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.
Argument | Alias | Description |
---|---|---|
--out | -o | filepath to save output |
--pages | -p | number of HTML pages to retrieve from server |
--truncate | -t | subsets a table with a start and end indices |
--filter | -f | filter the table by column headers |
Listed below are optional boolean flags:
Argument | Description |
---|---|
--no-header | excludes the column names when writing stdout to file |
--csv | writes output to file as csv |
--tsv | writes ouput to file as tsv |
--json | writes output to file as json |
--verbose | print out program messages |
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