refdbib - Online in the Cloud

PROGRAM:

NAME

refdbib - the bibliography client of RefDB

SYNOPSIS

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.

Table 1. 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.

Note
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

Note
The runbib script does exactly this kind of preprocessing automatically.

Use refdbib online using onworks.net services