Add Testing Script

[nguyenank]

Add a testing script (mapper-test.yml) that adds integration with the ontology-mapper-tests repo [OMT repo] to automatically evaluate the mapper performance against a gold standard.

The script runs for each push and pull-request for any branches in the list for the appropriate event under on:; add the name of the branch if you want the script to run for a given action.

The tool currently runs on terms from the UK Biobank (OMT repo: data/ukb-efo/terms.txt), using EFO 2.106 released on 2019-03-18 (OMT repo: data/ukb-efo/efo-v2019-03-18.owl) as referenced in the paper on hand-mapping UK Biobank terms to EFO. The output is saved in the OMT repo in mapper-outputs/ukb-efo/{commit SHA}.csv(.json).

A script then calculates the coverage error and one error (OMT repo: compare-scripts/coverage_one_error.py) between the mapper output and the mappings done by hand (OMT repo: data/ukb-efo/gold-standard.csv). Results are saved in a spreadsheet (OMT repo: summary.csv), with each row being a different run of the script. The spreadsheet has the following columns:

• branch - the branch on which either a push/pull-request was done that initiated the script run
• commit-sha - the identifier of the most recent commit that is used as an ID for the particular script run
• github-comment - the comment of the most recent commit
• ukb-efo_mapper_output_filename - the filename of the mapper output from running on the UK Biobank terms with the EFO ontology; should always be of the form:ukb-efo/{commit SHA}.csv
• coverage_error - the coverage error
• one_error - the one error