def test_update_phenotypes(self):
"""update of phenotypes adds new phenotypes."""
# rerun the update, should give twice the number of phenotypes
impc2 = Phenoscoring(IMPCTestConfig())
impc2.update()
phentab = ModelPhenotypeTable(self.dbfile)
self.assertEqual(phentab.count_rows(), 28, "phenotypes added twice")
def test_build_mgi(self):
"""can build a phenoscoring database using only MGI data"""
mgi = Phenoscoring(MGITestConfig())
mgi.update()
# in contrast to complete config, this db should have fewer rows
desctab = ModelDescriptionTable(self.dbfile)
self.assertEqual(desctab.count_rows(), 6)
modeltab = ModelPhenotypeTable(self.dbfile)
self.assertEqual(modeltab.count_rows(), 9)
def test_build_impc(self):
"""can build a phenoscoring database using only IMPC data"""
impc = Phenoscoring(IMPCTestConfig())
impc.update()
# in contrast to complete build, this db should have IMPC-only rows
desctab = ModelDescriptionTable(self.dbfile)
self.assertEqual(desctab.count_rows(), 8)
modeltab = ModelPhenotypeTable(self.dbfile)
self.assertEqual(modeltab.count_rows(), 14)
def test_update_phenotypes_badids(self):
"""update of phenotypes aborts when file contains incorrect ids."""
phentab = ModelPhenotypeTable(self.dbfile)
self.assertEqual(phentab.count_rows(), 14, "initial phenotypes")
config = IMPCTestConfig()
config.model_descriptions = None
config.model_phenotypes = "prep-IMPC-phenotypes-badids.tsv"
impc2 = Phenoscoring(config)
impc2.update()
self.assertEqual(phentab.count_rows(), 14, "phenotypes unchanged")
def setUp(self):
"""For setup, ensure db does not exist, then build a new one"""
config = CompleteTestConfig()
self.dbfile = config.db
remove_db(self.dbfile)
self.pipeline = Phenoscoring(config)
self.pipeline.build()
impc = Phenoscoring(IMPCTestConfig())
impc.update()
# handles for models
self.desctab = ModelDescriptionTable(self.dbfile)
self.phenstab = ModelPhenotypeTable(self.dbfile)
self.scoretab = ModelScoreTable(self.dbfile)
def test_build_both(self):
"""can update database sequentially with MGI and IMPC"""
mgi = Phenoscoring(MGITestConfig())
mgi.update()
impc = Phenoscoring(IMPCTestConfig())
impc.update()
desctab = ModelDescriptionTable(self.dbfile)
self.assertEqual(desctab.count_rows(), 14, "8 IMPC, 6 MGI")
modeltab = ModelPhenotypeTable(self.dbfile)
self.assertEqual(modeltab.count_rows(), 23, "9 MGI, 14 IMPC")
scoretab = ModelScoreTable(self.dbfile)
self.assertGreater(scoretab.count_rows(), 0,
"score table is non-empty")
def test_update_nowork(self):
"""can run build repeatedly without over-inserting"""
# run update again, but without setting phenotypes
impc = Phenoscoring(IMPCTestConfig())
impc.model_phenotypes = None
impc.update()
desctab = ModelDescriptionTable(self.dbfile)
self.assertEqual(desctab.count_rows(), 8,
"number of descriptions should be unchanged")
# run again without setting anything
impc.model_descriptions = None
impc.update()
self.assertEqual(desctab.count_rows(), 8,
"number of descriptions should be unchanged")
def test_update_descriptions(self):
"""run update multiple times to change content of model descriptions."""
desctab = ModelDescriptionTable(self.dbfile)
self.assertEqual(desctab.count_rows(), 8,
"initial set of model descriptions")
self.assertFalse(self.descriptions_contain("description", "UPDATED"))
# run an update operation with only model descriptions
config = IMPCTestConfig()
config.model_descriptions = "prep-IMPC-descriptions-update.tsv"
config.model_phenotypes = None
impc2 = Phenoscoring(config)
impc2.update()
self.assertEqual(desctab.count_rows(), 8,
"number of models should be unchanged")
self.assertTrue(self.descriptions_contain("description", "UPDATED"),
"descriptions in updated file contain string UPDATED")
def test_update_skip_compute(self):
"""run update but skip score calculation"""
# extract current number of models and scores
desctab = ModelDescriptionTable(self.dbfile)
scorestab = ModelScoreTable(self.dbfile)
num_models = desctab.count_rows()
num_scores = scorestab.count_rows()
# run an update, but without computing scores
config = MGITestConfig()
config.skip_compute = True
mgi = Phenoscoring(config)
mgi.update()
self.assertGreater(desctab.count_rows(), num_models,
"number of models should increase")
self.assertEqual(scorestab.count_rows(), num_scores,
"number of scores should remain")
def setUp(self):
"""At beginning of each test, make sure IMPC models are loaded."""
self.pipeline.clearmodels()
impc = Phenoscoring(IMPCTestConfig())
impc.update()
if __name__ == "__main__":
config = parser.parse_args()
pipeline = Phenoscoring(config)
if config.action == "build":
# create a new sqlite database with references
pipeline.build()
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