Paperboy

A command line program to check for the most recently published articles from specified scientific journals.

Features

What Paperboy does:

Pulls all articles, news, editorials, etc. published since the last check (or within the last 4 days if used the first time)
For the set of scientific journals specified from all journals curated in the NCBI Pubmed/Medline database.

Note: No publisher subscription is required, but only the identifying information is printed, not the abstract or full text.

Get started

Download/clone the code. Install required Python packages (see Requirements below).

Find your journal

Let say you want to add the journal PLOS Computational Biology. Find its NlmID. (The following command greps for the journal's Medline abbreviation, but you can grep for anything you want.)

$ python paperboy-cli.py journal-list-all|grep -e 'PLoS Comput Biol'
INFO: Found 33599 journals.
Journal: PLoS computational biology (PLoS Comput Biol) (NlmId: 101238922) (ISSN: 1553-734X, 1553-7358)

Mark your journal active

Add the NlmID to the active journal list.

$ python paperboy-cli.py journal-add 101238922
INFO: PLoS Comput Biol (NlmId: 101238922) was marked active.

(Optionally) Verify your journal was set active

$ python paperboy-cli.py journal-list-active
INFO: Found 1 active journals.
Journal: PLoS computational biology (PLoS Comput Biol) (NlmId: 101238922) (ISSN: 1553-734X, 1553-7358)

Check for new articles

Any new articles since the last check, or since 4 days ago if this is the first time, will be downloaded and shown.

$ python paperboy-cli.py 
INFO: Loading new articles since 2021/01/03.
INFO: Found 27 new articles from PLoS Comput Biol.
INFO: Displaying 26 articles, excluding 1 Letter, Editorial, News, Interview.
Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform.. Eyre, (4 more). PLoS Comput Biol (https://doi.org/10.1371/journal.pcbi.1008417) (PMID 33444378) (Journal Article)
Investigating the mitochondrial genomic landscape of Arabidopsis thaliana by long-read sequencing. Masutani, Arimura, Morishita. PLoS Comput Biol (https://doi.org/10.1371/journal.pcbi.1008597) (PMID 33434206) (Journal Article)
...

Once your set of journals is active, just repeat the last step.

Requirements

The following python packages are required: biopython, lxml, colorama, pyparsing, appdirs.

One way to set up an environment is by using conda.

conda create -n paperboy python=3.8 biopython lxml colorama pyparsing appdirs
conda activate paperboy

Usage

The usage help is:

paperboy-cli.py [-h] [-d] {update,update-show,show,show-last-update,set-last-update,journal-list-all,journal-list-active,journal-add,journal-remove}

The commands do the following:

update: Check for new published articles and download their IDs since the last update.
show: Show details about all new articles, including title, authors, and DOI link.
update-show: Run update followed by show. This is the default command.
show-last-update: Print the date of the last update.
set-last-update: Set the date of the last update if you want to check older articles again.
journal-list-all: List all journals available in the Pubmed/Medline database. This is a fairly large number (~30k at the time of writing) and can take a bit. This list is downloaded the first time and stored locally, and only updated periodically after that.
journal-list-active: List all journals for which new articles are pulled.
journal-add: Add a journal to the list of active journals; requires the journal's NlmID (listed by journal-list-all).
journal-remove: Remove a journal from the list of active journals; requires the journal's NlmID.

Output is formatted to terminal width, unless the terminal width is small, or the output is redirected.

Files

The code is contained in just one file, paperboy-cli.py.
One config file is stored in an OS-specific user-dependent location, e.g. on Linux in ~/.config/paperboy/paperboy.conf.

Contribute

Any help is welcome, bug reports, feature requests, or pull requests for code or documentation!

shze / paperboy