refdb handbook

covers version 0.9.4

Markus Hoenicka

mhoenicka@users.sourceforge.net

Table of Contents
Preface
I. Overview
1. Introduction
What is refdb?
Who should use refdb?
General features
Reference management features
Bibliography tool features
SGML and XML
LaTeX
Credits
2. System requirements
Operating system
Libraries necessary to build and run refdb
System libraries
Other libraries
Perl modules
External applications
3. Current limitations and platform issues
Limitations
Platform issues
II. Administrator manual
4. Installation
Quickstart guide
Upgrading from an older version
0.9.4
0.9.3
0.9
Things to know before you start
Which database server?
Where do the components go?
Installation on a standalone workstation
Installation in a network
Installation as a web application
The mystery of the configuration files
Types of configuration files
Configuration file syntax
A configuration example
Configuration file variables
Environment variables
Some notes on the filesystem
Installation on Linux and other Unix variants
Generic instructions
Prerequisites
Installation from the sources
Living on the bleeding edge: installing a CVS version
Installation of refdbd as a daemon
OS-specific hints
Linux
FreeBSD
NetBSD
Solaris
OSX
Installation on Windows NT/2000/XP
Prerequisites
External applications
Libraries
Installation from the sources
Installation of prebuilt binaries
Installation on Windows 95/98/ME
Other operating systems
Finishing the refdb installation
Creating the databases
MySQL
PostgreSQL
SQLite
Configuration files
The SGML/XML support files
The shell scripts
Testing your installation
Setting up the refdb web services
Logging data
What to log
Destinations
Log levels
Interpreting the log information
Security issues
Passwords
Database server access control
MySQL
PostgreSQL
Web access
5. refdb administration
Create a database
Delete a database
Add or remove a user
Add users
MySQL
PostgreSQL
Remove users
Configure the application server
Configuration at startup
Reconfiguring a running refdbd process
Add, edit, or delete bibliography styles
Backup your data
Creating a risx dump
Creating a SQL dump
III. User manual
6. Overview of the refdb clients
Quickstart guide
The interactive mode of refdba and refdbc
The non-interactive mode of refdba and refdbc
Example
The non-interactive mode of refdbib
Common command-line options for all clients
7. Data input
Writing RIS datasets
Overview
RIS tags
Examples
The Emacs RIS mode
Input filters
Writing risx datasets
Writing extended notes
8. Reference management
Add references
RIS datasets
Example
risx datasets
Example
Find and view references
Delete references
Example
Edit references
Use the personal reference list
Global edit references
Create periodical synonyms
Use pdfroot
Interaction with external applications
Editor
Viewer
9. Notes management
Add extended notes
Example
Find and view extended notes
Delete extended notes
Example
Edit extended notes
Link existing notes to other objects in the database
Example
10. Bibliographies
Quickstart guide
Manage bibliography styles
Write or modify a bibliography style file
Create bibliographies
SGML and XML documents
Prepare the document
Create citations
Generate the bibliography
Transform the document
The refdbnd shortcut
Other SGML or XML document types
LaTeX/BibTeX
11. Using the refdb web interface
Overview
The main screens
Search references
Search keywords, authors, journals
Add new references
Change database
Logout
IV. Reference manual
12. refdbd: the application server
Overview
Starting refdbd
Using the control script
Start refdbd directly
The refdbdrc variables
13. refdba: the administrative client
Overview
Starting refdba
The refdbarc variables
Commands
addstyle
Synopsis
Description
Example
adduser
Synopsis
Description
Examples
Alternatives on sites with restricted database server access
addword
Synopsis
Description
Example
confserv
Synopsis
Description
Example
createdb
Synopsis
Description
Example
Using SQL scripts to create databases
deletedb
Synopsis
Description
Example
deletestyle
Synopsis
Description
Example
getstyle
Synopsis
Description
Example
help
Synopsis
Description
Example
listdb
Synopsis
Description
Example
liststyle
Synopsis
Description
Example
listuser
Synopsis
Description
Example
listword
Synopsis
Description
Example
scankw
Synopsis
Description
set
Synopsis
Description
Example
verbose
Synopsis
Description
Example
viewstat
Synopsis
Description
Example
14. refdbc: the reference management client
Overview
Starting refdbc
The refdbc configuration file variables
Commands
addlink
Synopsis
Description
Example
addnote
Synopsis
Description
Example
addref
Synopsis
Description
Example
deletenote
Synopsis
Description
Example
deleteref
Synopsis
Description
Example
getau, geted, getas
Synopsis
Description
Example
getjo, getjf, getj1, getj2
Synopsis
Description
Example
getkw
Synopsis
Description
Example
getnote
Synopsis
Description
Example
getref
Synopsis
Description
Example
help, ?
Synopsis
Description
Example
listdb
Synopsis
Description
Example
liststyle
Synopsis
Description
Example
pickref
Synopsis
Description
Example
selectdb
Synopsis
Description
Example
set
Synopsis
Description
Example
updatenote
Synopsis
Description
Example
updateref
Synopsis
Description
Example
verbose
Synopsis
Description
Example
whichdb
Synopsis
Description
Example
Reference data output formats
scrn
html
xhtml
ris
risx
bibtex
db31
db31x
teix
Extended notes output formats
scrn
html
xhtml
xnote
The query language
The reference query language
The notes query language
Some example queries
Regular expressions
Unix-style regular expressions
SQL regular expressions
15. refdbib: the bibliography client
Overview
Starting refdbib
Examples
The refdbibrc variables
16. Reference data conversion tools
dos2unix
med2ris.pl
Starting med2ris.pl
The med2ris.pl configuration variables
med2ris' behind-the-scenes data mangling
nmed2ris
Starting nmed2ris
The nmed2ris configuration variables
nmed2ris' behind-the-scenes data mangling
Data sources
bib2ris
Starting bib2ris
The bib2ris variables
bib2ris' data mangling
Post-processing with tex2mail
en2ris.pl
Starting en2ris.pl
The en2ris.pl configuration variables
en2ris' behind-the-scenes data mangling
db2ris
Starting db2ris
The db2risrc variables
db2ris' data mangling
Modifying db2ris
marc2ris.pl
Starting marc2ris.pl
marc2ris.pl data mangling
The marc2ris.pl configuration variables
Convert SGML and XML data to risx
17. Bibliography tools
The refdbnd shell script
The runbib shell script
DocBook SGML output
DocBook and TEI XML output
BibTeX output
Example
The refdbjade shell script
Starting refdbjade
Examples
The refdbxml shell script
Starting refdbxml
Examples
The bibdb2tei.dsl stylesheet
refdbxp
Starting refdbxp
Examples
V. Programmer's manual
18. Reference database design
The table t_meta
The table t_refdb
The table t_author
The table t_keyword
The table t_periodical
The table t_user
The table t_xauthor
The table t_xkeyword
The table t_xuser
19. The refdb database design
The table t_journal_words
The table CITSTYLE
The table REFSTYLE
The table SEPARATORS
The table POSITION
20. RIS and risx format specifications
The refdb RIS implementation
The risx DTD
21. The Perl client module
Installation
Classes and their functions
RefDBClient::Client
set_conninfo
refdb_addstyle
refdb_adduser
refdb_addword
refdb_confserv
refdb_createdb
refdb_deletedb
refdb_deletestyle
refdb_getstyle
refdb_listdb
refdb_liststyle
refdb_listuser
refdb_listword
refdb_viewstat
refdb_addref
refdb_updateref
refdb_deleteref
refdb_getas
refdb_getau
refdb_geted
refdb_getkw
refdb_getjf
refdb_getjo
refdb_getj1
refdb_getj2
refdb_getref
refdb_pickref
refdb_selectdb
refdb_whichdb
refdb_texbib
refdb_dbib
id_from_aux
RefDBClient::Risdata
read_ris
get_ris
22. Using the backend API to implement new output formats
The backend API
How to insert a new backend into refdb
23. The refdb SGML/XML input and output formats
The XML input format for bibliographies
The XML input format for bibliographic styles
The XML input format for extended notes
Processing expectations for the refdb DocBook bibliography output
24. Customization of the refdb web interface
Modifying the stylesheet
Modify the HTML pages
List of Tables
4-1. Log level definitions
10-1. Bibliographic reference types
12-1. refdbdrc
13-1. refdbarc
14-1. refdbcrc
14-2. refdbcgirc
15-1. refdbibrc
16-1. med2risrc
16-2. med2riscgirc
16-3. nmed2risrc
16-4. nmed2riscgirc
16-5. bib2ris exit codes
16-6. bib2risrc
16-7. bib2riscgirc
16-8. bib2riscgirc
16-9. en2risrc
16-10. db2risrc
16-11. med2risrc
List of Figures
1-1. refdb three-tier architecture
4-1. refdb on a standalone workstation
4-2. refdb on a network
4-3. Example of refdb as a web application
10-1. Schematic representation of a CITESTYLE element
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