bibfuse

A CLI tool to manage bibtex entries using nickng/bibtex.

bibfuse creates an SQLite database file (--db) from given BibTex files (*.bib), and generates a single clean .bib file (--out).

The filtering formats can be defined in the config file (--config). bibfuse takes the bibfuse.toml in this package by default.

If no .bib files are given, it just reads the database and updates the BibTex file.

Table of Contents

• Synopsis
  • Usage
  • Usage with Docker
• bibfuse filters for BibTex format
  • todos and optionals filters
  • oneof_ filters with -smart
  • Citation Types
    • @article
    • @book
    • @incollection
    • @inproceedings
    • @mastersthesis
    • @misc
    • @phdthesis
    • @techreport
    • @unpublished
• Contribution
• License
• Author

Synopsis

Install

% go get -u github.com/iomz/bibfuse/...

Usage

% bibfuse -h
Usage of bibfuse: [options] [.bib ... .bib]
  -config string
        The bibfuse.[toml|yml] defining the filters. (default "bibfuse.toml")
  -db string
        The SQLite file to read/write. (default "bib.db")
  -no-optional
        Suppress "OPTIONAL" fields in the resulting bibtex.
  -no-todo
        Suppress "TODO" fields in the resulting bibtex.
  -out string
        The resulting bibtex to write (it overrides if exists). (default "out.bib")
  -show-empty
        Do not hide empty fields in the resulting bibtex.
  -smart
        Use oneof selectively filters when importing bibtex.
  -verbose
        Print verbose messages.
  -version
        Print version.

Example

% cat ref.bib
@article{someone2021a,
    title     = {{A Journal Article}},
}
% bibfuse ref.bib
2021/10/17 15:47:32 parsing ref.bib
2021/10/17 15:47:32 +1 new entries
2021/10/17 15:47:32 bib.db contains 1 entries
2021/10/17 15:47:32 1 entries written to out.bib
% cat out.bib
@article{someone2021a,
    title       = {{A Journal Article}},
    author      = "(TODO)",
    url         = "(OPTIONAL)",
    doi         = "(OPTIONAL)",
    isbn        = "(OPTIONAL)",
    issn        = "(OPTIONAL)",
    journal     = "(TODO)",
    metanote    = "(OPTIONAL)",
    number      = "(OPTIONAL)",
    numpages    = "(OPTIONAL)",
    pages       = "(OPTIONAL)",
    publisher   = "(OPTIONAL)",
    volume      = "(OPTIONAL)",
    year        = "(TODO)",
}

Usage with Docker

% cat ref.bib
@article{someone2021a,
    title     = {{A Journal Article}},
}
% docker run -v $(pwd):$(pwd) -w $(pwd) --rm iomz/bibfuse ref.bib
2021/10/17 13:53:33 parsing ref.bib
2021/10/17 13:53:33 +0 new entries
2021/10/17 13:53:33 bib.db contains 1 entries
2021/10/17 13:53:33 1 entries written to out.bib
% sqlite3 bib.db "SELECT * FROM entries;"
1|someone2021a|article|(TODO)|{A Journal Article}||(OPTIONAL)||(OPTIONAL)|(OPTIONAL)||(TODO)|(OPTIONAL)||(OPTIONAL)||(OPTIONAL)|(OPTIONAL)|(OPTIONAL)|(OPTIONAL)||||(OPTIONAL)||(OPTIONAL)|(TODO)

bibfuse filters for BibTex format

bibfuse reflects rather subjective opinion to filter and flag the required fields depending on the type, aiming for the compatibility with most of the research publication requirements.

todos and optionals filters

bibfuse filters fields for each entry depending on the type: @article, @book, @incollection, @inproceedings, @mastersthesis, @misc, @phdthesis, @techreport, and @unpublished as defined in bibfuse.toml.

Mandatory fields are filled with (TODO) while optional fileds are filled with (OPTIONAL).

oneof_ filters with -smart

In addition, you can define additional filters whose name starting with oneof_ to selectively discard some fields in presence of a specific fields with the -smart option. For example, by default for the @article type the default bibfuse.toml has the following oneof_ filter:

oneof_doi_page = [
    "doi",
    "pages",
    "numpages"
]

This checks each field in the order "doi", "pages", and "numpages" then after finding the first one of neither empty, "(OPTIONAL)", nor "(TODO)", bibfuse discards the remaining fields and does NOT store them in the database. Note that if you want to retain those fields, you should not use this -smart option.

This feature enables rather concise bibliography in your manuscript while maintaining the accessibility to the cited documents through more efficient identities (e.g., DOI).

Citation Types

Journal articles

@article{mizutani2021article
    title     = {{Title of the Article}},
    author    = "(TODO)",
    journal   = "(TODO)",
    year      = "(TODO)",
    doi       = "(OPTIONAL)",
    isbn      = "(OPTIONAL)", % removed if doi exists
    issn      = "(OPTIONAL)", % removed if doi exists
    metanote  = "(OPTIONAL)",
    number    = "(OPTIONAL)", % removed if doi exists
    numpages  = "(OPTIONAL)", % removed if doi exists
    pages     = "(OPTIONAL)", % removed if doi exists
    publisher = "(OPTIONAL)", % removed if doi exists
    url       = "(OPTIONAL)", % removed if doi exists
    volume    = "(OPTIONAL)", % removed if doi exists
}

Books

@book{mizutani2021book,
    title     = {{Title of the Book}},
    author    = "(TODO)"
    publisher = "(TODO)",     % removed if doi exists
    year      = "(TODO)",
    doi       = "(OPTIONAL)",
    edition   = "(OPTIONAL)", % removed if doi exists
    isbn      = "(OPTIONAL)", % removed if doi exists
    issn      = "(OPTIONAL)", % removed if doi exists
    metanote  = "(OPTIONAL)",
    url       = "(OPTIONAL)", % removed if doi exists
}

Chapters or articles in a book

@incollection{mizutani2012incollection,
    title     = {{Title of the Book Chapter}},
    author    = "(TODO)"
    booktitle = "(TODO)",
    publisher = "(TODO)",     % removed if doi exists
    year      = "(TODO)",
    doi       = "(OPTIONAL)",
    isbn      = "(OPTIONAL)", % removed if doi exists
    issn      = "(OPTIONAL)", % removed if doi exists
    metanote  = "(OPTIONAL)",
    numpages  = "(OPTIONAL)", % removed if doi exists
    pages     = "(OPTIONAL)", % removed if doi exists
    series    = "(OPTIONAL)",
    url       = "(OPTIONAL)", % removed if doi exists
}

Conference papers, lecture notes, extended abstract, etc.

@inproceedings{mizutani2012inproceedings,
    title     = {{Title of the Conference Paper}},
    author    = "(TODO)"
    booktitle = "(TODO)",
    year      = "(TODO)",
    doi       = "(OPTIONAL)",
    isbn      = "(OPTIONAL)", % removed if doi exists
    issn      = "(OPTIONAL)", % removed if doi exists
    metanote  = "(OPTIONAL)",
    numpages  = "(OPTIONAL)", % removed if doi exists
    pages     = "(OPTIONAL)", % removed if doi exists
    publisher = "(OPTIONAL)", % removed if doi exists
    series    = "(OPTIONAL)",
    url       = "(OPTIONAL)", % removed if doi exists
}

Master's theses

@mastersthesis{mizutani2021mastersthesis,
    title       = {{Title of the Master's Thesis}},
    author      = "(TODO)",
    url         = "(OPTIONAL)",
    metanote    = "(OPTIONAL)",
    school      = "(TODO)",
    year        = "(TODO)",
}

Online resources, artifacts, etc.

@misc{mizutani2021misc,
    title       = "Title of the Resource",
    author      = "(TODO)"
    note        = "(TODO)",
    url         = "(TODO)",
    year        = "(TODO)",
    institution = "(OPTIONAL)",
    metanote    = "(OPTIONAL)",
}

Ph.D. theses / dissertations

@phdthesis{mizutani2021phdthesis,
    title       = {{Title of the Ph.D. Thesis}},
    author      = "(TODO)",
    url         = "(OPTIONAL)",
    metanote    = "(OPTIONAL)",
    school      = "(TODO)",
    year        = "(TODO)",
}

Standards, specifications, white papers, etc.

@techreport{mizutani2021techreport,
    title       = {{Title of the Technical Document}},
    author      = "(TODO)",
    institution = "(TODO)",
    year        = "(TODO)",
    metanote    = "(OPTIONAL)",
    series      = "(OPTIONAL)",
    url         = "(OPTIONAL)",
    version     = "(OPTIONAL)",
}

Documents not formally published.

@unpublished{mizutani2021unpublished,
    title       = {{Title of the Unpublished Work}},
    author      = "(TODO)",
    url         = "(TODO)",
    metanote    = "(OPTIONAL)",
    note        = "(TODO)",
}

Contribution

See CONTRIBUTING.md.

License

See LICENSE.

Author

Iori Mizutani (@iomz)