Provided by: refdb-clients_1.0.2-3ubuntu1_amd64 
NAME
refdbc - the reference and note management client of RefDB
SYNOPSIS
Interactive mode:
refdbc [-c pager-command] [-d database] [-e log-destination] [-f stdin] [-F fields]
[-g deffile] [-G CSS-file] [-h] [-i IP-address] [-l log-level] [-L log-file]
[-p port] [-q] [-R pdfroot] [-T time] [-u name] [-v] [-V] [-w password] [-x]
[-y confdir]
Batch mode:
refdbc -C command [-c pager-command] [-d database] [-e log-destination] [-f stdin]
[-F fields] [-g deffile] [-G CSS-file] [-i IP-address] [-l log-level] [-L log-file]
[-p port] [-q] [-R pdfroot] [-T time] [-u name] [-v] [-V] [-w password] [-x]
[-y confdir]
DESCRIPTION
refdbc is a command-line client providing the commands to manage references and notes with
RefDB(7). refdbc can be started in an interactive mode, providing a command prompt. Type ?
or help to see a list of available commands. Alternatively you can start refdbc in
non-interactive mode. refdbc will execute the requested command and return. In this mode
refdbc will accept input on stdin for a variety of commands, allowing Unix piping.
OPTIONS
-c pager-command
The command line of the pager that is to be used. Instead of a pager you can of course
specify any valid command that accepts data on stdin. Use "stdout" to request data
output to stdout. This is the default, but you may want to specify it on the command
line if you need to temporarily override a default pager setting in your configuration
file.
-C command
The command to be run in non-interactive mode. You can supply all options and
parameters that the command accepts on the refdba command line.
-d database
The name of the default database. You can change the database anytime during an
interactive session.
-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.
-f stdin
Read data from stdin. refdbc usually knows when it should read from stdin. However, a
few commands use data supplied in the command line but also allow to read from a file.
Use this option to force refdbc to read from stdin in addition to values supplied on
the command line.
-F fields
Specify the default fields that are to be displayed in a getref query.
-g deffile
This option can be used to add some default fields to all RIS references that are
added or updated. The argument deffile is the filename of a RIS file containing these
additional fields. refdbc first tries the filename as is, so it should be a valid
relative or absolute path. If the file is not found, refdb looks for the file in
$HOME. The command aborts if the file cannot be found.
-G CSS-file
Specify the URL of a Cascading Style Sheets (CSS) file. This file will be used to
customize the HTML output of the getref command. The URL can be either a local path
(e.g. refdb.css, /home/myname/custom.css) or the web address of a file on a web
server (e.g. http://www.mycomp.com/refdb.css).
-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.
-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. Useful for
debugging configuration files.
-R pdfroot
Specify the root path of your collection of electronic offprints.
-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 (when run in batch mode)
or the last command (when run in interactive mode) returned an error, or if there was a
general error condition during startup like a lack of available memory.
CONFIGURATION
refdbc evaluates the refdbcrc configuration file at startup to initialize itself.
Table 1. refdbcrc
┌─────────────┬─────────────────────┬──────────────────────────┐
│Variable │ Default │ Comment │
├─────────────┼─────────────────────┼──────────────────────────┤
│cssurl │ (none) │ The URL of a Cascading │
│ │ │ Style Sheet (CSS) file. │
│ │ │ This file, if specified, │
│ │ │ is used to customize the │
│ │ │ visual appearance of the │
│ │ │ HTML output of the │
│ │ │ getref command. │
├─────────────┼─────────────────────┼──────────────────────────┤
│defaultdb │ (none) │ The default database. │
│ │ │ refdbc will try to use │
│ │ │ this database unless you │
│ │ │ select a different one │
│ │ │ with the selectdb │
│ │ │ command. │
├─────────────┼─────────────────────┼──────────────────────────┤
│defaultris │ (none) │ The path of a RIS file │
│ │ │ with entries that should │
│ │ │ be added to all new or │
│ │ │ updated references. This │
│ │ │ is typically used to set │
│ │ │ some default value for │
│ │ │ the RP field or to │
│ │ │ specify additional │
│ │ │ keywords. │
├─────────────┼─────────────────────┼──────────────────────────┤
│fields │ (none) │ A list of additional │
│ │ │ fields which should be │
│ │ │ displayed by default in │
│ │ │ the reference output. │
│ │ │ The list is a simple │
│ │ │ concatenation of the │
│ │ │ field names. Possible │
│ │ │ fields are N1, N2, NX, │
│ │ │ AB, AD, RP, SN, PB, CY, │
│ │ │ UR, U1 through U5, M1 │
│ │ │ through M3. Use the │
│ │ │ string "ALL" to request │
│ │ │ all available fields. │
├─────────────┼─────────────────────┼──────────────────────────┤
│fromencoding │ ISO-8859-1 │ The default encoding of │
│ │ │ RIS input data. You can │
│ │ │ use any encoding that │
│ │ │ your local libiconv │
│ │ │ implementation supports. │
├─────────────┼─────────────────────┼──────────────────────────┤
│logdest │ file │ Where the log output │
│ │ │ should be written to. │
│ │ │ Use either stderr, │
│ │ │ syslog, or file. For the │
│ │ │ latter to work, the │
│ │ │ logfile variable must be │
│ │ │ set appropriately │
├─────────────┼─────────────────────┼──────────────────────────┤
│logfile │ /var/log/refdbc.log │ The full path of a │
│ │ │ custom log file. │
├─────────────┼─────────────────────┼──────────────────────────┤
│loglevel │ info │ Set the level of log │
│ │ │ information that you │
│ │ │ would receive. Possible │
│ │ │ values, in order of │
│ │ │ increasing verbosity, │
│ │ │ are: emerg, alert, crit, │
│ │ │ err, warning, notice, │
│ │ │ info, debug │
├─────────────┼─────────────────────┼──────────────────────────┤
│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 configuration file │
│ │ │ is not readable for │
│ │ │ anyone else. The default │
│ │ │ setting causes refdbc to │
│ │ │ ask for your password │
│ │ │ interactively. │
├─────────────┼─────────────────────┼──────────────────────────┤
│pdfroot │ (none) │ This value will be used │
│ │ │ as the root of the paths │
│ │ │ to PDF or Postscript │
│ │ │ offprints that can be │
│ │ │ specified with the AV │
│ │ │ field in a RIS dataset. │
│ │ │ The path should not rely │
│ │ │ on shell expansion, e.g. │
│ │ │ use /home/me/literature/ │
│ │ │ instead of │
│ │ │ ~/literature/. The │
│ │ │ pdfroot allows you to │
│ │ │ shorten the paths that │
│ │ │ you enter for each │
│ │ │ dataset and to maintain │
│ │ │ a certain portability if │
│ │ │ you have to move the │
│ │ │ offprints to a different │
│ │ │ directory or want to │
│ │ │ access them remotely. │
│ │ │ The html output routine │
│ │ │ will concatenate the │
│ │ │ relative path of each │
│ │ │ dataset with the pdfroot │
│ │ │ to construct the link to │
│ │ │ the offprint. Instead of │
│ │ │ a local path name you │
│ │ │ can specify an URL │
│ │ │ starting with http:// or │
│ │ │ ftp:// if your offprints │
│ │ │ are accessible through a │
│ │ │ web server or ftp │
│ │ │ server. │
├─────────────┼─────────────────────┼──────────────────────────┤
│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 refdbs 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 refdbd │
│ │ │ overload. │
├─────────────┼─────────────────────┼──────────────────────────┤
│toencoding │ (none) │ The default encoding of │
│ │ │ output data. You can use │
│ │ │ any encoding that your │
│ │ │ local libiconv │
│ │ │ implementation supports. │
│ │ │ If this value is not │
│ │ │ set, the encoding of the │
│ │ │ database will be used │
│ │ │ without conversion. │
├─────────────┼─────────────────────┼──────────────────────────┤
│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. │
├─────────────┼─────────────────────┼──────────────────────────┤
│no_encrypt │ f │ If set to 't', passwords │
│ │ │ are transmitted │
│ │ │ unencrypted. The default │
│ │ │ is to encrypt passwords. │
└─────────────┴─────────────────────┴──────────────────────────┘
COMMANDS
All commands consist of a single word which specifies the command. This may be followed by
arguments and/or switches. The general syntax rules of the getopts library apply.
addlink
Synopsis
addlink [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
{note-specifier} {link-target...}
Description
The addlink command links an extended note to one or more link targets.
You have to specify exactly one note on the command line, either by using the :NID:
field selector to specify the note ID, or by using the :NCK: field selector to specify
the note key. Then you need at least one link target. This can be one of :ID:
(reference by ID), :CK: (reference by citation key), :AU: (author by name), :KW:
(keyword by name), or one of :JF:, :JO:, :J1:, :J2: (periodical by full name,
abbreviated name, or user abbreviations 1 and 2).
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
note-specifier
Specify one note by either its :NID: or its :NCK: value.
link-target
Specify one or more link targets by means of their :ID:, :CK:, :AU:, :KW:, :JF:,
:JO:, :J1:, or :J2: values.
Example
refdbc:
addlink :NID:=12 :CK:=Miller1999 :KW:=biochemistry
This command will link the note carrying the ID 12 with a reference specified by its
citation key "Miller1999" and with the keyword "biochemistry".
addnote
Synopsis
addnote [-d database] [-E encoding] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[file...]
Description
Adds the extended notes in file to the current database. You can specify several files
in one run. Any ID fields in the notes are ignored.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the input data if it is different from the
default UTF-8.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
Example
refdbc:
addnote foo.xml
This command will add the extended notes in foo.ris to the currently selected
database. If the notes do not specify a date, refdbd will insert a timestamp
automatically.
addref
Synopsis
addref [-d database] [-E encoding] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-t type] [-U username] [file...]
Description
Adds the references in file to the current database. You can specify several files in
one run. Any ID fields in the references are ignored unless you specify the -k option.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the input data if it is different from the
default setting. RIS datasets can use any encoding that your local libiconv
supports (see man iconv_open for a list of available encodings), except UTF-16 and
UTF-32. RISX datasets carry the encoding in the processing instructions, therefore
this option is not needed and ignored.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-t type
Select the input data type. Possible values are "ris" (default) and "risx". Other
data types have to be converted to one of these types before adding them to the
database.
-U username
Provide a different username than that of the current user, so e.g. some
technician or administrative staff can add references in behalf of a researcher.
file
All other command-line arguments will be interpreted as filenames to read
references from. If no filenames are specified, the data will be read from stdin.
Example
refdbc:
addref -U doe -g .refdbdefault.ris -E ISO-8859-1 foo.ris
$
refdbc -C addref -U doe -g .refdbdefault.ris -d db1 < foo.ris
These commands will add the references in foo.ris. The references will be associated
with the user “doe”. Every reference will use the specified values in
.refdbdefault.ris in the appropriate fields. In the first (interactive) command, the
active database will be used, and the encoding is set to ISO-8859-1, aka Latin-1. In
the second (non-interactive) command, the database has to be specified explicitly with
the -d option, and the default encoding (UTF-8) is assumed.
checkref
Synopsis
checkref [-A output-type] [-d database] [-E encoding] [-h] [[-c command] |
[-o outfile] | [-O outfile]] [-r field-list] [-s field-list] [-t input-type]
[-U username] [file...]
Description
Adds the references in file to temporary tables in the current database. The command
is similar to the addref command, except that it does not add the references
permanently to your database. Instead, the import is "simulated" in temporary tables,
and the resulting datasets are analyzed in terms of similarities to existing permanent
entries. If a reference is similar to an existing one in terms of the location
(periodical, volume, issue, startpage), of the titles, or of the citekey, you may want
to check these references manually as they are probably duplicates. If an abbreviated
periodical name is reported to match an existing full name, you may want to add both
names to the new reference to make refdb aware that it is dealing with the same
journal. If an author name using abbreviated first or middle names is reported to be a
possible duplicate of an existing author or vice versa, you may want to check if these
authors are indeed identical, and change the abbreviated one to the full version. In
addition, keywords are checked for similar existing keywords (often there are singular
and plural forms of the same keyword). You should prefer to use existing keywords if
possible to make your database more consistent and easier to search.
Options
-A outtype
Select the output type of the report. Currently supported values are "scrn" for a
terse screen output, and "xhtml" for a voluptuous xhtml report, bells and whistles
included.
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the input data if it is different from the
default setting. RIS datasets can use any encoding that your local libiconv
supports (see man iconv_open for a list of available encodings), except UTF-16 and
UTF-32. RISX datasets carry the encoding in the processing instructions, therefore
this option is not needed and ignored.
-G cssfile
Select the CSS stylesheet that is to be used for the xhtml output.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-r fieldlist
Select fields to check. If this option is not used, all available checks are
performed. This may result in a more comprehensive report than you want. You can
instead check for particular fields, or a subset of the available fields.
fieldlist is a concatenation of the two-letter (pseudo) field codes: TX (all
titles), PY (pubdate, volume, issue, pages), AX (all authors), JO (all journal
names), CK, and KW.
-s fieldlist
Select additional fields to display with the default xhtml output. fieldlist is a
concatenation of the two-letter field codes of those fields which are not printed
by default: N1, N2, NX, AB, AD, PB, CY, RP, SN, LX, U1-U5, and M1-M3.
-t input-type
Select the input data type. Possible values are "ris" (default) and "risx". Other
data types have to be converted to one of these types before adding them to the
database.
-U username
Provide a different username than that of the current user, so e.g. some
technician or administrative staff can add references in behalf of a researcher.
file
All other command-line arguments will be interpreted as filenames to read
references from. If no filenames are specified, the data will be read from stdin.
Example
refdbc:
checkref -A xhtml -G /usr/local/share/refdb/css/refdb-frequency.css -E ISO-8859-1 -s KW foo.ris
This command adds the data in foo.ris to temporary tables in the current database,
using the ISO-8859-1 encoding. The result of the duplicate checks is requested in
xhtml format using a stylesheet that displays frequency information graphically. In
addition to the default fields the keywords will be listed as well.
deletelink
Synopsis
deletelink [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
{note-specifier} {link-target...}
Description
The deletelink command removes links from an extended note to one or more link
targets.
You have to specify exactly one note on the command line, either by using the :NID:
field selector to specify the note ID, or by using the :NCK: field selector to specify
the note key. Then you need at least one link target. This can be one of :ID:
(reference by ID), :CK: (reference by citation key), :AU: (author by name), :KW:
(keyword by name), or one of :JF:, :JO:, :J1:, :J2: (periodical by full name,
abbreviated name, or user abbreviations 1 and 2).
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
note-specifier
Specify one note by either its :NID: or its :NCK: value.
link-target
Specify one or more link targets by means of their :ID:, :CK:, :AU:, :KW:, :JF:,
:JO:, :J1:, or :J2: values.
Example
refdbc:
deletelink :NID:=12 :CK:=Miller1999 :KW:=biochemistry
This command will delete the links from the note carrying the ID 12 to a reference
specified by its citation key "Miller1999" and to the keyword "biochemistry".
deletenote
Synopsis
deletenote [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]] {{ID...} |
{-f infile}}
Description
Deletes the extended note with the identifier ID from the current database. Several
extended notes may be specified in a single call of this command. Notes with
consecutive ID values may be specified as ranges.
Caution
It is not possible to delete a note if it belongs to a different user.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-f infile
Read a list of NID values in the RIS format from infile.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
NID
All other arguments are interpreted as a list of noteID values. Ranges may be used
to specify consecutive NIDs. If neither NIDs nor an infile are provided, refdbc
attempts to read the NIDs from stdin. You can ask refdbc to read NID values from
stdin in addition to other NIDs by using the -f stdin option.
Example
refdbc:
deletenote 3 5-10 26
This command will delete the extended notes with the ID values 3, 5 through 10, and
26.
deleteref
Synopsis
deleteref [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]] {{ID...} |
{-f infile}}
Description
Deletes the reference with the identifier ID from the current database. Several
references may be specified in a single call of this command. References with
consecutive ID values may be specified as ranges.
Caution
It is not possible to delete a reference if it belongs to the personal reference
list of more than one user.
If you're the only user of this reference and go ahead and delete it, all data
saved in the specified references will be gone, so be careful with this command.
Make sure you understand the difference between the deleteref command and the
dumpref command. The former deletes the data, the latter deletes only your
personal data associated with the specified references (the notes, availability,
and reprint data) and removes your association with this reference. In other
words, deleteref removes the reference from the database, whereas dumpref removes
the reference from your personal reference list, leaving the remaining data for
the other users of the database.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-f infile
Read a list of ID values in the RIS format from infile. This list may be the
result of a previous getref command.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
ID
All other arguments are interpreted as a list of ID values. Ranges may be used to
specify consecutive IDs. If neither IDs nor an infile are provided, refdbc
attempts to read the IDs from stdin. You can ask refdbc to read ID values from
stdin in addition to other IDs by using the -f stdin option.
Example
refdbc:
deleteref 3 5-10 26
This command will delete the references with the ID values 3, 5 through 10, and 26.
dumpref
Synopsis
dumpref [-b listname] [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
{[ID...] | [-f file]...}
Description
Removes references from the specified personal reference list in the current database.
If no personal reference list is specified, the default list (carrying the same name
as your database username) will be used instead.
Options
-b listname
Use the personal reference list named listname.
-c command
Pipe the output through command.
-d database
Specify the database.
-f infile
Read a list of ID values in the RIS format from infile. This list may be the
result of a previous getref command.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
ID
All other arguments are interpreted as a list of ID values. Ranges may be used to
specify consecutive IDs. If neither IDs nor an infile are provided, refdbc
attempts to read the IDs from stdin. You can ask refdbc to read ID values from
stdin in addition to other IDs by using the -f stdin option.
Example
refdbc:
dumpref -f foo.ris 3 5-10 26
This command will remove the references 3, 5 through 10, and 26 as well as those
listed in the file foo.ris from your personal reference list.
getau, geted, getas, getax
Synopsis
getau [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {unix-regexp}
geted [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {unix-regexp}
getas [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
getas [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
Description
Retrieve all author names that match the regular expression regexp in the current
database. If no regexp argument is given, all author names will be listed, which may
or may not be what you want. getau retrieves the primary authors which is the most
common case if you want to locate a publication. geted and getas retrieve book or
periodical editors and series authors, respectively. getax retrieves authors from any
level.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit author names are returned. If the optional offset argument is used as well,
the first offset author names will be skipped, and the next limit author names
will be returned.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-s format
Request additional frequency information. "freq" provides the absolute number of
references that contain the given author. "relfreq" reports a relative frequency
indicator as an integer between 0 and 10.
regexp
All other arguments are interpreted as a unix regular expression which limits the
results to matching author names.
Note
Some database engines, like SQLite, do not support Unix-style regular
expressions. Use SQL regular expressions instead.
Example
refdbc:
getau -o authors.txt '^Simpson'
This command will write a list of all authors starting with “Simpson” to the file
authors.txt.
refdbc:
getau -N 5:10
This command prints the author names 11 through 15.
getjo, getjf, getj1, getj2
Synopsis
getjo [-a] [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
getjf [-a] [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
getj1 [-a] [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
getj2 [-a] [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
Description
Retrieve all journal names that match the regular expression regexp in the current
database. The regexp will be matched to the journal abbreviation, the full name, the
custom abbreviation 1, and the custom abbreviation 2, respectively. If no regexp
argument is given, all available journal names will be listed.
Options
-a
Return all synonymous journal names, i.e. full name, abbreviation, custom
abbreviation 1, and custom abbreviation 2. If the option is absent, only the name
that you search for will be returned, e.g. only the full name in the case of
getjf.
-c command
Pipe the output through command.
-d database
Specify the database.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit journal names are returned. If the optional offset argument is used as well,
the first offset journal names will be skipped, and the next limit journal names
will be returned.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-s format
Request additional frequency information. "freq" provides the absolute number of
references that contain the given journal name. "relfreq" reports a relative
frequency indicator as an integer between 0 and 10.
regexp
All other arguments are interpreted as a unix regular expression which limits the
results to matching journal names.
Note
Some database engines, like SQLite, do not support Unix-style regular
expressions. Use SQL regular expressions instead.
Example
refdbc:
getjo -a -o journals.txt '^J'
This command will list all synonyms of the journals whose abbreviations start with a
capital J. The output will be redirected into the file journals.txt.
getkw
Synopsis
getkw [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-s format] {regexp}
Description
Retrieve all keywords that match the regular expression regexp in the current
database. If no regexp argument is specified, all keywords in the database will be
listed.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit keywords are returned. If the optional offset argument is used as well, the
first offset keywords will be skipped, and the next limit keywords will be
returned.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-s format
Request additional frequency information. "freq" provides the absolute number of
references that contain the given keyword. "relfreq" reports a relative frequency
indicator as an integer between 0 and 10.
regexp
All other arguments are interpreted as a unix regular expression which limits the
results to matching keywords.
Note
Some database engines, like SQLite, do not support Unix-style regular
expressions. Use SQL regular expressions instead.
Examples
refdbc:
getkw -o keywords.txt '^An.*l$'
This command will request a list of all keywords that start with “An” and end with the
letter “l”, like “Animal”, and write the result to the file keywords.txt.
~#
refdbc -C getkw -s freq -c "sort -r|cut -d ':' -f 2"|less
Here we run the getkw command from the shell. The result list contains the frequency
of each returned keyword. The data are sorted in descending order according to the
frequency, and the frequency information itself is stripped off. Of course there is
more than one way to arrive here. E.g. you could use the -c option to send the data to
stdout and pipe them through the argument of the -c option in the example shown above.
getnote
Synopsis
getnote [-d database] [-E encoding] [-h] [[-c command] | [-o outfile] | [-O outfile]]
[-N limit[:offset]] [-P] [-S sort-string] [-t output-type] {[search-string] |
[-f file]}
Description
Displays all extended notes which match the search-string in the current database.
Refer to the section The query language for a description of the syntax of a search
string.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the output data if it is different from the
database encoding. You can request any encoding that your local libiconv supports
(see man iconv_open for a list of available encodings).
-f infile
Read the search string from infile. This is a simple way to re-run saved queries.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit extended notes are returned. If the optional offset argument is used as
well, the first offset notes will be skipped, and the next limit notes will be
returned.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-P
Limit the search to the notes which were added by the current user. If this switch
is absent, the whole database will be searched.
-S sort-string
Sort the output. Currently you can sort only by ID (the default) or by PY
(publication year).
-t output-type
Select the type of output. Available are "scrn", "html", "xhtml", and "xnote" for
a compact format suitable for terminal browsing, HTML, XHTML, or the native XML
format, respectively.
search-string
The remainder of the arguments is interpreted as a search string. The syntax of
the queries is described in the section query language.
Example
refdbc:
getnote -t xnote :CK:=Miller1999
This command retrieves notes which are attached to the reference with the citation key
"Miller1999" and displays them in the xnote format.
getref
Synopsis
getref [-b listname] [-d database] [-E encoding] [-h] [[-c command] | [-o outfile] |
[-O outfile]] [-N limit[:offset]] [-s format-string] [-S sort-string]
[-t output-format] {[search-string] | [-f file]}
Description
Displays all datasets which match the search-string in the current database. Refer to
the section The query language for a description of the syntax of a search string. See
the countref command if you want to know how many references match your current query
without actually retrieving a possibly large amount of reference data.
Options
-b listname
Limit the search to the personal reference list named listname.
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the output data if it is different from the
database encoding. You can request any encoding that your local libiconv supports
(see man iconv_open for a list of available encodings).
-f infile
Read the search string from infile. This is a simple way to re-run saved queries.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit matching references are returned. If the optional offset argument is used as
well, the first offset matching references will be skipped, and the next limit
matching references will be returned.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-s format-string
Specify additional fields and pseudo-fields (N1, N2/AB, NX, RP, SN, AD, CY, PB,
LX, U1 through U5, M1 through M3) that are not displayed by default, except for
the RIS and risx output formats. Use "ALL" as an argument to display all available
fields. If several fields are specified, the argument has to be enclosed by single
quotation marks. If applied to RIS output, you can specify ID as format-string to
get only a list of ID values in RIS format for all references that match the
search. This is a convenient way to generate ID lists for later operations like
deleteref.
-S sort-string
Sort the output. Currently you can sort only by ID (the default) or by PY
(publication year).
-t output-type
Select the type of output. Available are "scrn", "ris", "risx", "html", "xhtml",
"db31", "db31x", "db50x, "teix", "tei5x", "mods", and "bibtex" for a compact
format suitable for terminal browsing, the native RIS and risx (XML) formats,
HTML, XHTML, DocBook SGML, DocBook XML (DTD-based), DocBook XML (schema-based),
TEI P4 XML, TEI P5 XML, MODS, or BibTeX format, respectively.
search-string
The remainder of the arguments is interpreted as a search string. The syntax of
the queries is described in the section query language.
Example
refdbc:
getref -t ris -o temp.sgml -E ISO-8859-15 ":AU:='& ^Doe ^Jones' AND :KW:=circular\ dichroism"
This command retrieves articles with both an author starting with “Doe” and an author
starting with “Jones” that have the keyword “circular dichroism”. The output will be
saved in RIS format to the file temp.sgml using the character encoding ISO-8859-15.
help, ?
Synopsis
help
?
Description
Displays a brief summary of the available commands.
Note
This command is not available in the batch mode (use the -h option instead to
review the command line usage).
Example
refdbc:
help
This will list the available commands.
listdb
Synopsis
listdb [-h] [database-regexp]
Description
Lists all available databases if no argument is specified. If database-regexp is
specified, only the databases matching this expression will be listed.
Options
-h
Displays a help message explaining the listdb command.
database-regexp
A valid SQL regular expression which limits the output to matching database names.
Example
refdbc:
listdb db%
This command will list all available databases that start with “db”.
liststyle
Synopsis
liststyle {style-regexp}
Description
Lists all available bibliography styles that match style-regexp.If no argument is
specified, all available styles will be listed.
Options
-h
Displays a help message explaining the listdb command.
style-regexp
A valid Unix regular expression which limits the output to matching style names.
Note
Some database engines, like SQLite, do not support Unix-style regular
expressions. Use SQL regular expressions instead.
Example
refdbc:
liststyle ^J.*
This will list all bibliography styles that start with a capital “J”.
pickref
Synopsis
pickref [-b listname] [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]]
{[ID...] | [-f file]}
Description
Adds references to the specified personal reference list in the current database. If
no personal reference list is specified, the default list (carrying the same name as
your database username) will be used instead.
Options
-b listname
Use the personal reference list named listname.
-c command
Pipe the output through command.
-d database
Specify the database.
-f infile
Read a list of ID values in the RIS format from infile. This list may be the
result of a previous getref command.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
ID
All other arguments are interpreted as a list of ID values. Ranges may be used to
specify consecutive IDs. If neither IDs nor an infile are provided, refdbc
attempts to read the IDs from stdin. You can ask refdbc to read ID values from
stdin in addition to other IDs by using the -f stdin option.
Example
refdbc:
pickref -f foo.ris 3 5-10 26
This command will add the references 3, 5 through 10, and 26 as well as those listed
in the file foo.ris to your personal reference list.
countnote
Synopsis
countnote [-b listname] [-c command] [-d database] [-h] [-N limit[:offset]]
{[search-string] | [-f file]}
Description
Counts all extended notes which match the search-string in the current database. Refer
to the section The query language for a description of the syntax of a search string.
This command is equivalent to the getnote command except that it does not return the
matching notes. It just counts them.
Options
-b listname
Limit the search to the personal reference list named listname.
-c command
Pipe the output through command.
-d database
Specify the database.
-f infile
Read the search string from infile. This is a simple way to re-run saved queries.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit matching references are returned. If the optional offset argument is used as
well, the first offset matching references will be skipped, and the next limit
matching references will be returned.
search-string
The remainder of the arguments is interpreted as a search string. The syntax of
the queries is described in the section query language.
Example
refdbc:
countnote :KW:~[rR]eview
This command looks for extended notes that are linked to references which contain
keywords like "review" or "Review". The command will return the number of matching
notes in the result summary.
countref
Synopsis
countref [-b listname] [-c command] [-d database] [-h] [-N limit[:offset]]
{[search-string] | [-f file]}
Description
Counts all datasets which match the search-string in the current database. Refer to
the section The query language for a description of the syntax of a search string.
This command is equivalent to the getref command except that it does not return the
matching references. It just counts them.
Options
-b listname
Limit the search to the personal reference list named listname.
-c command
Pipe the output through command.
-d database
Specify the database.
-f infile
Read the search string from infile. This is a simple way to re-run saved queries.
-h
Display a help message explaining the command.
-N limit[:offset]
Limit the number of returned datasets. If limit is used all by itself, the first
limit matching references are returned. If the optional offset argument is used as
well, the first offset matching references will be skipped, and the next limit
matching references will be returned.
search-string
The remainder of the arguments is interpreted as a search string. The syntax of
the queries is described in the section query language.
Example
refdbc:
countref ":AU:='& ^Doe ^Jones' AND :KW:=circular\ dichroism"
This command looks for articles with both an author starting with “Doe” and an author
starting with “Jones” that have the keyword “circular dichroism”. The command will
return the number of matching references in the result summary.
selectdb
Synopsis
selectdb [-h] {database}
Description
Select database as the current database. This current database will be used in all
queries unless you specify a different database with the -d option of the query
commands.
Note
This command is not available in the batch mode. Use the -d command line option
instead.
Options
-h
Display a help message explaining the command.
database
The name of the database to be selected.
Example
refdbc:
selectdb db1
This command will make the database db1 the active database. All further queries and
operations will affect this database.
set
Synopsis
set [-h] [varname] [varvalue]
Description
The set command displays or modifies the values of configuration variables.
If you call set without any arguments, it will display a list of all configuration
variables with their current values.
If you call set with one argument, it will display the value of this particular
variable.
If you call set with two arguments, it will set the variable (first argument) to the
new value (second argument). To specify an empty value, use two quotation marks like
this:"".
Note
For obvious reasons, set will never display the current password although you can
certainly change the password with this command. To make sure no one else sees the
new password that you enter, run the command set passwd *. You will then be asked
to enter a password which will not be echoed on the screen.
This command is not available in batch mode, use the command line switches
instead. In the interactive mode, the changes to the configuration variables are
limited to the current session. If you want to change the values permanently, you
should rather edit one of the configuration files.
Options
-h
Displays a help message explaining the set command.
varname
The name of the variable whose value should be displayed or set.
varvalue
The new value of the variable to be set.
Example
refdbc:
set timeout 90
This command will set the timeout to 90 seconds for the current session.
updatejo
Synopsis
updatejo [-d database] [-h] [[-c command] | [-o outfile] | [-O outfile]] {:XY:=name}
{:XY:=name...}
Description
Updates the list of synonyms of a particular periodical.
Each periodical can have up to four synonymous names. The full name and an official
abbreviation (e.g. according to the Index Medicus for biomedical publications) should
always be supplied if available. In addition, refdb can store up to two user-defined
abbreviations which may serve as shorthands when adding datasets.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
:XY:=name
XY stands for one of JF, JO, J1, or J2 which denote the full name, the abbreviated
name, and the user abbreviations 1 and 2, respectively. You have to supply at
least two of these items. The first one selects the periodical by one of its
existing names in the database. All other items update or add the names as
provided.
Example
refdbc:
updatejo :JO:="J.Biol.Chem." :JF:="The Journal of Biological Chemistry"
Adds (or changes) the full name of the periodical known by its official abbreviation
as "J.Biol.Chem." to read "The Journal of Biological Chemistry".
updatenote
Synopsis
updatenote [-d database] [-E encoding] [-h] [[-c command] | [-o outfile] |
[-O outfile]] [file...]
Description
Updates the extended notes in file in the current database.
This command is essentially the same as addnote, but it uses the citekey or id
attributes (in this order) to update an existing note in the database. If the
specified note does not exist in the database, a new one will be created.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the input data if it is different from the
default UTF-8.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
Example
refdbc:
updatenote foo.xml
This command will update the extended notes in foo.ris in the currently selected
database. If the notes do not specify a date, refdbd will insert a timestamp
automatically.
updateref
Synopsis
updateref [-d database] [-E encoding] [-h] [[-c command] | [-o outfile] |
[-O outfile]] [-t type] [-P] [-U username] [file]
Description
Updates the references in RIS format in file in the current database.
This command is essentially the same as addref, but it uses the ID fields in the input
data to update existing references with the same ID. If the ID of a reference is not
existent in the database, a new entry is created, ignoring the ID specified in the RIS
or risx file. Currently refdb does not check whether the new dataset has any
similarity with the old one having the same ID. If you tell refdb to update a
reference, it uses whatever you send to this end.
Options
-c command
Pipe the output through command.
-d database
Specify the database.
-E encoding
Select the character encoding for the input data if it is different from the
default setting. RIS datasets can use any encoding that your local libiconv
supports (see man iconv_open for a list of available encodings), except UTF-16 and
UTF-32. RISX datasets carry the encoding in the processing instructions, therefore
this option is not needed and ignored.
-h
Display a help message explaining the command.
-o filename
Write the output to filename instead of to stdout.
-O filename
Append the output to filename instead of sending it to stdout.
-t type
Select the input data type. Possible values are "ris" (default) and "risx". Other
data types have to be converted to one of these types before adding them to the
database.
-P
Update only the personal information for this reference, i.e. the N1 (notes), RP
(reprint status), and AV (availability) fields. This will automatically add the
reference to your personal reference list. All other fields will be ignored.
Combine this option with the -g option e.g. to quickly change the reprint status
of existing references to “IN FILE” from “NOT IN FILE” or from “ON REQUEST”.
-U username
Provide a different username than that of the current user, so e.g. some
technician or administrative staff can add references in behalf of a researcher.
file
All other command-line arguments will be interpreted as filenames to read
references from. If no filenames are specified, the data will be read from stdin.
Example
refdbc:
updateref -P foo.ris
This command will update the references in foo.ris in the previously selected active
database. Only the personal information (AV, N1, RP) will be added or modified for the
current user.
verbose
Synopsis
verbose [-h]
Description
Toggles the verbose mode on or off. If the verbose mode is on, the error messages and
warnings may be some more comprehensible.
Options
-h
Displays a help message explaining the verbose command.
Example
refdbc:
verbose
Depending on the previous value, this command will either turn the verbose mode on or
off.
whichdb
Synopsis
whichdb [-h]
Description
Displays a plethora of information about the currently selected database.
Options
-h
Displays a help message explaining the whichdb command.
Example
refdbc:
whichdb
This will print the information about the active database. Refer to the selectdb
command for information how to change the active database. The whichdb output looks
like this:
Current database: alltypes
Number of references: 45
Highest reference ID: 45
Number of notes: 2
Highest note ID: 2
Encoding: ISO-8859-1
Database type: risx
Server type: pgsql
Created: 2003-12-24 22:27:43 UTC
Using refdb version: 0.9.4-pre2
Last modified: 2003-12-24 22:29:05 UTC
FILES
PREFIX/etc/refdb/refdbcrc
The global configuration file of refdbc.
$HOME/.refdbcrc
The user configuration file of refdbc.
SEE ALSO
RefDB (7), refdbd (1), refdba (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
refdbc was written by Markus Hoenicka <markus@mhoenicka.de>.