Command Line Interface

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

sssom_pydantic

CLI for sssom_pydantic.

Usage

sssom_pydantic [OPTIONS] COMMAND [ARGS]...

format

Lint a SSSOM TSV file.

Usage

sssom_pydantic format [OPTIONS] PATH

Options

--standardize

Standardize against Bioregistry preferred CURIE prefixes and (RDF) URI prefixes

Arguments

PATH

Required argument

subset

Implement the filter workflow for a given prefix.

This workflow removes negative mappings, unsure mappings, and non-exact mappings.

Usage

sssom_pydantic subset [OPTIONS]

Options

-p, --prefix <prefix>

Required The prefix that becomes the subjects of all mappings. If used in combination with –standardize, will get automatically standardized.

--target-prefix <target_prefix>

The prefix that becomes the object of all mappings. If used in combination with –standardize, will get automatically standardized.

-i, --input <input>

Path to a local file or URL to a remote file. If not given, will get input from STDIN

-o, --output <output>

Path to a local file to output. If not given, will write to STDOUT

--justification-policy

When inverting mappings, should the justification be derived to semapv:MappingInversion and reference be made back to the original mapping, or should the original jusitication be retained?

Options:

retain | derive

--standardize

Standardize against Bioregistry preferred CURIE prefixes and (RDF) URI prefixes

web

Run the web app (with SQL backend).

Usage

sssom_pydantic web [OPTIONS]

Options

--add-examples

Add example SSSOM records.

--tab

--host <host>

Default:

'0.0.0.0'

--port <port>

Default:

8876