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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>refdbib</title><link rel="stylesheet" type="text/css" href="manual.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.79.1" /><link rel="home" href="index.html" title="RefDB handbook" /><link rel="up" href="ch15.html" title="Chapter 15. Tools for bibliographies" /><link rel="prev" href="ch15.html" title="Chapter 15. Tools for bibliographies" /><link rel="next" href="re21.html" title="refdbnd" /></head><body><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">refdbib</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="ch15.html">Prev</a> </td><th width="60%" align="center">Chapter 15. Tools for bibliographies</th><td width="20%" align="right"> <a accesskey="n" href="re21.html">Next</a></td></tr></table><hr /></div><div class="refentry"><a id="refentry-refdbib"></a><div class="titlepage"></div><div class="refnamediv"><a id="refdbib-name"></a><h2>Name</h2><p>refdbib — the bibliography client of RefDB</p></div><div class="refsynopsisdiv"><a id="refdbib-synopsis"></a><h2>Synopsis</h2><div class="cmdsynopsis"><p><code class="command">refdbib</code> [<code class="option">-d</code> <em class="replaceable"><code>database</code></em>] [<code class="option">-D</code> <em class="replaceable"><code>stylespec-directory</code></em>] [<code class="option">-e</code> <em class="replaceable"><code>log-destination</code></em>] [<code class="option">-E</code> <em class="replaceable"><code>encoding</code></em>] [<code class="option">-f</code> <em class="replaceable"><code>stdin</code></em>] [<code class="option">-h</code> ] [<code class="option">-i</code> <em class="replaceable"><code>IP-address</code></em>] [<code class="option">-l</code> <em class="replaceable"><code>log-level</code></em>] [<code class="option">-L</code> <em class="replaceable"><code>log-file</code></em>] [<code class="option">-m</code> ] [<code class="option">-N</code> <em class="replaceable"><code>number</code></em>] [<code class="option">-p</code> <em class="replaceable"><code>port</code></em>] [<code class="option">-q</code> ] [<code class="option">-r</code> ] [<code class="option">-S</code> <em class="replaceable"><code>style</code></em>] [<code class="option">-t</code> <em class="replaceable"><code>output-type</code></em>] [<code class="option">-T</code> <em class="replaceable"><code>time</code></em>] [<code class="option">-u</code> <em class="replaceable"><code>name</code></em>] [<code class="option">-v</code> ] [<code class="option">-V</code> ] [<code class="option">-w</code> <em class="replaceable"><code>password</code></em>] [<code class="option">-x</code> ] [<code class="option">-y</code> <em class="replaceable"><code>confdir</code></em>] <em class="replaceable"><code>filename</code></em> </p></div></div><div class="refsect1"><a id="refdbib-description"></a><h2>Description</h2><p>refdbib is a command-line client to generate bibliographies with RefDB(7). refdbib reads the contents of <span class="emphasis"><em>filename</em></span>, which contains a list of citations as an XML document according to <span class="emphasis"><em>citationlistx.dtd</em></span>, and sends a bibliography in the requested format to stdout. If no input file is specified, refdbib tries to read the data from stdin. Unless suppressed, it also writes a style specification file (either a DSSSL or an XSLT stylesheet) and a CSS stylesheet for HTML output to your disk.</p><p>refdbib is a low-level tool. It is advisable to use one of the wrappers shipped with RefDB. runbib(1) is a shell script which creates the list of citations, runs refdbib on this list, and transforms the document. refdbnd(1) is a Makefile-based system that encapsulates the bibliography generation and document transformation conveniently.</p><p>This man page describes only the startup options of refdbib. Please consult the RefDB manual (see below) for a description of the input and output formats, as well as for post-processing instructions that are required for some output types.</p></div><div class="refsect1"><a id="refdbib-options"></a><h2>Options</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="option">-d</code> <em class="replaceable"><code>database</code></em></span></dt><dd><p>The name of the default database. You can change the database anytime during an interactive session.</p></dd><dt><span class="term"><code class="option">-D</code> <em class="replaceable"><code>stylespec-directory</code></em></span></dt><dd><p>Specify either a full path or <code class="literal">.</code> to use the current working directory for the output of the style specification and CSS files. The latter case is what you usually want if you run refdbib from the directory where your LaTeX or SMGL/XML document is stored. This is also the default if you do not specify a directory at all.</p></dd><dt><span class="term"><code class="option">-e</code> <em class="replaceable"><code>log-destination</code></em></span></dt><dd><p>log-destination can have the values 0, 1, or 2, or the equivalent strings <span class="emphasis"><em>stderr</em></span>, <span class="emphasis"><em>syslog</em></span>, or <span class="emphasis"><em>file</em></span>, respectively. This value specifies where the log information goes to. <code class="literal">0</code> (zero) means the messages are sent to stderr. They are immediately available on the screen but they may interfere with command output. <code class="literal">1</code> will send the output to the syslog facility. Keep in mind that syslog must be configured to accept log messages from user programs, see the syslog(8) man page for further information. Unix-like systems usually save these messages in <code class="filename">/var/log/user.log</code>. <code class="literal">2</code> will send the messages to a custom log file which can be specified with the <code class="option">-L</code> option.</p></dd><dt><span class="term"><code class="option">-E</code> <em class="replaceable"><code>encoding</code></em></span></dt><dd><p>Select an output character encoding. If this option is not used, the bibliography data will use the character encoding of the database. See iconv_open(3) for a list of available encodings.</p></dd><dt><span class="term"><code class="option">-f</code> <em class="replaceable"><code>stdin</code></em></span></dt><dd><p>This is a crutch to make reading data from stdin possible on platforms that do not allow automatic detection of data on stdin, like Windows/Cygwin. On other platforms, refdbib automatically reads data from stdin if data are available.</p></dd><dt><span class="term"><code class="option">-h</code></span></dt><dd><p>Displays help and usage screen, then exits.</p></dd><dt><span class="term"><code class="option">-i</code> <em class="replaceable"><code>IP-address</code></em></span></dt><dd><p>Set the IP address of the box which is running the application server refdbd(1). Instead of the IP address you can also specify the hostname as long as it can be properly resolved by your system.</p></dd><dt><span class="term"><code class="option">-l</code> <em class="replaceable"><code>log-level</code></em></span></dt><dd><p>Specify the priority up to which events are logged. This is either a number between <code class="literal">0</code> and <code class="literal">7</code> or one of the strings <span class="emphasis"><em>emerg</em></span>, <span class="emphasis"><em>alert</em></span>, <span class="emphasis"><em>crit</em></span>, <span class="emphasis"><em>err</em></span>, <span class="emphasis"><em>warning</em></span>, <span class="emphasis"><em>notice</em></span>, <span class="emphasis"><em>info</em></span>, <span class="emphasis"><em>debug</em></span>, respectively (see also Log level definitions). <code class="option">-1</code> disables logging completely. A low log level like <code class="literal">0</code> means that only the most critical messages are logged. A higher log level means that less critical events are logged as well. <code class="literal">7</code> will include debug messages. The latter can be verbose and abundant, so you want to avoid this log level unless you need to track down problems.</p></dd><dt><span class="term"><code class="option">-L</code> <em class="replaceable"><code>log-file</code></em></span></dt><dd><p>Specify the full path to a log file that will receive the log messages. Typically this would be <code class="filename">/var/log/refdba</code>.</p></dd><dt><span class="term"><code class="option">-m</code></span></dt><dd><p>This switch turns errors caused by missing references (i.e. cited but not available in the database) into warnings, causing refdbib to return 0 instead of an error code.</p></dd><dt><span class="term"><code class="option">-N</code> <em class="replaceable"><code>number</code></em></span></dt><dd><p>Use this option to specify where the numbering of the references is supposed to start. The default is 1. This option comes in handy if you need to cobble together composite bibliographies or per-chapter bibliographies that still need to be numbered consecutively.</p></dd><dt><span class="term"><code class="option">-p</code> <em class="replaceable"><code>port</code></em></span></dt><dd><p>Set the port of the box which is running the application server.</p></dd><dt><span class="term"><code class="option">-q</code></span></dt><dd><p>Start without reading the configuration files. The client will use the compile-time defaults for all values that you do not set with command-line switches.</p></dd><dt><span class="term"><code class="option">-r</code></span></dt><dd><p>Use this option to request a raw instead of a cooked bibliography. Raw bibliographies are not formatted in any way and are processed with the standard DocBook or TEI stylesheets instead of with the RefDB driver files.</p></dd><dt><span class="term"><code class="option">-S</code> <em class="replaceable"><code>style</code></em></span></dt><dd><p>Specifies the bibliography style. This controls the formatting of the bibliography and the in-text citations when the document is processed.</p></dd><dt><span class="term"><code class="option">-t</code> <em class="replaceable"><code>output-type</code></em></span></dt><dd><p>Select the output type. Use <span class="emphasis"><em>db31</em></span> to generate DocBook SGML bibliographies, <span class="emphasis"><em>db31x</em></span> for DocBook XML bibliographies (DTD-based, up to 4.3), <span class="emphasis"><em>db50x</em></span> for Docbook V5 XML bibliographies (schema-based), <span class="emphasis"><em>teix</em></span> for TEI P4 XML bibliographies, <span class="emphasis"><em>tei5x</em></span> for TEI P5 XML bibliographies, <span class="emphasis"><em>bibtex</em></span> for BibTeX bibliographies, and <span class="emphasis"><em>rtf</em></span> for RTF bibliographies. The type of output also determines the type of style specification file, if any, that will be generated in addition to the bibliography for formatting purposes. This is only a matter of concern if you want to process a DocBook XML document with the DSSSL stylesheets: In this case you should use <span class="emphasis"><em>db31</em></span> with this option. The SGML bibliography element is also a valid XML element, but you will get a DSSSL driver file instead of a XSL driver file when you use <span class="emphasis"><em>db31x</em></span>.</p><p>Note: In the current implementation, the <code class="option">-t</code> <em class="replaceable"><code>teix</code></em> option will also return a DocBook bibliography which needs to be transformed to a TEI bibliography with the <span class="emphasis"><em>bibdb2tei.xsl</em></span> stylesheet. The <code class="option">-t</code> <em class="replaceable"><code>tei5x</code></em> option creates a directly usable TEI bibliography.</p></dd><dt><span class="term"><code class="option">-T</code> <em class="replaceable"><code>time</code></em></span></dt><dd><p>Set the timeout for client/application server dialogue in seconds. A connection with unsuccessful read or write attempts will be considered as dead and taken down after this amount of time has elapsed.</p></dd><dt><span class="term"><code class="option">-u</code> <em class="replaceable"><code>name</code></em></span></dt><dd><p>Set the username for the database access.
Note: This username need not be identical to the login name of the user. This is the username required to access the database server.</p></dd><dt><span class="term"><code class="option">-v</code></span></dt><dd><p>Prints version and copyright information, then exits.</p></dd><dt><span class="term"><code class="option">-V</code></span></dt><dd><p>Switches to verbose mode.</p></dd><dt><span class="term"><code class="option">-w</code> <em class="replaceable"><code>password</code></em></span></dt><dd><p>Set the password for the database access.
Note: This password need not be identical to the login password of the user. This is the password required to access the database server.</p></dd><dt><span class="term"><code class="option">-x</code></span></dt><dd><p>Send passwords unencrypted.</p></dd><dt><span class="term"><code class="option">-y</code> <em class="replaceable"><code>confdir</code></em></span></dt><dd><p>Specify the directory where the global configuration files are
Note: By default, all RefDB applications look for their configuration files in a directory that is specified during the configure step when building the package. That is, you don't need the <code class="option">-y</code> option unless you use precompiled binaries in unusual locations, e.g. by relocating a rpm package.</p></dd></dl></div></div><div class="refsect1"><a id="refdbib-diagnostics"></a><h2>Diagnostics</h2><p>The exit code is 0 if all went fine. It will be 1 if the command returned an error, or if there was a general error condition during startup like a lack of available memory.</p></div><div class="refsect1"><a id="refdbib-configuration"></a><h2>Configuration</h2><p>refdbib evaluates the <code class="filename">refdbibrc</code> configuration file at startup to initialize itself.</p><div class="table"><a id="idp67412576"></a><p class="title"><strong>Table 15.1. refdbibrc</strong></p><div class="table-contents"><table class="table" summary="refdbibrc" border="1"><colgroup><col /><col /><col /></colgroup><thead><tr><th>Variable</th><th>Default</th><th>Comment</th></tr></thead><tbody><tr><td>refdblib</td><td>(none)</td><td>The path of a directory containing shareable files like DTDs, HTML templates etc.</td></tr><tr><td>defaultdb</td><td>(none)</td><td>The default database. <span class="application">refdbib</span> will use this database unless you specify the databases in the citation elements of your documents.</td></tr><tr><td>pager</td><td>stdout</td><td>The command line of a pager that accepts the output of refdb on stdin to allow scrolling and other nifty things. <span class="quote">“<span class="quote">stdout</span>”</span> sends the data to stdout.</td></tr><tr><td>passwd</td><td>*</td><td>The password which is used for authentication with the database server. It is potentially evil to store unencrypted passwords in disk files. At least make sure that the init file is not readable for anyone else. The default setting causes refdbib to ask for your password interactively.</td></tr><tr><td>port</td><td>9734</td><td>The port on which <span class="application">refdbd</span> listens. Change this for all clients and the server if this value interferes with another program using this port.</td></tr><tr><td>serverip</td><td>127.0.0.1</td><td>The IP address or hostname of the machine where <span class="application">refdbd</span> runs. Use the default (localhost) address if the clients and refdbd run on the same machine.</td></tr><tr><td>timeout</td><td>180</td><td>The timeout in seconds. After this time has elapsed, a stalled connection is taken down. Increase this value if you encounter frequent timeout errors due to high network traffic or refdbs overload.</td></tr><tr><td>username</td><td>login name</td><td>The username which is used for authentication with the database server. This may be different from the login name of the user.</td></tr><tr><td>verbose</td><td>f</td><td>Set this to t if you prefer verbose error messages.</td></tr><tr><td>logfile</td><td>/var/log/refdbib.log</td><td>The full path of a custom log file. This is used only if logdest is set appropriately.</td></tr><tr><td>logdest</td><td>1</td><td>The destination of the log information. 0 = print to stderr; 1 = use the syslog facility; 2 = use a custom logfile. The latter needs a proper setting of logfile.</td></tr><tr><td>loglevel</td><td>6</td><td>The log level up to which messages will be sent. A low setting (0) allows only the most important messages, a high setting (7) allows all messages including debug messages. -1 means nothing will be logged.</td></tr><tr><td>outtype</td><td>db31</td><td>The type of output generated. Use <em class="replaceable"><code>db31</code></em> for DocBook SGML bibliographies, <em class="replaceable"><code>db31x</code></em> for DocBook XML bibliographies, <em class="replaceable"><code>teix</code></em> for TEI XML bibliographies, and <em class="replaceable"><code>bibtex</code></em> for BibTeX bibliographies.</td></tr><tr><td>outformat</td><td>(none)</td><td>The bibliographic style to be used for the output. This is the name of a style as it was previously <a class="link" href="re06.html#app-a-command-addstyle" title="addstyle">added</a> to the database.</td></tr><tr><td>stylespecdir</td><td>.</td><td>A path to a directory (including the trailing directory separator) that will receive the stylesheet driver files. The default setting will direct the driver files to the current working directory that most likely contains the input files. It should rarely be necessary to use a different setting.</td></tr><tr><td>startnumber</td><td>1</td><td>The number where the reference numbering starts at. This option is mostly useful for compiling advanced bibliographies or for C boneheads who insist that counting starts at zero.</td></tr><tr><td>toencoding</td><td>(the database encoding)</td><td>The character encoding for the bibliography output. If this is not specified, the data will use the same encoding as the database.</td></tr><tr><td>ignore_missing</td><td>f</td><td>If this is set to "f", missing references (i.e. cited but not in the database) will throw an error. If set to "t", you'll get a warning but missing references will not cause refdbib to return an error.</td></tr><tr><td>no_encrypt</td><td>f</td><td>If set to 't', passwords are transmitted unencrypted. The default is to encrypt passwords.</td></tr></tbody></table></div></div><br class="table-break" /></div><div class="refsect1"><a id="refdbib-examples"></a><h2>Examples</h2><p>The first example shows how to create a DocBook SGML bibliography file.</p><pre class="screen">
<code class="prompt">$~ </code>
<strong class="userinput"><code>refdbib -d myrefs -S "Br.J.Pharmacol." -t db31 -D "." mypaper.id.xml > mypaper.bib.sgml</code></strong>
</pre><p>This command will use the database <span class="quote">“<span class="quote">myrefs</span>”</span> to retrieve the references defined in <code class="filename">mypaper.id.xml</code>. They will be formatted according to the bibliography style called <span class="quote">“<span class="quote">Br.J.Pharmacol.</span>”</span> and will be redirected into the bibliography file <code class="filename">mypaper.bib.sgml</code>. The DSSSL driver file (it will be automatically named after the bibliography style, that is <code class="filename">Br.J.Pharmacol.dsl</code>) will be stored in the current working directory.</p><p>The second example shows how to create the BibTeX bibliography from your LaTeX document (it is assumed that you ran <span class="command"><strong>latex</strong></span> at least once before this command.</p><pre class="screen">
<code class="prompt">$~ </code>
<strong class="userinput"><code>refdbib -d myrefs -S "name" -t bibtex mypaper.aux > mypaper.bib</code></strong>
</pre><p>This command will use the database <span class="quote">“<span class="quote">myrefs</span>”</span> to retrieve the references defined in <code class="filename">mypaper.aux</code>. The intermediate bibliography database will be stored in <code class="filename">mypaper.bib</code> and will serve as an input file for <span class="command"><strong>bibtex</strong></span>.</p><div class="note" style="margin-left: 0.5in; margin-right: 0.5in;"><h3 class="title">Note</h3><p>For the sake of consistency with <span class="command"><strong>bibtex</strong></span>, it is possible to specify the auxiliary file without the <code class="filename">.aux</code> extension (<code class="filename">mypaper</code> in the above example).</p></div><p>If you are working on a long document that cites the same references over and over again, it may be prudent to preprocess the <code class="filename">.aux</code> file in order to eliminate duplicates (duplicates do not confuse <span class="command"><strong>bibtex</strong></span> but they waste space):</p><pre class="screen">
<code class="prompt">$~ </code>
<strong class="userinput"><code>sort mypaper.aux | uniq | refdbib -d myrefs -S "name" -t bibtex > mypaper.bib</code></strong>
</pre><div class="note" style="margin-left: 0.5in; margin-right: 0.5in;"><h3 class="title">Note</h3><p>The <a class="link" href="re22.html" title="runbib">runbib</a> script does exactly this kind of preprocessing automatically.</p></div></div><div class="refsect1"><a id="refdbib-files"></a><h2>Files</h2><div class="variablelist"><dl class="variablelist"><dt><span class="term"><code class="filename">PREFIX/etc/refdb/refdbibrc</code></span></dt><dd><p>The global configuration file of refdbib.</p></dd><dt><span class="term"><span class="emphasis"><em>$HOME/.refdbibrc</em></span></span></dt><dd><p>The user configuration file of refdbib.</p></dd></dl></div></div><div class="refsect1"><a id="refdbib-see_also"></a><h2>See also</h2><p><span class="emphasis"><em>RefDB</em></span> (7),
<span class="emphasis"><em><a class="link" href="re02.html" title="refdbd">refdbd</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re22.html" title="runbib">runbib</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re21.html" title="refdbnd">refdbnd</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re06.html" title="refdba">refdba</a></em></span> (1),
<span class="emphasis"><em><a class="link" href="re11.html" title="refdbc">refdbc</a></em></span> (1).</p><p><span class="emphasis"><em>RefDB manual (local copy) </em></span> PREFIX/share/doc/refdb-<version>/refdb-manual/index.html</p><p><span class="emphasis"><em>RefDB manual (web) </em></span> <<a class="ulink" href="http://refdb.sourceforge.net/manual/index.html" target="_top">http://refdb.sourceforge.net/manual/index.html</a>></p><p><span class="emphasis"><em>RefDB on the web </em></span> <<a class="ulink" href="http://refdb.sourceforge.net/" target="_top">http://refdb.sourceforge.net/</a>></p></div><div class="refsect1"><a id="refdbib-author"></a><h2>Author</h2><p>refdbib was written by Markus Hoenicka <markus@mhoenicka.de>.</p></div></div><div class="navfooter"><hr /><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="ch15.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="ch15.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="re21.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">Chapter 15. Tools for bibliographies </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> refdbnd</td></tr></table></div></body></html>
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