refdbd - Online in the Cloud

PROGRAM:

NAME

refdbd - the application server of RefDB

SYNOPSIS

refdbd [-b dbs-port] [-d default-database] [-D dbserver] [-e log-destination]
[-E encoding] [-h] [-i IP-address] [-I] [-k] [-K] [-l log-level] [-L log-file]
[-p port] [-P PID-file] [-q] [-r] [-s] [-S note-share-mode] [-T time] [-U] [-v]
[-V] [-x] [-y confdir] [-Y libdbidir]

refdbd {[-a] | [-c]} [-b dbs-port] [-D dbserver] [-e log-destination] [-E encoding] [-h]
[-i IP-address] [-l log-level] [-L log-file] [-p port] [-P PID-file] [-q]
[-u username] [-v] [-V] [-w password] [-x] [-y confdir] [-Y libdbidir]

DESCRIPTION

refdbd is the application server of RefDB(7). refdbd contains most of the application
logic of RefDB and interacts with the database engine. refdbd must run somewhere in your
network to do anything useful with the RefDB clients. refdbd usually runs as a daemon and
responds to client requests, but it can be started as a regular process for debugging
purposes. To start refdbd as a server, use the first command synopsis shown above.

It is recommended to use a wrapper script to start and stop refdbd. If you want to start
and stop refdbd manually, use refdbctl(1). If you want to run refdbd as a daemon, use
refdb(8). Edit the configuration file (see below) to permanently configure refdbd.

In addition to being run as a server, refdbd can also be invoked to check, install, or
upgrade the main database. Refer to the second command synopsis shown above.

OPTIONS

-a
Runs refdbd to install or upgrade the main database. refdbd will exit after performing
the maintenance tasks. In order to perform the maintenance tasks you have to provide a
database administrator username and password using the -u and -w options,
respectively, if your database engine uses access control. Some database
configurations (e.g. PostgreSQL on Debian) further require you to run the
administrative tasks from a special privileged user account (often called pgsql or
postgres). If you use one of the file-based engines (SQLite or SQLite3), you must run
the tool from an account which has write permissions in the database folder. refdbd
first checks whether a main database already exists. If not, it will attempt to
install it. Otherwise, it will upgrade the database to the current version if
required. refdbd will print an error message to stderr if the maintenance job fails,
and exit with a non-zero exit code.

-b dbs-port
Set the port on which the database server listens for incoming connections. The
default is 3306 for MySQL and 5432 for PostgreSQL. This option does not apply if you
use SQLite as your database engine.

-c
Runs refdbd to check the main database version and the database engine connection.
refdbd will exit after performing the maintenance tasks. In order to perform the
maintenance tasks you have to provide a database administrator username and password
using the -u and -w options, respectively, if your database engine uses access
control. If you use one of the file-based engines (SQLite or SQLite3), you must run
the tool from an account which has read permissions for the main database file. refdbd
will print an error message to stderr if the check fails, and exit with a non-zero
exit code.

-d default-database
Set a default database to be used for all client queries that do not specify a
database.

-D dbserver
Select the database server. Currently the values mysql, pgsql, and sqlite are
supported to select MySQL, PostgreSQL, and SQLite, respectively.

-e log-destination
This specifies the destination of the log information. If destination is 0 or
"stderr", the log output is sent to stderr. This should only be used for debugging
purposes when refdbd is not run as a daemon. If destination is 1 or "syslog", the
syslog facility of the system is used. syslog has to be configured properly to accept
refdb's log output. Consult the syslogd(8) man page how to achieve this. If
destination is 2 or "file", a custom log file as defined by the -L switch is used
instead. If this log file cannot be written to, refdbd falls back to using syslog.

-E encoding
Select the default character encoding for new reference databases. Specify the IANA
name of the encoding. You can override this default by using the -E option of the
createdb command.

-h
Displays help and usage screen, then exits.

-i IP-address
For external database servers, set the IP address of the box which is running the
database server. Instead of the IP address you can also specify the hostname as long
as it can be properly resolved by your system. If the database server runs on the same
box as refdbd, use the string localhost. Note: If localhost does not seem to work, try
specifying the real IP address of the box instead - some database client libraries
refuse to use TCP/IP for local connections which may cause mayhem on particular
systems. For embedded database engines, this option sets the directory which contains
the database files. The default is /usr/local/share/refdb/db. Note: SQLite on Cygwin
has a bug which prevents the use of absolute paths. Use a relative path instead by
leaving out the leading slash. This assumes that refdbd is started from the root
directory. The start script refdbctl does this automatically.

-I
Set this switch to allow remote connections to refdbd. Otherwise only connections from
localhost (127.0.0.1) will be answered.

-k
refdb stores up to four names (full name, official abbreviation, and two user-defined
abbreviations) of each periodical. These synonyms are shared by all references that
use one of these periodical names. As it sometimes requires some effort to get at the
synonyms (public reference data often contains only the official abbreviation), it is
desirable to keep these synonyms even if you remove the last reference that uses a
particular periodical name. If you use the -k option, the synonyms will not be removed
from the database and will be available immediately if you add a new reference using
that particular periodical name.

-K
If this option is used, refdbd will run an automatic keyword scan each time you add or
update references. refdbd will scan the title fields and the abstract field of the
modified references for any keywords already present in the database but not in the
particular reference. This increases the usability of keywords in queries. There is no
speed decrease for the user interaction as the keyword scan is performed in the
background. See also the related refdba command scankw which performs a more thorough
manual keyword scan.

-l log-level
Set the log level to a value between 0 and 7 or to a string value as described in log
level definitions. 0 means that only critical log messages will be logged, while a
value of 7 means that every log message will be logged. Set level to -1 to disable
logging.

-L log-file
This switch specifies a custom log file (full path please). This will only be used if
the -e switch is set accordingly.

-p port
Set the port on which refdbd listens for incoming connections. The default is 9734.

-P PID-file
Specify the full path of the file that refdbd writes its process ID to. This PID
simplifies stopping and reconfiguring the application server from the command line.
The default value is /var/log/refdbd.pid.

-q
Start without reading the configuration file. Useful for debugging purposes

-r
Enables remote administration via refdba.

-s
Starts as a standalone application, not as daemon.

-S note-share-mode
Set the default extended note share mode to either public or private. This setting
affects the accessibility of extended notes if they do not explicitly carry a share
attribute. See the section about notes sharing for more information.

-T time
Set the timeout for client/application server dialogue in seconds.

-u name
Set the username of the database administrator account.

-U
This switch causes refdbd to automatically uppercase all citation keys of newly added
references. This makes it more convenient to work with SGML bibliographies.

-v
Prints version and copyright information, then exits.

-V
Switches to verbose mode. To be honest, currently this doesn't make much of a
difference.

-w password
The password of the database administrator account. You can pass an asterisk to let
refdbd ask for a password interactively. This keeps your password from showing up in
the process list. Keep in mind that you have to protect the asterisk on the command
line by surrounding it with single quotes.

-x
Assume incoming passwords are 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.

-Y libdbidir
Specify the directory where the libdbi drivers are Note: By default, libdbi (the
database abstraction library used by refdbd) looks for its driver 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 libdbi binaries in unusual
locations, e.g. by relocating a rpm package.

CONFIGURATION

Table 1. refdbdrc
┌──────────────┬─────────────────────────────┬──────────────────────────┐
│Variable │ Default │ Comment │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│refdblib │ /usr/local/share/refdb │ The path of the │
│ │ │ directory containing │
│ │ │ shareable refdb files │
│ │ │ like DTDs, HTML │
│ │ │ templates etc. Actually, │
│ │ │ most of the files are in │
│ │ │ subdirectories of │
│ │ │ refdblib. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│dbsport │ 3306 │ The port on which the │
│ │ │ database server listens. │
│ │ │ Use either 3306 or 5432 │
│ │ │ for MySQL and │
│ │ │ PostgreSQL, │
│ │ │ respectively. This │
│ │ │ variable is ignored if │
│ │ │ you use SQLite as your │
│ │ │ database engine. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│dbserver │ sqlite │ The database server you │
│ │ │ want to connect to. Use │
│ │ │ one of mysql, pgsql, or │
│ │ │ sqlite to select MySQL, │
│ │ │ PostgreSQL, or SQLite as │
│ │ │ your database engine, │
│ │ │ respectively. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│dbpath │ /usr/local/var/lib/refdb/db │ The directory that │
│ │ │ contains the database │
│ │ │ files of an embedded │
│ │ │ database engine. Leave │
│ │ │ out the leading slash if │
│ │ │ you use SQLite on │
│ │ │ Cygwin. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│logdest │ 2 │ The destination of the │
│ │ │ log information. 0 = │
│ │ │ print to stderr (for │
│ │ │ debugging only, don't │
│ │ │ use when running as a │
│ │ │ daemon); 1 = use the │
│ │ │ syslog facility; 2 = use │
│ │ │ a custom logfile. The │
│ │ │ latter needs a proper │
│ │ │ setting of logfile. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│logfile │ /var/log/refdbd.log │ The full path of a │
│ │ │ custom log file. This is │
│ │ │ used only if logdest is │
│ │ │ set appropriately. If │
│ │ │ you start refdbd from │
│ │ │ the command line as a │
│ │ │ regular user, you should │
│ │ │ specify a file that you │
│ │ │ have write access to │
│ │ │ (you may not be allowed │
│ │ │ to create │
│ │ │ /var/log/refdbd.log or │
│ │ │ write to this file as a │
│ │ │ regular user). │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│loglevel │ 6 │ The log level up to │
│ │ │ which messages will be │
│ │ │ sent. A low setting (0) │
│ │ │ will notify you only in │
│ │ │ case of a meltdown, │
│ │ │ whereas a high setting │
│ │ │ (7) allows all messages │
│ │ │ including debug messages │
│ │ │ (this is a lot). -1 │
│ │ │ means nothing will be │
│ │ │ logged. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│pidfile │ /var/log/refdb.pid │ The file refdbd writes │
│ │ │ its process ID to. If │
│ │ │ you start refdbd from │
│ │ │ the command line as a │
│ │ │ regular user, you should │
│ │ │ specify a file that you │
│ │ │ have write access to │
│ │ │ (you may not be allowed │
│ │ │ to create │
│ │ │ /var/log/refdbd.pid or │
│ │ │ write to this file as a │
│ │ │ regular user). │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│port │ 9734 │ The port on which refdbd │
│ │ │ listens. The server and │
│ │ │ all clients that are │
│ │ │ supposed to connect to │
│ │ │ it must agree on the │
│ │ │ same port. Obviously, │
│ │ │ this option allows to │
│ │ │ run several instances of │
│ │ │ refdbd on the same box │
│ │ │ if there is a good │
│ │ │ reason to do so. In this │
│ │ │ case you should also use │
│ │ │ separate log and pid │
│ │ │ files. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│remoteadmin │ f │ Set this to 't' to allow │
│ │ │ remote administration │
│ │ │ via refdba. Be aware │
│ │ │ that this is a security │
│ │ │ risk. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│serverip │ localhost │ The IP address or │
│ │ │ hostname of the machine │
│ │ │ where the database │
│ │ │ server runs. Use the │
│ │ │ default (localhost) │
│ │ │ address if the database │
│ │ │ server and refdbd 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. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│keep_pnames │ t │ Set this to 't' to keep │
│ │ │ periodical names and │
│ │ │ synonyms if you remove │
│ │ │ references. If set to │
│ │ │ 'f', the names will be │
│ │ │ removed from the │
│ │ │ database if the last │
│ │ │ reference using these │
│ │ │ names is deleted. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│db_encoding │ (none) │ Specify the default │
│ │ │ character encoding for │
│ │ │ new refdb reference │
│ │ │ databases. If the │
│ │ │ database server supports │
│ │ │ this feature (currently │
│ │ │ only PostgreSQL does), │
│ │ │ all new databases will │
│ │ │ use this encoding unless │
│ │ │ a different one is │
│ │ │ specified with the │
│ │ │ createdb command. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│in_encoding │ ISO-8859-1 │ Specify the default │
│ │ │ character encoding for │
│ │ │ RIS data being added to │
│ │ │ databases. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│dbi_driverdir │ (none) │ Specify the directory │
│ │ │ containing the libdbi │
│ │ │ driver files. As │
│ │ │ mentioned above, this is │
│ │ │ only necessary if you │
│ │ │ use precompiled libdbi │
│ │ │ binaries in funny │
│ │ │ locations. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│keyword_scan │ t │ Set this to 't' to allow │
│ │ │ an automatic keyword │
│ │ │ scan after references │
│ │ │ are added or updated. │
│ │ │ 'f' will switch off this │
│ │ │ feature. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│upper_citekey │ f │ Set this to 't' to │
│ │ │ uppercase all citation │
│ │ │ keys of newly added │
│ │ │ references (this makes │
│ │ │ sure they work with SGML │
│ │ │ bibliographies). │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│share_default │ public │ Whether ("public") or │
│ │ │ not ("private") to share │
│ │ │ extended notes between │
│ │ │ users by default. See │
│ │ │ the section about notes │
│ │ │ sharing for more │
│ │ │ information. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│remoteconnect │ f │ Set this to 't' to allow │
│ │ │ remote connections to │
│ │ │ refdbd. By default, │
│ │ │ refdbd accepts only │
│ │ │ local connections due to │
│ │ │ security concerns. │
├──────────────┼─────────────────────────────┼──────────────────────────┤
│no_decrypt │ f │ If set to 't', incoming │
│ │ │ passwords are assumed to │
│ │ │ be unencrypted. The │
│ │ │ default is to expect │
│ │ │ encrypted passwords. │
└──────────────┴─────────────────────────────┴──────────────────────────┘

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