Command-line interface

Some wags-tails functions are executable via a provided command-line interface, enabling usage from non-Python environments or for general data management purposes.

Note

Currently, the CLI routes data requests through the explicitly defined source modules within wags-tails. This means that the CLI cannot be used to manage custom sources.

wags-tails

wags-tails [OPTIONS] COMMAND [ARGS]...

Manage data files from genomics databases and knowledge sources.

get-latest

wags-tails get-latest [OPTIONS] {chemidplus|chembl|do|drugbank|drugsatfda|ense
                      mbl|ensembl_transcript_mappings|guidetopharmacology|hemo
                      nc|hgnc|hpo|moalmanac|mondo|ncbi|ncbi_lrg_refseqgene|ncb
                      i_mane_summary|ncit|oncotree|rxnorm}

Get latest version of specified data.

For example, to retrieve the latest Disease Ontology release:

% wags-tails get-version do

Unless --from_local is declared, wags-tails will first make an API call against the resource to determine the most recent release version, and then either provide a local copy if already available, or first download from the data origin and then return a link.

The --help option for this command will display all legal inputs for DATA; alternatively, use the list-sources command to show them in a computable (line-delimited) format.

Options

-s, --silent

Suppress intermediary printing to stdout.

--from_local

Use latest available local file.

--force_refresh

Retrieve data from source regardless of local availability.

Arguments

DATA

Required argument

list-sources

wags-tails list-sources [OPTIONS]

List supported sources.

path

wags-tails path [OPTIONS]

Get path to wags-tails storage directory given current environment configuration.