File Release Notes and Changelog
Notes:
refbase 0.9.5 README
====================
About refbase
-------------
refbase is a web-based solution for managing scientific literature,
references and citations.
Currently, the following features have been implemented for:
EVERYONE
- search the database using different search forms
- search within results
- browse found records and sort results by any database field
- view results in different views (list view, citations, details,
print view)
- display results in different citation styles & output formats
- export selected records to XML (Atom, MODS, OAI_DC, ODF) and (via
the GPLed Bibutils programs) to ADS, BibTeX, EndNote, ISI, RIS and
Word XML
- display rich text (i.e., italics, super/sub-script, greek letters)
- extract citations from a text & build an appropriate reference list
- track additions via RSS and generate custom RSS feeds from searches
- web services (SRU & OpenSearch) that allow clients to access a
refbase database using a standard query syntax and retrieve results
in structured XML format
- dissemination of bibliographic data via standard methods (COinS &
unAPI) allowing clients to automatically discover and extract data
from refbase
- search a refbase online database from the command line and retrieve
results in various export & citation formats
LOGGED IN USERS
- user-specific fields which are stored individually for each user
- import of records from common bibliographic formats and online
databases via the web interface or the command line
- automatic email announcements for newly added records
- save and recall search queries
- adding records to user-specific groups
- add/edit/delete records as well as file upload & download links
ADMINISTRATOR
- user management interface provided to the database admin
- set access permissions on a per-user basis
More information is given at:
<http://features.refbase.net>
Credits
-------
See AUTHORS
Requirements
------------
refbase requires:
- a web server (like the Apache HTTP Server <http://httpd.apache.org/>)
- PHP <http://www.php.net/> (version 4.4.0 or greater) with enabled
session support & installed PHP MySQL module
- MySQL <http://www.mysql.com/> (version 4.1.x or greater required for
Unicode support)
- for import and export of various formats (e.g., Endnote & BibTeX):
Bibutils <http://www.scripps.edu/~cdputnam/software/bibutils/>
(version 3.21 or greater)
More detailed information is available at:
<http://requirements.refbase.net>
Installation & Import
---------------------
See INSTALL
Update
------
See UPDATE
New Features
------------
See NEWS
Changelog
---------
See ChangeLog
Known issues
------------
See BUGS
What is missing?
----------------
See TODO
License
-------
See COPYING
Further information
-------------------
For more information about the refbase project and pointers to working
examples of refbase please visit:
<http://www.refbase.net/> or <http://refbase.sourceforge.net/>
Changes:
Below is a summary of the main fixes and enhancements since refbase-0.9.0.
See the 'ChangeLog' or the commit messages on SourceForge for a detailed history:
<http://refbase.svn.sourceforge.net/viewvc/refbase/>
refbase-0.9.5
-------------
[19-Nov-2008]
Feature additions
-------------------
Import/Add Records:
- New resource types: Abstract, Conference Article, Conference Volume, Magazine
Article, Manual, Miscellaneous, Newspaper Article, Patent, Report, Software
- Import from Endnote XML and SciFinder
- Direct import from arXiv IDs, DOIs and OpenURLs
- Direct upload of references from Bookends <http://www.sonnysoftware.com>
Search/Display:
- Improved interface:
- Redesigned main page, page footer/header & forms on results pages
- Quick Search form now always available in the page header
- Search suggestions for text entered by the user
- Forms on results pages can be hidden
- Search results can be browsed & searched in three different views:
List view, Citations, Details
- Additional record info (keywords, abstract, etc) and links to cite
or export the record can be displayed underneath each citation
- OpenSearch support (which e.g. enables Firefox & IE users to search refbase
directly from their browser's toolbar)
- Initial support for searching & managing of duplicate records
- New query history with links to any previous search results
- New customizable "main fields" search option that allows to search across
multiple fields at once
- New option to customize the default number of records per page
- Results can be dynamically included in foreign web pages
Export/Citation:
- New export formats: ADS, Atom XML, ISI Web of Science, OAI_DC XML, SRW_DC XML,
Word XML
- New citation styles: AMA, APA, Chicago, Harvard (3 variants), MLA, Vancouver
- Output of citations in LaTeX bibliography (.bbl) format
- Cite, group or export ALL found records (instead of just the selected ones)
- For PDF output, US letter is now supported as page format
- The 'headerMsg' URL parameter adds a header to any of the citation formats
- Upon export, links to corresponding files are now included if the export
format and user permissions allow so
Localization:
- Added chinese localization
Command Line Clients:
- Added support for all new export formats
- Added new options that allow to append found records to a local BibTeX or
MODS/SRW XML file (if they don't yet exist in that file), and update existing
records in that file if their modification date on the server is more recent
- Added new option to extract citation IDs from a file and retrieve matching
records from refbase (supported file types: .aux, .bbl, .bib, .enw, .ris,
.tex, (MODS|SRW|Endnote) .xml)
Miscellaneous:
- Added a refbase extension for MediaWiki which allows to place a serial number
within <refbase>...</refbase>' markup tags; metadata for the reference is
retrieved from refbase and marked-up according to a MediaWiki citation template
- Added support for the sitemaps.org protocol which allows for better indexing
by search engines
- Added unAPI support for the new export formats 'atom', 'oai_dc' and 'srw_dc'
Changes
---------
Security:
- Introduced measures to better prevent cross-site scripting (XSS) attacks
- For security reasons, HTML tags are now stripped from the 'headerMsg' URL
parameter; string formatting can now be done using the refbase markup syntax
Installation/Update:
- Improved support for PHP installations running with 'safe_mode=On'
Import/Add Records:
- The 'edition' field now accepts string values
- After any add/edit/delete action, refbase now includes a link to the last
multi-record search results list in the feedback message if the previous query
resulted in a single record; Along with other changes, this obviates
'receipt.php'
- When importing multiple records, ALL records are now imported by default
- Improved UTF-8 handling on import so that e.g. a best-effort conversion is
done for UTF-8 data which are imported into a latin1-based database
- When importing (or exporting) RIS records, the type of thesis (such as
"Masters thesis" or "Ph.D. thesis") is now taken from (or exported to) the
'U1' field (as is supported by Bibutils v3.35 or greater)
- Upon import, if the given URL actually is a DOI prefixed with
<http://dx.doi.org/>, we'll extract the DOI and move it to the 'doi' field
- Improved recognition of PubMed resource types
Search/Display:
- refbase now remembers many more search & display options while navigating or
refining the results list
- Changed the HTTP transfer method in most forms from POST to GET; this helps to
avoid warnings about re-sending POST data in some browsers (such as Firefox)
- When linking to particular records via 'show.php', one can now use consecutive
serial number ranges as values of the 'records' URL parameter; examples:
<show.php?records=123-131> or <show.php?records=123-141,145,147,150-152>
- One can now specify 'creation-date' as value for the 'citeOrder' parameter in
'show.php' URLs (or the '--order' option of the 'refbase' CLI); this allows to
sort records such that newly added/edited records get listed top of the list
- One can now specify 'Mobile' as value for the 'viewType' URL parameter (or the
'--view' option of the 'refbase' CLI); this will return results in simple HTML
suitable for mobile devices or any postprocessing
- Refined layout of 'user_receipt.php'
- Added many CSS attributes (id/class names) to HTML output where appropriate;
this allows to easier refine the CSS styling of the refbase interface
Export/Citation:
- By default, export via the refbase GUI is now enabled for anonymous users
- By default, the SRU formats SRW_DC XML and SRW_MODS XML are now transformed to
HTML via XSL stylesheets
- MODS XML exports include file links that Zotero is able to download
- Renamed the Bibutils 'xml2word' command line tool to 'xml2wordbib' according
to the name changes in Bibutils v3.40; note that if you're using a Bibutils
version prior to Bibutils v3.40, you must revert this change in file
'export/bibutils/export_xml2word.php'
- The citation output options (previously located in the results footer) have
been moved to the Display Options form of the results header in Citation view
Admin settings:
- The admin can now define any of the supported views (List view, Citations,
Details) as the default view
- For each view, the admin can now define whether the results header & footer
should be displayed open or closed by default, or whether they should be
entirely hidden from the interface
- The admin can now customize the list of fields that are displayed by default
in List & Details view; similarly, the list of fields that are available in
dropdown menus of the results header can also be customized
- The admin can now define 'accesskey' values which allow for keyboard
navigation of the main parts of the refbase interface
- The '$databaseBaseURL' in 'ini.inc.php' is now auto-generated by default
- The refbase logo image files have been updated to the new refbase logo, and
the logo URL path & dimensions can now be customized easily via 'ini.inc.php'
- The session/temp dir path can now be specified explicitly in 'ini.inc.php';
this allows you to define a custom directory path that's used on your server
to save session data and to write any temporary files
Localization:
- Improved internationalization and added many additional localization strings
- Changed or merged some localization strings to allow for better translations
to languages such as Spanish or Chinese
Miscellaneous:
- Underline fontshape markup is now supported in various import and citation
formats as well as in refbase markup (use: '__underlined text__')
- For the "Extract citations" functionality, refbase now checks whether the
extracted serial numbers and cite keys exist in the database and report any
missing record identifiers
Bug fixes
-----------
- Fixed bug that prevented correct directory creation/renaming and/or file
upload on some platforms
- Fixed 'preg_match()' compilation errors when importing BibTeX records into a
refbase UTF-8 database
- Worked around an error in Internet Explorer when importing single records via
the web interface
- When importing PubMed MEDLINE source data, refbase now extracts author
information from the 'AU' field if the 'FAU' field is not available
- refbase now converts Endnote XML text style markup into appropriate refbase
markup
- Upon RIS import, refbase now makes sure that HTML encoded source data (such as
'ä', 'ö' or 'é') get decoded before import
- Fixed an issue were it wasn't possible to correctly import (or cite) records
which contained non-ASCII characters in author's given names
- Records of unrecognized resource type were omitted upon citation output; fixed
- When outputting to LaTeX or RIS, curly brackets are now escaped to avoid
incorrect output
- Fixed an error when exporting data to ODF XML and when the user-specific
fields were missing from the SQL query