This PR includes a command line regnum2phyx script that can convert Regnum database dumps into a directory of Phyx files. It also includes tests for the output of that script, by ensuring that (1) the JSON file produced is identical to the expected JSON file we've previous calculated, and (2) whether it can be validated against a first draft of a JSON schema for Phyx files.
Should be merged after RT #70, as otherwise the Travis CI tests fail in phyx2ontology.
The current conversion test is based on a single Regnum dump written by hand and based on the Crocodylia phyloreference from the Brochu 2003 test file. We should eventually expand this to a partial Regnum dump once parts of Regnum have become public.
Note that the JSON schema is a model 2.0 schema rather than a model 1.0 schema: the next step is to update the Curation Tool and phyx.js to model 2.0, at which point they will be able to use Phyx in those schemas.
This PR includes a command line regnum2phyx script that can convert Regnum database dumps into a directory of Phyx files. It also includes tests for the output of that script, by ensuring that (1) the JSON file produced is identical to the expected JSON file we've previous calculated, and (2) whether it can be validated against a first draft of a JSON schema for Phyx files.
Should be merged after RT #70, as otherwise the Travis CI tests fail in phyx2ontology.
The current conversion test is based on a single Regnum dump written by hand and based on the Crocodylia phyloreference from the Brochu 2003 test file. We should eventually expand this to a partial Regnum dump once parts of Regnum have become public.
Note that the JSON schema is a model 2.0 schema rather than a model 1.0 schema: the next step is to update the Curation Tool and phyx.js to model 2.0, at which point they will be able to use Phyx in those schemas.