term>
141        <listitem>
142          <para>
143            There are several ways to download BASE. Please refer to
144            section <xref linkend="resources.home_page.download"/> for
145            information on downloading BASE, and select the item
146            matching your download option:
147          </para>
148
149          <variablelist>
150            <varlistentry>
151              <term><emphasis>Pre-compiled package</emphasis></term>
152              <listitem>
153                <para>
154                  If you selected to download a pre-compiled package,
155                  unpack the downloaded file with <command>tar zxpf
156                  base-...tar.gz</command>.
157                </para>
158              </listitem>
159            </varlistentry>
160
161            <varlistentry>
162              <term><emphasis>Source package</emphasis></term>
163              <listitem>
164                <para>
165                  If you selected to download a source package, unpack
166                  the downloaded file with <command>tar zxpf
167                  base-...src.tar.gz</command>. Change to the new
168                  directory, and issue <command>ant
169                  package.bin</command>. This will create a binary
170                  package in the current directory. Unpack this new
171                  package (outside of the source file hierarchy).
172                </para>
173              </listitem>
174            </varlistentry>
175
176            <varlistentry>
177              <term><emphasis>Subversion checkout</emphasis></term>
178              <listitem>
179                <para>
180                  This option is for advanced users only and is not
181                  covered here. Please refer to
182                  <xref linkend="core_ref.build"/> for information on
183                  this download option.
184                </para>
185              </listitem>
186            </varlistentry>
187
188          </variablelist>
189        </listitem>
190
191      </varlistentry>
192
193      <varlistentry>
194        <term>Transfer files and settings</term>
195        <listitem>
196          <para>
197            Settings from the previous installation must be
198            transferred to the new installation. This is most easily
199            done by comparing the configuration files from the
200            previous install with the new files. Do not just copy the
201            old files to the new install since new options may have
202            appeared.
203          </para>
204          <para>
205            In the main BASE configuration file,
206            <filename>&lt;base-dir&gt;/www/WEB-INF/classes/base.config</filename>,
207            fields that needs to be transferred are usually
208            <emphasis>db.username</emphasis>,
209            <emphasis>db.password</emphasis>,
210            and <emphasis>userfiles</emphasis>.
211          </para>
212          <para>
213            Local settings in the raw data
214            tables, <filename>&lt;base-dir&gt;/www/WEB-INF/classes/raw-data-types.xml</filename>,
215            may need to be transferred.
216          </para>
217        </listitem>
218      </varlistentry>
219
220      <varlistentry>
221        <term>Updating database schema</term>
222        <listitem>
223          <para>
224            It is recommended that you also perform an update of your
225            database schema.  Running the update scripts are not
226            always necessary when upgrading BASE, but the running the
227            update scripts are safe even in cases when there is no
228            need to run them. Change directory
229            to <filename
230            class="directory">&lt;base-dir&gt;/bin/</filename> and issue
231<programlisting>
232sh ./updatedb.sh [base_root_login] <emphasis>base_root_password</emphasis>
233sh ./updateindexes.sh <emphasis>base_root_password</emphasis>
234</programlisting>
235            where <emphasis>base_root_login</emphasis> is the login
236            for the root user and <emphasis>base_root_password</emphasis> is the
237            password. The login is optional. If not specified,
238            <constant>root</constant> is used as the login.
239          </para>
240        </listitem>
241      </varlistentry>
242
243      <varlistentry>
244        <term>Remove tomcat cache</term>
245        <listitem>
246          <para>
247            As tomcat user, remove cached files and directories. Do
248            something like
249<programlisting>cd /usr/share/apache-tomcat-5.5.15/
250rm -rf work/Catalina</programlisting>
251          </para>
252        </listitem>
253      </varlistentry>
254
255      <varlistentry>
256        <term>Start tomcat</term>
257        <listitem>
258          <para>
259            Start the tomcat server: <command>sudo
260              /etc/init.d/tomcat5.5 start</command>
261          </para>
262        </listitem>
263      </varlistentry>
264
265    </variablelist>
266
267    <para>
268      Done! Upgrade of BASE is finished.
269    </para>
270
271  </sect1>      <!-- Upgrade instructions -->
272
273
274  <sect1 id="installation_upgrade.jobagents">
275    <title>Installing job agents</title>
276
277    <para>
278      It is important to understand that the BASE application can be
279      spread on to several computers. The main BASE application is
280      serving HTTP requests, the underlying database engine is
281      providing storage and persistence of data, and job agents can be
282      installed on computers that will serve the BASE installation
283      with computing power and perform analysis and run plug-in. In a
284      straight forward setup one computer provides all services needed
285      for running BASE. From this starting point it is easy to add
286      computers to shares load from the BASE server by installing job
287      agents on these additional computers.
288    </para>
289
290    <para>
291      A job agent is a program running on a computer regularly
292      checking the BASE job queue for jobs awaiting execution. When
293      the job agent finds a job that it is enabled to execute, it
294      loads the plug-in and executes it. Job agents will in this way
295      free up resources on the BASE application server, and thus allow
296      the BASE server to concentrate on serving web pages. Job agents
297      are optional and must be installed and setup
298      separately. However, BASE is prepared for job agent setup and to
299      utilize the agents, but the agent are not required.
300    </para>
301
302    <para>
303      A job agent supports many configuration options that are not
304      supported by the internal job queue. For example, you can
305      <itemizedlist>
306        <listitem>
307          <para>
308            Specify exactly which plug-ins each job agent should be
309            able to execute.
310          </para>
311        </listitem>
312        <listitem>
313          <para>
314            Give some plug-ins higher priority than other plug-ins.
315          </para>
316        </listitem>
317        <listitem>
318          <para>
319            Specify which users/groups/projects should be able to use
320            a specific job agent.
321          </para>
322        </listitem>
323        <listitem>
324          <para>
325            Override memory settings and more for each plug-in.
326          </para>
327        </listitem>
328        <listitem>
329          <para>
330            Execute plug-ins in separate processes. Thus, a misbehaving
331            plug-in cannot bring the main application server down.
332          </para>
333        </listitem>
334        <listitem>
335          <para>
336            Add more computers with job agents as needed.
337          </para>
338        </listitem>
339      </itemizedlist>
340      All these options make it possible to create a very flexible
341      setup. For example one job agent can be assigned for importing
342      data only, another job agent can be assigned for running
343      analysis plug-ins for specific project only, and a third may be a
344      catch-all job agent that performs all low-priority jobs.
345    </para>
346
347    <sect2 id="installation_upgrade.jobagents.serverside">
348      <title>BASE application server side setup</title>
349      <para>
350        <variablelist>
351          <varlistentry>
352            <term>Make sure the internal job queue doesn't execute all plug-ins</term>
353            <listitem>
354              <para>
355                The setting <command>jobqueue.internal.runallplugins</command>
356                should be set to <command>false</command> for the
357                BASE server. This setting is found in
358                the <filename>&lt;base-dir&gt;/www/WEB-INF/classes/base.config</filename>
359                file. The changes will not take effect until the
360                application server is restarted.
361              </para>
362             
363              <note>
364                Prior to BASE 2.5 the internal job queue had to be disabled
365                completely. This is no longer the case since it is possible to
366                enable/disable the internal job queue separately for
367                each plug-in.
368              </note>
369             
370            </listitem>
371          </varlistentry>
372          <varlistentry id="installation_upgrade.jobagent.user_account">
373            <term>Enable the job agent user account</term>
374            <listitem>
375              <para>
376                During installation of BASE a user account is created
377                for the job agent. This account is used by the job
378                agents to log on to BASE. The account is disabled by
379                default and must be enabled. Enable the account and
380                set a password using the BASE web interface.
381                The same password must also be set in the
382                <filename>jobagent.properties</filename> file, see
383                item
384                <xref linkend="installation_upgrade.jobagent.client.properties"/>
385                below.
386              </para>
387            </listitem>
388          </varlistentry>
389        </variablelist>
390      </para>
391    </sect2>
392
393    <sect2 id="installation_upgrade.jobagents.database">
394      <title>Database server setup</title>
395      <para>
396        <variablelist>
397          <varlistentry id="installation_upgrade.jobagent.database">
398            <term>Create a user account on the database</term>
399            <listitem>
400              <para>
401                This is the similar to granting database access for
402                the BASE server user in the in the regular BASE
403                installation, cf.
404                <xref
405                linkend="installation_upgrade.installation.database"/>.
406                You must create an account in the database that is
407                allowed to connect from the job agent server. MySQL
408                example:
409<programlisting>GRANT ALL ON base2.* TO db_user@job.agent.host IDENTIFIED BY 'db_password';
410GRANT ALL ON base2dynamic.* TO db_user@job.agent.host;</programlisting>
411
412                Replace <command>job.agent.host</command> with the
413                host name of the server that is going to run the job
414                agent. You should also set password. This password is
415                used in item
416                <xref linkend="installation_upgrade.jobagent.client.config"/>
417                below in job agent server setup. You can use the same
418                database user and password as in the regular database
419                setup.
420              </para>
421            </listitem>
422          </varlistentry>
423        </variablelist>
424      </para>
425    </sect2>
426
427    <sect2 id="installation_upgrade.jobagents.client">
428      <title>Job agent client setup</title>
429      <para>
430        <variablelist>
431          <varlistentry>
432            <term>Download and unpack a regular BASE 2 distribution</term>
433            <listitem>
434              <para>
435                You <emphasis>must</emphasis> use the same version on
436                the web server and all job agents. You find the
437                downloads at
438                <ulink
439                url="http://base.thep.lu.se/wiki/DownloadPage">http://base.thep.lu.se/wiki/DownloadPage</ulink>
440              </para>
441            </listitem>
442          </varlistentry>
443          <varlistentry id="installation_upgrade.jobagent.client.config">
444            <term>Edit the <filename>base.config</filename> file</term>
445            <listitem>
446              <para>
447                The <filename>&lt;base-dir&gt;/www/WEB-INF/classes/base.config</filename>
448                file must be configured as in regular BASE
449                installation, cf.
450                <xref
451                linkend="installation_upgrade.installation.configuration"/>,
452                to use the same database as the web server
453                application. The most important settings are
454                <itemizedlist>
455                  <listitem>
456                    <para>
457                      <command>db.username</command>: The database
458                      user you created in item
459                      <xref
460                      linkend="installation_upgrade.jobagent.database"/>
461                      above.
462                    </para>
463                  </listitem>
464                  <listitem>
465                    <para>
466                      <command>db.password</command>: The password for
467                      the user.
468                    </para>
469                  </listitem>
470                  <listitem>
471                    <para>
472                      <command>db.url</command>: The connection url to
473                      the database.
474                    </para>
475                  </listitem>
476                  <listitem>
477                    <para>
478                      <command>userfiles</command>: The path to the
479                      directory where user files are located. This
480                      directory must be accessible from all job
481                      agents, i.e., by nfs or other file system
482                      sharing method.
483                    </para>
484                  </listitem>
485                </itemizedlist>
486                See the <xref linkend="appendix.base.config"/> for
487                more information about the settings in
488                the <filename>base.config</filename> file.
489              </para>
490            </listitem>
491          </varlistentry>
492          <varlistentry id="installation_upgrade.jobagent.client.properties">
493            <term>Edit
494            the <filename>jobagent.properties</filename> file</term>
495            <listitem>
496              <para>
497                The <filename>&lt;base-dir&gt;/www/WEB-INF/classes/jobagent.properties</filename>
498                file contains settings for the job agent. The most
499                important ones to specify value for are
500                <itemizedlist>
501                  <listitem>
502                    <para>
503                      <command>agent.password</command>: The password
504                      you set for the job agent user account in item
505                      <xref
506                      linkend="installation_upgrade.jobagent.user_account"/>
507                      above.
508                    </para>
509                  </listitem>
510                  <listitem>
511                    <para>
512                      <command>agent.id</command>: An ID that must be
513                      unique for each job agent accessing the BASE application.
514                    </para>
515                  </listitem>
516                  <listitem>
517                    <para>
518                      <command>agent.remotecontrol</command>: The
519                      name/ip address of the web server if you want it
520                      to be able to display info about running
521                      jobs. The job agent will only allow connections
522                      from computers specified in this setting.
523                    </para>
524                  </listitem>
525                </itemizedlist>
526              </para>
527              <para>
528                The <filename>jobagent.properties</filename> file
529                contains many more configuration options. See
530                the <xref linkend="appendix.jobagent.properties"/> for
531                more information.
532              </para>
533            </listitem>
534          </varlistentry>
535          <varlistentry>
536            <term>Register the job agent</term>
537            <listitem>
538              <para>
539                From the <filename>bin</filename> directory, register
540                the job agent with
541                <programlisting>./jobagent.sh register</programlisting>
542              </para>
543            </listitem>
544          </varlistentry>
545          <varlistentry>
546            <term>Start the job agent</term>
547            <listitem>
548              <para>
549                From the <filename>bin</filename> directory, start the
550                job agent with
551                <programlisting>./jobagent.sh start &amp;</programlisting>
552              </para>
553              <para>
554                See the <xref linkend="appendix.jobagent.sh"/>
555                for more information about what you can do
556                with the job agent command line interface.
557              </para>
558            </listitem>
559          </varlistentry>
560        </variablelist>
561      </para>
562    </sect2>
563
564    <sect2 id="installation_upgrade.jobagents.configuration">
565      <title>Configuring the job agent</title>
566      <para>
567        Before the job agent starts executing jobs for you it must be
568        configured. The configuration is done through the BASE web
569        interface. See <xref linkend="plugins.jobagents" />
570        <variablelist>
571          <varlistentry>
572            <term>Configure the plug-ins the job agent should handle</term>
573            <listitem>
574              <para>
575                <itemizedlist>
576                  <listitem>
577                    <para>
578                      Go to the
579                      <menuchoice>
580                        <guimenu>Administrate</guimenu>
581                        <guisubmenu>Plugins</guisubmenu>
582                        <guimenuitem>Job agents</guimenuitem>
583                      </menuchoice> menu.
584                    </para>
585                  </listitem>
586                  <listitem>
587                    <para>
588                      Select the job agent and click on the &gbEdit;
589                      button.
590                    </para>
591                  </listitem>
592                  <listitem>
593                    <para>
594                      On the <guilabel>Plugins</guilabel> tab you can
595                      specify which plug-ins the job agent should
596                      handle. Note that if you have installed external
597                      plug-ins on the web server, those plug-ins must be
598                      installed on the job agent as well. It is
599                      possible to specify different paths to the JAR
600                      file for each job agent.
601                    </para>
602                  </listitem>
603                </itemizedlist>
604              </para>
605            </listitem>
606          </varlistentry>
607          <varlistentry>
608            <term>Grant users access to the job agent</term>
609            <listitem>
610              <para>
611                Use the regular <guilabel>Share</guilabel>
612                functionality to specify which users/groups/projects
613                should be able to use the job agent. You must give
614                them at least <command>USE</command> permission.
615              </para>
616            </listitem>
617          </varlistentry>
618        </variablelist>
619      </para>
620    </sect2>
621
622  </sect1>      <!-- job agent setup -->
623
624
625  <sect1 id="installation_upgrade.installation">
626    <title>Installation instructions</title>
627
628    <variablelist>
629
630      <varlistentry>
631        <term>Java</term>
632        <listitem>
633          <para>
634            Download and install Java SDK 1.5, available from
635            <ulink url="http://java.sun.com/" />. Make sure that you
636            download the JDK version (<emphasis>not</emphasis> the JRE
637            version). <command>Java 6 is currently not
638            supported</command> (this will change starting with
639            BASE version 2.5 whereafter only Java 6 will be supported).
640          </para>
641        </listitem>
642      </varlistentry>
643
644      <varlistentry>
645        <term>Tomcat</term>
646        <listitem>
647          <para>
648            Download and install tomcat 5.5.16 or later, available
649            from <ulink
650            url="http://jakarta.apache.org/tomcat/" />
651            <important>
652              You MUST make sure that Tomcat uses the SERVER mode of
653              the Java run time engine
654              (see <ulink
655              url="http://lev.thep.lu.se/trac/base/ticket/99">ticket:99</ulink>).
656            </important>
657            On Linux you do this by setting the environment variable:
658            <code>CATALINA_OPTS</code> to <code>-server</code>. It is
659            also a good idea to specify the maximum allowed memory to
660            use: <code>-server -Xmx500m</code> sets it to 500
661            megabytes. Basically add the next line close to the top of
662            the <filename>catalina.sh</filename> script that comes
663            with tomcat
664            (directory <filename
665            class="directory">bin</filename>):
666<programlisting>CATALINA_OPTS="-server -Xmx500m"</programlisting>
667          </para>
668          <para>
669            For more information about Tomcat options see
670            <ulink url="http://www.chemaxon.com/jchem/doc/admin/tomcat.html" />.
671          </para>
672        </listitem>
673      </varlistentry>
674
675      <varlistentry>
676        <term>Set up SQL database</term>
677        <listitem>
678          <para>
679            BASE 2
680            utilize <ulink
681            url="http://www.hibernate.org/">Hibernate</ulink> for
682            object persistence to a relational database. Hibernate
683            supports many database engines, but so far we only work
684            with <ulink url="http://www.mysql.com">MySQL</ulink>
685            and <ulink
686            url="http://www.postgresql.org/">PostgreSQL</ulink>.
687          </para>
688
689          <variablelist>
690            <varlistentry>
691              <term>MySQL</term>
692              <listitem>
693                <para>
694                  Download and install MySQL (tested with version
695                  5.0), available from
696                  <ulink url="http://www.mysql.com/" />. You need to
697                  be able to connect to the server over TCP, so
698                  the <emphasis>skip-networking</emphasis> option
699                  must <command>not</command> be used. The InnoDB
700                  table engine is also needed, so do not disable them
701                  (not that you would) but you may want to tune the
702                  InnoDB behaviour before creating BASE
703                  databases. BASE comes pre-configured for MySQL so
704                  there is no need to change database settings in the
705                  BASE configuration files.
706                </para>
707              </listitem>
708            </varlistentry>
709            <varlistentry>
710              <term>PostgreSQL</term>
711              <listitem>
712                <para>
713                  PostgreSQL 8.2 seems to be working very well with
714                  BASE and Hibernate. Download and install PostgreSQL,
715                  available from
716                  <ulink url="http://www.postgresql.org/" />. you must
717                  edit
718                  your <filename>&lt;base-dir&gt;/www/WEB-INF/classes/base.config</filename>
719                  file. Uncomment the settings for Postgres and
720                  comment out the settings for MySQL.
721                </para>
722               
723                <note>
724                  <para>
725                  Postgres versions prior to 8.2 have a non-optimal solution
726                  for locking rows in certain situations. This may cause two
727                  seemingly independent transactions to lock if they just
728                  reference a common database row. This may happen, for example,
729                  when importing raw data that have references to the same
730                  reporters. The problem has been solved in Postgres 8.2.
731                  </para>
732                </note>
733               
734              </listitem>
735            </varlistentry>
736          </variablelist>
737
738        </listitem>
739      </varlistentry>
740
741      <varlistentry>
742        <term>BASE (download and unpacking)</term>
743        <listitem>
744          <para>
745            <ulink
746            url="http://base.thep.lu.se/wiki/DownloadPage">Download
747            BASE</ulink> and unpack the downloaded file,
748            i.e. <command>tar zxpf base-...tar.gz</command>. If you
749            prefer to have the bleeding edge version of BASE, perform
750            a checkout of the source from the subversion repository
751            (subversion checkout instructions at
752            <ulink url="http://base.thep.lu.se/wiki/DownloadPage">BASE
753            trac site</ulink>).
754          </para>
755          <para>
756            If you choose to download the binary package, skip to the
757            next item. The rest of us, read on and compile BASE 2. If
758            you downloaded a source distribution, unpack the
759            downloaded file <command>tar zxpf
760            base-...src.tar.gz</command>, or you may have performed a
761            subversion checkout.  Change to the 'root' base2
762            directory, and issue <command>ant
763            package.bin</command>. This will create a binary package
764            in the base2 'root' directory. Unpack this new package
765            (outside of the source file hierarchy), and from now on
766            the instructions are the same irrespective where you got
767            the binary package.
768          </para>
769          <para>
770            <emphasis>This section is intended for advanced users and
771              programmers only. In cases when you want to change the
772              BASE code and try out personalized features it may be
773              advantageous to run the tweaked BASE server against the
774              development tree. Instructions on how to accomplish this
775              is available in the
776              <ulink
777              url="http://base.thep.lu.se/chrome/site/doc/development/build.html">building
778              BASE document</ulink>. When you return back after
779              compiling in the subversion tree you can follow the
780              instruction here (with obvious changes to
781              paths).</emphasis>
782          </para>
783        </listitem>
784      </varlistentry>
785
786      <varlistentry id="installation_upgrade.installation.database">
787        <term>BASE (database engine)</term>
788        <listitem>
789          <para>
790            Instructions for MySQL and PostgreSQL are available
791            below. The database names (base2 and base2dynamic is used
792            here), the <emphasis>db_user</emphasis>, and
793            the <emphasis>db_password</emphasis> can be changed during
794            the creation of the databases. It is recommended to change
795            the <emphasis>db_password</emphasis>, the other changes
796            can be made if desired. The database names,
797            the <emphasis>db_user</emphasis>, and
798            the <emphasis>db_password</emphasis> are needed in a later
799            step below when configuring BASE.
800          </para>
801          <note>
802            Note that the <emphasis>db_user</emphasis> name
803            and <emphasis>db_password</emphasis> set here is used
804            internally by BASE in communication with the database and
805            is never used to log on to the BASE application.
806          </note>
807          <variablelist>
808            <varlistentry>
809              <term>MySQL</term>
810              <listitem>
811                <para>
812                  Create a new database for BASE, and add a
813                  <emphasis>db_user</emphasis> with at least
814                  <emphasis>SELECT</emphasis>, <emphasis>INSERT</emphasis>,
815                  <emphasis>UPDATE</emphasis>, <emphasis>DELETE</emphasis>,
816                  <emphasis>CREATE</emphasis>, <emphasis>DROP</emphasis>,
817                  <emphasis>INDEX</emphasis>,
818                  and <emphasis>ALTER</emphasis> permission for the
819                  new database. To do this, connect to your MySQL
820                  server and issue the next lines:
821<programlisting>CREATE DATABASE base2;
822CREATE DATABASE base2dynamic;
823GRANT ALL ON base2.* TO db_user@localhost IDENTIFIED BY 'db_password';
824GRANT ALL ON base2dynamic.* TO db_user@localhost;</programlisting>
825                </para>
826                <para>
827                  The <filename>&lt;base-dir&gt;/misc/sql/createdb.mysql.sql</filename>
828                  file contains the above statements and can be used
829                  by the <filename>mysql</filename> command-line tool
830                  (remember to edit
831                  the <emphasis>db_user</emphasis>,
832                  <emphasis>db_password</emphasis>,
833                  and the database names in the script file before
834                  executing the command): <command>mysql -uroot -p
835                  &lt; ./misc/sql/createdb.mysql.sql</command>. The
836                  header in the script file contains further
837                  information about the script.
838                </para>
839              </listitem>
840            </varlistentry>
841            <varlistentry>
842              <term>PostgreSQL</term>
843              <listitem>
844                <para>
845                  Create a new database for BASE, and add a
846                  <emphasis>db_user</emphasis> with the proper
847                  privileges. To do this, log in as your PostgreSQL
848                  user and issue these lines (omit comments):
849<programlisting>createuser db_user -P
850  # this will prompt for an password for the new user, and issue two
851  # more question that should be answered with character 'n' for no.
852createdb --owner db_user --encoding UNICODE base2
853psql base2
854  # this will start the psql command line tool. Issue the next line
855  # within the tool and quit with a '\q'.
856CREATE SCHEMA "dynamic" AUTHORIZATION "db_user";</programlisting>
857                  The <filename>&lt;base-dir&gt;/misc/sql/createdb.postgresql.sql</filename>
858                  file contains the above statements and can be used
859                  by the <filename>psql</filename> command-line tool:
860                  <command>psql -f ./misc/sql/createdb.posgres.sql
861                    template1</command> The header in the script file
862                  contains further information about the script.
863                </para>
864              </listitem>
865            </varlistentry>
866          </variablelist>
867        </listitem>
868      </varlistentry>
869
870      <varlistentry>
871        <term>BASE (file storage setup)</term>
872        <listitem>
873          <para>
874            An area for file storage must be setup. Create an empty
875            directory in a proper location in your file system, and
876            set the owner to be the same as the one that the tomcat
877            server will be running as. Remember this location for
878            later use.
879          </para>
880        </listitem>
881      </varlistentry>
882
883      <varlistentry id="installation_upgrade.installation.configuration">
884        <term>BASE (configuration)</term>
885        <listitem>
886          <para>
887            Basic BASE configuration is done in
888            <filename>&lt;base-dir&gt;/www/WEB-INF/classes/base.config</filename>:
889            <itemizedlist>
890              <listitem>
891                Uncomment the database engine section that match your setup.
892              </listitem>
893              <listitem>
894                Modify the <emphasis>db.url</emphasis>,
895                <emphasis>db.dynamic.catalog</emphasis>,
896                <emphasis>db.username</emphasis>,
897                and <emphasis>db.password</emphasis> settings to match
898                your choice above. (<emphasis>database host and
899                database name (e.g. base2)</emphasis>,
900                <emphasis>e.g. base2dynamic</emphasis>,
901                <emphasis>db_user</emphasis>, and
902                <emphasis>db_password</emphasis>, respectively.)
903              </listitem>
904              <listitem>
905                Modify the <emphasis>userfiles</emphasis> setting to
906                match your choice above.
907              </listitem>
908            </itemizedlist>
909            See the <xref linkend="appendix.base.config"/> for more
910            information about the settings in
911            the <filename>base.config</filename> file.
912          </para>
913          <para>
914            <emphasis>Optional but recommended.</emphasis> You may want
915            to modify extended properties to fit your needs. Extended
916            properties are defined in
917            <filename>&lt;base-dir&gt;/www/WEB-INF/classes/extended-properties.xml</filename>.
918            There is an
919            administrator <ulink
920            url="http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html">document
921            discussing extended properties</ulink> available. If you
922            plan to perform a migration of a BASE 1.2 database you
923            should probably not remove any extended properties
924            columns (this is not tested so the outcome is currently
925            undefined). However, adding columns does not affect
926            migration.
927          </para>
928        </listitem>
929      </varlistentry>
930
931      <varlistentry>
932        <term>BASE (database initialization)</term>
933        <listitem>
934          <para>
935            Change directory to
936            <filename class="directory">&lt;base-dir&gt;/bin</filename>
937            and run <filename>initdb.sh</filename> as
938<programlisting>./initdb.sh [base_root_login] base_root_password</programlisting>
939
940            <important>
941            <para>
942            The <emphasis>base_root_login</emphasis> and
943            <emphasis>base_root_password</emphasis> you use here
944            is given to the BASE web application root user account.
945            The <emphasis>base_root_login</emphasis> is optional. If
946            not specified, <constant>root</constant> is used for
947            the login.
948            </para>
949            </important>
950            If the initialisation script fail, it is most probably a
951            problem related to the underlying database. Make sure that
952            the database accepts network connection and make sure that
953            <emphasis>db_user</emphasis> has proper credentials.
954          </para>
955        </listitem>
956      </varlistentry>
957
958      <varlistentry>
959        <term>BASE and tomcat</term>
960        <listitem>
961          <para>
962            Either move the <filename
963            class="directory">&lt;base-dir&gt;/www</filename> directory
964            to the tomcat <filename class="directory">webapps</filename>
965            directory or create a symbolic link from the tomcat
966            <filename class="directory">webapps</filename> directory to
967            the <filename class="directory">&lt;base-dir&gt;/www</filename>
968            directory
969<programlisting>cd /path/to/tomcat/webapps
970ln -s /path_to_base/www base2</programlisting>
971            Start/restart tomcat, and try http://hostname:8080/base2
972            (change <emphasis>hostname</emphasis> to your hostname) in
973            your favourite browser. BASE log-in page should appear
974            after a few seconds.
975          </para>
976        </listitem>
977      </varlistentry>
978
979      <varlistentry>
980        <term>BASE, apache, and apache/tomcat connector</term>
981        <listitem>
982          <para>
983            <emphasis>This step is optional</emphasis>.
984          </para>
985          <para>
986            If you want run the tomcat server through the apache web
987            server, you need to install the apache version 2 web
988            server, available
989            from <ulink
990            url="http://www.apache.org/">http://www.apache.org/</ulink>,
991            and a apache-tomcat connector, available
992            from <ulink
993            url="http://jakarta.apache.org/tomcat/connectors-doc/index.html">http://jakarta.apache.org/tomcat/connectors-doc/index.html</ulink>.
994            So, we got you there;-) To be honest, this step is not
995            really well documented since we previously used SuSE 9.3
996            on our demo/test server, and apache/tomcat/mod_jk comes
997            pre-installed. The current server does not use the
998            apache/tomcat connector. What you need to do is something
999            like this
1000            <itemizedlist>
1001              <listitem>
1002                Get that tomcat server running in stand-alone
1003                mode.
1004              </listitem>
1005              <listitem>
1006                Get the apache 2 server running.
1007              </listitem>
1008              <listitem>
1009                Install mod_jk. Note, different version are used for
1010                apache 1.3 and 2. In SuSE 9.3 this step is done by
1011                installing <filename>mod_jk-ap20</filename>.
1012              </listitem>
1013              <listitem>
1014                Create a <filename>workers.properties</filename> file
1015                in the
1016                tomcat <filename class="directory">base</filename>
1017                directory (commonly copied from a template).
1018              </listitem>
1019              <listitem>
1020                Create a <filename>jk.conf</filename> file in the
1021                apache <filename class="directory">conf</filename>
1022                directory (commonly copied from a template), and make
1023                sure that <emphasis>jk</emphasis> is added to the
1024                modules to be loaded when apache starts.
1025              </listitem>
1026              <listitem>
1027                In <filename>jk.conf</filename> add the lines below
1028                and change paths appropriately.
1029<programlisting># The following lines makes apache aware of the location of
1030# the /base2 context
1031Alias /base2 "/srv/www/tomcat5/base/webapps/base2"
1032&lt;Directory "/srv/www/tomcat5/base/webapps/base2"&gt;
1033Options Indexes FollowSymLinks
1034allow from all
1035&lt;/Directory&gt;
1036# The following lines mounts all base2 jsp files to tomcat
1037JkMount /base2 ajp13
1038JkMount /base2/* ajp13
1039# The following lines prohibits users from directly accessing WEB-INF
1040&lt;Location "/base2/WEB-INF/"&gt;
1041AllowOverride None
1042deny from all
1043&lt;/Location&gt;</programlisting>
1044              </listitem>
1045            </itemizedlist>
1046            You must restart the apache and the tomcat server after above steps.
1047          </para>
1048        </listitem>
1049      </varlistentry>
1050
1051      <varlistentry>
1052        <term>Setup done!</term>
1053        <listitem>
1054          <para>
1055            Happy BASEing. Now you can log on to your BASE 2 server as
1056            user <emphasis>root</emphasis> (use
1057            the <emphasis>base_root_password</emphasis> from the
1058            database initialization step above). You should begin with
1059            creating a couple user accounts, for more information on
1060            how to create user accounts please refer to
1061            <xref linkend="user_administration"/>.
1062          </para>
1063          <para>
1064            If you are planning to perform a migration of data from
1065            BASE 1.2.x please perform the steps in
1066            <xref linkend="installation_upgrade.migration"/> before
1067            doing anything else with your new BASE installation.
1068          </para>
1069        </listitem>
1070      </varlistentry>
1071
1072    </variablelist>
1073
1074  </sect1>      <!-- Installation instructions -->
1075
1076
1077  <sect1 id="installation_upgrade.migration">
1078    <title>Migration instructions</title>
1079
1080    <caution>
1081      <title>The disclaimer section</title>
1082      <para>
1083        We have made extensive testing of the migration from BASE1.2
1084        to BASE2. To our knowledge the migration works but we cannot
1085        guarantee perfect functionality. The migration tool is
1086        supplied as is and usage is done at your risk. We are
1087        committed to solve migration problems at the level of
1088        transferring data from BASE 1.2 to 2.2.x, but cannot resolve
1089        data loss issues in a running BASE 2 server due to imperfect
1090        migration. When you start the migration tool you are required
1091        to pass parameter <emphasis>"disclaimer_understood"</emphasis>
1092        to the <filename>migrate_from_1.2.sh</filename>
1093        script. Remember to check that the migration performed well
1094        before you decide to delete your 1.2 installation.
1095      </para>
1096      <para>
1097        Migration from the latest BASE 1.2.x release to the latest is
1098        supported.
1099      </para>
1100    </caution>
1101
1102    <para>
1103      Verify that your BASE 2 installation is up and running before
1104      attempting migration. Preferably try to log in using the root
1105      user through the web interface.
1106    </para>
1107
1108    <para>
1109      Make sure your BASE 1.2 runs with the latest
1110      (<emphasis>pristine</emphasis>) schema
1111      version, <emphasis>i.e.,</emphasis> the migration will only
1112      support an unmodified BASE 1.2 installation. If you have an out
1113      of date schema version, please upgrade to the latest schema
1114      using BASE 1.2 tools before migrating. If you have made local
1115      changes to the BASE 1.2 schema you need to patch the BASE 2
1116      schema as well as make proper changes to the migration program.
1117      If there are added columns to the reporter table in your BASE
1118      1.2 database you need to transfer the additional information
1119      after migration (even if you modified the BASE
1120      2 <filename>extended-properties.xml</filename> file).
1121    </para>
1122
1123    <para>
1124      The behaviour of migration is controlled
1125      through <filename>migration.properties</filename> file (see
1126      <xref linkend="appendix.migrate.properties"/>), but you should
1127      know what you do when you change parameters in this file.
1128    </para>
1129
1130    <para>
1131      Migration can be restarted in one specific case only; If the
1132      migration fails during the RawBioAssaysData transfer simply
1133      restart the migration and the script will ask you to verify that
1134      a restart should be attempted. For all other failure points the
1135      migration has to be restarted with an empty database.
1136    </para>
1137
1138    <para>
1139      Migration is performed with the following steps:
1140      <orderedlist>
1141
1142        <listitem>
1143          <para>
1144            To transfer files from BASE 1.2 (default migration
1145            behaviour), you must have file system access to BASE 1.2
1146            files, <emphasis>i.e.,</emphasis> the <filename
1147            class="directory">/ 1.2/data</filename>
1148            directory containing directories
1149            <filename class="directory">rawdata</filename>,
1150            <filename class="directory">uploads</filename>,
1151            <filename class="directory">protocols</filename>, ...
1152          </para>
1153        </listitem>
1154
1155        <listitem>
1156          <para>
1157            Change settings in the file
1158            <filename>&lt;base-dir&gt;/dist/www/WEB-INF/classes/migrate.properties</filename>.
1159            The available options are commented:
1160            <itemizedlist>
1161              <listitem>
1162                <para>
1163                  Modify <emphasis>db1.*</emphasis> parameters to
1164                  match your BASE 1.2 installation.
1165                </para>
1166              </listitem>
1167              <listitem>
1168                <para>
1169                  Set <emphasis>userfiles</emphasis> (note, this is
1170                  not the same parameter as
1171                  in <filename>base.config</filename>) to point to the
1172                  directory containing the BASE 1.2 files (defined in a
1173                  previous step above).
1174                </para>
1175              </listitem>
1176              <listitem>
1177                <para>
1178                  Set the <emphasis>pluginDir</emphasis> to point to
1179                  the directory where your BASE 1.2 plug-ins are
1180                  installed. The default is
1181                  <filename
1182                  class="directory">/usr/local/base/plugins</filename>.
1183                </para>
1184              </listitem>
1185              <listitem>
1186                <para>
1187                  Modify <emphasis>root.password</emphasis>.
1188                </para>
1189              </listitem>
1190              <listitem>
1191                <para>
1192                  Change the <emphasis>deletefiles</emphasis> setting
1193                  wisely. If you
1194                  set <emphasis>deletefiles=yes</emphasis> all BASE
1195                  1.2 files will be physically removed when copied to
1196                  BASE 2. Leave this options
1197                  as <emphasis>deletefiles=no</emphasis> unless you
1198                  are absolutely sure of what you are doing.
1199                </para>
1200              </listitem>
1201            </itemizedlist>
1202          </para>
1203        </listitem>
1204
1205        <listitem>
1206          <para>
1207            Run migration utility:
1208<programlisting>cd /path_to_base/dist/bin
1209./migrate_from_1.2.sh</programlisting>
1210          </para>
1211          <para>
1212            If the migration fails during the RawBioAssaysData
1213            transfer you can restart the migration at the point of
1214            failure. Simply restart the migration and the script will
1215            ask you to verify that a restart should be attempted. For
1216            all other failure points the migration has to be restarted
1217            with an empty database.
1218          </para>
1219        </listitem>
1220
1221        <listitem>
1222          <para>
1223            <emphasis>Optional, depends on your BASE 1.2 reporter
1224            table.</emphasis> Additional columns (as compared with a
1225            pristine database schema) in the reporter table in the
1226            BASE 1.2 schema are not transferred during migration. You
1227            have to perform the transfer manually after
1228            migration. Simply export the reporter information from
1229            BASE 1.2, and import the data into BASE 2. In BASE 1.2: i)
1230            View the reporters, ii) Use `Get as tab-separated text` to
1231            create a tab separated file (right click and save). In
1232            BASE 2, to import the file follow the instructions in
1233            <xref linkend="reporters.import"/>.
1234          </para>
1235        </listitem>
1236
1237        <listitem>
1238          <para>
1239            Migration done! Happy BASEing.
1240          </para>
1241        </listitem>
1242
1243      </orderedlist>
1244
1245    </para>
1246
1247  </sect1>      <!-- Migration instructions -->
1248
1249</chapter>
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