refdbc
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## 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 14.1. 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>.

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