def test_export(self):
"""export a table with reference priors"""
config = MGITestConfig()
config.table = "reference_priors"
# export the table
out = StringIO()
pipeline = Phenoscoring(config)
pipeline.export(out)
# check some basic properties
outvalue = out.getvalue().strip().split("\n")
self.assertGreater(len(outvalue), 4)
self.assertEqual(outvalue[0], "id\tvalue")
if config.action == "clearmodels":
# remove all models and model scores from the database
pipeline.clearmodels()
if config.action == "update":
# add new or update existing model defintions/phenotypes
pipeline.update()
if config.action == "remove":
# remove a subset of models from the database
pipeline.remove()
if config.action == "recompute":
# remove all scores and re-generate them from scratch
pipeline.recompute()
if config.action == "export":
# write a database table into a tsv file
pipeline.export()
if config.action == "representations":
# compute complete representations for references and models
pipeline.export_representations()
if config.action == "explain":
# provide step-by-step explanation of scoring
result = pipeline.explain()
if config.pretty:
result = json.dumps(json.loads(result), indent=2)
print(result)