BibTex import error: Unrecognized data format

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2010-01-13
2013-05-28
  • Allan Streib
    Allan Streib
    2010-01-13

    Hi,

    I just found refbase and am attempting to evaluate it.  I would need to migrate a large amount of publication data from Drupal (Biblio module) to refbase.  To see if I could use BibTex as a format to do this, I exported an article citation from Drupal in BibTex format, and attempted to import it into refbase.  I got an error message stating "Unrecognized data format!" but no detail on what the problem was.

    The record I was attempting to import:

    @article {9426,
        title = {Cloud Technologies for Bioinformatics Applications},
        year = {2010},
        month = {01/04/2010},
        institution = {Indiana University},
        address = {Bloomington, IN},
        abstract = {Executing large number of independent jobs or jobs comprising of large number of tasks that perform minimal inter-task communication is a common requirement in many domains. Various technologies ranging from classic job schedulers to latest cloud technologies such as MapReduce can be used to execute these {\textquotedblleft}many-tasks{\textquotedblright} in parallel. In this paper, we present our experience in applying two cloud technologies Apache Hadoop and Microsoft DryadLINQ to two bioinformatics applications with the above characteristics. The applications are a pairwise Alu sequence alignment application and an EST (Expressed Sequence Tag) sequence assembly program. First we compare the performance of these cloud technologies using the above case and also compare them with traditional MPI implementation in one application. Next we analyze the effect of inhomogeneous data on the scheduling mechanisms of the cloud technologies. Finally we present a comparison of performance of the cloud technologies under virtual and non-virtual hardware platforms.},
        keywords = {Distributed Programming, Parallel Systems, Performance, Programming Paradigms},
        url = {http://grids.ucs.indiana.edu/ptliupages/publications/BioCloud_TPDS_Journal_Jan4_2010.pdf},
        author = {Jaliya Ekanayake and Thilina Gunarathne and Judy Qiu}
    }
    

    Can anyone help me out? Anyone done a migration of data from Drupal Biblio before?

    Thanks,

     
  • Allan Streib
    Allan Streib
    2010-01-13

    OK so it seems to be the space between @article and the opening { that is the problem.

    Is that bibutils or refbase that is being so strict?

     
  • refbase.  See includes/import.inc.php, in function identifySourceFormat($sourceText).  You can edit the regex to allow any character between @ and {, rather than non-whitespace characters.  Though this is the first time I think I've seen an app that puts the space there, it is valid BibTeX.

     
  • Allan Streib
    Allan Streib
    2010-01-13

    Thanks!  And incidentally, I had not looked at any of the refbase code yet.  I must say this is some of the most nicely commented code I've ever seen.