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REFDBC(1) RefDB Manual REFDBC(1) 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] [-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] [-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, pro- viding a command prompt. Type ? or help to see a list of available com- mands. Alternatively you can start refdbc in non-interactive mode. refdbc will execute the requested command and return. In this mode refdbc will ac- cept 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 temporar- ily override a default pager setting in your configuration file. -C command The command to be run in non-interactive mode. You can supply all op- tions 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 sys- log facility. Keep in mind that syslog must be configured to accept log messages from user programs, see the syslog(8) man page for further in- formation. 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 refer- ences 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 com- mand 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.my- comp.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 defini- tions). -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 de- bug 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 com- mand-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 re- quired 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. -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 precom- piled binaries in unusual locations, e.g. by relocating a rpm package. DIAGNOSTICS The exit code is 0 if all went fine. It will be 1 if the command (when run in batch mode) or the last command (when run in interactive mode) returned an error, or if there was a general error condition during startup like a lack of available memory. CONFIGURATION refdbc evaluates the refdbcrc configuration file at startup to initialize itself. Table-1.-refdbcrc--------------------+----------------------+ | Variable | Default | Comment | +--------------+---------------------+----------------------+ | cssurl | (none) | The URL of a Cascad- | | | | ing Style Sheet | | | | (CSS) file. This | | | | file, if specified, | | | | is used to customize | | | | the visual appear- | | | | ance of the HTML | | | | output of the getref | | | | command. | +--------------+---------------------+----------------------+ | passwd | * | The password which | | | | is used for authen- | | | | tication with the | | | | database server. It | | | | is potentially evil | | | | to store unencrypted | | | | passwords in disk | | | | files. At least make | | | | sure that the con- | | | | figuration file is | | | | not readable for | | | | anyone else. The de- | | | | fault setting causes | | | | refdbc to ask for | | | | your password inter- | | | | actively. | +--------------+---------------------+----------------------+ | pdfroot | (none) | This value will be | | | | used as the root of | | | | the paths to PDF or | | | | Postscript offprints | | | | that can be speci- | | | | fied with the AV | | | | field in a RIS | | | | dataset. The path | | | | should not rely on | | | | shell expansion, | | | | e.g. use | | | | /home/me/literature/ | | | | instead of ~/litera- | | | | ture/. 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 dif- | | | | ferent directory or | | | | want to access them | | | | remotely. The html | | | | output routine will | | | | concatenate the rel- | | | | ative path of each | | | | dataset with the | | | | pdfroot to construct | | | | the link to the off- | | | | print. 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 an- | | | | other program using | | | | this port. | +--------------+---------------------+----------------------+ | serverip | 127.0.0.1 | The IP address or | | | | hostname of the ma- | | | | chine where refdbd | | | | runs. Use the de- | | | | fault (localhost) | | | | address if the | | | | clients and refdbs | | | | run on the same ma- | | | | chine. | +--------------+---------------------+----------------------+ | timeout | 180 | The timeout in sec- | | | | onds. After this | | | | time has elapsed, a | | | | stalled connection | | | | is taken down. In- | | | | crease this value if | | | | you encounter fre- | | | | quent 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 li- | | | | biconv implementa- | | | | tion supports. If | | | | this value is not | | | | set, the encoding of | | | | the database will be | | | | used without conver- | | | | sion. | +--------------+---------------------+----------------------+ | username | login name | The username which | | | | is used for authen- | | | | tication with the | | | | database server. | | | | This may be differ- | | | | ent from the login | | | | name of the user. | +--------------+---------------------+----------------------+ | verbose | f | Set this to t if you | | | | prefer verbose error | | | | messages. | +--------------+---------------------+----------------------+ | defaultdb | (none) | The default data- | | | | base. refdbc will | | | | try to use this | | | | database unless you | | | | select a different | | | | one with the se- | | | | lectdb command. | +--------------+---------------------+----------------------+ | defaultris | (none) | The path of a RIS | | | | file with entries | | | | that should be added | | | | to all new or up- | | | | dated references. | | | | This is typically | | | | used to set some de- | | | | fault value for the | | | | RP field or to spec- | | | | ify additional key- | | | | words. | +--------------+---------------------+----------------------+ | fields | (none) | A list of additional | | | | fields which should | | | | be displayed by de- | | | | fault in the refer- | | | | ence output. The | | | | list is a simple | | | | concatenation of the | | | | field names. Possi- | | | | ble fields are N1, | | | | N2, NX, AB, AD, RP, | | | | SN, PB, CY, UR, U1 | | | | through U5, M1 | | | | through M3. Use the | | | | string "ALL" to re- | | | | quest all available | | | | fields. | +--------------+---------------------+----------------------+ | fromencoding | ISO-8859-1 | The default encoding | | | | of RIS input data. | | | | You can use any en- | | | | coding that your lo- | | | | cal libiconv imple- | | | | mentation 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. Pos- | | | | sible values, in or- | | | | der of increasing | | | | verbosity, are: | | | | emerg, alert, crit, | | | | err, warning, no- | | | | tice, 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. "std- | | | | out" sends the data | | | | to stdout. | +--------------+---------------------+----------------------+ 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 out- file]] {note-specifier} {link-target...} Description The addlink command links an extended note to one or more link tar- gets. 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: (key- word 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 out- file] | [-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 ig- nored. 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 dif- ferent 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 ig- nored 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 dif- ferent from the default setting. RIS datasets can use any encod- ing 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 file- names 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 explic- itly with the -d option, and the default encoding (UTF-8) is as- sumed. checkref Synopsis checkref [-A output-type] [-d database] [-E encoding] [-h] [[-c com- mand] | [-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 data- base. 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 in- deed identical, and change the abbreviated one to the full version. In addition, keywords are checked for similar existing keywords (of- ten 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 volup- tuous 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 dif- ferent from the default setting. RIS datasets can use any encod- ing 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 out- put. -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 avail- able checks are performed. This may result in a more comprehen- sive 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 out- put. 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 file- names 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: (key- word 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 out- file]] {{ID...} | {-f infile}} Description Deletes the reference with the identifier ID from the current data- base. 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 per- sonal 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 associ- ated 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 data- base. 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 addi- tion 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 out- file] | [-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 addi- tion 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 refer- ence list. getau, geted, getas, getax Synopsis getau [-d database] [-h] [[-c command] | [-o outfile] | [-O out- file]] [-N limit[:offset]] [-s format] {unix-regexp} geted [-d database] [-h] [[-c command] | [-o outfile] | [-O out- file]] [-N limit[:offset]] [-s format] {unix-regexp} getas [-d database] [-h] [[-c command] | [-o outfile] | [-O out- file]] [-N limit[:offset]] [-s format] {regexp} getas [-d database] [-h] [[-c command] | [-o outfile] | [-O out- file]] [-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 pe- riodical 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 op- tional 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 in- stead. Example refdbc: getau -o authors.txt '^Simpson' This command will write a list of all authors starting with "Simp- son" 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 cus- tom 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, abbrevia- tion, custom abbreviation 1, and custom abbreviation 2). If the option is absent, only the name that you search for will be re- turned, 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 op- tional 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 in- teger 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 in- stead. Example refdbc: getjo -a -o journals.txt '^J' This command will list all synonyms of the journals whose abbrevia- tions 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 out- file]] [-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 key- words 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 in- stead. 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 re- sult 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 con- tains the frequency of each returned keyword. The data are sorted in descending order according to the frequency, and the frequency in- formation 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 out- file] | [-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 de- scription 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 dif- ferent 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 op- tional 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 for- mat-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 dif- ferent 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 for- mats. 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 data- base-regexp is specified, only the databases matching this expres- sion 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 match- ing 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 in- stead. 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 out- file] | [-O outfile]] {[ID...] | [-f file]} Description Adds references to the specified personal reference list in the cur- rent database. If no personal reference list is specified, the de- fault 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 addi- tion 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 cur- rent database. Refer to the section The query language for a de- scription of the syntax of a search string. This command is equiva- lent 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 refer- ences. 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 al- though 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 con- figuration 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 ses- sion. updatejo Synopsis updatejo [-d database] [-h] [[-c command] | [-o outfile] | [-O out- file]] {: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 offi- cial abbreviation as "J.Biol.Chem." to read "The Journal of Biologi- cal Chemistry". updatenote Synopsis updatenote [-d database] [-E encoding] [-h] [[-c command] | [-o out- file] | [-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 data- base, 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 dif- ferent 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 cur- rently 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 out- file] | [-O outfile]] [-t type] [-P] [-U username] [file] Description Updates the references in RIS format in file in the current data- base. 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 simi- larity with the old one having the same ID. If you tell refdb to up- date 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 dif- ferent from the default setting. RIS datasets can use any encod- ing 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 per- sonal 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 file- names 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 data- base. 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 /usr/local/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-man- ual/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 2005-10-15 REFDBC(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | DIAGNOSTICS | CONFIGURATION | COMMANDS | FILES | SEE ALSO | AUTHOR
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