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REFDBC(1) | RefDB Manual | REFDBC(1) |
NAME¶
refdbc - the reference and note management client of RefDBSYNOPSIS¶
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-commandThe 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.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¶
Synopsisaddlink [-d database] [-h]
[[-c command] | [-o outfile] |
[-O outfile]] {note-specifier} {link-target...}
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).
-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.
refdbc: addlink :NID:=12 :CK:=Miller1999 :KW:=biochemistry
addnote¶
Synopsisaddnote [-d database]
[-E encoding] [-h]
[[-c command] | [ -o outfile] |
[-O outfile]] [file...]
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.
-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.
refdbc: addnote foo.xml
addref¶
Synopsisaddref [-d database]
[-E encoding] [-h]
[[-c command] | [ -o outfile] |
[-O outfile]] [-t type]
[-U username] [file...]
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.
-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.
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
checkref¶
Synopsischeckref [-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...]
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.
-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.
refdbc: checkref -A xhtml -G /usr/local/share/refdb/css/refdb-frequency.css -E ISO-8859-1 -s KW foo.ris
deletelink¶
Synopsisdeletelink [-d database] [-h]
[[ -c command] | [-o outfile] |
[-O outfile]] {note-specifier} {link-target...}
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).
-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.
refdbc: deletelink :NID:=12 :CK:=Miller1999 :KW:=biochemistry
deletenote¶
Synopsisdeletenote [-d database] [-h]
[[ -c command] | [-o outfile] |
[-O outfile]] {{ID...} |
{-f infile}}
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.
-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.
refdbc: deletenote 3 5-10 26
deleteref¶
Synopsisdeleteref [-d database] [-h]
[[ -c command] | [-o outfile] |
[-O outfile]] {{ID...} |
{-f infile}}
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.
-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.
refdbc: deleteref 3 5-10 26
dumpref¶
Synopsisdumpref [-b listname]
[-d database] [-h]
[[-c command] | [ -o outfile] |
[-O outfile]] {[ID...] |
[-f file]...}
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.
-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.
refdbc: dumpref -f foo.ris 3 5-10 26
getau, geted, getas, getax¶
Synopsisgetau [-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}
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.
-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.
refdbc: getau -o authors.txt '^Simpson'
refdbc: getau -N 5:10
getjo, getjf, getj1, getj2¶
Synopsisgetjo [-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}
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.
-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.
refdbc: getjo -a -o journals.txt '^J'
getkw¶
Synopsisgetkw [-d database] [-h]
[[-c command] | [-o outfile] |
[-O outfile]] [-N limit[:offset]]
[-s format] {regexp}
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.
-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.
refdbc: getkw -o keywords.txt '^An.*l$'
~# refdbc -C getkw -s freq -c "sort -r|cut -d ':' -f 2"|less
getnote¶
Synopsisgetnote [-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]}
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.
-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.
refdbc: getnote -t xnote :CK:=Miller1999
getref¶
Synopsisgetref [-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]}
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.
-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.
refdbc: getref -t ris -o temp.sgml -E ISO-8859-15 ":AU:='& ^Doe ^Jones' AND :KW:=circular\ dichroism"
help, ?¶
Synopsishelp
?
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).
refdbc: help
listdb¶
Synopsislistdb [-h] [database-regexp]
Lists all available databases if no argument is specified. If
database-regexp is specified, only the databases matching this
expression will be listed.
-h
Displays a help message explaining the listdb
command.
database-regexp
A valid SQL regular expression which limits the output to
matching database names.
refdbc: listdb db%
liststyle¶
Synopsisliststyle {style-regexp}
Lists all available bibliography styles that match style-regexp.If no
argument is specified, all available styles will be listed.
-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.
refdbc: liststyle ^J.*
pickref¶
Synopsispickref [-b listname]
[-d database] [-h]
[[-c command] | [ -o outfile] |
[-O outfile]] {[ID...] |
[-f file]}
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.
-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.
refdbc: pickref -f foo.ris 3 5-10 26
countnote¶
Synopsiscountnote [-b listname]
[-c command] [-d database]
[-h] [ -N limit[:offset]] {[search-string]
| [ -f file]}
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.
-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.
refdbc: countnote :KW:~[rR]eview
countref¶
Synopsiscountref [-b listname]
[-c command] [-d database]
[-h] [ -N limit[:offset]] {[search-string]
| [ -f file]}
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.
-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.
refdbc: countref ":AU:='& ^Doe ^Jones' AND :KW:=circular\ dichroism"
selectdb¶
Synopsisselectdb [-h] {database}
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.
-h
Display a help message explaining the command.
database
The name of the database to be selected.
refdbc: selectdb db1
set¶
Synopsisset [-h] [varname] [varvalue]
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.
-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.
refdbc: set timeout 90
updatejo¶
Synopsisupdatejo [-d database] [-h]
[[ -c command] | [-o outfile] |
[-O outfile]] {:XY:=name}
{:XY:=name...}
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.
-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.
refdbc: updatejo :JO:="J.Biol.Chem." :JF:="The Journal of Biological Chemistry"
updatenote¶
Synopsisupdatenote [-d database]
[-E encoding] [-h]
[[-c command] | [ -o outfile] |
[-O outfile]] [file...]
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.
-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.
refdbc: updatenote foo.xml
updateref¶
Synopsisupdateref [-d database]
[-E encoding] [-h]
[[-c command] | [ -o outfile] |
[-O outfile]] [-t type] [-P]
[ -U username] [file]
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.
-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.
refdbc: updateref -P foo.ris
verbose¶
Synopsisverbose [-h]
Toggles the verbose mode on or off. If the verbose mode is on, the error
messages and warnings may be some more comprehensible.
-h
Displays a help message explaining the verbose
command.
refdbc: verbose
whichdb¶
Synopsiswhichdb [-h]
Displays a plethora of information about the currently selected database.
-h
Displays a help message explaining the whichdb
command.
refdbc: whichdb
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/refdbcrcThe 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>.2005-10-15 | RefDB Manual |