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Full Discussion: Dynamically parse BibTeX and create hash of hash
Top Forums Shell Programming and Scripting Dynamically parse BibTeX and create hash of hash Post 302740963 by wakatana on Friday 7th of December 2012 08:51:49 AM
Old 12-07-2012
Dynamically parse BibTeX and create hash of hash
Hello gurus, Iam trying to parse following BibTex file (bibliography.bib):

Code:
@book{Lee2000a,
abstract = {Abstract goes here},
author = {Lee, Wenke and Stolfo, Salvatore J},
title = {{Data mining approaches for intrusion detection}},
year = {2000}
}
@article{Forrest1996,
abstract = {Abstract goes here},
author = {Forrest, Stephanie and Hofmeyr, Steven A. and Anil, Somayaji},
title = {{Computer immunology}},
year = {1996}
}

I am using BibTeX-Parser for this which works as expected, problem that I have is with creating hash of hash array. Following code:

Code:
#!/usr/bin/perl
# http://search.cpan.org/~gerhard/BibTeX-Parser-0.62/lib/BibTeX/Parser.pm
use BibTeX::Parser;
use IO::File;
use Data::Dumper;
use strict;
use warnings;

my $filename="bibliography.bib";
my (%bibliography, %article);
my $i;
my ($entry, @entries, $type, $key);
my (my $hkey, my $hvalue);

# open BibTeX
my $fh = IO::File->new("$filename") or die "could not open $filename: $!\n";

# create parser object ...
my $parser = BibTeX::Parser->new($fh);
    
# ... and iterate over entries
while ($entry = $parser->next ) {
  if ($entry->parse_ok) {
  
    # return BibTeX elements like abstract, author, title ...
    @entries = $entry->fieldlist();
    
    # create %article as a hash array e.g. year -> 1996; isbn -> 1581138709 etc.
    foreach (@entries) {
      $article{"$_"} = $entry->field("$_");
    }
    
    # return article's key (Lee2000a, Forrest1996)
    $key = $entry->key;
    
    # append %article into %bibliography with approporiate key
    $bibliography{"$key"} = \%article;
    
    #Debug
    #print $entry->key, "\n";
    #print Dumper (\%article);

    # removes all elements of %article (prepare for next iteration)
    %article = ();
    
    #Debug
    #print "================================\n";
  }
  
  else {
    warn "Error parsing file: " . $entry->error;
 }
}

    #Debug
    #print Dumper (\%bibliography);

CURRENT output of Dumper (\%bibliography);
Code:
$VAR1 = {
          'Lee2000a' => {},
          'Forrest1996' => $VAR1->{'Lee2000a'}
        };

EXPECTED output of Dumper (\%bibliography);
Code:
$VAR1 = {
          'Lee2000a' => {
                'abstract' => 'Abstract goes here',
                'author' => 'Lee, Wenke and Stolfo, Salvatore J'
                'title' => 'Data mining approaches for intrusion detection'
                'year' => '2000'
              },
          'Forrest1996' => {
                'abstract' => 'Abstract goes here',
                'author' => 'Forrest, Stephanie and Hofmeyr, Steven A. and Anil, Somayaji'
                'title' => 'Computer immunology'
                'year' => '1996'
                }
        };

What I am doing Wrong ? Many thanks.
 

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LEARN ABOUT DEBIAN

nbibtex

NBIBTEX(1)						      General Commands Manual							NBIBTEX(1)

NAME

       nbibtex - make a bibliography for LaTeX

SYNOPSIS

       nbibtex [options] auxname[.aux] [bibname...]

DESCRIPTION

       NbibTeX	is  a drop-in replacement for BibTeX.  It reads the top-level auxiliary (.aux) file that was output during the running of latex(1)
       or tex(1) and creates a bibliography (.bbl) file that will be incorporated into the document on subsequent runs of LaTeX or TeX.

       NbibTeX looks up, in bibliographic database (.bib) files specified by the ibliography command, the entries specified  by  the	cite  and
       
ocite	commands  in  the  LaTeX  or TeX source file.  The association of cite command with .bib entry is made by a simple query language
       described below.  NbibTeX formats the information from the .bib entries according to instructions  in  a  bibliography  style  (.nbs)  file
       (specified by the ibliographystyle command, and it outputs the results to the .bbl file.

       If  the	optional  bibnames are used, NbibTeX looks in the named bibliographies instead of those specified by the ibliography command.  A
       bibname without a slash (/) character means the same thing it would mean in a ibliographystyle command: it is looked up according to  the
       rules  of BibTeX.  A bibname with a slash character is taken to be the absolute or relative pathname of a .bib file.  Explicit bibnames can
       be used with the -bib and -o options to make a paper-specific .bib file from larger .bib files.

       The LaTeX manual explains what a LaTeX source file must contain to work with NbibTeX.  Appendix B of the manual describes the format of the
       .bib files. The `NbibTeXing' document describes extensions and details of this format, and it gives other useful hints for using NbibTeX.

OPTIONS

       -min-crossrefs=number
	      The  -min-crossrefs  option  defines  the minimum number of crossref required for automatic inclusion of the crossref'd entry on the
	      citation list; the default is 2.

       -terse Accepted for backward compatibility with BibTeX; NbibTeX is terse by default.

       -permissive
	      Enables NbibTeX to continue working even when some of the .bib files mentioned in the ibliography command are missing.	Also tells
	      NbibTeX not to object if duplicate entries are found in multiple .bib files.

       -strict
	      Tells  NbibTeX  to  complain  about all irregularities it spots in any .bib file it parses.  By default,	NbibTeX (like BibTeX) com-
	      plains only about entries it actually intends to use.

       -o file
	      Writes the bibliography to file instead of to the default auxname.bbl.  If file is -, writes to standard output.

       -bib   Instead of writing a bibliography for use by LaTeX, writes exactly those NbibTeX entries	needed	by  auxname.   Useful  for  making
	      paper-specific .bib files.

       -help  Emit a short help message and exit.

       -version
	      Emit version information and exit.

EXAMPLES

       To make a normal bibliography for file paper.tex:

	      nbibtex paper
																	    b
       To  use	the  personal .bib file personal.bib to make a paper-specific bibliography for file paper.tex, which should use the command logra-
       phy{paper}:

	      nbibtex -o paper.bib -bib paper personal

       The file personal.bib should be found on the usual BIBINPUTS path.

       To extend the bibliography paper.bib by filling in missing entries from personal.bib:

	      nbibtex -permissive -o paper.bib -bib paper paper personal

QUERY LANGUAGE

       To specify a paper you wish to cite, classic BibTeX requires an arbitrary key.  The advantage of NbibTeX is that you cite a  paper  by  the
       contents of the NbibTeX entry.

	      The citation consists of a sequence of one or more constraints separated by colons.  A constraint may be empty.

	      A nonempty constraint is of the form key=words, where key is the name of a field in the NbibTeX entry and words is a sequence of one
	      or more words separated by dashes.  The contraint is satisfied if every word in words is found in the field named by key.  (The  key
	      may also be [type], which matches agains the type of the entry, or *, which looks for words in any field.)

       For example, the following queries might match an entry for a useful source on arithmetic:

	      author=knuth:series=art-programming:volume=2
	      author=knuth:title=seminumerical:year=1981

       As  a convenience, keys may be defaulted in up to three constraints.  In the first constraint, the default key is author (or if there is no
       author, editor).  In the second constraint, the default key is year if words is all digits, and is title  otherwise.   In  the  third  con-
       straint, the default key is year if words is all digits, and is [type] otherwise.  So for example, we could have written

	      knuth:seminumerical:1981

       To match a word in words, BX uses the Boyer-Moore string-matching algorithm, so longer words are usually faster.

       NbibTeX's query language can be used on the command line by nbibfind(1).

NBIBTEX STYLES AND COMPATIBILITY WITH BibTeX
       Like  BibTeX,  NbibTeX supports a variety of "styles" of bibliography.  Each style is defined by a program written in Lua, using additional
       primitives suitable to construction of bibliographies.  NbibTeX provides the three standard styles in a form suitable for use with the nat-
       bib  package.   Two of these styles (abbrvnat and unsrtnat) are completely compatible with the corresponding BibTeX styles; the third style
       (plainnat) has been changed to more closely follow the Chicago Manual of Style.	A compatible version is available as style plainnatc.

       Additional styles may be created by writing new Lua code; for example, an author wishing to create a style called mcbride would put a  file
       called  mcbride.nbs  (for  New  BibTeX Style) in the directory /usr/share/nbibtex.  For guidance on what goes into such a file, consult the
       other files in that directory and the literate source code for NbibTeX.

ENVIRONMENT

       For .bib files, NbibTeX searches the directories in the path defined by the BIBINPUTS environment variable if that is  set,  otherwise  the
       default.  For details of the searching, see tex(1) and kpsewhich(1).

       No special searching is done for the .aux file.

FILES

       /usr/share/nbibtex/*.nbs
	      New bibliography style files.

BUGS

       Although  I  have  made some effort in this direction, compatibility with BibTeX does not extend to .bib files containing non-ASCII charac-
       ters.

SEE ALSO

       nbibfind(1), latex(1), tex(1), kpsewhich(1), bibtex(1).
       Leslie Lamport, LaTeX - A Document Preparation System, Addison-Wesley, 1985, ISBN 0-201-15790-X.
       The NbibTeX home page at http://www.eecs.harvard.edu/~nr/nbibtex.
       The Lua home page at http://www.lua.org.

AUTHOR

       Norman Ramsey, Harvard University.

								    15 May 2006 							NBIBTEX(1)
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