tpub: TESS publication database

A database of scientific publications related to NASA's TESS mission.

tpub is a mission-specific tool that enables NASA's TESS Guest Investigator 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. This is a fork of kpub which is used to track Kepler/K2 publications. kpub was written by Geert Barentsen

Example use

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

tpub --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:

tpub-add 2015arXiv150204715F

Remove an article using its bibcode:

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

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

tpub-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/tessgi/tpub.git
cd tpub
python setup.py install

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

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

The tpub-addand tpub-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

tpub 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 GI 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:

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

Listed below are the usage instructions for each command:

tpub

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

View the TESS publication list in markdown format.

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

kpub-update

$ tpub-update --help
usage: tpub-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 TESS publication list db. Defaults to
              ~/.tpub.db.

tpub-add

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

Add a paper to the TESS 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 TESS publication list db. Defaults to
              ~/.tpub.db.

tpub-delete

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

Deletes a paper from the TESS 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 TESS publication list db. Defaults to
              ~/.tpub.db.

kpub-import

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

Batch-import papers into the TESS publication list from a CSV file. The
CSV file must have three columns (bibcode,mission,science) separated by
commas. For example: '2004ApJ...610.1199G,tess,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 TESS publication list db. Defaults to
              ~/.tpub.db.

tpub-export

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

Export the TESS publication list in CSV format.

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

tpub-spreadsheet

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

Export the TESS publication list in XLS format.

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

Author

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

tpub is a fork of kpub that creates a list of TESS publications, rather than Kepler/K2. The tpub fork was created by Tom Barclay (thomas.barclay at nasa.gov) on behalf of the TESS Guest Investigator 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.

We also thank Geert cos he wrote nearly all the code here.