Bibtexautocomplete 1.3.3

Description:

bibtexautocomplete 1.3.3

Bibtex Autocomplete

bibtex-autocomplete or btac is a simple script to autocomplete BibTeX
bibliographies. It reads a BibTeX file and looks online for any additional data
to add to each entry. It can quickly generate entries from minimal data (a lone
title is often sufficient to generate a full entry). You can also use it to only
add specific fields (like DOIs, or ISSN) to a manually curated bib file.
It is designed to be as simple to use as possible: just give it a bib file and
let btac work its magic! It combines multiple sources and runs consistency
and normalization checks on the added fields (check that URLs lead to a valid
webpage, that DOIs exist at https://dx.doi.org/).
It attempts to complete a BibTeX file by querying the following domains:

openalex.org: ~240 million entries
www.crossref.org: ~150 million entries
arxiv.org: open access archive, ~2.4 million entries
semanticscholar.org: ~215 million entries
unpaywall.org: database of open access articles, ~48 million entries
dblp.org: computer science, ~7 million entries
researchr.org: computer science
inspirehep.net: high-energy physics, ~1.5 million entries

Big thanks to all of them for allowing open, easy and well-documented access to
their databases. This project wouldn't be possible without them. You can easily
narrow down the list of sources if some aren't relevant using command line options.
Contents

New in version 1.3
Demo
Quick overview
Installation

Dependencies

Usage
Command line arguments

Specifying output
Query filtering
New field formatting
Global output formatting
Optional flags

Credit and license

New in version 1.3
Added OpenAlex and Inspire HEP as sources. Switched to a majority vote between source
to find new field, along with smart field normalization and comparison. And of course,
bug fixes!
See the changelog for full details.
Demo

Quick overview
How does it find matches?
btac queries the websites using the entry DOI (if known) or its title. So
entries that don't have one of those two fields will not be completed.

DOIs are only used if they can be recognized, so the doi field should
contain "10.xxxx/yyyy" or an URL ending with it.
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 formats 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)
If the year is known, entries with different years will also not match.

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 by performing a majority vote among the
source. To do so it uses smart normalization and merging tactics for each field:

Authors (and editors) match if they have same last names and, if both first
names present, the first name of one is equal/an abbreviation of the other.
Author list match if their intersection is non-empty.
ISSN and ISBN are normalized their check digits verified. ISBN are converted
to their 13 digit representation
URL and DOI are checked for valid format, and further validated by querying
them online to ensure they exist
Many fields match with abbreviation detection (journal, institution, booktitle,
organization, publisher, school and series). So ACM will match
Association for Computer Machinery
Pages are normalized to use -- as separator
All other fields are compared excluding case and punctuation.

The script will not overwrite any user given non-empty fields, unless the
-f/--force-overwrite flag is given. If you want to check what fields are
added, you can use -v/--verbose to have them printed to stdout (with
source information), or -p/--prefix to have the new fields be prefixed with
BTAC in the output file.
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

Note: pip no longer allows installing scripts globally in systems with other
package managers (like most Linux distros). You can install the script locally in
a virtual environment or globally
using pipx:
sudo apt install pipx
pipx install bibtexautocomplete

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

bibtexparser (<2.0.0)
alive_progress (>= 3.0.0) for the fancy progress bar

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.
A different output file can be specified with -o.
btac -i db.bib : reads from db.bib and overwrites it (inplace flag).
Avoid on non backed-up/version-controlled files, I'd hate it if my script
corrupted your data.
btac folder : reads from all files ending with .bib in folder. Excludes
.btac.bib files unless they are the only .bib files present. Writes to
folder/file.btac.bib unless inplace flag is set.
btac with no inputs is same as btac ., reads file from current working directory
btac -c doi ... only completes DOI fields, leave others unchanged
btac -v ... verbose mode, pretty prints all new fields when done.
See this image for a preview of verbose output.

Note: the parser doesn't preserve
format information, so this script will reformat your files. Some formatting
options are provided to control output format.
Slow responses: Sometimes due to server traffic, a source DB may take significantly longer
to respond and slow btac.

You can increase timeout with btac ... -t 60 (60s) or btac ... -t -1 (no timeout)
You can disable queries to the offender btac ... -Q <website>
You can try again at another time

Command line arguments
As btac has a lot of option I'd recommend setting up an alias if you use a lot
regularly.
Specifying output

-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. If there are extra inputs,
uses default name (old_name.btac.bib). Ignored in inplace (-i) mode.
For example btac db1.bib db2.bib db3.bib -o out1.bib -o out2.bib reads db1.bib,
db2.bib and db3.bib, and write their outputs to out1.bib, out2.bib
and db3.btac.bib respectively.

-i --inplace Modify input files inplace, ignores any specified output files.
Avoid on non backed-up/version-controlled files, I'd hate it if my script
corrupted your data.

-O --no-output don't write any output files (except the one specified by --dump-data)
can be used with -v/--verbose mode to only print a list of changes to the terminal

Query filtering

-q --only-query <site> or -Q --dont-query <site>
Restrict which websites to query from. <site> must be one of: openalex,
crossref, arxiv, s2, unpaywall, dblp, researchr, hep. These arguments
can be used multiple times, for example to only query Crossref and DBLP use
-q crossref -q dblp or
-Q openalex -Q researchr -Q unpaywall -Q arxiv -Q s2 -Q hep

-e --only-entry <id> or -E --exclude-entry <id>
Restrict which entries should be autocompleted. <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 DOIs use -c doi.

-b --filter-fields-by-entrytype <required|optional|all> only add fields that correspond to
the given entry type in bibtex's data model. Disabled by default. required
only adds required fields, optional adds required and optional fields, and
all adds required, optional and non-standard fields (doi, issn and isbn).
A list of required/optional fields by entry type can be found
on the tex stackexchange

-w --overwrite <field> or -W --dont-overwrite <field>
Force overwriting of the selected fields. If using -W author -W journal
your force overwrite of all fields except author and journal. The
default is to override nothing (only complete absent and blank fields).
For a more complex example btac -C doi -w author means complete all fields
save DOI, and only overwrite author fields.
You can also use the -f flag to overwrite everything or the -p flag to add
a prefix to new fields, thus avoiding overwrites.

-m --mark and -M --ignore-mark
This is useful to avoid repeated queries if you want to run btac many times
on the same (large) file.
By default, btac ignores any entry with a BTACqueried field. --ignore-mark
overrides this behavior.
When --mark is set, btac adds a BTACqueried = {yyyy-mm-dd} field to each entry
it queries.

New field formatting
You can use the following arguments to control how btac formats the new fields

--fu --escape-unicode replace unicode symbols by latex escapes sequence (for
example: replace é with {\'e}). The default is to keep unicode symbols as is.
--fp --protect-uppercase <field> or --FP --dont-protect-uppercase <field> or
--fpa --protect-all-uppercase, insert braces around words containing uppercase
letters in the given fields to ensure bibtex will preserve them. The three
arguments are mutually exclusive, and the first two can be used multiple times
to select/deselect multiple fields.

Global output formatting
Unfortunately bibtexparser doesn't
preserve format information, so this script will reformat your BibTeX file. Here
are a few options you can use to control the output format:

--fa --align-values pad field names 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.
Can be specified as a number (number of spaces) or a string with spaces
and _, t, and n characters to mark space, tabs and newlines.

Optional flags

-p --prefix Write new fields with a prefix. The script will add BTACtitle = ... instead of title = ... in the bib file. This can be combined with -f
to safely show info for already present fields.
Note that this can overwrite existing fields starting with BTACxxxx, even
without the -f option.

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

-D --diff only print the new fields in the output file. In this mode, old
fields are removed and entries with no new fields are deleted. This cannot be
used with the -i --inplace flag for safety reasons. If you really want to overwrite
your input file (and delete a bunch of data in the process), you can do so with
by specifying it explicitly via the -o --output option.

-u --copy-doi-to-url If a DOI is found but no URL, set the URL field
to https://dx.doi.org/<doi>

-t --timeout <float> set timeout on request in seconds, default: 20.0 s,
increase this if you are getting a lot of timeouts. Set it to -1 for no timeout.

-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 structure:
[
{
"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!",
"..." : "..."
},
"openalex": ...,
"arxiv": null, // null when no match found
"unpaywall": ...,
"dblp": ...,
"researchr": ...,
"inspire": ...
},
...
]

-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 than once prints debug info (up to four times).
Verbose mode looks like this:

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

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

--version show version number

-h --help show help

Credit and license
This project was first inspired by the solution provided by
thando in this
TeX stack exchange post. I worked on as
part of a course on
Web data management in
2021-2022 as part of my masters (MPRI).
This project is free and open-source. It is distributed under terms of the
MIT License. See the
LICENSE
file for more information