bibtexautocomplete 1.1.2

Module to complete bibtex files by polling online databases

Bibtex Autocomplete

bibtexautocomplete or btac is a python package to autocomplete bibtex bibliographies. It is inspired and expanding on the solution provided by thando in this tex stackexchange post.

It attempts to complete a bibtex file by querying the following domains:

• www.crossref.org
• arxiv.org
• dlbp.org
• researchr.org
• unpaywall.org

Big thanks to all of them for allowing open, easy and well-documented access to their databases.

Demo

Quick overview

How does it find matches?

btac queries the websites using the entry doi if known otherwise the title. So entries that don't have one of those two fields will not be completed.

• Titles should be the full title, they are compared excluding case and punctuation, but titles with missing words will not match.
• If one or more authors are present, entries with no common authors will not match. Authors are compared using lower case last names only. Be sure to use one of the correct Bibtex format for the author field:

  author = {First Last and Last, First and First von Last}
  

  (see https://www.bibtex.com/f/author-field/ for full details)

Disclaimers

• There is no guarantee that the script will find matches for your entries, or that the websites will have any data to add to your entries, (or even that the website data is correct, but that's not for me to say...)

• The script is designed to minimize the chance of false positives - that is adding data from another similar-ish entry to your entry. If you find any such false positive please report them using the issue tracker.

How are entries completed?

Once responses from all websites have been found, the script will add fields from website with the following priority : crossref > arxiv > dblp > researchr > unpaywall.

So if both crossref's and dblp's response contain a publisher, the one from crossref will be used.

The script will not overwrite any user given non-empty fields, unless the -f/--force-overwrite flag is given.

The script checks that the DOIs or URLs found correspond (or redirect to) a valid webpage before adding them to an entry.

Installation

Can be installed with pip :

pip install bibtexautocomplete

You should now be able to run the script using either command:

btac --version
python3 -m bibtexautocomplete --version

Dependencies

This package has two dependencies (automatically installed by pip) :

• bibtexparser
• alive_progress (>= 2.4.0) for the fancy progressbar

Usage

The command line tool can be used as follows:

btac [-flags] <input_files>

Examples :

• btac my/db.bib : reads from ./my/db.bib, writes to ./my/db.btac.bib
• btac -i db.bib : reads from db.bib and overwrites it (inplace flag)
• btac db1.bib db2.bib -o out1.bib -o out2.bib reads multiple files and write their outputs to out1.bib and out2.bib respectively

Optional arguments:

• -o --output <file.bib>

  Write output to given file. Can be used multiple times when also giving multiple inputs. Maps inputs to outputs in order in that case If there are extra inputs, use default name (old_name.btac.bib). Ignored in inplace (-i) mode.

• -q --only-query <website> or -Q --dont-query <website>

  Restrict which websites to query from. <site> must be one of: crossref, dblp, researchr, unpaywall. These arguments can be used multiple times, for example to only query crossref and dblp use -q crossref -q dblp or -Q researchr -Q unpaywall -Q arxiv

• -e --only-entry <id> or -E --exclude-entry <id>

  Restrict which entries should be autocomplete. <id> is the entry id used in your bibtex file (e.g. @inproceedings{<id> ... }). These arguments can also be used multiple times to select only/exclude multiple entries

• -c --only-complete <field> or -C --dont-complete <field>

  Restrict which fields you wish to autocomplete. Field is a bibtex field (e.g. author, doi,...). So if you only wish to add missing doi's used -c doi.

Output formatting:

• --fa --align-values pad fieldnames to align all values

  @article{Example,
    author = {Someone},
    doi    = {10.xxxx/yyyyy},
  }
  

• --fc --comma-first use comma first syntax

  @article{Example
    , author = {Someone}
    , doi = {10.xxxx/yyyyy}
    ,
  }
  

• --fl --no-trailing-comma don't add the last trailing comma

• --fi --indent <space> space used for indentation, default is a tab

Flags:

• -i --inplace Modify input files inplace, ignores any specified output files

• -f --force-overwrite Overwrite already present fields. The default is to overwrite a field if it is empty or absent

• -t --timeout <float> set timeout on request in seconds, default: 10.0 s, increase this if you are getting a lot of timeouts.

• -S --ignore-ssl bypass SSL verification. Use this if you encounter the error:

  [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate has expired (_ssl.c:1129)
  

  another (better) fix for this is to run pip install --upgrade certifi to update python's certificates.

• -d --dump-data <file.json> writes matching entries to the given JSON files.

  This allows to see duplicate fields from different sources that are otherwise overwritten when merged into a single entry.

  The JSON file will have the following formatting:

  [
    {
      "entry": "<entry_id>",
      "new-fields": 8,
      "crossref": {
        "query-url": "https://api.crossref.org/...",
        "query-response-time": 0.556,
        "query-response-status": 200,
        "author" : "Lastname, Firstnames and Lastname, Firstnames ...",
        "title" : "super interesting article!",
        "..." : "..."
      },
      "arxiv": null, // null when no match found
      "dblp": ...,
      "researchr": ...,
      "unpaywall": ...
    },
    ...
  ]
  

• -O --no-output don't write any output files (except the one specified by --dump-data)

• -v --verbose verbose mode shows more info. It details entries as they are being processed and shows a summary of new fields and their source at the end. Using it more then once prints debug info (up to four times).

• -s --silent hide info and progressbar. Keep showing warnings and errors. Use twice to also hide warnings, thrice to also hide errors and four times to also hide critical error, effectively killing all output.

• -n --no-color don't color use ANSI codes to color and stylise output

• --version show version number

• -h --help show help