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SVN updated with new features & bug fixes

2007-05-23
2013-05-28
  • Hi,

    the "trunk" in the refbase SVN repository has been updated, here's an overview of the major additions, changes and fixes since refbase-0.9.0:

      Feature additions
    -------------------

    Import/Add Records:

    - Added support for resource types Conference Article, Conference Volume,
      Manual, Miscellaneous, Newspaper Article, Patent, Report, Software

    - Added import capabilities from SciFinder and Endnote XML

    Export/Citation:

    - Added APA and MLA citation styles

    - Added support for new export formats: Word XML and ISI Web of Science

    - When outputting citations as PDF, US letter is now supported as page format

    - Headers can now be added to cite formats via the 'headerMsg' URL parameter

    - Links to corresponding files are now included in the export data if the
      export format and user permissions allow so

    Search/Display:

    - Initial support for searching & managing of duplicate records

    - Many more minor enhancements

      Changes
    ---------

    - 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

    - Improved recognition of PubMed resource types

    - Improved support for PHP installations running with 'safe_mode=On'

    - The '$databaseBaseURL' in 'ini.inc.php' is now auto-generated by default

      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

    - When importing PubMed MEDLINE source data, we now extract author information
      from the 'AU' field if the 'FAU' field is not available

    - Records of unrecognized resource type were omitted upon citation output; fixed

    - Many more minor bug fixes

    ------------------------

    To use this new version:

    1. Backup your existing refbase scripts (especially those in 'initialize/') as
       well as your refbase database: http://backup.refbase.net/

    2. Checkout the refbase SVN trunk: http://svn.refbase.net/

    3. Replace all your old refbase scripts with the updated ones from the trunk

    4. Re-enter your custom settings in files 'db.inc.php' and 'ini.inc.php'

    5. Execute 'update.php' in your browser to update your refbase MySQL database

    6. Enjoy

    The update process is described in more detail in file 'UPDATE'.

    Matthias

     
    • Knut Krüger
      Knut Krüger
      2007-06-05

      are the files in the Directory revision: 953?
      and is there a possibility do download them all together?

      Kknut

       
    • My initial message in this thread regards the trunk at revision 953:

      http://refbase.svn.sourceforge.net/viewvc/refbase/trunk/

      A list of modified files is given here:

      http://cia.vc/stats/project/refbase/.message/44bcd

      files that are marked with a colored symbol have "real" changes, while all other listed files have only SVN property changes.

      I wouldn't recommend to manually download these files to your computer. You should use an SVN client instead:

      http://sourceforge.net/svn/?group_id=64647

      Using the SVN command line client, the refbase SVN trunk can be fetched (checked out) in one go using this command:

      svn co https://refbase.svn.sourceforge.net/svnroot/refbase/trunk refbase

      You can then copy all refbase scripts from your local SVN directory (the working copy into which you've checked out the refbase SVN trunk) to your actual deployment directory (or another web directory if you'd just want to test and try out things).

      Matthias

       
    • Knut Krüger
      Knut Krüger
      2007-06-05

      https://refbase.svn.sourceforge.net/svnroot/refbase/trunk
      there is no server connection to this URL.
      I forgot to wrote it in the last post, sorry
      Knut

       
    • > https://refbase.svn.sourceforge.net/svnroot/refbase/trunk
      > there is no server connection to this URL.

      You're not supposed to click this URL and view it in your web browser, instead you need to install an SVN client, then use this SVN client to download (check out) the refbase SVN trunk to a local directory on your machine. When using the SVN command line client, the above given command (note the "svn co " at the beginning and the trailing " refbase" which both belong to this command) will work to checkout the refbase SVN trunk.

      For further information on SVN and how to install/use it, please see the above given links (and the links given on those pages), or you could ask Google for more help:

      http://www.google.com/search?q=SVN+installation+tutorial
      http://www.google.com/search?q=Subversion+howto+tutorial

      Matthias

       
    • Knut Krüger
      Knut Krüger
      2007-06-05

      Works thank you  - great :-)

      Knut

       
    • Knut Krüger
      Knut Krüger
      2007-06-05

      The find duplicates feature is very helpful
      Knut

       
    • Knut Krüger
      Knut Krüger
      2007-07-06

      Hi Richard,
      indeed its working :-)
      Seems that I choosed one time the right url and the other times the wrong one.

      Thank you

       
    • FYI, the "trunk" in the refbase SVN repository was again updated on 07-Nov-2007,
      below is an overview of the major additions, changes and fixes since the last
      update of the trunk[1].

      [1]: http://sourceforge.net/forum/message.php?msg_id=4327638

        Feature additions
      -------------------

      Import/Add Records:

      - Added support for resource types Abstract and Magazine Article

      - Added support for direct upload of references from Bookends
        (http://www.sonnysoftware.com/)

      Export/Citation:

      - refbase can now output citations in LaTeX bibliography (.bbl) format

      Search/Display:

      - The 'show.php' API now allows to include results from a refbase server into
        foreign web pages; this makes it possible to dynamically include results from
        a refbase database into static HTML pages (using an <iframe> or AJAX-style
        JavaScript)

      - Added a "main fields" search option to the "Quick Search" form which allows to
        search all of the main fields at once; the list of "main fields" can be
        specified individually for each user

      - The default number of records per page can now be specified individually for
        each user

      Localization:

      - Added initial support for spanish and chinese localizations

      Command Line Clients:

      - 'refbase' command line client: added options '-A|--append' and '-B|--update'
        which let you 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; by default, a backup
        file is created before adding or changing anything in the local file

      - 'refbase' command line client: added '-E|--extract' option which extracts
        citation IDs from a file and retrieves matching records from refbase
        (supported file types: .aux, .bbl, .bib, .enw, .ris, .tex, and
        (MODS|SRW|Endnote) .xml)

        Changes
      ---------

      - 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

      - When importing multiple records, ALL records are now imported by default

      - 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

      - For the "Extract citations" functionality, we now check whether the extracted
        serial numbers and cite keys exist in the database and report any missing
        record identifiers

      - Changed or merged some localization strings to allow for better translations
        to languages such as Spanish or Chinese

      - Refined layout of 'user_receipt.php'

        Bug fixes
      -----------

      - We now convert Endnote XML text style markup into appropriate refbase markup

      - Upon RIS import, we now make sure that HTML encoded source data (such as
        "&auml;", "&#xF6;" or "&#233;") get decoded before import

      - When outputting to LaTeX or RIS, curly brackets are now escaped to avoid
        incorrect output

      - Additional minor bug fixes

      ------------------------

      As before, if you'd like to use this new version, perform these steps:

      1. Backup your existing refbase scripts (especially those in 'initialize/') as
         well as your refbase database: http://backup.refbase.net/

      2. Checkout the refbase SVN trunk: http://svn.refbase.net/

      3. Replace all your old refbase scripts with the updated ones from the trunk

      4. Re-enter your custom settings in files 'db.inc.php' and 'ini.inc.php'

      5. Execute 'update.php' in your browser to update your refbase MySQL database

      6. Enjoy

      The update process is described in more detail in file 'UPDATE'.

      Matthias

       
    • FYI, the "trunk"[1] in the refbase SVN repository[2] was again updated on
      29-Aug-2008, below is an overview of the major additions, changes and fixes
      since the last update of the trunk[3].

      A list of modified files is given at [4]. Files that are marked with a colored
      symbol have "real" changes, while all other listed files have only SVN property
      changes.

      [1]: http://refbase.svn.sourceforge.net/viewvc/refbase/trunk/
      [2]: http://svn.refbase.net/
      [3]: http://sourceforge.net/forum/message.php?msg_id=4675976
      [4]: http://cia.vc/stats/project/refbase/.message/7efb8

      You can try out this new version online at:

      http://beta.refbase.net/

      Btw, commit messages to the SVN bleeding-edge branch can be tracked via RSS:

      http://cia.vc/stats/project/refbase/.rss

      Feature additions
      -----------------

      Import/Add Records:

      - If you paste one or more DOI numbers (or OpenURLs) into the "Import IDs" form,
        refbase can now fetch matching record metadata from CrossRef.org and create a
        new record for each of the given DOIs (or OpenURLs)

      - refbase can now import records directly from arXiv.org: enter one or more
        arXiv IDs into the "Import IDs" form, and refbase will fetch & import record
        metadata from arXiv.org

      Export/Citation:

      - Added new citation styles: AMA, Chicago, Harvard (3 variants), and Vancouver

      - Additional record info (keywords, abstract, etc) can now be displayed in
        Citation view via a small triangle widget below each citation; this section
        also includes a permalink as well as links to cite/export the record

      - refbase can now export data to (and serve feeds as) Atom XML which, for each
        record, includes direct links to export & citation formats, OpenURL & unAPI
        links, Dublin Core metadata, as well as the formatted citation. Example:
        http://beta.refbase.net/opensearch.php?query=dc.title%3DBaltic&maximumRecords=15

      - refbase can now export data as Simple Dublin Core XML ("OAI_DC XML", as
        recommended by the Open Archives Initiative); this format is also available
        via the refbase SRU gateway ("SRW_DC XML")

      - refbase can now export data in the "ADS" tagged format that's used by the
        SAO/NASA Astrophysics Data System (via Bibutils 'xml2ads')

      - It is now possible to cite, group, or export ALL found records (instead of
        only the selected records)

      Search/Display:

      - Search results can now be browsed & searched in three different views: List
        view, Citations, and Details -- i.e. the latter two have been made first class
        citizens, and the admin can also define them as the default view

      - Added support for the OpenSearch.org protocol which (similar to SRU) allows
        clients to search refbase and retrieve results in a standardized manner; this
        allows e.g. browsers such as Firefox 2 or Internet Explorer 7 (and above) to
        auto-detect the refbase search engine, and to let users search refbase
        directly from the browser's toolbar

      - refbase can now display a query history for the user's current session, i.e.
        it will display links to any previous search results

      - Added JavaScript functions which allow to dynamically include references from
        a refbase database within foreign web sites

      - Added initial support for output to mobile devices ('viewType=Mobile')

      Command Line Clients:

      - the 'refbase' command line client now supports the new export formats 'atom',
        'oai_dc' and 'srw_dc' as well as '--view=Mobile' and '--order=creation-date'

      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. More info: <http://www.mediawiki.org/wiki/Extension:Refbase>

      - Added support for the sitemaps.org protocol which allows for better indexing
        by search engines

      - the refbase unAPI service now supports the new export formats 'atom', 'oai_dc'
        and 'srw_dc'

      - Many more minor enhancements

      Changes
      -------

      - Changed the appearance of the forms in the results header & footer which can
        now be displayed (or hidden) via a little triangle widget; for each view, the
        admin can 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 citation output options (previously located in the results footer) have
        been moved to the Display Options form of the results header in Citation view

      - By default, export of data via the refbase GUI is now enabled for anonymous
        users

      - After any add, edit, or delete action, we now include a link to the last
        multi-record search result list in the feedback header message if the previous
        query resulted in a single record; together with other changes, this obviates
        'receipt.php'

      - refbase now remembers many more search & display options while navigating or
        refining the results list

      - Improved the APA and MLA citation styles

      - For citation formats other than HTML, header messages passed via the
        'headerMsg' URL parameter are now correctly rendered, and any contained
        refbase markup is converted into format-specific markup & entities

      - Underline fontshape markup is now supported in various import and citation
        formats as well as in refbase markup (use: "__underlined text__")

      - The admin can now customize the list of fields that are displayed by default
        in List view, as well as the fields that are available in dropdown menus of
        the results header

      - The admin can now specify whether additional (i.e. usually less important)
        fields & user-specific fields shall be displayed in Details view by default;
        this allows to setup a stripped down Details view that e.g. only shows the
        main fields plus the abstract & keywords fields

      - The maximum number of links to found results pages that are displayed per page
        can now be customized by the admin

      - The admin can now define 'accesskey' values which allow for keyboard
        navigation of the main parts of the refbase interface

      - By default, the SRU formats "SRW_DC XML" and "SRW_MODS XML" are now
        transformed to HTML via XSL stylesheets

      - 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

      - 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)

      - We now use a 'show.php' URL for the "show details" link in the search results
        list since it is much shorter and easier to bookmark as a permanent link

      - When linking to particular records via 'show.php', one can now use consecutive
        serial number ranges as values of the 'records' 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; this allows to sort records such that newly added/edited
        records get listed top of the list

      - Redesigned the page footer to make it fit on one line (and thus less heavy)

      - Added many CSS attributes (id/class names) to HTML output where appropriate;
        this allows to easier refine the CSS styling of the refbase interface

      - The 'edition' field now accepts string values

      - 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'

      Bug fixes
      ---------

      - Fixed an issue were it wasn't possible to correctly import (or cite) records
        which contained non-ASCII characters in author's given names

      - Worked around an error in Internet Explorer when importing single records
        via the web interface

      - Fixed an error when exporting data to ODF XML and when the user-specific
        fields were missing from the SQL query

      - Additional minor bug fixes

      ------------------------

      As before, if you'd like to use this new version, perform these steps:

      1. Backup your existing refbase scripts (especially those in 'initialize/') as
         well as your refbase database: http://backup.refbase.net/

      2. Checkout the refbase SVN trunk: http://svn.refbase.net/

      3. Replace all your old refbase scripts with the updated ones from the trunk

      4. Re-enter your custom settings in files 'db.inc.php' and 'ini.inc.php'

      5. Execute 'update.php' in your browser to update your refbase MySQL database

      6. Enjoy

      The update process is described in more detail in file 'UPDATE'.

      Matthias

       
    • Hi,

      since my last post in this thread, the "trunk"[1] in the refbase SVN
      repository[2] was updated twice (on 04-Nov-2008 and on 07-Nov-2008). This latest
      trunk version is the *release candidate*, and we don't anticipate more changes
      (unless some major issues emerge) before the release.

      We'd appreciate if you could try out[3] this new version, and report any issues
      you encounter. Upgrading from this trunk version to the final release version
      will be easy.

      Below is an overview of the major additions, changes and fixes since the last
      major update of the trunk[4] (back in August).

      For the merge on 04-Nov-2008, a list of modified files is given at [5]. Files
      that are marked with a colored symbol have "real" changes, while all other
      listed files have only SVN property changes.

      [1]: http://refbase.svn.sourceforge.net/viewvc/refbase/trunk/
      [2]: http://svn.refbase.net/
      [3]: http://wiki.refbase.net/index.php/SVN_version#Deploying_refbase_from_SVN
      [4]: https://sourceforge.net/forum/message.php?msg_id=5209693
      [5]: http://cia.vc/stats/project/refbase/.message/958f5

      You can try out this new version online at:

      http://beta.refbase.net/

      Feature additions
      -----------------

      Search/Display:

      - Revamped the refbase main page: all forms are now styled via CSS, and
        citations of the most recent publications are now dynamically included upon
        page load

      - Redesigned the right-hand side of the page header which now holds the "Quick
        Search" form (thus, the "Quick Search" form is now available across all pages)

      - For a given CQL query, the refbase OpenSearch API can now return search
        suggestions in JSON (or HTML) format; this allows browsers such as Firefox to
        present search suggestions for search terms entered in the browser's search box

      - We now make use of the Prototype & script.aculo.us JavaScript frameworks to
        offer auto-completions (search suggestions) for text entered by the user

      - If enabled by the admin, we now use a sliding effect when a user toggles the
        display of the results header & footer or the "more info" section underneath
        of a citation

      Localization:

      - Added locales for localization of the interface to Chinese

      Changes
      -------

      - Import of user-specific fields into the "Add record" form is now possible

      - We now generate (or honour existing) cite keys/IDs for the import data, and
        copy them to the user's 'cite_key' field; the uniqueness of cite keys is
        ensured among all imported records as well as the user's existing records

      - For output to Atom XML, OAI_DC XML and SRW_DC XML, the chosen citation style
        is now honoured; where appropriate, the citation style & sort order is also
        maintained in link URLs

      - Authenticated users can now use 'opensearch.php' or 'sru.php' to query any of
        their user-specific fields

      - For OpenSearch & SRU searches, the 'keywords' field will now be queried by
        default if no context set & index name is given ("cql.serverChoice")

      - When viewing/outputting citations, the list of citations can now be sorted by
        record creation date ('citeOrder=creation-date')

      - The admin can now customize the list of fields that are made available in the
        "main fields" selector of the user's account options page

      - Internationalized and localized many more interface elements & strings

      - Added more CSS attributes (id/class names) to the HTML output to allow for
        easier CSS styling of the refbase interface

      - The 'refbase_import' command line client now supports common output options
        from the 'refbase' CLI client; this allows to instruct the refbase server to
        return all imported records in any of the supported export or citation formats
        & styles

      Bug fixes
      ---------

      - When including refbase results into foreign web pages, the use of some forms &
        links caused unexpected behaviour; fixed

      - Fixed referrer-related problems that could cause unexpected behaviour and
        incorrect warning/error messages; however note that working simultaneously in
        different browser windows or tabs can still cause some unexpected results

      - Worked around PREG compilation errors on some UTF8-based systems

      - For theses, the corporate author (i.e. the corporate body granting the degree)
        is now labeled correctly in MODS XML output; as a result, the degree grantor
        is now recognized correctly by Bibutils and copied to the BibTeX 'school' field

      - Additional minor bug fixes

      ------------------------

      As before, if you'd like to use this new version, perform these steps:

      1. Backup your existing refbase scripts (especially those in 'initialize/') as
         well as your refbase database: http://backup.refbase.net/

      2. Checkout the refbase SVN trunk: http://svn.refbase.net/

      3. Replace all your old refbase scripts with the updated ones from the trunk

      4. Re-enter your custom settings in files 'db.inc.php' and 'ini.inc.php'

      5. Execute 'update.php' in your browser to update your refbase MySQL database

      6. Enjoy

      The update process is described in more detail in file 'UPDATE'.

      Matthias

       
    • Hi,

      refbase-0.9.5 has been released on 19-Nov-2008. This release incorporates all the additions, changes and bug fixes outlined in this thread.

      The release announcement is here:

      https://sourceforge.net/forum/forum.php?forum_id=889500

      Matthias