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BibTex Cleaner

This is just a little tool to clean up your BibTeX .bib file.

The idea is to turn this:

@inproceedings{10.1145/3341162.3349306, author = {Marini, Gabriele},
title = {Towards Indoor Localisation Analytics for Modelling Flows of Movements},
booktitle = {whbatevas},
pages = {377–382},
}

@Article{info:doi/10.2196/19874, author="Marini, Gabriele and Tag, Benjamin and Goncalves, Jorge and Velloso, Eduardo and Jurdak, Raja and Capurro, Daniel and McCarthy, Clare and Shearer, William and Kostakos, Vassilis",
title="Measuring Mobility and Room Occupancy in Clinical Settings: System Development and Implementation",
number="10",
pages="e19874",
keywords="localization; indoor; efficiency; Bluetooth; occupancy; mobility; metrics; smartphone; mobile phone",
}

Into this:

@InProceedings{Marini_2019,
    author		= {Gabriele Marini},
    title		= {Towards indoor localisation analytics for modelling flows of movements},
    booktitle	= {Adjunct Proceedings of the 2019 ACM International Joint Conference on Pervasive and Ubiquitous Computing and Proceedings of the 2019 ACM International Symposium on Wearable Computers},
    pages		= {377–382},
    doi			= {10.1145/3341162.3349306},
    url			= {https://doi.org/10.1145/3341162.3349306},
    year		= {2019},
    month		= {sep},
    publisher	= {ACM},
    r_updated	= {YES},
}
@Article{Marini_2020,
    author		= {Gabriele Marini and Benjamin Tag and Jorge Goncalves and Eduardo Velloso and Raja Jurdak and Daniel Capurro and Clare McCarthy and William Shearer and Vassilis Kostakos},
    title		= {Measuring Mobility and Room Occupancy in Clinical Settings: System Development and Implementation (Preprint)},
    pages		= {e19874},
    doi			= {10.2196/preprints.19874},
    url			= {https://doi.org/10.2196/preprints.19874},
    year		= {2020},
    month		= {may},
    publisher	= {JMIR Publications Inc.},
    number		= {10},
    keywords		= {localization; indoor; efficiency; Bluetooth; occupancy; mobility; metrics; smartphone; mobile phone},
    r_updated	= {YES},
}

Features

  • DOI lookup from title through rcrossref and aRxiv
title <- "Towards indoor localisation analytics for modelling flows of movements"
resCR <- cr_works(query = title, format = "text", style = "acm", limit=10) 
resArxiv <- arxiv_search(query = noquote(paste0('ti:\"', title, '\"')), limit=10)
  • Metadata update from DOI through rcrossref
style <- "acm"
cr_cn(dois = doi, format = "bibtex", style=style, locale="en-US")
  • Multi-Threaded
  • Only updates data if titles are similar
  • Keeps all the extra metadatata already in the bibentry (including abstracts)
  • Outputs to file AND also returns a data.table (data.frame)
  • Sort result by key (e.g by title or year)
  • Updated entries are marked with:
r_updated = {YES}

Instructions

  1. Clone the repository
  2. Install all the required libraries by running lib_install.R (need R >= 3.6)
  3. Open clean_refs.R, edit path, options and filename
  4. Call updateReferences (Multithreaded is highly recommended)
bib_df <- updateReferences(..., multithreaded = TRUE)
  1. The output will already be written in out_file but you can check the resulting df for any missing data
  2. Use CTRL+F on the output file and look for {NO} to double check the entries that have not been updated

Options

  • multithreaded: If TRUE it will create a cluster for each worker to call crossref asynchronously.
  • workers_log_folder: The folder where individual log files for each worker will be stored (files are deleted whenever the script is run)
  • style: The reference style to use, you can have a look at the list of available styles by calling rcrossref::get_styles()
  • upd_bibkey: Whether to update the bibkey or not. The bibkey is the identifier at the beginning of the ref. (If you have already cited the references in your LaTeX I'd leave this as FALSE so you won't need to update your \cite{...} in LaTeX) E.g. Marini_2019 is the bibkey here:
@InProceedings{Marini_2019,
    author		= {Gabriele Marini},
    title		= {Towards indoor localisation analytics for modelling flows of movements},
    booktitle	= {Adjunct Proceedings of the 2019 ACM International Joint Conference on Pervasive and Ubiquitous Computing and Proceedings of the 2019 ACM International Symposium on Wearable Computers},
    ...,
    r_updated	= {YES},
}

  • upd_author: Whether to updated the list of authors or not (useful when changing the reference style)

  • upd_title: Whether to update the title or not. Some works might have different titles online. For instance looking up this work's DOI will return a citation whose title is just WebClip. In this case it might be a good idea to keep the original title.

@InProceedings{kubitza2013webclip:1,
    title		= {WebClip: a connector for ubiquitous physical input and output for touch screen devices},
    author		= {Thomas Kubitza and Norman Pohl and Tilman Dingler and Albrecht Schmidt},
    doi			= {10.1145/2493432.2493520},
    url			= {https://doi.org/10.1145/2493432.2493520},
    ...
    r_updated	= {YES},
}
  • upd_abstract: Whether to look for the abstract and update it or not (if FALSE the abstract won't be retreived from crossref)
  • sorting_key: The key to use to sort the references before outputting to file. If NULL or file it will follow the input file's order
  • decreasing: Sorting order based on the key above (won't work if sorting key is null or file)