register-globas, publication types, endnote

rob stone
  • rob stone

    rob stone - 2004-02-18

    -- firts off i like this project seems tidy and compact and quite useful. Im also looking at refdb but that seems a bit mre heavy handed.

    couple of things ..

    1) i think register globasl should be eliminated ASAP
    as its a setting used by all php apps and i have a few running on this box. I know this is in your todo list ..

    2) i think the publication type should be another table,
    (ID,REF_TYPE) it would extensible without codeing changes and be more 'relational'. at the moment its limited to book whole, book chapter, journal (i wanted to add conference ...)

    3) im trying t get refs from enote into refbase in the simplest manner, i ve started trying to wrtie an export filter or endnote, i started think about writing a sql exporter, then
    thought about rewriting import.csa, but am at the momet trying to get Ennote to export in CSA mode so i can use that to import it.

    I wonder if a better approach would be to write a more universally accepted importer for refbase
    (bibtex, refer, RIS ?)

    cheers, and nice one :-)

    • Matthias Steffens

      Hi Rob!

      The next release version will work indepent of the setting of the 'register_globals' directive in 'php.ini'. The fix has been implemented already but needs some additional testing (since we had to re-structure quite a lot of code for this).

      When designing the refbase database, we decided against a separate publication database (for several reasons). Still, we are planning to add a 'journals' table to support auto-fill of publication fields (like publication, abbrev_journal, publisher, place, language, summary_language, isbn, issn) when adding records manually. Your suggestions are appreciated and we may have to re-think our current implementation. However, I fear this won't happen in the near future (since this would mean almost a complete re-write of the application).

      Currently, import & export capabilities are poor. Hopefully, this will change in the future. Import from (and export to) BibTeX, EndNote, ProCite, and RIS has a very high priority for us. The biggest problem is development time available... :-/

      Right now, the only way to batch import data into refbase is to export data from your reference manager to a tab-separated file. Then, you'll need to import records directly into the MySQL database by use of a utility like 'mysqlimport'. You'll need to specify the order of fields when importing. Sorry for the inconvenience!

      For future versions of refbase we plan to standardize the import & export interface. For example, when exporting data, refbase would handover all data in a universal format, a separate script would then handle the export for a particular output format. By that it should be easy to add additional formats (or change existing ones).

      Rob, thanks your feedback!

      Best regards, Matthias

    • rob stone

      rob stone - 2004-02-19

      Hi Matthias,

      thanks for the response, and consideration,

      gald to hear about register- i knew you were on it - i saw some docs  somehere.

      the problem i think with the journal type is its embeddedness within the code, and it 'll be easier to take it out now rather than later.  At worst you could define a matching string somewhere in the header (Book Whole|Book Chapter|Journal) etc and then use that in the code ?

      re import  - i guess my suggestion was to pick one that all the others reference applications can export to (like RIS) and write that one first, then leave the  others to
      other developers.  SO id get Endote to export RIs and then refbase to import it.  Lots of things can export to RSI already,

      I like the universal approach that you mention for export etc but sounds quite a task.

      anyways - tope effort, ill keep you posted on anything i produce- tinker with :-)

    • Ray

      Ray - 2004-02-20

      Hi Rob

      I've been trying to help out a bit also - there is code out there that is PHP based for input of a variety of formats (I've found bibtex, for example). As you've probably already noticed, the import_csa and related functions handle the importation. Theoretically, the modificiation of that for other purposes would be relatively straight-forward, especially if there is also code to handle the parsing of the incoming format. If you happen to find code for the formats you mentioned, can you point it out?


    • Derek Lackaff

      Derek Lackaff - 2004-09-23


      Let me add to the kudos given to the developers -- Refbase is a great project! It does all we need for our citation index project and more.

      This is an old thread, but I was wondering if anyone had any updates. I am in the same situation as Rob was back in February, and would like to import a database from Endnote into Refbase. As a complete novice with scripting languages and text-file parsing, I'd be happy to read about anyone else's experiences with a similar project, or advice on how to proceed.

      Again, cheers for the hard work going into this project!


      • Richard Karnesky

        Matthias made a nice post[1] on how to format a text file for import.  I do know that endnote's export types can be customized, so you might be able to make an output filter to do a lot of this work for you.  I'm not an endnote user myself, so don't know if you'll be able to cleanly handle white space, character sets, setc.  Try to get the output as close as possible.  If you won't be doing this data dump frequently in the near future, you should be able to do any other editing in a good text editor--you won't have to touch any scripting language at all.

        If you do get stuck, please don't hesitate to make another post about where you got stuck.  I can then talk to you off-list & try to hammer out a quick script with you to finish the job (we can even contribute the endnote export you write and any scripts back to the project). 

        I am currently working on adding the ability to import from MODS XML.  Because there are already great converters to put endnote into this format, this will eventually be a solution.




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