def test_get_name_type(self):
"""should return the (latin|common) name given a latin, common or ensembl
db prefix names"""
self.assertEqual(Species.get_species_name("human"), "H**o sapiens")
self.assertEqual(Species.get_species_name("homo_sapiens"),
"H**o sapiens")
self.assertEqual(Species.get_common_name("Mus musculus"), "Mouse")
self.assertEqual(Species.get_common_name("mus_musculus"), "Mouse")
def test_amend_existing(self):
"""should correctly amend an existing species"""
species_name = "Ochotona princeps"
common_name1 = "american pika"
common_name2 = "pika"
ensembl_pref = "ochotona_princeps"
Species.amend_species(species_name, common_name1)
self.assertEqual(Species.get_common_name(species_name), common_name1)
Species.amend_species(species_name, common_name2)
self.assertEqual(Species.get_species_name(common_name2), species_name)
self.assertEqual(Species.get_species_name(ensembl_pref), species_name)
self.assertEqual(Species.get_common_name(species_name), common_name2)
self.assertEqual(Species.get_common_name(ensembl_pref), common_name2)
self.assertEqual(Species.get_ensembl_db_prefix(species_name), ensembl_pref)
self.assertEqual(Species.get_ensembl_db_prefix(common_name2), ensembl_pref)
def test_add_new_species(self):
"""should correctly add a new species/common combination and infer the
correct ensembl prefix"""
species_name, common_name = "Otolemur garnettii", "Bushbaby"
Species.amend_species(species_name, common_name)
self.assertEqual(Species.get_species_name(species_name), species_name)
self.assertEqual(Species.get_species_name("Bushbaby"), species_name)
self.assertEqual(Species.get_species_name(common_name), species_name)
self.assertEqual(Species.get_common_name(species_name), common_name)
self.assertEqual(Species.get_common_name("Bushbaby"), common_name)
self.assertEqual(Species.get_ensembl_db_prefix("Bushbaby"),
"otolemur_garnettii")
self.assertEqual(Species.get_ensembl_db_prefix(species_name),
"otolemur_garnettii")
self.assertEqual(Species.get_ensembl_db_prefix(common_name),
"otolemur_garnettii")
def test_synonyms_work(self):
"""species with synonyms should allow correct lookups"""
self.assertEqual(Species.get_species_name("Canis lupus familiaris"),
"Canis familiaris")
self.assertEqual(Species.get_common_name("Canis lupus familiaris"),
"Dog")
self.assertEqual(
Species.get_ensembl_db_prefix("Canis lupus familiaris"),
"canis_familiaris")
self.assertEqual(Species.get_compara_name("Canis lupus familiaris"),
"Dog")