ysbach / ads2bibtex

Make ADS library auto-synchronized to the local file, preferably in BibTeX format.

ads2bibtex

Make ADS library auto-synchronized to the local file (recommeneded: BibTeX).

Purpose

I created this script to reduce the time I waste on creating BibTeX files for multiple journals and my thesis. I did not care about the usage when the journals do not support BibTeX, and that's why the name is ads2bibtex. However, this should generally be useful because ADS supports various output formats (See Usage Tips below).

Also, it is intended to be run in the background on my terminal while I crawl references on ADS. When I add a paper to my library on ADS, this script automatically detects the change by checking the last-modified timestamp and updates the local BibTeX file accordingly.

Installation

Clone this repo and

$ pip install -e .

Later, you may git pull. Currently pip install ads2bibtex is unavailable (to be available 2023 Fall)

How to get the API Token? (click)

• Go to NASA ADS
• Top right: Log In. After logging in...
• Top right: Account → Settings
• Left: API Token

Do NOT click Generate a new key unless you really need it!!

How do I make an ADS Library? (click)

• Top right: Account → ADS Libraries
• Left: ADD A LIBRARY → Set the name of the library (e.g., "PhDT", "everything", "Bach+2023AJ").
• Select Manage Access Tab → copy Library ID: https://ui.adsabs.harvard.edu/public-libraries/<Library ID>

See this to learn how to add a paper to your library on ADS.

Check if installed by printing all the help messages:

ads2bibtex -h

Usage

1. The simplest usage:

   ads2bibtex <library ID> -o ysBach_PhDT_SNU/references.bib
   

2. My intentention when I made this package (see "Additional" Entry section below):

   ads2bibtex <library ID> -a bib_add.txt -o ../ysBach_PhDT_SNU/references.bib
   

• Please read the message printed on terminal for more information.
• NOTE: Paste your API token if asked. It will be saved as .ads-token file for later use.
• NOTE: To update the token, simply rm .ads-token.

"Additional" Entry

There are things that are not registered to ADS. If you have an additional file for them:

ads2bibtex <library ID> -a bib_add.txt -o outputdir/references.bib

Contents of my bib_add.txt as an example (click)

I always use `-f bibtex` as default. Thus, my "additional file" is in BibTeX format:

% A part of my own bib_add.txt
@ARTICLE{2022_SAG_NICpolpy,
       author = {{Bach}, Yoonsoo P. and {Ishiguro}, Masateru and {Takahashi}, Jun and {Geem}, Jooyeon},
        title = "{Data Reduction Process and Pipeline for the NIC Polarimetry Mode in Python, NICpolpy}",
      journal = {Stars and Galaxies (arXiv:2212.14167)},
     keywords = {methods: data analysis, methods: observational, techniques: image processing, techniques: polarimetric},
         year = 2022,
        month = dec,
       volume = {5},
          eid = {4},
        pages = {4},
archivePrefix = {arXiv},
       eprint = {2212.14167},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2022arXiv221214167B},
      adsnote = {}
}

@INPROCEEDINGS{gil-hutton-data,
title= {Catalogue of asteroid polarization curves},
author = {Gil-Hutton, R.},
year = {2017},
booktitle= {ACM (Asteroid, Comets, Meteors) 2017, Montevideo},
pages={Poster1.d.17},
URL= {http://gcpsj.sdf-eu.org/catalogo.html},
       adsurl = {},
      adsnote = {}
}

• Important Note: The journal names in the additional file (-a, --additional-file) will also be changed based on -j (--journal) option.
• Important Note: Note that "full/ISO-4 journal name → ADS macro (e.g., \apj)" is designed to be impossible (why not use ADS entry?).
  • To simply append the additional file to the resulting BibTeX without altering the contents of journal = {} field, use -j ads option, which is the default.

Journal Names

For different journals/formats other than BibTeX when querying from the ADS, use -f (see ads2bibtex -h).

\apj → Astrophysicial Journal (full name):

ads2bibtex <library ID> -o outputdir/references.bib -j full

\apj → Astrophys. J. (ISO-4 style):

ads2bibtex <library ID> -o outputdir/references.bib -j iso4

(You need to install nltk to use -j iso4)

ISO-4 is useful for, e.g., non-astronomy specific journals like Nature/Science (I actually made this for my thesis).

Less Useful Functionalities

Some tips for other arguments (use ads2bibtex -h for full help)

• -n (-num-iter): number of iterations (default=500)
  • Warning: Although I could not find the description, ADS "limits users to 5000 requests/day (on a rolling 24-hour window)", and there is no way to circumvent this limit [Lockhart, K. 2023-03-07, priv. comm. via email through help desk].
• -t (--dtime): time between iterations (default=5s)
• -i (--info-interval): number of iterations between info prints (default=20)

For debugging purpose...

If you want to save a separate output as ADS-Export functionality as bib_raw.txt for some reason (for me, I made it purely for debugging purpose):

ads2bibtex <library ID> -r bib_raw.txt -o outputdir/references.bib

Use -f or -F (--format or --format-raw) to set the save style of output file and raw file, respectively. By default, -f is "bibtex" and -F is %R # %3h_%Y_%q_%V_%p %T (a random testing format I used for debugging).

ads2bibtex <library ID> -r bib_raw.txt -o outputdir/references.bib -F "%R  # %10.5N_%Y_%q_%V_%p %T"

This is the same as ADS's "Export → Custom Format". See this help page of ADS.

Requirements

• regex (also used in nltk https://pypi.org/project/regex/)
• colorama (for colorful output on terminal)

To use abbreviation of words (-j iso4), you need nltk.

Other Notes

TODO?

At the moment, you cannot change the original journal name into the ADS style macro. (macro -> full/iso4 is possible).

iso4

The iso4/ is directly adopted from adlpr/iso4 (MIT license), and underwent minor tweaks to cope with the more recent LTWA version.

The Abbreviation file from LTWA (version 2021-07-02, retrieved 2022-12-27): http://www.issn.org/services/online-services/access-to-the-ltwa/

Notes by ADS

ADS provides some example notes:

• GitHub
• nbviewer

Explanations are scattered to many places, such as:

• Full API Docs
• Export API
• Search API: this explains most of the APIs I guess.

Bugs

• I sometimes encounter a crash. However, I can just re-run the script and then everything is fine 🤷