bibliography-organizer-sebastian-achim-mueller 1.1.4

Organize your bibliography

Helps you to organize and search your local bibliography. biborg is not invasive, it does not touch your cited documents or bibtex-files. biborg only offers suggestions to organize your files, as well as a full-text-search. biborg acts in the filesystem. Its interface is motivated by the version-control-tool git.

Commands

A set of command-line-tools to help you managing your bibliography. The interface is similar to git.

bib status

Prints a list of errors and warnings when your entries are not structrured as expected, or when entries are missing crucial parts.

bib update

Tries to update the optical-character-recognition ocr, the icon.jpg in each entry. Finally updates the search-index in your bibliography directory. When new originals were added, they are read and added to the ocr. Likewise ocr-records will be ignored when the corresponding original does not longer exist. The icon.jpg is extracted from the primary original.

bib search

Searches for your search-PHRASE in the search-index. Results are printed to the command-line. The search-PHRASE may contain logical operators such as AND, OR, NOT, ANDNOT, ANDMAYBE, (, and ). See documnetation of Whoosh.

Structure

The bibliography_organizer, or biborg for short, acts in your bibliography directory bib_dir. The bib_dir can be any directory in your filesystem. biborg’s command-line-interface expects the current working directory to be a bib_dir.

bib_dir
|-- citekey_A
|   |-- original
|   |   |-- citekey_A.pdf
|   |   |-- comments.ps
|   |   |-- preprint.pdf
|   |
|   |-- reference.bib
|
|-- citekey_B                       <-- you
|   |-- original                    <-- you
|   |   |-- citekey_B.html          <-- you
|   |
|   |-- reference.bib               <-- you
|   |
|   |-- ocr                         <-- biborg
|   |   |-- citekey_B.html.tar      <-- biborg
|   |
|   |-- icon.jpg                    <-- biborg
|
|-- .bibliography_organizer         <-- biborg
    |-- full_text_search_index

Terminology

citekey

The citekey is a string to identify your reference, e.g. ‘darwin1859origin’. In LaTex you use \cite{citekey}.

bib_dir

The base directory of your local bibliography. Here, you create and collect your entries in entry_dir``s. ``biborg will create a hidden cache in here named .bibliography_organizer.

entry_dir

An entry_dir is directory inside your bib_dir. An entry_dir has the name of the citekey. The entry_dir contains the original files and a bibtex reference. You create, and populate the entry_dir``s in your ``bib_dir.

original

In every entry_dir is the original directory. It contains the original files to be cited. Usually, there is only one original-file corresponding to one citekey. But sometimes the original might be a collection of files like a web-page or such. You create the original directory and populate it with your originals.

reference.bib

A bibtex-file in the entry_dir that you create. It contains exactly one bibtex-entry. The citekey in the bibtex-entry is expected to match the entry_dir.

ocr

The ocr directory is created and updated by biborg. The ocr directory contains the extracted text from the original files. The text is extracted using optical character recognition. Each original file has one archive in the ocr directory. The archive contains the text of the individual pages from the original. This is used to fill the search-index.

icon

The icon.jpg is a small image rendered from the first page of the primary original-file. The icon.jpg is created by biborg. The primary original file has the citekey as its basename.

full_text_search_index

This is a hidden directory in bib_dir/.bibliography_organizer/full_text_search_index. It is a cache for the search created and updated by biborg.

To use optical character recognition

sudo apt-get install tesseract-ocr
sudo apt-get install imagemagig