Using BibTool with BibLaTeX, again

Question

I've installed BibTool and it seems to work for e.g. printing a formatted bibliography to the terminal. I'm trying to extract a bibliography from an .aux file from a document compiled with BibLaTeX. As a MWE here's such a document:

\documentclass[12pt, oneside, article, a4paper]{memoir}

\usepackage[backend=biber, natbib, style=authoryear-comp]{biblatex}
\ExecuteBibliographyOptions{alldates=short, language=british, sortcites}

\usepackage{kantlipsum}

\title{BibTool MWE}
\author{Thomas Hodgson}
\date{11 May 2013}
\bibliography{bibtool_mwe}

\begin{document}
\maketitle

\kant

\citet{Melville2007}

\printbibliography
\end{document}

This compiles, and generates a bib tool_mwe.aux file that looks like this:

\relax 
\providecommand*{\memsetcounter}[2]{}
\abx@aux@sortscheme{nyt}
\@writefile{toc}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
\@writefile{lof}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
\@writefile{lot}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
\abx@aux@cite{Melville2007}
\abx@aux@page{1}{3}
\@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\contentsline {section}{References}{3}}
\abx@aux@page{2}{3}
\memsetcounter{lastsheet}{3}
\memsetcounter{lastpage}{3}

And, in case it's necessary here's the .bib file:

@book{Melville2007,
    Author = {Melville, Herman},
    Booktitle = {Moby-Dick},
    Date-Added = {2013-05-12 09:35:11 +0000},
    Date-Modified = {2013-05-12 09:37:33 +0000},
    Location = {London},
    Publisher = {Vintage},
    Title = {Moby-Dick},
    Year = {2007}}

When I put the following in the command line BibTool produces a blank line, when I leave it with ctrl-D it generates a .bib file, but it's empty.

bibtool -x bibtool_mwe.aux -o test.bib

For a while I thought this was the same problem as this question. I'm using BibLaTeX as well. But I was getting similar error messages only when I got BibTool's syntax one. In any case, my problem couldn't be solved in the way suggested by the answer to that question because my .aux file is different to the one described there.

Answer 1

Just run biber as follows:

biber mainfile --output_format bibtex

where mainfile.tex is your tex file. You will then get an file

mainfile_biber.bib

contained the relevant bib entries.

Answer 2

I wrote, or at least adopted from the answers to this question on Stack Overflow, the following (in Python) to extract a regular expression from a .bcf file:

def xmltocitekeys(file):

    from xml.dom import minidom

    xmldoc = minidom.parse(file)
    taglist = xmldoc.getElementsByTagName('bcf:citekey')
    keylist = []

    for x in taglist:
        keylist.append(str(x.childNodes[0].nodeValue))

    print('\|'.join(keylist))

The output can then be used with BibTool, for example:

bibtool -X "output" -o extract.bib -i bibliography.bib

By the way, I needed to set an option in BibTool in order to preserve the capitalisation of my citekeys.

Answer 3

Biber can do this for you in "tool" mode. Put this in your biber.conf file (or in any file which you then tell biber about with the -g option):

<config>
  <sourcemap>
    <maps datatype="bibtex" map_overwrite="1">
      <map>
        <map_step map_field_source="entrykey" map_match="^(?!(?:key1|key2))" map_final="1"/>
        <map_step map_entry_null="1"/>
      </map>
    </maps>
  </sourcemap>
</config>

and call biber like this (assuming your .bib file is called "foo.bib"):

biber --tool foo.bib

or if you are not using the default biber.conf file:

biber -g <conf_file> --tool foo.bib

This will output another .bib file called foo_bibertool.bib with only the entries with "key1" and "key2". You can change the regexp accordingly to select what you want. I will add a "map_not_match" option to biber as a convenience for the next version so you don't have to use negative regexps. This config file essentially goes through the .bib file you pass and ignores any entries which match the regexp.

This is completely independent of any .bcf or .aux etc. See the biber manual, section 3.12.