Command Line Interface

pubmed_downloader automatically installs the command pubmed_downloader. See pubmed_downloader --help for usage details.

pubmed_downloader

CLI for pubmed_downloader.

Usage

pubmed_downloader [OPTIONS] COMMAND [ARGS]...

articles

Download and process articles.

Usage

pubmed_downloader articles [OPTIONS]

Options

-f, --force-process

If given, re-processes the articles. Does not re-download.

-m, --multiprocessing

Should multiprocessing get used?

-v, --verbose

Enable verbose mode. More -v’s means more verbose.

--source <source>

Choose where the index of files comes from. Remote means that the NCBI FTP server is queried, which is flaky. Local means a previous cache of the index is used.

Options:

remote | local

--ground, --no-ground

Should MeSH terms, organizations, and authors get grounded?

Default:

True

--clear

Delete cached JSON/JSONL files for articles, then exit without doing any processing. Useful for cleaning up and iteratively developing the processor.

catalog

Download and process the NLM catalog.

Usage

pubmed_downloader catalog [OPTIONS]

Options

-f, --force-process