2005-10-15
refdbib 1 2005-10-15 RefDB Manual
refdbib the bibliography client of RefDB
`refdbib` `-d` database `-D` stylespec-directory `-e` log-destination `-E` encoding `-f` stdin `-h` `-i` IP-address `-l` log-level `-L` log-file `-m` `-N` number `-p` port `-q` `-r` `-S` style `-t` output-type `-T` time `-u` name `-v` `-V` `-w` password `-x` `-y` confdir filename

## Description

refdbib is a command-line client to generate bibliographies with RefDB(7). refdbib reads the contents of filename, which contains a list of citations as an XML document according to citationlistx.dtd, 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.

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.

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.

## Options

`-d` database

  The name of the default database. You can change the database anytime during an interactive session.

`-D` stylespec-directory

  Specify either a full path or `.` 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.

`-e` log-destination

  log-destination can have the values 0, 1, or 2, or the equivalent strings stderr, syslog, or file, respectively. This value specifies where the log information goes to. `0` (zero) means the messages are sent to stderr. They are immediately available on the screen but they may interfere with command output. `1` 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 `/var/log/user.log`. `2` will send the messages to a custom log file which can be specified with the `-L` option.

`-E` encoding

  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.

`-f` stdin

  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.

`-h`

  Displays help and usage screen, then exits.

`-i` IP-address

  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.

`-l` log-level

  Specify the priority up to which events are logged. This is either a number between `0` and `7` or one of the strings emerg, alert, crit, err, warning, notice, info, debug, respectively (see also Log level definitions). `-1` disables logging completely. A low log level like `0` means that only the most critical messages are logged. A higher log level means that less critical events are logged as well. `7` 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.

`-L` log-file

  Specify the full path to a log file that will receive the log messages. Typically this would be `/var/log/refdba`.

`-m`

  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.

`-N` number

  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` port

  Set the port of the box which is running the application server.

`-q`

  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.

`-r`

  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.

`-S` style

  Specifies the bibliography style. This controls the formatting of the bibliography and the in-text citations when the document is processed.

`-t` output-type

  Select the output type. Use db31 to generate DocBook SGML bibliographies, db31x for DocBook XML bibliographies (DTD-based, up to 4.3), db50x for Docbook V5 XML bibliographies (schema-based), teix for TEI P4 XML bibliographies, tei5x for TEI P5 XML bibliographies, bibtex for BibTeX bibliographies, and rtf 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 db31 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 db31x.

  Note: In the current implementation, the `-t` teix option will also return a DocBook bibliography which needs to be transformed to a TEI bibliography with the bibdb2tei.xsl stylesheet. The `-t` tei5x option creates a directly usable TEI bibliography.

`-T` time

  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.

`-u` name

  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.

`-v`

  Prints version and copyright information, then exits.

`-V`

  Switches to verbose mode.

`-w` password

  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.

`-x`

  Send passwords unencrypted.

`-y` confdir

  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 `-y` option unless you use precompiled binaries in unusual locations, e.g. by relocating a rpm package.

## Diagnostics

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.

## Configuration

refdbib evaluates the `refdbibrc` configuration file at startup to initialize itself.

refdbibrc

Variable | Default | Comment
--- | --- | ---
refdblib | (none) | The path of a directory containing shareable files like DTDs, HTML templates etc.
defaultdb | (none) | The default database. refdbib will use this database unless you specify the databases in the citation elements of your documents.
pager | stdout | The command line of a pager that accepts the output of refdb on stdin to allow scrolling and other nifty things. stdout sends the data to stdout.
passwd | * | 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.
port | 9734 | The port on which refdbd listens. Change this for all clients and the server if this value interferes with another program using this port.
serverip | 127.0.0.1 | The IP address or hostname of the machine where refdbd runs. Use the default (localhost) address if the clients and refdbd run on the same machine.
timeout | 180 | 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.
username | login name | The username which is used for authentication with the database server. This may be different from the login name of the user.
verbose | f | Set this to t if you prefer verbose error messages.
logfile | /var/log/refdbib.log | The full path of a custom log file. This is used only if logdest is set appropriately.
logdest | 1 | 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.
loglevel | 6 | 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.
outtype | db31 | The type of output generated. Use db31 for DocBook SGML bibliographies, db31x for DocBook XML bibliographies, teix for TEI XML bibliographies, and bibtex for BibTeX bibliographies.
outformat | (none) | The bibliographic style to be used for the output. This is the name of a style as it was previously added to the database.
stylespecdir | . | 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.
startnumber | 1 | 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.
toencoding | (the database encoding) | The character encoding for the bibliography output. If this is not specified, the data will use the same encoding as the database.
ignore_missing | f | 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.
no_encrypt | f | If set to 't', passwords are transmitted unencrypted. The default is to encrypt passwords.

## Examples

The first example shows how to create a DocBook SGML bibliography file.

          $~
          refdbib -d myrefs -S "Br.J.Pharmacol." -t db31 -D "." mypaper.id.xml > mypaper.bib.sgml

This command will use the database myrefs to retrieve the references defined in `mypaper.id.xml`. They will be formatted according to the bibliography style called Br.J.Pharmacol. and will be redirected into the bibliography file `mypaper.bib.sgml`. The DSSSL driver file (it will be automatically named after the bibliography style, that is `Br.J.Pharmacol.dsl`) will be stored in the current working directory.

The second example shows how to create the BibTeX bibliography from your LaTeX document (it is assumed that you ran `latex` at least once before this command.

          $~
          refdbib -d myrefs -S "name" -t bibtex mypaper.aux > mypaper.bib

This command will use the database myrefs to retrieve the references defined in `mypaper.aux`. The intermediate bibliography database will be stored in `mypaper.bib` and will serve as an input file for `bibtex`.

For the sake of consistency with `bibtex`, it is possible to specify the auxiliary file without the `.aux` extension (`mypaper` in the above example).

If you are working on a long document that cites the same references over and over again, it may be prudent to preprocess the `.aux` file in order to eliminate duplicates (duplicates do not confuse `bibtex` but they waste space):

          $~
          sort mypaper.aux | uniq | refdbib -d myrefs -S "name" -t bibtex > mypaper.bib

The runbib script does exactly this kind of preprocessing automatically.

## Files

`PREFIX/etc/refdb/refdbibrc`

  The global configuration file of refdbib.

$HOME/.refdbibrc

  The user configuration file of refdbib.

## See also

RefDB (7), refdbd (1), runbib (1), refdbnd (1), refdba (1), refdbc (1).

RefDB manual (local copy) PREFIX/share/doc/refdb-<version>/refdb-manual/index.html

RefDB manual (web) <http://refdb.sourceforge.net/manual/index.html>

RefDB on the web <http://refdb.sourceforge.net/>

## Author

refdbib was written by Markus Hoenicka <markus@mhoenicka.de>.