kpub: Kepler/K2 publication database

A database of scientific publications related to NASA's Kepler/K2 mission.

kpub is a mission-specific tool that enables NASA's Kepler/K2 Guest Observer Office to keep track of its mission's scientific publications in an easy way. It leverages SQLite and the ADS API (using Andy Casey's awesome Python client) to create and curate a database that contains the metadata of mission-related articles.

Example use

Print a nicely-formatted list of Kepler-related exoplanet publications in markdown format:

kpub --exoplanets

Add a new article to the database using its bibcode. This command will display the article's metadata and ask the user to classify the science:

kpub-add 2015arXiv150204715F

Remove an article using its bibcode:

kpub-delete 2015ApJ...800...46B

Search ADS interactively for new Kepler-related articles and try to add them:

kpub-update 2015-07

For example output, see the data/output/ sub-directory in this repository.

Installation

To install the latest version from source:

git clone https://github.com/KeplerGO/kpub.git
cd kpub
python setup.py install

Note that the kpub tools will use ~/.kpub.db as the default database file. This repository contains a recent version of the database file (data/kpub.db), which you may want to link to the default file as follows:

ln -s /path/to/git/repo/data/kpub.db ~/.kpub.db

The kpub-addand kpub-update tools that come with this package require an api key from NASA ADS labs to retrieve publication meta-data. You need to follow the installation instructions of the ads client by @andycasey to make this work.

Usage

kpub adds a number of tools to the command line (described below).

There is a Makefile which makes your life easy if you work for the GO office and are updating the database. Simply type:

• make update to search for new publications;
• make push to push the updated database to the git repo;
• make refresh to export and import all publications, this is slow and necessary only if you want to remove duplicates and fetch fresh citation statistics.

Command-line tools

After installation, this package adds the following command-line tools to your path:

• kpub prints the list of publications in markdown format;
• kpub-update adds new publications by searching ADS (interactive);
• kpub-add adds a publication using its ADS bibcode;
• kpub-delete deletes a publication using its ADS bibcode;
• kpub-import imports bibcodes from a csv file;
• kpub-export exports bibcodes to a csv file;
• kpub-plot creates a visualization of the database;
• kpub-spreadsheet exports the publications to an Excel spreadsheet.

Listed below are the usage instructions for each command:

kpub

$ kpub --help
usage: kpub [-h] [-f dbfile] [-e] [-a] [-k] [-2] [-m]

View the Kepler/K2 publication list in markdown format.

optional arguments:
  -h, --help          show this help message and exit
  -f dbfile           Location of the Kepler/K2 publication list db. Defaults 
                      to ~/.kpub.db.
  -e, --exoplanets    Only show exoplanet publications.
  -a, --astrophysics  Only show astrophysics publications.
  -k, --kepler        Only show Kepler publications.
  -2, --k2            Only show K2 publications.
  -m, --month         Group the papers by month rather than year.

kpub-update

$ kpub-update --help
usage: kpub-update [-h] [-f dbfile] [month]

Interactively query ADS for new publications.

positional arguments:
  month       Month to query, e.g. 2015-06.

optional arguments:
  -h, --help  show this help message and exit
  -f dbfile   Location of the Kepler/K2 publication list db. Defaults to
              ~/.kpub.db.

kpub-add

$ kpub-add --help
usage: kpub-add [-h] [-f dbfile] bibcode [bibcode ...]

Add a paper to the Kepler/K2 publication list.

positional arguments:
  bibcode     ADS bibcode that identifies the publication.

optional arguments:
  -h, --help  show this help message and exit
  -f dbfile   Location of the Kepler/K2 publication list db. Defaults to
              ~/.kpub.db.

kpub-delete

$ kpub-delete --help
usage: kpub-delete [-h] [-f dbfile] bibcode [bibcode ...]

Deletes a paper from the Kepler/K2 publication list.

positional arguments:
  bibcode     ADS bibcode that identifies the publication.

optional arguments:
  -h, --help  show this help message and exit
  -f dbfile   Location of the Kepler/K2 publication list db. Defaults to
              ~/.kpub.db.

kpub-import

$ kpub-import --help 
usage: kpub-import [-h] [-f dbfile] csvfile

Batch-import papers into the Kepler/K2 publication list from a CSV file. The
CSV file must have three columns (bibcode,mission,science) separated by
commas. For example: '2004ApJ...610.1199G,kepler,astrophysics'.

positional arguments:
  csvfile     Filename of the csv file to ingest.

optional arguments:
  -h, --help  show this help message and exit
  -f dbfile   Location of the Kepler/K2 publication list db. Defaults to
              ~/.kpub.db.

kpub-export

$ kpub-export --help
usage: kpub-export [-h] [-f dbfile]

Export the Kepler/K2 publication list in CSV format.

optional arguments:
  -h, --help  show this help message and exit
  -f dbfile   Location of the Kepler/K2 publication list db. Defaults to
              ~/.kpub.db.

kpub-spreadsheet

$ kpub-spreadsheet --help
usage: kpub-spreadsheet [-h] [-f dbfile]

Export the Kepler/K2 publication list in XLS format.

optional arguments:
  -h, --help  show this help message and exit
  -f dbfile   Location of the Kepler/K2 publication list db. Defaults to
              ~/.kpub.db.

Author

Created by Geert Barentsen (geert.barentsen at nasa.gov) on behalf of the Kepler/K2 Guest Observer Office.

Acknowledgements

This tool is made possible thanks to the efforts made by NASA ADS to provide a web API, and thanks to the excellent Python client that Andy Casey (@andycasey) wrote to use the API. Thanks ADS, thanks Andy!