A command-line interface for retrieving preprint information from bioRxiv.

© Jan Samson (reach out at [email protected])

The field argument is the only required parameter. This pertains to the research area of interest. Optional flags are listed below.

Listed below are optional boolean flags:

Retrieve the most recent pre-prints in the field of bioinformatics.

# returns 10 articles by default
biorx.py bioinformatics

Retrieve article information from the first 3 pages of bioRxiv.

biorx.py bioinformatics --pages 3

Display the first five articles.

biorx.py bioinformatics --truncate 5

Extract all articles between the 8th and 15th articles.

biorx.py bioinformatics --pages 2 --truncate 8:15

Return the first 8 articles and sort by title.

biorx.py bioinformatics --truncate 8 --sort title

Display article information as json.

biorx.py bioinformatics --json

• create tree object for navigating the HTML/XML document
• generate dataclasses for storing article information
  • Author
  • Article
• command line parser for providing program arguments
• design command line interface with custom flags
• convert API to client that supports HTTP connection pooling
• support for stdin, stdout for piping operations
• display output as json
• download full article text to a specified file

I should be able retrieve the most recent biorxiv pre-prints for a given field.

For each article, I should be able to view its TITLE, AUTHORS, DATE OF PUBLICATION, DOI, and ABSTRACT