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Tests

As well as aiming to provide good coverage of the Phenoflow codebase, tests can also be used to populate a local development instance of the Phenoflow library with definitions.

NB: Tests that are used to populate local instances should be run in a development environment (i.e. without a NODE_ENV=test prefix).

Example 1: Importing from CALIBER

CALIBER (or the HDR UK phenotype library) stores phenotype definitions as markdown files, each of which links to a set of codelists that form the definition.

To import CALIBER definitions into Phenoflow:

  1. Clone [email protected]:kclhi/hdr-caliber-phenome-portal.git into fixtures/importer/caliber.
  2. Run npx mocha -g "CI1|CI2"
  3. Run npx mocha -g "IM7", to manually connect the definitions with different connectors.

Example 2: Importing from SAIL databank

SAIL databank stores phenotypes remotely, as a part of a web library.

To import SAIL definitions into Phenoflow:

  1. Inside web/.env specify SAIL API credentials:
SAIL_USERNAME=
SAIL_PASSWORD=
  1. Run npx mocha -g "web"
  2. Run npx mocha -g "IM7", to manually connect the definitions with different connectors.