Command Line Interface

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

semra

CLI for SeMRA.

Usage

semra [OPTIONS] COMMAND [ARGS]...

Options

--version: Show the version and exit.

build

Construct the SeMRA Raw Semantic Mappings Database.

Usage

semra build [OPTIONS]

Options

--include-wikidata, --no-include-wikidata

Default:: True

--write-labels: If set to true, writes subject and object labels in the SSSOM file.

--prune-sssom: If true, will try and prune unused SSSOM columns during output. Note that this significantly increases memory requirement during construction, but results in a smaller database file.

--upload: If set to true, upload the generated artifacts to the SeMRA Raw Semantic Mappings Database record on Zenodo (https://doi.org/10.5281/zenodo.11082038)

--refresh-source: Enable this to fully re-process source data, e.g., parse source OBO files and re-build mapping caches. This is more aggressive than –refresh-process and –refresh-raw

--refresh-raw: Re-process mapping sources to produce raw mappings and process them again. This is more aggressive than –refresh-process.

--test: Run in test mode on a subset of resources.

--skip-below <skip_below>

landscape

Construct pre-configured domain-specific mapping databases and run landscape analyses.

Usage

semra landscape [OPTIONS]

Options

--refresh-source: Enable this to fully re-process source data, e.g., parse source OBO files and re-build mapping caches. This is more aggressive than –refresh-process and –refresh-raw

--refresh-raw: Re-process mapping sources to produce raw mappings and process them again. This is more aggressive than –refresh-process.

--refresh-processed: Re-process raw mappings. This is the least aggressive ‘refresh’ option.

--upload: If enabled, upload each landscape to their respective Zenodo records.

--build-docker: If activated, docker build is invoked as a test to make sure that the construction of the Neo4j database works correctly. E.g., this can catch data issues that result in invalid Neo4j nodes or edges files.

-v, --verbose: Enable verbose mode. More -v’s means more verbose.

--only <only>: if given, only runs this configuration

--readme-only: if given, only creat ethe readme