source: trunk/doc/src/docbook/developerdoc/documentation.xml @ 4477

Last change on this file since 4477 was 4477, checked in by Jari Häkkinen, 14 years ago

Addresses #1106. Moving to GPLv3 in chunked commits.

File size: 64.2 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  $Id$
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 3
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="documentation">
30  <?dbhtml dir="write_doc"?>
31  <title>Write documentation</title>
32
33  <sect1 id="documentation.docbook">
34    <title>User, administrator and developer documentation with Docbook</title>
35
36    <para>
37      This chapter is for those who intent to contribute to the BASE2 user documentation.
38      The chapter contains explanations of how the documentation is organized, what the
39      different parts is about and other things that will make it easier to know
40      where to insert new text.
41    </para>
42    <para>
43      The documentation is written with the docbook standard, which is a bunch of defined XML
44      elements and XSLT style sheets that are used to format the text. Later on in this chapter
45      is a reference, over those docbook elements that are recommended to use when writing BASE2
46      documentation. Further information about docbook can be found in the on-line version of
47      O'Reilly's
48      <ulink url="http://www.docbook.org/tdg/en/html/">DocBook: The Definitive Guide</ulink>
49      by Norman Walsh and Leonard Muellner.
50    </para>
51   
52
53  <sect2 id="docbook.layout">
54    <title>Documentation layout</title>
55    <para>
56      The book, which is the main element in this docbook documentation, is divided into four
57      separated parts, depending on who the information is directed to. What kind of
58      documentation each one of these parts contains or should contain is described here
59      below.
60    </para>
61    <variablelist>
62      <varlistentry>
63        <term>Overview documentation</term>
64        <listitem>
65          <para>
66            The overview part contains, like the name says, an overview of BASE2.
67            For example an explanation about what the purpose with BASE2 is, the terms
68            that are used in the program and other general things that anyone that is
69            interested in the program wants/needs to know before exploring it further.
70          </para>
71        </listitem>
72      </varlistentry>
73      <varlistentry>
74        <term>User documentation</term>
75        <listitem>
76          <para>
77            This part contains information that are relevant for the common BASE2-user.
78            More or less should everything that a power user role or an user role needs
79            to know be included here.
80          </para>
81        </listitem>
82      </varlistentry>
83      <varlistentry>
84        <term>Administrator documentation</term>
85        <listitem>
86          <para>
87            Things that only an administrator-role can do is documented in this part. It
88            can be how to install the program, how to configure the server for best
89            performance or other subjects that are related to the administration.
90          </para>
91        </listitem>
92      </varlistentry>
93      <varlistentry>
94        <term>Developer documentation</term>
95        <listitem>
96          <para>
97            Documentation concerning the participation of BASE2 development should be placed
98            in this part, e.g. coding standards, the java doc from the source code, how
99            to develop a plugin etc.
100          </para>
101        </listitem>
102      </varlistentry>
103    </variablelist>
104  </sect2>
105
106
107  <sect2 id="docbook.begin">
108    <title>Getting started</title>
109    <para>
110      Before writing any documentation in BASE2 there are a couple of things, some
111      rules and standards, to have in mind.
112    </para>
113    <sect3 id="docbook.begin.sourcefiles">
114      <title>Organization of source files</title>
115      <para>
116        The source files of the documentation are located in
117        <filename class='directory'>&lt;base-dir&gt;/doc/src/docbook</filename>.
118        The different parts of the documentation are organized into separate folders and
119        each one of the folders contains one index file and one file for each chapter in
120        that part. The index file joins the chapters, in current part/folder, together and
121        does not really contain any text. The documentation root directory also contains an
122        <filename class='headerfile'>index.xml</filename>
123        file which joins the index files from the different parts together.
124      </para>
125      <figure id="docbook.figures.fileorganization">
126        <title>The organization of documentation files</title>
127        <screenshot>
128          <mediaobject>
129            <imageobject>
130              <imagedata fileref="figures/fileorganization.png" format="PNG" />
131            </imageobject>
132          </mediaobject>
133        </screenshot>
134      </figure>
135      <sect4 id="docbook.begin.sourcefiles.newfile">
136        <title>Create new chapter/file</title>
137        <para>
138          Most files in the documentation, except the index files, represents a chapter.
139          Here is how to create a new chapter and include it in the main documentation:
140          <orderedlist numeration='arabic' spacing='compact'>
141            <listitem>
142              <para>
143                Create a new XML-file in the folder for the part where the new chapter
144                should be included. Give it a name that is quite similar to the
145                new chapter's title but use <userinput>_</userinput> instead of
146                blank space and keep it down to one or a few words.
147              </para>
148            </listitem>
149            <listitem>
150              <para>
151                Begin to write the chapter's body, here is an example:
152                <example id="docbook.examples.chapterbody">
153                  <title>Example of a chapter</title>
154<programlisting language="xml">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
155&lt;!DOCTYPE chapter PUBLIC
156  "-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN"
157  "../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"&gt;
158
159&lt;chapter id="example_chapter"&gt;
160   &lt;?dbhtml dir="folder name to put the chapter's files in"?&gt;
161   &lt;title&gt;Example of a chapter &lt;/title&gt;
162   &lt;para&gt;
163      &hellip;
164   &lt;/para&gt;
165   &lt;sect1 id="example_chapter.sect1"&gt;
166      &lt;title&gt;Example of top level section &lt;/title&gt;
167      &lt;para&gt;
168         &hellip;
169      &lt;/para&gt;
170      &lt;sect2 id="example_chapter.sect1.sect2"&gt;
171         &lt;title&gt;Example of second level section &lt;/title&gt;
172         &lt;para&gt;
173            &hellip;
174         &lt;/para&gt;
175         &lt;sect3 id="example_chapter.sect1.sect2.sect3"&gt;
176            &lt;title&gt;Example of third level section&lt;/title&gt;
177            &lt;para&gt;
178               &hellip;
179            &lt;/para&gt;
180         &lt;/sect3&gt;
181      &lt;/sect2&gt;     
182   &lt;/sect1&gt;
183&lt;/chapter&gt;</programlisting>
184                </example>
185              </para>
186              <note>
187                <para>
188                  Do not forget to include the
189                  <sgmltag>dbhtml</sgmltag>
190                  tag with the attribute
191                  <sgmltag class="attribute">dir</sgmltag>
192                  set to the value that the chapter's output folder should have as a
193                  name.
194                </para>
195              </note>
196            </listitem>
197            <listitem>
198              <para>
199                The last step is to get the new chapter included in the documentation. This is done by including the file's name in
200                the file
201                <filename>index.xml</filename>
202                that's located in the current part's folder.
203                The following example
204                shows how the chapter that was created above is included in the user
205                documentation part.
206              </para>
207              <example id="docbook.examples.include_chapter">
208                <title>Include a chapter</title>
209<programlisting language="xml:nogutter:nocontrols">&lt;part id="userdoc"&gt;
210   &lt;title&gt;User documentation&lt;/title&gt;
211   &lt;include file= "about.xml"/&gt;
212   &lt;include file="webclient.xml"/&gt;
213   &lt;include file="project_permission.xml"/&gt;
214   &lt;include file="trashcan.xml"/&gt;
215   &lt;include file="file_system.xml"/&gt;
216   &lt;include file="jobs.xml"/&gt;
217   &lt;include file="reporters.xml"/&gt;
218   &lt;include file="annotations.xml"/&gt;
219   &lt;include file="protocols.xml"/&gt;
220   &lt;include file="hardware.xml"/&gt;
221   &lt;include file="example_chapter.xml"/&gt;
222   &lt;include file="software.xml"/&gt;
223   &lt;include file="array_lims.xml"/&gt;
224   &lt;include file="biomaterials.xml"/&gt;
225   &lt;include file="experiments_analysis.xml"/&gt;
226   &lt;include file="import_export_data.xml"/&gt;
227&lt;/part&gt;</programlisting>
228                </example>
229              <note>
230                <title>Order of chapters</title>
231                <para>
232                  The chapters will come in the same order as they are included in
233                  the index file.
234                </para>
235              </note>
236            </listitem>     
237          </orderedlist>
238          Now it's only to go ahead with the documentation writing.
239        </para>
240      </sect4>
241    </sect3>
242   
243    <sect3 id="docbook.begin.chunking">
244      <title>Controlling chunking</title>
245      <para>
246        We have configured docbook to create a new subdirectory for each
247        <sgmltag class="starttag">chapter</sgmltag> and a new output file for each
248        <sgmltag class="starttag">sect1</sgmltag> tag. In most cases this
249        gives each page a relatively good size. Not too long and not too short.
250        However, if a chapter contains many small <sgmltag class="starttag">sect1</sgmltag>
251        sections (for example, <xref linkend="resources"/>), you end up with many
252        pages with just a few lines of text on each page. This is not so
253        good and can be avoided by adding <sgmltag class="attribute">chunked="0"</sgmltag>
254        as an attribute to the <sgmltag class="starttag">chapter</sgmltag> tag, for example:
255      </para>
256      <programlisting language="xml">&lt;chapter id="resources" chunked="0"&gt;</programlisting>
257      <para>
258        This will stop the chunking of <sgmltag class="starttag">sect1</sgmltag>
259        sections in this chapter.
260      </para>
261     
262      <para>
263        On the other
264        hand, if you have a <sgmltag class="starttag">sect1</sgmltag>
265        that contains many long <sgmltag class="starttag">sect2</sgmltag>
266        sections you might want to put each <sgmltag class="starttag">sect2</sgmltag>
267        section in a separate chunk:
268      </para>
269      <programlisting language="xml">&lt;sect1 id="sect.with.large.sect2" chunked="1"&gt;</programlisting>
270   
271    </sect3>
272   
273    <sect3 id="docbook.begin.id">
274      <title>
275        The
276        <sgmltag class="attribute">id</sgmltag>
277        attribute
278      </title>
279      <para>
280        Common to all elements is that they have an <sgmltag class="attribute">id</sgmltag>
281        attribute that can be used to identify the
282        element with. The value must be unique for the entire documentation.
283        Most of the elements that are used inside the BASE2 documentation do not
284        need to have an id if they do not are used in any cross references from other part of
285        the text.
286      </para>
287      <para>
288        There are some elements that always should have the
289        <sgmltag class="attribute">id</sgmltag>
290        set. Which these elements are and how the
291        <sgmltag class="attribute">id</sgmltag>
292        should look like for each one of those is described below. All values should be as
293        short as possible and associated to the current element. The
294        <sgmltag class="attribute">id</sgmltag>
295        value should only consist of the lowercase characters a-z, '_' instead of blank
296        spaces and '.' to symbolize the different levels in the document.
297        <variablelist>
298          <varlistentry>
299            <term>chapter</term>
300            <listitem>
301              <para>
302                The chapter should have an
303                <sgmltag class="attribute">id</sgmltag>
304                that is identical or almost identical to the chapter's title.
305                <synopsis>chapter_title</synopsis>
306              </para>
307            </listitem>
308          </varlistentry>
309          <varlistentry>
310            <term>sect1-sect5</term>
311            <listitem>
312              <para>
313                The creation of a section's id is done by using the upper level's id
314                and add the section's title or a part of the title. For
315                &lt;sect2&gt; it should be like this;
316                <synopsis>chapter_title.sect1_title.sect2_title</synopsis>
317              </para>
318            </listitem>
319          </varlistentry>
320          <varlistentry>
321            <term>examples</term>
322            <listitem>
323              <para>
324                The naming of an example's
325                <sgmltag class="attribute">id</sgmltag>
326                is a bit different compare to the chapter's and section's id. It
327                should begin with the chapter's id followed by
328                <userinput>examples</userinput>
329                and the caption of the example.
330                <synopsis>chapter_title.examples.example_caption</synopsis>
331              </para>
332            </listitem>
333          </varlistentry>
334          <varlistentry>
335            <term>figures</term>
336            <listitem>
337              <para>
338                The figure's
339                <sgmltag class="attribute">id</sgmltag>
340                should have the following layout
341                <synopsis>chapter_title.figures.figure_name</synopsis>
342              </para>
343            </listitem>
344          </varlistentry>
345        </variablelist>
346      </para>
347    </sect3>
348    <sect3 id="docbook.begin.helptext">
349      <title>Mark help texts</title>
350      <para>
351        This documentation is also use to create the help texts that show up
352        in the web client when clicking on the question mark icons.
353        The parts of the text that also should be used as help texts in the web must be
354        inside
355        <sgmltag class="starttag">helptext</sgmltag>
356        tags. These texts will be exported to a XML-file at the same time as the
357        HTML-documentation is generated. The generated XML-file is compatible with the help
358        text importer in BASE2 and will be imported when running the update script or
359        installation script.
360      </para>
361      <note>
362      <para>
363        The
364        <sgmltag class="starttag">helptext</sgmltag>
365        must be outside the
366        <sgmltag class="starttag">para</sgmltag>
367        tag but inside a
368        <sgmltag class="starttag">sect</sgmltag> 
369        tag to work properly. Do not put any <sgmltag class="starttag">sect</sgmltag>
370        tags inside the helptext. This will make the automatic chapter and section
371        numbering confused.
372      </para>
373      </note>
374      <para>
375        The tag supports the following attributes
376        <variablelist>
377          <varlistentry>
378            <term>
379              <sgmltag class="attribute">external_id</sgmltag>
380            </term>
381            <listitem>
382              <para>
383                Is used to identify and to find a help text in the web client.
384                BASE2's web client already has several IDs to help texts defined,
385                it could therefore be a good idea to have a look in the
386                program to see if there already is an external id to use for the
387                particular help text.
388              </para>
389            </listitem>
390          </varlistentry>
391          <varlistentry>
392            <term>
393              <sgmltag class="attribute">title</sgmltag>
394            </term>
395            <listitem>
396              <para>
397                Is directly connected to the name/title property for a help text
398                item in BASE2.
399              </para>
400            </listitem>
401          </varlistentry>
402          <varlistentry>
403            <term>
404              <sgmltag class="attribute">webonly</sgmltag>
405            </term>
406            <listitem>
407              <para>
408                If set to a non-zero value, the contents of the tag
409                will not be outputted in the HTML or PDF documentation.
410                This is useful for minor functionality that is not
411                important enough to be mentioned in the documentation but has
412                a help icon in the web client.
413              </para>
414            </listitem>
415          </varlistentry>
416        </variablelist>
417      </para>
418      <example id="docbook.examples.helptexttag">
419        <title>How to use the help text tag</title>
420<programlisting language="xml">&lt;sect1&gt;
421   &lt;helptext external_id="helptexts.external.id" title="The title"&gt;
422      The text that also should be used as a helptext in the program.
423      &lt;seeother&gt;
424         &lt;other external_id="other.external.id"&gt;
425            Related info here...&lt;/other&gt;
426      &lt;/seeother&gt;
427   &lt;/helptext&gt;
428&lt;/sect1&gt;</programlisting>
429      </example>
430     
431      <sect4 id="docbook.begin.helptext.nohelp">
432        <title>Skip parts of a help text</title>
433        <para>
434          From time to time, it may happen that you find that
435          some parts of the text inside a <sgmltag class="starttag">helptext</sgmltag>
436          tag does not make sense. It may, for example, be a reference to
437          an image or an example, or a link to another chapter or
438          section. Put a <sgmltag class="starttag">nohelp</sgmltag>
439          tag around the problematic part to avoid it from beeing
440          outputted to the help texts.
441        </para>     
442        <programlisting language="xml">&lt;nohelp&gt;see &lt;xref linkend="chapter11" /&gt;&lt;/nohelp&gt;</programlisting>
443      </sect4>
444     
445      <sect4 id="docbook.begin.helptext.link">
446      <title>Link to other help texts</title>
447     
448      <para>
449        You can use <sgmltag class="starttag">seeother</sgmltag> and
450        <sgmltag class="starttag">other</sgmltag>
451        to create links between different help texts. The
452        <sgmltag  class="starttag">seeother</sgmltag>
453        tag does not have any attributes and is just a container for one or more
454        <sgmltag  class="starttag">other</sgmltag> tags. Each tag requires a single attribute.
455      </para>
456        <variablelist>
457          <varlistentry>
458            <term>
459              <sgmltag class="attribute">external_id</sgmltag>
460            </term>
461            <listitem>
462              <para>
463                The external ID of the other help text to link to.
464              </para>
465            </listitem>
466          </varlistentry>
467        </variablelist>
468       
469<programlisting language="xml">&lt;seeother&gt;
470  &lt;other external_id="userpreferences.password"&gt;Change password&lt;/other&gt;
471  &lt;other external_id="userpreferences.other"&gt;Other information&lt;/other&gt;
472&lt;/seeother&gt;</programlisting>
473       
474        <para>
475          We recommend that you place the links at the end of the
476          help text section. The links will not show up in the HTML or PDF version.
477        </para>
478      </sect4>
479     
480      <sect4 id="docbook.begin.helptext.import">
481      <title>Import help texts into BASE</title>
482
483      <para>
484        Import the generated XML-file manually by uploading it from the
485        <filename class="directory">data</filename>
486        directory to the BASE-server's file system and then use the help text importer
487        plugin to import the help text items from that file.
488      </para>
489     
490      <para>
491        The help texts can also be imported by running the TestHelp
492        test program. In short, here are the commands you need to
493        import the help texts:
494      </para>
495     
496<programlisting>ant docbook
497ant test
498cd build/test
499./run.sh TestHelp</programlisting>
500      </sect4>
501     
502    </sect3>
503    <sect3 id="docbook.begin.generate">
504      <title>Generate output</title>
505
506      <sect4 id="docbook.begin.generate.requirements">
507        <title>Requirements</title>
508        <para>
509          Those who have checked out the documentation source from repository or got the
510          source from a distribution package needs to compile it to get the PDF and HTML
511          documentation files. The compilation of the documentation source requires, beside Ant, that the XML-parser
512          Xsltproc is installed on the local computer. More information about
513          XsltProc and how it is installed, can be found at
514          <ulink url="http://xmlsoft.org/XSLT/index.html"></ulink>.
515        </para>
516        <note>
517          <para>
518            There is an xml-parser in newer java-versions that can be used instead of
519            XsltProc but the compilation will most likely take much much longer time.
520            Therefore it's not recommended to be used when generating/compiling the
521            documentation in BASE 2.
522          </para>
523        </note>
524      </sect4>
525      <sect4 id="docbook.begin.generate.compile">
526        <title>Compile - generate output files</title>
527        <para>
528          There are two different types of format that is generated from the documentation
529          source. The format to view the documentation on-line will be the one with
530          chunked HTML pages where each chapter and section of first level are on separate
531          pages/files. The other format is a PDF-file that are most useful for printing
532          and distribution. Those two types of output are generated with the ant-target:
533          <command>ant docbook</command>. This documentation is also generated with
534          <command>ant dist</command>, which will put the output files in the right location for distribution with
535          BASE 2.
536        </para>
537      </sect4>
538    </sect3>
539  </sect2>
540
541  <sect2 id="docbook.usedtags">
542    <title>Docbook tags to use</title>
543    <para>
544      The purpose with this section is to give an overview of those docbook elements that are
545      most common in this documentation and to give some example on how they should be used.
546      There will not be any detailed explanation of the tags here, instead the reader is
547      recommended to get more information from
548      <ulink url="http://www.docbook.org/tdg/en/html/docbook.html">
549        Docbook's documentation
550      </ulink>
551      or other references.
552    </para>
553    <sect3 id="docbook.usedtags.text">
554      <title>Text elements</title>
555      <para>
556       
557      </para>
558      <informaltable frame="none">
559        <tgroup cols="3" rowsep="1" colsep="1">
560          <colspec align="left" />
561          <colspec align="center" />
562          <colspec align="left" />
563          <thead>
564            <row>
565              <entry>Define</entry>
566              <entry>Element to use</entry>
567              <entry>Comments</entry>
568            </row>
569          </thead>
570          <tbody>
571            <row>
572              <entry>Chapter</entry>
573              <entry>
574                <sgmltag class="starttag">chapter</sgmltag>
575              </entry>
576              <entry>
577                <para>
578                  See
579                  <xref linkend="docbook.examples.chapterbody" />
580                </para>
581              </entry>
582            </row>
583            <row>
584              <entry>Title</entry>
585              <entry>
586                <sgmltag class="starttag">title</sgmltag>
587              </entry>
588              <entry>
589                <xref linkend="docbook.examples.chapterbody" />
590                shows how this can be implemented
591              </entry>
592            </row>
593            <row>
594              <entry>Paragraph</entry>
595              <entry>
596                <sgmltag class="starttag">para</sgmltag>
597              </entry>
598              <entry>Used almost everywhere around real text.</entry>
599            </row>
600            <row>
601              <entry>Top-level subsection</entry>
602              <entry>
603                <sgmltag class="starttag">sect1</sgmltag>
604              </entry>
605              <entry>
606                See
607                <xref linkend="docbook.begin.id" />
608              </entry>
609            </row>
610            <row>
611              <entry>Second level section</entry>
612              <entry>
613                <sgmltag class="starttag">sect2</sgmltag>
614              </entry>
615              <entry>
616                See
617                <xref linkend="docbook.begin.id" />
618              </entry>
619            </row>
620            <row>
621              <entry>Third level section</entry>
622              <entry>
623                <sgmltag class="starttag">sect3</sgmltag>
624              </entry>
625              <entry>
626                See
627                <xref linkend="docbook.begin.id" />
628              </entry>
629            </row>
630            <row>
631              <entry>Fourth level section</entry>
632              <entry>
633                <sgmltag class="starttag">sect4</sgmltag>
634              </entry>
635              <entry></entry>
636            </row>
637            <row>
638              <entry>Fith level section</entry>
639              <entry>
640                <sgmltag class="starttag">sect5</sgmltag>
641              </entry>
642              <entry></entry>
643            </row>
644          </tbody>
645        </tgroup>
646      </informaltable>
647
648      <sect4 id="docbook.usedtags.text.keywords">
649        <title>Code elements</title>
650        <para>
651          These elements should be used to mark up words and phrases that have a special
652          meaning in a coding environment, like method names, class names and
653          user inputs, etc.
654        </para>
655        <informaltable frame="none">
656          <tgroup cols="3" rowsep="1" colsep="1">
657            <colspec align="left" />
658            <colspec align="center" />
659            <colspec align="left" />
660            <thead>
661              <row>
662                <entry>Define</entry>
663                <entry>Element to use</entry>
664                <entry>Comment</entry>
665              </row>
666            </thead>
667            <tbody>
668              <row>
669                <entry>Class name</entry>
670                <entry>
671                  <sgmltag class="starttag">classname</sgmltag>
672                </entry>
673                <entry>
674                  The name of a (Java) class.
675                  <sgmltag class="attribute">docapi</sgmltag>-attribute
676                  can be used to link the class to it's javadoc(only
677                  html-version). This is done by setting the attribute to the
678                  package name of the class, like
679                  <synopsis>net.sf.basedb.core</synopsis> 
680                </entry>
681              </row>
682              <row>
683                <entry>Interface name</entry>
684                <entry>
685                  <sgmltag class="starttag">interfacename</sgmltag>
686                </entry>
687                <entry>
688                  The name of an (Java) interface. Has a
689                  <sgmltag class="attribute">docapi</sgmltag>-attribute
690                  which has the same functionality as in
691                  <sgmltag>classname</sgmltag> above.                 
692                </entry>
693              </row>
694              <row>
695                <entry>User input</entry>
696                <entry>
697                  <sgmltag class="starttag">userinput</sgmltag>
698                </entry>
699                <entry>Text that is entered by a user.</entry>
700              </row>
701              <row>
702                <entry>Variable name</entry>
703                <entry>
704                  <sgmltag class="starttag">varname</sgmltag>
705                </entry>
706                <entry>The name of a variable in a program.</entry>
707              </row>
708              <row>
709                <entry>Constant</entry>
710                <entry>
711                  <sgmltag class="starttag">constant</sgmltag>
712                </entry>
713                <entry>The name of a variable in a program.</entry>
714              </row>
715              <row>
716                <entry>Method definition</entry>
717                <entry>
718                  <sgmltag class="starttag">methodsynopsis</sgmltag>
719                </entry>
720                <entry>
721                  See
722                  <xref linkend="docbook.examples.methodimpl" />
723                </entry>
724              </row>
725              <row>
726                <entry>Modifier of a method</entry>
727                <entry>
728                  <sgmltag class="starttag">modifier</sgmltag>
729                </entry>
730                <entry>
731                  See
732                  <xref linkend="docbook.examples.methodimpl" />
733                </entry>
734              </row>
735              <row>
736                <entry>Classification of return value</entry>
737                <entry>
738                  <sgmltag class="starttag">type</sgmltag>
739                </entry>
740                <entry>
741                  See
742                  <xref linkend="docbook.examples.methodimpl" />
743                </entry>
744              </row>
745              <row>
746                <entry>Method name</entry>
747                <entry>
748                  <sgmltag class="starttag">methodname</sgmltag>
749                </entry>
750                <entry>
751                  See
752                  <xref linkend="docbook.examples.methodimpl" />
753                </entry>
754              </row>
755              <row>
756                <entry>No parameter/type</entry>
757                <entry>
758                  <sgmltag class="starttag">void</sgmltag>
759                </entry>
760                <entry>
761                  See
762                  <xref linkend="docbook.examples.methodimpl" />
763                </entry>
764              </row>
765              <row>
766                <entry>Define a parameter</entry>
767                <entry>
768                  <sgmltag class="starttag">methodparam</sgmltag>
769                </entry>
770                <entry>
771                  See
772                  <xref linkend="docbook.examples.methodimpl1" />
773                </entry>
774              </row>
775              <row>
776                <entry>Parameter type</entry>
777                <entry>
778                  <sgmltag class="starttag">type</sgmltag>
779                </entry>
780                <entry>
781                  See
782                  <xref linkend="docbook.examples.methodimpl1" />
783                </entry>
784              </row>
785              <row>
786                <entry>Parameter name</entry>
787                <entry>
788                  <sgmltag class="starttag">parameter</sgmltag>
789                </entry>
790                <entry>
791                  See
792                  <xref linkend="docbook.examples.methodimpl1" />
793                </entry>
794              </row>
795            </tbody>
796          </tgroup>
797        </informaltable>
798        <para>
799          Follow one of the examples below to insert a method definition in the document.
800        </para>
801        <example id="docbook.examples.methodimpl">
802          <title>
803            Method with no arguments and a return value
804          </title>
805<programlisting language="xml">
806&lt;methodsynopsis language="java"&gt;
807   &lt;modifier&gt;public&lt;/modifier&gt;
808   &lt;type&gt;Plugin.MainType&lt;/type&gt;
809   &lt;methodname&gt;getMainType&lt;/methodname&gt;
810   &lt;void /&gt;
811&lt;/methodsynopsis&gt;
812</programlisting>
813        </example>
814        <example id="docbook.examples.methodimpl1">
815          <title>
816            Method with arguments and no return value
817          </title>
818<programlisting language="xml">
819&lt;methodsynopsis language="java"&gt;
820   &lt;modifier&gt;public&lt;/modifier&gt;
821   &lt;void /&gt;
822   &lt;methodname&gt;init&lt;/methodname&gt;
823   &lt;methodparam&gt;
824      &lt;type&gt;SessionControl&lt;/type&gt;
825      &lt;parameter&gt;sc&lt;/parameter&gt;
826   &lt;/methodparam&gt;
827   &lt;methodparam&gt;
828      &lt;type&gt;ParameterValues&lt;/type&gt;
829      &lt;parameter&gt;configuration&lt;/parameter&gt;
830   &lt;/methodparam&gt;
831   &lt;methodparam&gt;
832      &lt;type&gt;ParameterValues&lt;/type&gt;
833      &lt;parameter&gt;job&lt;/parameter&gt;
834   &lt;/methodparam&gt;
835&lt;/methodsynopsis&gt;
836</programlisting>
837        </example>
838       
839      </sect4>
840      <sect4 id="docbook.usedtags.text.gui">
841        <title>Gui elements</title>
842        <para>
843          Docbook has some elements that can be used to symbolize gui items in a program.
844          Following list contains the ones that are most common in this document.
845        </para>
846        <informaltable frame="none">
847          <tgroup cols="3" rowsep="1" colsep="1">
848            <colspec align="left" />
849            <colspec align="center" />
850            <colspec align="left" />
851            <thead>
852              <row>
853                <entry>Define</entry>
854                <entry>Element to use</entry>
855                <entry>Comment</entry>
856              </row>
857            </thead>
858            <tbody>
859              <row>
860                <entry>Button</entry>
861                <entry>
862                  <sgmltag class="starttag">guibutton</sgmltag>
863                </entry>
864                <entry></entry>
865              </row>
866              <row>
867                <entry>Label</entry>
868                <entry>
869                  <sgmltag class="starttag">guilabel</sgmltag>
870                </entry>
871                <entry></entry>
872              </row>
873              <row>
874                <entry>Menu choice</entry>
875                <entry>
876                  <sgmltag class="starttag">menuchoice</sgmltag>
877                </entry>
878                <entry></entry>
879              </row>
880              <row>
881                <entry>Menu</entry>
882                <entry>
883                  <sgmltag class="starttag">guimenu</sgmltag>
884                </entry>
885                <entry></entry>
886              </row>
887              <row>
888                <entry>Submenu</entry>
889                <entry>
890                  <sgmltag class="starttag">guisubmenu</sgmltag>
891                </entry>
892                <entry></entry>
893              </row>
894              <row>
895                <entry>Menu item</entry>
896                <entry>
897                  <sgmltag class="starttag">guimenuitem</sgmltag>
898                </entry>
899                <entry></entry>
900              </row>
901              <row>
902                <entry>Icon</entry>
903                <entry>
904                  <sgmltag class="starttag">guiicon</sgmltag>
905                </entry>
906                <entry></entry>
907              </row>
908            </tbody>
909          </tgroup>
910        </informaltable>
911        <para>
912          <xref linkend="docbook.examples.guielements" />
913          shows how the menu choice in figure
914          <xref linkend="docbook.figures.menuchoice" />
915          can be described.
916        </para>
917        <figure id="docbook.figures.menuchoice">
918          <title>Menu choice</title>
919          <screenshot>
920            <mediaobject>
921              <imageobject>
922                <imagedata 
923                  fileref="figures/menuchoice.png" format="PNG" 
924                />
925              </imageobject>
926            </mediaobject>
927          </screenshot>
928        </figure>
929        <example id="docbook.examples.guielements">
930          <title>Describe a menu choice</title>
931<programlisting language="xml">
932&lt;menuchoice&gt;
933   &lt;guimenu&gt;Administrate&lt;/guimenu&gt;
934   &lt;guisubmenu&gt;Plugins&lt;/guisubmenu&gt;
935   &lt;guimenuitem&gt;Types&lt;/guimenuitem&gt;
936&lt;/menuchoice&gt;
937</programlisting>
938          <para>
939            In the text it will look like this:
940            <menuchoice>
941              <guimenu>Administrate</guimenu>
942              <guisubmenu>Plugins</guisubmenu>
943              <guimenuitem>Types</guimenuitem>
944            </menuchoice>
945          </para>
946        </example>
947      </sect4>
948    </sect3>
949    <sect3 id="docbook.usedtags.images">
950      <title>Images and figures</title>
951      <para>
952        Images and figures are normally implemented like the following example. The
953        image-file must be located in
954        <filename class="directory">doc/src/docbook/figures</filename>,
955        otherwise the image will not be visible in the generated output files.
956      </para>
957
958      <example id="docbook.examples.screenshot">
959        <title>Screen-shot in the documentation</title>
960        <para>
961          <xref linkend="webclient.figures.homepage" />
962          is implemented with the following code
963        </para>
964<programlisting language="xml">&lt;figure id="docbook.figures.menuchoice"&gt;
965  &lt;title&gt;The home page&lt;/title&gt;
966  &lt;screenshot&gt;
967    &lt;mediaobject&gt;
968      &lt;imageobject&gt;
969        &lt;imagedata
970          scalefit="1"
971          width="100%"
972          fileref="figures/homapage.png" format="PNG"
973        /&gt;
974      &lt;/imageobject&gt;
975    &lt;/mediaobject&gt;
976  &lt;/screenshot&gt;
977&lt;/figure&gt;</programlisting>
978      </example>
979      <warning>
980        <para>
981          When using images in docbook you will always have problems with image
982          resolution and scaling. Since we are generating output for both HTML
983          and PDF it is even worse. What we have found to work is this:
984         
985          <itemizedlist>
986          <listitem>
987            <para>
988            The screenshots must be saved without any resolution information
989            in them, or with the resolution set to 96 dpi. We have configured PDF to
990            use 96 dpi instead of 72 dpi to make the HTML and PDF output
991            look as similar as possible.
992            </para>
993          </listitem>
994         
995          <listitem>
996            <para>
997            Scaling in HTML has been disabled. The images will always be the
998            same size (number of pixels) as they actually are. Please, do not
999            make the screenshots too wide!
1000           
1001            <tip>
1002              <para>
1003                Change your BASE preferences, see
1004                <xref linkend="webclient.configuration.preferences" />,
1005                to a smaller font size or use the zoom functionality in the web
1006                browser to make more information fit in the same image width.
1007              </para>
1008            </tip>
1009           
1010            </para>
1011          </listitem>
1012         
1013          <listitem>
1014            <para>
1015            For small images, less than the width of the PDF page,
1016            do not specify scaling factors or widths.
1017            </para>
1018          </listitem>
1019         
1020          <listitem>
1021            <para>
1022            Images that are wider than the PDF page will be clipped. To
1023            prevent this you must add the following attributes to the
1024            <sgmltag class="starttag">imagedata</sgmltag> tag:
1025            <code>scalefit="1" width="100%"</code>. This will scale down
1026            the image so that it fits the available width.
1027            </para>
1028          </listitem>
1029         
1030          <listitem>
1031            <para>
1032            If you still need to scale the image differently in the PDF use
1033            the <sgmltag>width</sgmltag> and <sgmltag>depth</sgmltag>
1034            attributes.
1035            </para>
1036          </listitem>
1037          </itemizedlist>
1038        </para>
1039      </warning>
1040    </sect3>
1041    <sect3 id="docbook.usedtags.examples">
1042      <title>Examples and program listing</title>
1043      <para>
1044        Following describes how to insert an example in the documentation.The examples in
1045        this document are often some kind of program listing but they can still be examples
1046        of something else.
1047      </para>
1048      <warning>
1049        <title>Use spaces instead of tabs for indentation</title>
1050        <para>
1051          Use spaces for indentation in program listing, this is because of the
1052          tab-indentations will sooner or later cause corrupt text.
1053        </para>
1054      </warning>
1055
1056      <itemizedlist>
1057        <listitem>
1058          <simpara>
1059            The verbatim text is splitted into several lines if the text contains
1060            more then 80 characters. This could give the text an unwanted look and
1061            it's therefore recommended to manually insert new lines to have controll
1062            over layout of the text
1063          </simpara>
1064        </listitem>
1065        <listitem>
1066          <simpara>
1067            We have added support for syntax highlightning of program
1068            examples in the HTML version. To enable it add a
1069            <sgmltag class="attribute">language</sgmltag>
1070            attribute with one of the following values: <constant>java</constant>,
1071            <constant>xml</constant> or <constant>sql</constant>. The highlightning engine
1072            support more languages. To add support for those in docbook, change
1073            the <filename>customized.chunked.xsl</filename> file. The syntax highlightning
1074            engine doesn't handle markup inside the <sgmltag class="starttag">programlisting</sgmltag>
1075            tag very well. You should avoid that. By default, java program examples
1076            include line numbering, but not xml examples. To disable line numbering
1077            for java add <constant>:nogutter</constant> to the <sgmltag>language</sgmltag> 
1078            attribute: <constant>&lt;programlisting language="java:nogutter"&gt;</constant>.
1079            To enable line numbering for xml add <constant>:gutter</constant> to the <sgmltag>language</sgmltag> 
1080            attribute: <constant>&lt;programlisting language="xml:gutter"&gt;</constant>.
1081          </simpara>
1082        </listitem>
1083      </itemizedlist>
1084
1085      <example id="docbook.examples.example">
1086        <title>Example in the documentation</title>
1087        <para>
1088          This shows how 
1089          <xref linkend="net.sf.basedb.core.plugin.Plugin.getAbout" />
1090          is written in the corresponding XML-file.
1091        </para>
1092<programlisting language="xml">
1093&lt;example id="net.sf.basedb.core.plugin.Plugin.getAbout"&gt;
1094   &lt;title&gt;A typical implementation stores this information
1095      in a static field&lt;/title&gt;
1096   &lt;programlisting language="java"&gt;
1097private static final About about = new AboutImpl
1098(
1099   "Spot images creator",
1100   "Converts a full-size scanned image into smaller preview jpg " +
1101   "images for each individual spot.",
1102   "2.0",
1103   "2006, Department of Theoretical Physics, Lund University",
1104   null,
1105   "base@thep.lu.se",
1106   "http://base.thep.lu.se"
1107);
1108 
1109public About getAbout()
1110{
1111   return about;
1112}
1113&lt;/programlisting&gt;
1114&lt;/example&gt;
1115</programlisting>
1116      </example>     
1117    </sect3>
1118    <sect3 id="docbook.usedtags.admonitions">
1119      <title>Admonitions</title>
1120      <para>
1121        The admonitions that are used in this document can be found in the table below.
1122      </para>
1123      <informaltable frame="none">
1124        <tgroup cols="3" rowsep="1" colsep="1">
1125          <colspec align="left" />
1126          <colspec align="center" />
1127          <colspec align="left" />
1128          <thead>
1129            <row>
1130              <entry>Define</entry>
1131              <entry>Element to use</entry>
1132              <entry>Comment</entry>
1133            </row>
1134          </thead>
1135          <tbody>
1136            <row>
1137              <entry>Warning text</entry>
1138              <entry>
1139                <sgmltag class="starttag">warning</sgmltag>
1140              </entry>
1141              <entry></entry>
1142            </row>
1143            <row>
1144              <entry>Notification text</entry>
1145              <entry>
1146                <sgmltag class="starttag">note</sgmltag>
1147              </entry>
1148              <entry></entry>
1149            </row>
1150            <row>
1151              <entry>A tip</entry>
1152              <entry>
1153                <sgmltag class="starttag">tip</sgmltag>
1154              </entry>
1155              <entry></entry>
1156            </row>
1157            <row>
1158              <entry>Important text</entry>
1159              <entry>
1160                <sgmltag class="starttag">important</sgmltag>
1161              </entry>
1162              <entry></entry>
1163            </row>
1164            <row>
1165              <entry>Something to be cautious about</entry>
1166              <entry>
1167                <sgmltag class="starttag">caution</sgmltag>
1168              </entry>
1169              <entry></entry>
1170            </row>
1171          </tbody>
1172        </tgroup>
1173      </informaltable>
1174    </sect3>
1175    <sect3 id="docbook.usedtags.lists">
1176      <title>Lists</title>
1177      <para>
1178        Following items can be used to define different kind of lists in the documentation.
1179        Some common elements for the lists are also described here.
1180      </para>
1181      <informaltable frame="none">
1182        <tgroup cols="3" rowsep="1" colsep="1">
1183          <colspec align="left" />
1184          <colspec align="center" />
1185          <colspec align="left" />
1186          <thead>
1187            <row>
1188              <entry>Define</entry>
1189              <entry>Element</entry>
1190              <entry>Comment</entry>
1191            </row>
1192          </thead>
1193          <tbody>           
1194            <row>
1195              <entry>None-ordered list</entry>
1196              <entry>
1197                <sgmltag class="starttag">itemizedlist</sgmltag>
1198              </entry>
1199              <entry></entry>
1200            </row>
1201            <row>
1202              <entry>Term definition list</entry>
1203              <entry>
1204                <sgmltag class="starttag">variablelist</sgmltag>
1205              </entry>
1206              <entry></entry>
1207            </row>
1208            <row>
1209              <entry>Ordered list</entry>
1210              <entry>
1211                <sgmltag class="starttag">orderedlist</sgmltag>
1212              </entry>
1213              <entry></entry>
1214            </row>
1215            <row>
1216              <entry>List item</entry>
1217              <entry>
1218                <sgmltag class="starttag">listitem</sgmltag>
1219              </entry>
1220              <entry></entry>
1221            </row>
1222          </tbody>
1223        </tgroup>
1224      </informaltable>
1225      <para>The example below shows how to create a list for term definition in the text.</para>
1226      <example id="docbook.examples.variablelist">
1227        <title>Example how to write a variable list</title>
1228<programlisting language="xml">
1229&lt;variablelist&gt;
1230   &lt;varlistentry&gt;
1231      &lt;term&gt;Term1&lt;/term&gt;
1232      &lt;listitem&gt;
1233         &lt;para&gt;
1234            Definition/explanation of the term
1235         &lt;/para&gt;
1236      &lt;/listitem&gt;
1237   &lt;/varlistentry&gt;
1238   
1239   &lt;varlistentry&gt;
1240      &lt;term&gt;Term2&lt;/term&gt;
1241      &lt;listitem&gt;
1242         &lt;para&gt;
1243            Definition/explanation of the term
1244         &lt;/para&gt;
1245      &lt;/listitem&gt;
1246   &lt;/varlistentry&gt;
1247&lt;/variablelist&gt;</programlisting>
1248      </example>
1249    </sect3>
1250   
1251    <sect3 id="docbook.usedtags.links">
1252      <title>Link elements</title>
1253      <para></para>
1254      <informaltable frame="none">
1255        <tgroup cols="3" rowsep="1" colsep="1">
1256          <colspec align="left" />
1257          <colspec align="center" />
1258          <colspec align="left" />
1259          <thead>
1260            <row>
1261              <entry>Define</entry>
1262              <entry>Element</entry>
1263              <entry>Comment</entry>
1264            </row>
1265          </thead>
1266          <tbody>
1267            <row>
1268              <entry>Cross reference</entry>
1269              <entry>
1270                <sgmltag class="starttag">xref linkend=""</sgmltag>
1271              </entry>
1272              <entry>Use this to linke to other parts of the document.</entry>
1273            </row>
1274            <row>
1275              <entry>Cross reference with own text</entry>
1276              <entry>
1277                <sgmltag class="starttag">link</sgmltag>
1278              </entry>
1279              <entry>
1280                Can be used as an alternative to
1281                <sgmltag>xref</sgmltag>
1282              </entry>
1283            </row>
1284            <row>
1285              <entry>External URLs</entry>
1286              <entry>
1287                <sgmltag class="starttag">ulink url=""</sgmltag>
1288              </entry>
1289              <entry></entry>
1290            </row>
1291          </tbody>
1292        </tgroup>
1293      </informaltable>
1294      <example id="docbook.examples.links">
1295        <title>Links</title>
1296<programlisting language="xml">
1297&lt;xref linkend="docbook.usedtags.links" /&gt;
1298&lt;link linkend="docbook.usedtags.links"&gt;Link to this section&lt;/link&gt;
1299&lt;ulink url="http://base.thep.lu.se"&gt;Base2's homepage&lt;/ulink&gt;
1300</programlisting>
1301        <para>
1302          The first element will autogenerate the linked section's/chapter's title as a
1303          hyperlinked text. As an alternative to
1304          <sgmltag>xref</sgmltag>
1305          is
1306          <sgmltag>link</sgmltag>
1307          that lets you write your own hyperlinked text. The third and last one should be
1308          used to link to any URL outside the document.
1309        </para>
1310      </example>
1311    </sect3>
1312  </sect2>
1313 
1314  </sect1>
1315 
1316  <sect1 id="documentation.magicdraw">
1317    <title>Create UML diagrams with MagicDraw</title>
1318
1319    <para>
1320      UML or UML-like diagrams are used to document the relationship of
1321      classes in the Core API. To create the diagrams we use the community edition (version 12.5)
1322      of a program called MagicDraw. This is a Java program and it should be possible
1323      to run it on any platform which has at least a Java 1.5 runtime.
1324      To get more information about MagicDraw and to download the program
1325      go to their website:
1326      <ulink url="http://www.magicdraw.com/">http://www.magicdraw.com/</ulink>
1327    </para>
1328   
1329
1330    <sect2 id="magicdraw.organisation">
1331      <title>Organisation</title>
1332     
1333      <para>
1334        All classes and diagrams are in a single UML file. It can be
1335        found at <filename>&lt;base-dir&gt;/doc/src/uml/base.mdzip</filename>
1336      </para>
1337     
1338      <para>
1339        Everything in MagicDraw has been organised into packages and
1340        modules. At the top we have the <code>Core layer</code> and
1341        the <code>Data layer</code>. The <code>Java</code> moduled is
1342        for classes that related to the Java programming language, such
1343        as <code>Map</code> and <code>Set</code> that are not pre-defined
1344        by MagicDraw.
1345      </para>
1346     
1347      <figure id="magicdraw.figures.organisation">
1348        <title>MagicDraw organisation</title>
1349        <screenshot>
1350          <mediaobject>
1351            <imageobject>
1352              <imagedata 
1353                fileref="figures/magicdraw/organisation.png" format="PNG" />
1354            </imageobject>
1355          </mediaobject>
1356        </screenshot>
1357      </figure>
1358    </sect2>
1359   
1360    <sect2 id="magicdraw.classes">
1361      <title>Classes</title>
1362        <para>
1363          New classes should be added to one of the subpackages inside
1364          the <code>Data layer/Classes</code> or <code>Core layer/Classes</code>
1365          modules. It is very simple:
1366        </para>
1367         
1368        <orderedlist>
1369        <listitem>
1370          <para>
1371          Select the subpackage in the overview and click with the right mouse button.
1372          </para>
1373        </listitem>
1374        <listitem>
1375          <para>
1376          Select the
1377          <menuchoice>
1378            <guimenu>New element</guimenu>
1379            <guimenuitem>Class</guimenuitem>
1380          </menuchoice>
1381          menu item in the menu that pops up.
1382          </para>
1383        </listitem>
1384        <listitem>
1385          <para>
1386          The overview will expand to add a new class. Enter the name of the class
1387          and press enter.
1388          </para>
1389        </listitem>
1390        </orderedlist>
1391       
1392        <sect3 id="magicdraw.classes.data">
1393          <title>Data layer classes</title>
1394         
1395          <para>
1396            If you added a class to the data layer you also need to
1397            record some important information.
1398          </para>
1399
1400          <itemizedlist>
1401          <listitem>
1402            <para>
1403            The database table the data is stored in
1404            </para>
1405          </listitem>
1406          <listitem>
1407            <para>
1408            If the second-level cache is enabled or not
1409            </para>
1410          </listitem>
1411          <listitem>
1412            <para>
1413            If proxies are enabled or not
1414            </para>
1415          </listitem>
1416          <listitem>
1417            <para>
1418            The superclass
1419            </para>
1420          </listitem>
1421          <listitem>
1422            <para>
1423            Implemented interfaces
1424            </para>
1425          </listitem>
1426          <listitem>
1427            <para>
1428            Simple properties, ie. strings, numbers, dates
1429            </para>
1430          </listitem>
1431          <listitem>
1432            <para>
1433            Associations to other classes
1434            </para>
1435          </listitem>
1436          </itemizedlist>
1437
1438          <para>
1439            To achive this we have slightly altered the meaning of some UML symbols.
1440            For example we use the access modified symbols (+, ~ and -) to indicate
1441            if a property is updatable or not.
1442          </para>
1443
1444          <sect4 id="magicdraw.classes.data.tags">
1445            <title>Setting tagged values</title>
1446           
1447            <para>
1448              Some of the information needed is specified as <emphasis>tagged values</emphasis>
1449              that can be attached to a class.
1450              Double-click on the new class to bring up it's properties dialog
1451              box. Switch to the <guilabel>Tags</guilabel> configuration page.
1452              We have defined the following tags:
1453            </para>
1454             
1455            <variablelist>
1456            <varlistentry>
1457              <term><guilabel>table</guilabel></term>
1458              <listitem>
1459                <para>
1460                The name of the database table where the items should be stored.
1461                </para>
1462              </listitem>
1463            </varlistentry>
1464            <varlistentry>
1465              <term><guilabel>cache</guilabel></term>
1466              <listitem>
1467                <para>
1468                The number of items to store in the second-level cache of Hibernate.
1469                Only specify a value if caching should be enabled.
1470                </para>
1471              </listitem>
1472            </varlistentry>
1473            <varlistentry>
1474              <term><guilabel>proxy</guilabel></term>
1475              <listitem>
1476                <para>
1477                A boolean flag to indicate if proxies should be used or not.
1478                </para>
1479              </listitem>
1480            </varlistentry>
1481            <varlistentry>
1482              <term><guilabel>extends</guilabel></term>
1483              <listitem>
1484                <para>
1485                Select the superclass of this class.
1486                </para>
1487              </listitem>
1488            </varlistentry>
1489            <varlistentry>
1490              <term><guilabel>implements</guilabel></term>
1491              <listitem>
1492                <para>
1493                Specify which interfaces the class implements. To save space
1494                we use the following one-letter abbreviations:
1495                </para>
1496               
1497                <itemizedlist>
1498                <listitem><para>A = AnnotatableData</para></listitem>
1499                <listitem><para>B = BatchableData</para></listitem>
1500                <listitem><para>D = DiskConsumableData</para></listitem>
1501                <listitem><para>E = ExtendableData</para></listitem>
1502                <listitem><para>F = FileAttachableData</para></listitem>
1503                <listitem><para>N = NameableData</para></listitem>
1504                <listitem><para>O = OwnableData</para></listitem>
1505                <listitem><para>R = RemoveableData</para></listitem>
1506                <listitem><para>S = ShareableData</para></listitem>
1507                <listitem><para>T = SystemData</para></listitem>
1508                </itemizedlist>
1509              </listitem>
1510            </varlistentry>
1511            </variablelist>
1512           
1513            <figure id="magicdraw.figures.classtags">
1514              <title>Setting tagged values</title>
1515              <screenshot>
1516                <mediaobject>
1517                  <imageobject>
1518                    <imagedata 
1519                      scalefit="1" width="100%"
1520                      fileref="figures/magicdraw/classtags.png" format="PNG" />
1521                  </imageobject>
1522                </mediaobject>
1523              </screenshot>
1524            </figure>
1525          </sect4>
1526         
1527          <sect4 id="magicdraw.classes.data.properties">
1528            <title>Specifying simple properties for a class</title>
1529            <para>
1530              Simple properties are strings, numbers, dates, etc. that are part of an object.
1531              Properties are entered as attributes of the class. The easiest way to enter
1532              properties are by typing directly in a diagram. It can also be done
1533              from the <guilabel>Attributes</guilabel> configuration page.
1534            </para>
1535           
1536            <para>
1537              Each attribute must have information about:
1538            </para>
1539           
1540            <itemizedlist>
1541            <listitem>
1542              <para>
1543              The name of the attribute, ie. the name of the get/set method without the
1544              get or set part and starting with a lowercase letter.
1545              </para>
1546            </listitem>
1547            <listitem>
1548              <para>
1549              The data type: enter or select the Java object type in the
1550              <guilabel>Type</guilabel> selection list.
1551              </para>
1552            </listitem>
1553            <listitem>
1554              <para>
1555              If null values are allowed or not: specify a multiplicity of 1 if a
1556              non-null value is required.
1557              </para>
1558            </listitem>
1559            <listitem>
1560              <para>
1561              If it is modifiable or not. From the <guilabel>Visibility</guilabel> 
1562              list, select one of the following:
1563              </para>
1564             
1565              <itemizedlist>
1566              <listitem>
1567                <para>
1568                public (+): the attribute is modifiable. This translates to public get and set methods.
1569                </para>
1570              </listitem>
1571              <listitem>
1572                <para>
1573                package (~): the attribute can only be set once. This translates to public get and set methods
1574                and an <code>update="false"</code> tag in the Hibernate mapping.
1575                </para>
1576              </listitem>
1577              <listitem>
1578                <para>
1579                private (-): the attribute is private (will this ever be used?).
1580                This translates to package private get and set methods.
1581                </para>
1582              </listitem>
1583              </itemizedlist>
1584             
1585            </listitem>
1586            </itemizedlist>
1587     
1588            <figure id="magicdraw.figures.attributes">
1589              <title>Class attributes</title>
1590              <screenshot>
1591                <mediaobject>
1592                  <imageobject>
1593                    <imagedata 
1594                      scalefit="1" width="100%"
1595                      fileref="figures/magicdraw/attributes.png" format="PNG" />
1596                  </imageobject>
1597                </mediaobject>
1598              </screenshot>
1599            </figure>         
1600          </sect4>
1601         
1602          <sect4 id="magicdraw.classes.data.associations">
1603            <title>Associations to other classes</title>
1604
1605            <para>
1606              Associations to other classes are easiest created from
1607              a diagram view by drawing an <guilabel>Association</guilabel>
1608              link between the two classes. The ends should be given a name,
1609              multiplicity and visibility should be selected. For the visibility
1610              we use the same options as for attributes, but with a slightly different
1611              interpretation.
1612            </para>
1613           
1614            <itemizedlist>
1615            <listitem>
1616              <para>
1617              public (+): the association is modifiable. This translates to public get and
1618              set methods for many-to-one associations. Many-to-many associations must have a
1619              package private set method since the set or map must never be replaced.
1620              </para>
1621            </listitem>
1622 
1623            <listitem>
1624              <para>
1625              package (~): same as public but the association cannot be changed once it has
1626              been created. For many-to-one associations an <code>update="false"</code> tag in
1627              the Hibernate mapping should be used. For many-to-many association there is
1628              no corresponding tag. It will be the responsibility of the core to make sure
1629              no modifications are done.
1630              </para>
1631            </listitem>
1632           
1633            <listitem>
1634              <para>
1635              private (-): this is the inverse end of an association. Only used for one-to-many
1636              and many-to-many associations and translates to package private get and set
1637              methods.
1638              </para>
1639            </listitem>
1640            </itemizedlist>
1641           
1642            <para>
1643              If the association involves a join table (many-to-many) the name of that
1644              table should be entered as a tagged value to the association.
1645            </para>
1646           
1647            <para>
1648              If the association have values attached to it, use the
1649              <guilabel>Association class</guilabel> link type and enter information about
1650              the values in the attached class.
1651            </para>         
1652
1653          </sect4>
1654
1655          <para>
1656            A lot more can be said about this, but
1657            it is probably better to have a look at already existing diagrams if you have
1658            any questions. The authentication overview shown below is one of the most
1659            complex diagrams that involves many different links.
1660          </para>
1661         
1662          <figure id="magicdraw.figures.realexample">
1663            <title>Authentication UML diagram</title>
1664            <screenshot>
1665              <mediaobject>
1666                <imageobject>
1667                  <imagedata 
1668                    scalefit="1" width="100%"
1669                    fileref="figures/uml/datalayer.authentication.png" format="PNG" />
1670                </imageobject>
1671              </mediaobject>
1672            </screenshot>
1673          </figure>
1674         
1675        </sect3>
1676       
1677        <sect3 id="magicdraw.classes.core">
1678          <title>Core layer classes</title>
1679          <para>
1680          TODO
1681          </para>
1682        </sect3>
1683       
1684      </sect2>
1685     
1686      <sect2 id="magicdraw.diagrams">
1687        <title>Diagrams</title>
1688
1689        <sect3 id="magicdraw.diagrams.create">
1690          <title>Create a new diagram</title>
1691         
1692          <para>
1693            New diagrams should be added to one of the subpackages inside
1694            the <code>Data layer/Diagrams</code> or <code>Core layer/Diagrams</code>
1695            modules. It is very simple:
1696          </para>
1697 
1698          <orderedlist>
1699          <listitem>
1700            <para>
1701            Select the subpackage in the overview and click with the right mouse button.
1702            </para>
1703          </listitem>
1704          <listitem>
1705            <para>
1706            Select the
1707            <menuchoice>
1708              <guimenu>New diagram</guimenu>
1709              <guimenuitem>Class diagram</guimenuitem>
1710            </menuchoice>
1711            menu item in the menu that pops up.
1712            </para>
1713          </listitem>
1714          <listitem>
1715            <para>
1716            The overview will expand to add a new diagram. A new empty diagram
1717            frame is also opened on the right part of the screen. Enter the name of the diagram
1718            and press enter.
1719            </para>
1720          </listitem>
1721          </orderedlist>
1722 
1723          <note>
1724            <title>Only class diagrams are fully supported</title>
1725            <para>
1726              The community edition of MagicDraw only has full support for
1727              class diagrams. The other diagram types has limitations, in the number of
1728              objects that can be created.
1729            </para>
1730          </note>
1731         
1732          <para>
1733            To display a class in a diagram, simply select the class in the overview
1734            and drag it into to the diagram.
1735          </para>
1736        </sect3>
1737
1738        <sect3 id="magicdraw.diagrams.appearance">
1739          <title>Visual appearance and style</title>
1740           
1741          <para>
1742            We have defined several different display style for classes. To set a
1743            style for a class right click on it in a diagram and select the
1744            <menuchoice><guimenuitem>Symbol properties</guimenuitem></menuchoice>
1745            menu item. In the bottom of the
1746            popup, use the <guilabel>Apply style</guilabel> selection list to select
1747            one of the predefined styles.
1748          </para>
1749           
1750          <itemizedlist>
1751          <listitem>
1752            <para>
1753            Data class: Use this style for all primary data classes in a diagram. It will
1754            display all info that we are interested in.
1755            </para>
1756          </listitem>
1757          <listitem>
1758            <para>
1759            External class: Use this style for related classes that are actaully part of
1760            another diagram. This style will hide all information except the class name.
1761            This style can be used for both data layer and core layer classes.
1762            </para>
1763          </listitem>
1764          <listitem>
1765            <para>
1766            Association class: Use this style for classes that hold information
1767            related to an association between two other classes. Classes with this
1768            style are displayed in a different color. This style can be used for both
1769            data layer and core layer classes.
1770            </para>
1771          </listitem>
1772          </itemizedlist>     
1773        </sect3>
1774
1775        <sect3 id="magicdraw.diagrams.save">
1776          <title>Save diagram as image</title>
1777          <para>
1778            When the diagram is complete, save it as a PNG image in the
1779            <filename class="directory">&lt;base-dir&gt;/doc/src/docbook/figures/uml</filename>
1780            directory.
1781          </para>
1782        </sect3>
1783      </sect2>     
1784     
1785  </sect1>
1786 
1787  <sect1 id="documentation.javadoc">
1788    <title>Javadoc</title>
1789
1790    <para>
1791      Existing Javadoc documentation is available online at:
1792      <ulink url="http://base.thep.lu.se/chrome/site/doc/api/index.html"
1793        >http://base.thep.lu.se/chrome/site/doc/api/index.html</ulink>.
1794    </para>
1795   
1796    <para>
1797      The BASE API is devided into four different parts on the package level.
1798    </para>
1799   
1800    <itemizedlist>
1801    <listitem>
1802      <para>
1803      Public API - All classes and methods in the package are public. May be
1804      used by client applications and plug-ins. In general, backwards compatibility
1805      will be maintained.
1806      </para>
1807    </listitem>
1808   
1809    <listitem>
1810      <para>
1811      Extension API - All classes and methods in the package intended for
1812      internal extensions only. Not part of the public API and should not be used
1813      by client applications or plug-in.
1814      </para>
1815    </listitem>
1816
1817    <listitem>
1818      <para>
1819      Internal API - All classes and methods in the package are internal. Should
1820      never be used by client application or plug-ins.
1821      </para>
1822    </listitem>
1823
1824    <listitem>
1825      <para>
1826      Mixed Public and Internal API - Contains a mix of public and internal
1827      classes. Check the javadoc for each class/method before using it.
1828      </para>
1829    </listitem>
1830
1831    </itemizedlist>
1832    <para>
1833      Introduction to the Base API and it's parts can be
1834      found on the start page of Base Javadoc. Plugin developers and other external developers
1835      should pay most attention to the public API. What we consider to be the public part of the API is discussed in
1836      <xref linkend="api_overview.public_api" />.
1837    </para>
1838
1839    <sect2 id="javadoc.writing">
1840      <title>Writing javadoc</title>
1841      <para>
1842        This section only covers Javadoc comments, how to write proper none-Javadoc comments
1843        are described in
1844        <xref linkend="core_ref.rules.style" />
1845      </para>
1846      <para>
1847        General information about Javadoc and how it is written in a proper way can be found
1848        at
1849        <ulink url="http://java.sun.com/j2se/javadoc/writingdoccomments/index.html">
1850          http://java.sun.com/j2se/javadoc/writingdoccomments/index.html</ulink>.
1851        The rule when coding in Base is that all packages, classes, interfaces, public
1852        methods and public attributes must be commented in Javadoc style. It is also
1853        recommended that private and protected methods has some comments, but maybe not as
1854        detailed as the public ones. Below follow more specific details what to have in mind
1855        when writing Javadoc in the Base project.
1856      </para>
1857      <variablelist>
1858        <varlistentry>
1859          <term>General</term>
1860          <listitem>
1861            <para>
1862              General things that are common for all Javadocs comments in Base.
1863            </para>
1864            <itemizedlist>
1865              <listitem>
1866                <para>All comments should be in English.</para>
1867              </listitem>
1868              <listitem>
1869                <para>Do not start each new line of comment with a star.</para>
1870              </listitem>
1871              <listitem>
1872                <para>
1873                  If a comment only should be shown in the internal documentation
1874                  and not in the public, it should be tagged with
1875                  <synopsis>@base.internal</synopsis>
1876                </para>
1877              </listitem>
1878            </itemizedlist>
1879          </listitem>
1880        </varlistentry>
1881       
1882        <varlistentry>
1883          <term>Package comments</term>
1884          <listitem>
1885            <para>
1886              Package comments should be placed in a file named <filename>package.html</filename>
1887              in the source code directory.
1888            </para>
1889           
1890            <important>
1891              <title>Is the package public or internal?</title>
1892              <para>
1893                This information should be added in the <filename>package.html</filename>
1894                file. You must also modify the <filename>build.xml</filename> file.
1895                The <emphasis>doc.javadoc</emphasis> target contains
1896                <sgmltag class="starttag">group</sgmltag> tags which lists all
1897                packages that are part of each group.
1898              </para>
1899            </important>
1900           
1901          </listitem>
1902        </varlistentry>
1903       
1904        <varlistentry>
1905          <term>Class and interface comments</term>
1906          <listitem>
1907            <para>
1908              A comment for a class or interface should start with a general
1909              description. The class comment should then give information about what
1910              the class can be used for, while an interface comment more should inform
1911              which kinds of classes that are supposed to implement the interface.
1912            </para>
1913            <variablelist>
1914              <varlistentry>
1915                <term><synopsis>@author</synopsis></term>
1916                <listitem>
1917                  <para>The first name of the author(s) of the class.</para>
1918                </listitem>
1919              </varlistentry>
1920              <varlistentry>
1921                <term><synopsis>@version</synopsis></term>
1922                <listitem>
1923                  <para>From which version of Base the class is available.</para>
1924                </listitem>
1925              </varlistentry>
1926              <varlistentry>
1927                <term><synopsis>@see</synopsis></term>
1928                <listitem>
1929                  <para>Optional. Links to some related subjects.</para>
1930                </listitem>
1931              </varlistentry>
1932              <varlistentry>
1933                <term><synopsis>@base.modified</synopsis></term>
1934                <listitem>
1935                  <para>
1936                    Optional. Some classes has this tag too. This is for give the
1937                    class-file a time stamp when it is checked in to subversion.
1938                  </para>
1939                </listitem>
1940              </varlistentry>
1941            </variablelist>
1942          </listitem>
1943        </varlistentry>
1944       
1945        <varlistentry>
1946          <term>Method comments</term>
1947          <listitem>
1948            <para>
1949              A method comment should start with a general description of the method
1950              and what it does. The following tags must be present in this order:
1951            </para>
1952            <variablelist>
1953              <varlistentry>
1954                <term>
1955                  <synopsis>@param</synopsis></term>
1956                <listitem>
1957                  <para>
1958                    One tag for each parameter of the method. Make sure to tell
1959                    what values are allowed and what will happen if a disallowed
1960                    value is passed.
1961                  </para>
1962                </listitem>
1963              </varlistentry>
1964              <varlistentry>
1965                <term><synopsis>@return</synopsis></term>
1966                <listitem>
1967                  <para>
1968                    What is returned by the method. Make sure to tell what
1969                    values can be returned (ie. if it can be null).
1970                  </para>
1971                </listitem>
1972              </varlistentry>
1973              <varlistentry>
1974                <term><synopsis>@throws</synopsis></term>
1975                <listitem>
1976                  <para>
1977                    One tag for each exception that the method can throw and
1978                    describe when and why it will be thrown.
1979                  </para>
1980                </listitem>
1981              </varlistentry>
1982              <varlistentry>
1983                <term>
1984                  <synopsis>@since</synopsis>
1985                </term>
1986                <listitem>
1987                  <para>
1988                    Use only this tag together with methods added in a later
1989                    version then the one the class was created in. It holds which
1990                    version the method first was available in.
1991                  </para>
1992                </listitem>
1993              </varlistentry>                           
1994              <varlistentry>
1995                <term>
1996                  <synopsis>@see</synopsis></term>
1997                <listitem>
1998                  <para>
1999                    Optional. Link to relevant information, one tag for each
2000                    link.
2001                  </para>
2002                </listitem>
2003              </varlistentry>
2004            </variablelist>
2005          </listitem>
2006        </varlistentry>
2007       
2008        <varlistentry>
2009          <term>Attribute comments</term>
2010          <listitem>
2011            <para>
2012              If the attribute is a static final, describe what the attribute is for
2013              an where it is typically used. Other attributes can often be explained
2014              through their getter and setter methods.
2015            </para>
2016          </listitem>
2017        </varlistentry>
2018      </variablelist>
2019    </sect2>
2020  </sect1>
2021</chapter>
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