RefDB handbook
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RefDB handbook

covers version 0.9.9

Markus Hoenicka

<mhoenicka@users.sourceforge.net>

Revision History
Revision 1.23	2007-11-03
Revision 1.22	2006-12-06
Revision 1.21	2006-05-27
Revision 1.20	2005-11-14
Revision 1.19	2004-12-12
Revision 1.18	2004-02-18
Revision 1.17	2003-12-20
Revision 1.16	2003-08-15
Revision 1.15	2003-02-16
Revision 1.14	2002-11-29
Revision 1.13	2002-11-11
Revision 1.12	2002-9-1
Revision 1.11	2002-7-23
Revision 1.10	2002-5-13
Revision 1.9	2002-3-2
Revision 1.8	2002-1-1
Revision 1.7	2001-11-22
Revision 1.6	2001-10-1
Revision 1.5	2001-8-9
Revision 1.4	2001-8-5
Revision 1.3	2001-7-21
Revision 1.2	2001-6-25
Revision 1.1	2001-6-18
Revision 1.0	2001-5-22

Table of Contents

RefDB in a nutshell
Organization of this manual
Further information

I. Overview

1. Introduction

What is RefDB?

Who should use RefDB?

General features

Reference management features

Bibliography tool features

SGML and XML
LaTeX

2. System requirements

Operating system

Libraries necessary to build and run refdb

System libraries
Other libraries

Perl modules

External applications

Related Software

3. Current limitations and platform issues

Limitations
Platform issues

II. Administrator manual

4. Installation

Quickstart guide

Upgrading from an older version

0.9.9
0.9.8
0.9.7

Things to know before you start

Which database server?
Where do the components go?
The mystery of the configuration files
Environment variables
Some notes on the filesystem

Installation on Linux and other Unix variants

Generic instructions
OS-specific hints

Installation on Windows NT/2000/XP

Prerequisites
Installation from the sources
Installation of prebuilt binaries

Installation on Windows 95/98/ME

Other operating systems

Finishing the RefDB installation

Using the interactive setup script
Manual setup

Testing your installation

SRU support

Setting up SRU support as a CGI program
Setting up SRU support using a standalone web server

Install the PHP interface

Prerequisites
Web server configuration
Test your PHP interface

5. refdbd administration

Create a database

Delete a database

Add or remove a user

Add users
Remove users

Configure the application server

Configuration at startup
Reconfiguring a running refdbd process

Add, edit, or delete bibliography styles

Logging data

What to log
Destinations
Log levels
Interpreting the log information

Security issues

Passwords
Database server access control

How to run several refdb instances

Backup your data

Creating a risx dump
Creating a SQL dump

III. User manual

6. Overview of the RefDB command-line clients

Quickstart guide
The interactive mode of refdba and refdbc
The non-interactive mode of refdba and refdbc
The non-interactive mode of refdbib
Common command-line options for all clients

7. Data input

Writing RIS datasets

Overview
Character encodings
RIS tags
Examples

The Emacs helpers

Input filters

Writing risx datasets

Writing extended notes

Input data mangling

Information that RefDB generates for you
Information that RefDB mangles

8. Reference management

Add references

RIS datasets
risx datasets

Find and view references

Delete references

Edit references

Print references

Managing personal reference lists

Creating and deleting personal reference lists
Accessing references in personal reference lists
Advanced use of personal reference lists

Global edit references

Create periodical synonyms

Character encoding issues

Character encodings of databases
Character encodings of imported data
Character encodings of exported data

Use pdfroot

Interaction with external applications

Editor
Viewer

9. Notes management

Add extended notes

Find and view extended notes

Delete extended notes

Edit extended notes

Link existing notes to other objects in the database

To share or not to share extended notes

The refdbd default
The share attribute of the extended notes
Data privacy

10. Bibliographies

Quickstart guide

Manage bibliography styles

Write or modify a bibliography style file

Create bibliographies

SGML and XML documents
Other SGML or XML document types
LaTeX/BibTeX

11. RefDB SRU interface

What SRU is all about

SRU Operations

The explain operation
The searchRetrieve operation
The scan operation

IV. Reference manual

12. The application server

Description
Options
Files
See also
Author

Description
Options
Configuration
Files
See also
Author

Description
Options
See also
Author

Description
Configuration
Environment
Files
See also
Author

refdb-sruserver

Description
Configuration
Files
See also
Author

13. Administration tools

Description

Diagnostics

Configuration

addstyle
adduser
addword
confserv
createdb
deletedb
deletestyle
deleteuser
deleteword
getstyle
help
listdb
liststyle
listuser
listword
scankw
set
verbose
viewstat

refdb-backup

Description
Options
See also
Author

refdb-restore

Description
Options
See also
Author

Description
Files
See also
Author

Description
See also
Author

14. Tools for reference and notes management

Description

Diagnostics

Configuration

addlink
addnote
addref
checkref
deletelink
deletenote
deleteref
dumpref
getau, geted, getas, getax
getjo, getjf, getj1, getj2
getkw
getnote
getref
help, ?
listdb
liststyle
pickref
countnote
countref
selectdb
set
updatejo
updatenote
updateref
verbose
whichdb

Description
Options
Diagnostics
Configuration
Data Processing
Files
See also
Author

Description
Options
Configuration
Data Processing
Modifying db2ris
Files
See also
Author

Description
Options
Configuration
Data Processing
Files
See also
Author

Description
Options
Configuration
Data Processing
Files
See also
Author

Description
Options
Configuration
Data Processing
Files
See also
Author

refdb_dos2unix

Description
See also
Author

refdb_latex2utf8txt

Description
Diagnostics
Data Processing
See also
Author

Reference data output formats

scrn
html
xhtml
ris
risx
mods
bibtex
db31
db31x
db50x
teix
tei5x

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. Tools for bibliographies

Description
Options
Diagnostics
Configuration
Examples
Files
See also
Author

Description
Options
Makefile Targets
Files
See also
Author

Description
Options
Configuration
SGML Output
XML Output
Bibtex Output
Example
Files
See also
Author

Description
Options
Configuration
Environment
Example
See also
Author

Description
Options
Configuration
Resolving Public Identifiers
Files
Example
See also
Author

Description
Options
Example
See also
Author

Description
Files
See also
Author

V. Programmer's manual

16. 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_note
The table t_user
The table t_link
The table t_xauthor
The table t_xkeyword
The table t_xuser
The table t_xnote
The table t_xlink

17. The RefDB database design

The table t_journal_words
The table CITSTYLE
The table REFSTYLE
The table SEPARATORS
The table POSITION

18. RIS and risx format specifications

The RefDB RIS implementation
The risx DTD

19. Using RefDB in your programs

General thoughts

Call the C clients from your program
Directly talk to refdbd

Tips and tricks

Paging output

20. The Perl client module

Installation

Classes and their functions

RefDBClient::Risdata
RefDBClient::Simplelist
RefDBClient::Enigma
RefDBClient::Client

21. Using the backend API to implement new output formats

The backend API
How to insert a new backend into RefDB

22. 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

23. The RefDB client/server communication protocol

Prerequisites

Basic principles

Message format
First stage
Second stage

Commented abstract representation of the client/server protocol

First stage
Second stage
Status messages

Tools for the client-server protocol

Description
Options
See also
Author

List of Figures

1.1. RefDB three-tier architecture
1.2. RefDB character encoding support
4.1. RefDB on a standalone workstation
4.2. RefDB on a network
10.1. Schematic representation of a CITESTYLE element

List of Tables

5.1. Log level definitions
9.1. Sharing extended notes
10.1. Bibliographic reference types
11.1. Context sets
11.2. Percent-encoding special characters
12.1. refdbdrc
12.2. refdbsrurc
12.3. refdb-sruserverrc
13.1. refdbarc
14.1. refdbcrc
14.2. bib2risrc
14.3. db2risrc
14.4. en2risrc
14.5. marc2risrc
14.6. med2risrc
15.1. refdbibrc
15.2. refdbjaderc
15.3. refdbjaderc
15.4. refdbxmlrc

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