addlink [-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

-d database

-h

-o filename

-O filename

note-specifier

link-target

	  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 [-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

-d database

-E encoding

-h

-o filename

-O filename

	  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 [-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

-d database

-E encoding

-h

-o filename

-O filename

-t type

-U username

file

	  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 [-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

-c command

-d database

-E encoding

-G cssfile

-h

-o filename

-O filename

-r fieldlist

-s fieldlist

-t input-type

-U username

file

	  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 [-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

-d database

-h

-o filename

-O filename

note-specifier

link-target

	  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 [-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

-d database

-f infile

-h

-o filename

-O filename

NID

	  refdbc: 
	  deletenote 3 5-10 26
	

This command will delete the extended notes with the ID values 3, 5 through 10, and 26.

deleteref [-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

-d database

-f infile

-h

-o filename

-O filename

ID

	  refdbc: 
	  deleteref 3 5-10 26
	

This command will delete the references with the ID values 3, 5 through 10, and 26.

dumpref [-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

-c command

-d database

-f infile

-h

-o filename

-O filename

ID

	  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 [-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

-d database

-h

-N limit[:offset]

-o filename

-O filename

-s format

regexp

	  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 [-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

-c command

-d database

-h

-N limit[:offset]

-o filename

-O filename

-s format

regexp

	  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 [-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

-d database

-h

-N limit[:offset]

-o filename

-O filename

-s format

regexp

	  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 [-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

-d database

-E encoding

-f infile

-h

-N limit[:offset]

-o filename

-O filename

-P

-S sort-string

-t output-type

search-string

	  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 [-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

-c command

-d database

-E encoding

-f infile

-h

-N limit[:offset]

-o filename

-O filename

-s format-string

-S sort-string

-t output-type

search-string

	  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

?

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
	

This will list the available commands.

listdb [-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

database-regexp

	  refdbc: 
	  listdb db%
	

This command will list all available databases that start with “db”.

liststyle {style-regexp}

Lists all available bibliography styles that match style-regexp.If no argument is specified, all available styles will be listed.

-h

style-regexp

	  refdbc: 
	  liststyle ^J.*
	

This will list all bibliography styles that start with a capital “J”.

pickref [-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

-c command

-d database

-f infile

-h

-o filename

-O filename

ID

	  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 [-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

-c command

-d database

-f infile

-h

-N limit[:offset]

search-string

	  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 [-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

-c command

-d database

-f infile

-h

-N limit[:offset]

search-string

	  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 [-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

database

	  refdbc: 
	  selectdb db1
	

This command will make the database db1 the active database. All further queries and operations will affect this database.

set [-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

varname

varvalue

	  refdbc: 
	  set timeout 90
	

This command will set the timeout to 90 seconds for the current session.

updatejo [-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

-d database

-h

-o filename

-O filename

:XY:=name

	  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 [-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

-d database

-E encoding

-h

-o filename

-O filename

	  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 [-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

-d database

-E encoding

-h

-o filename

-O filename

-t type

-P

-U username

file

	  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 [-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

	  refdbc: 
	  verbose
	

Depending on the previous value, this command will either turn the verbose mode on or off.

whichdb [-h]

Displays a plethora of information about the currently selected database.

-h

	  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