refdb handbook

covers version 0.9.6

Markus Hoenicka

Table of Contents
Preface
1. refdb in a nutshell
2. Organization of this manual
3. Further information
I. Overview
1. Introduction
1.1. What is refdb?
1.2. Who should use refdb?
1.3. General features
1.4. Reference management features
1.5. Bibliography tool features
1.5.1. SGML and XML
1.5.2. LaTeX
1.6. Credits
2. System requirements
2.1. Operating system
2.2. Libraries necessary to build and run refdb
2.2.1. System libraries
2.2.2. Other libraries
2.3. Perl modules
2.4. External applications
3. Current limitations and platform issues
3.1. Limitations
3.2. Platform issues
II. Administrator manual
4. Installation
4.1. Quickstart guide
4.2. Upgrading from an older version
4.2.1. 0.9.5
4.2.2. 0.9.4
4.2.3. 0.9.3
4.2.4. 0.9
4.3. Things to know before you start
4.3.1. Which database server?
4.3.2. Where do the components go?
4.3.3. The mystery of the configuration files
4.3.4. Environment variables
4.3.5. Some notes on the filesystem
4.4. Installation on Linux and other Unix variants
4.4.1. Generic instructions
4.4.2. OS-specific hints
4.5. Installation on Windows NT/2000/XP
4.5.1. Prerequisites
4.5.2. Installation from the sources
4.5.3. Installation of prebuilt binaries
4.6. Installation on Windows 95/98/ME
4.7. Other operating systems
4.8. Finishing the refdb installation
4.8.1. Configuring your database server
4.8.2. Creating the databases
4.8.3. Configuration files
4.8.4. The SGML/XML support files
4.8.5. The shell scripts
4.9. Testing your installation
5. refdb administration
5.1. Create a database
5.2. Delete a database
5.3. Add or remove a user
5.3.1. Add users
5.3.2. Remove users
5.4. Configure the application server
5.4.1. Configuration at startup
5.4.2. Reconfiguring a running refdbd process
5.5. Add, edit, or delete bibliography styles
5.6. Logging data
5.6.1. What to log
5.6.2. Destinations
5.6.3. Log levels
5.6.4. Interpreting the log information
5.7. Security issues
5.7.1. Passwords
5.7.2. Database server access control
5.8. How to run several refdb instances
5.9. Backup your data
5.9.1. Creating a risx dump
5.9.2. Creating a SQL dump
III. User manual
6. Overview of the refdb clients
6.1. Quickstart guide
6.2. The interactive mode of refdba and refdbc
6.3. The non-interactive mode of refdba and refdbc
6.3.1. Example
6.4. The non-interactive mode of refdbib
6.5. Common command-line options for all clients
7. Data input
7.1. Writing RIS datasets
7.1.1. Overview
7.1.2. Character encodings
7.1.3. RIS tags
7.1.4. Examples
7.2. The Emacs RIS mode
7.3. Input filters
7.4. Writing risx datasets
7.5. Writing extended notes
7.6. Input data mangling
7.6.1. Information that refdb generates for you
7.6.2. Information that refdb mangles
8. Reference management
8.1. Add references
8.1.1. RIS datasets
8.1.2. risx datasets
8.2. Find and view references
8.3. Delete references
8.3.1. Example
8.4. Edit references
8.5. Print references
8.6. Use the personal reference list
8.7. Global edit references
8.8. Create periodical synonyms
8.9. Character encoding issues
8.9.1. Character encodings of databases
8.9.2. Character encodings of imported data
8.9.3. Character encodings of exported data
8.10. Use pdfroot
8.11. Interaction with external applications
8.11.1. Editor
8.11.2. Viewer
9. Notes management
9.1. Add extended notes
9.1.1. Example
9.2. Find and view extended notes
9.3. Delete extended notes
9.3.1. Example
9.4. Edit extended notes
9.5. Link existing notes to other objects in the database
9.5.1. Example
9.6. To share or not to share extended notes
9.6.1. The refdbd default
9.6.2. The share attribute of the extended notes
9.6.3. Data privacy
10. Bibliographies
10.1. Quickstart guide
10.2. Manage bibliography styles
10.2.1. Write or modify a bibliography style file
10.3. Create bibliographies
10.3.1. SGML and XML documents
10.3.2. Other SGML or XML document types
10.3.3. LaTeX/BibTeX
IV. Reference manual
11. refdbd: the application server
11.1. Overview
11.2. Starting refdbd
11.2.1. Using the control script
11.2.2. Start refdbd directly
11.3. The refdbdrc variables
12. refdba: the administrative client
12.1. Overview
12.2. Starting refdba
12.3. The refdbarc variables
12.4. Commands
12.4.1. addstyle
12.4.2. adduser
12.4.3. addword
12.4.4. confserv
12.4.5. createdb
12.4.6. deletedb
12.4.7. deletestyle
12.4.8. deleteuser
12.4.9. deleteword
12.4.10. getstyle
12.4.11. help
12.4.12. listdb
12.4.13. liststyle
12.4.14. listuser
12.4.15. listword
12.4.16. scankw
12.4.17. set
12.4.18. verbose
12.4.19. viewstat
13. refdbc: the reference management client
13.1. Overview
13.2. Starting refdbc
13.3. The refdbc configuration file variables
13.4. Commands
13.4.1. addlink
13.4.2. addnote
13.4.3. addref
13.4.4. deletelink
13.4.5. deletenote
13.4.6. deleteref
13.4.7. dumpref
13.4.8. getau, geted, getas
13.4.9. getjo, getjf, getj1, getj2
13.4.10. getkw
13.4.11. getnote
13.4.12. getref
13.4.13. help, ?
13.4.14. listdb
13.4.15. liststyle
13.4.16. pickref
13.4.17. selectdb
13.4.18. set
13.4.19. updatenote
13.4.20. updateref
13.4.21. verbose
13.4.22. whichdb
13.5. Reference data output formats
13.5.1. scrn
13.5.2. html
13.5.3. xhtml
13.5.4. ris
13.5.5. risx
13.5.6. bibtex
13.5.7. db31
13.5.8. db31x
13.5.9. teix
13.6. Extended notes output formats
13.6.1. scrn
13.6.2. html
13.6.3. xhtml
13.6.4. xnote
13.7. The query language
13.7.1. The reference query language
13.7.2. The notes query language
13.7.3. Some example queries
13.8. Regular expressions
13.8.1. Unix-style regular expressions
13.8.2. SQL regular expressions
14. refdbib: the bibliography client
14.1. Overview
14.2. Starting refdbib
14.3. Examples
14.4. The refdbibrc variables
15. Reference data conversion tools
15.1. dos2unix
15.2. med2ris
15.2.1. Starting med2ris
15.2.2. The med2ris configuration variables
15.2.3. med2ris' behind-the-scenes data mangling
15.3. nmed2ris
15.3.1. Starting nmed2ris
15.3.2. The nmed2ris configuration variables
15.3.3. nmed2ris' behind-the-scenes data mangling
15.3.4. Data sources
15.4. bib2ris
15.4.1. Starting bib2ris
15.4.2. The bib2ris variables
15.4.3. bib2ris' data mangling
15.4.4. Post-processing with tex2mail
15.5. en2ris
15.5.1. Starting en2ris
15.5.2. The en2ris configuration variables
15.5.3. en2ris' behind-the-scenes data mangling
15.6. db2ris
15.6.1. Starting db2ris
15.6.2. The db2risrc variables
15.6.3. db2ris' data mangling
15.6.4. Modifying db2ris
15.7. marc2ris
15.7.1. Starting marc2ris
15.7.2. marc2ris data mangling
15.7.3. The marc2ris configuration variables
15.8. Convert SGML and XML data to risx
16. Bibliography tools
16.1. The refdbnd shell script
16.2. The runbib shell script
16.2.1. DocBook SGML output
16.2.2. DocBook and TEI XML output
16.2.3. BibTeX output
16.2.4. Example
16.3. The refdbjade shell script
16.3.1. Starting refdbjade
16.3.2. Resolution of public identifiers
16.3.3. Examples
16.4. The refdbxml shell script
16.4.1. Starting refdbxml
16.4.2. Configuring refdbxml
16.4.3. Resolution of public identifiers
16.4.4. Examples
16.5. The bibdb2tei.xsl stylesheet
16.6. refdbxp
16.6.1. Starting refdbxp
16.6.2. Examples
V. Programmer's manual
17. Reference database design
17.1. The table t_meta
17.2. The table t_refdb
17.3. The table t_author
17.4. The table t_keyword
17.5. The table t_periodical
17.6. The table t_user
17.7. The table t_xauthor
17.8. The table t_xkeyword
17.9. The table t_xuser
18. The refdb database design
18.1. The table t_journal_words
18.2. The table CITSTYLE
18.3. The table REFSTYLE
18.4. The table SEPARATORS
18.5. The table POSITION
19. RIS and risx format specifications
19.1. The refdb RIS implementation
19.2. The risx DTD
20. The Perl client module
20.1. Installation
20.2. Classes and their functions
20.2.1. RefDBClient::Risdata
20.2.2. RefDBClient::Simplelist
20.2.3. RefDBClient::Enigma
20.2.4. RefDBClient::Client
21. Using the backend API to implement new output formats
21.1. The backend API
21.2. How to insert a new backend into refdb
22. The refdb SGML/XML input and output formats
22.1. The XML input format for bibliographies
22.2. The XML input format for bibliographic styles
22.3. The XML input format for extended notes
22.4. Processing expectations for the refdb DocBook bibliography output
23. The refdb client/server communication protocol
23.1. Prerequisites
23.2. Basic principles
23.2.1. Message format
23.2.2. First stage
23.2.3. Second stage
23.3. Commented abstract representation of the client/server protocol
23.3.1. First stage
23.3.2. Second stage
23.3.3. Status messages
Colophon
List of Tables
5-1. Log level definitions
9-1. Sharing extended notes
10-1. Bibliographic reference types
11-1. refdbdrc
12-1. refdbarc
13-1. refdbcrc
14-1. refdbibrc
15-1. med2risrc
15-2. nmed2risrc
15-3. bib2ris exit codes
15-4. bib2risrc
15-5. bib2risrc
15-6. en2risrc
15-7. db2risrc
15-8. marc2risrc
16-1. refdbxmlrc
List of Figures
1-1. refdb three-tier architecture
4-1. refdb on a standalone workstation
4-2. refdb on a network
10-1. Schematic representation of a CITESTYLE element
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  Preface