class ZFINTestCase(SourceTestCase):
def setUp(self):
self.source = ZFIN('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
@unittest.skip(
'Will eventually write test to check if phenotype sextuples' +
'are mapped to ZP ids')
def test_allZPAvailable(self):
"""
This test will identify if there are
any missing ZP terms in the mapping file
:return:
"""
# TODO add this test to check if all phenotype sextuples
# are mapped to ZP ids
return
class ZFINTestCase(SourceTestCase):
def setUp(self):
self.source = ZFIN('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
return
def tearDown(self):
self.source = None
return
@unittest.skip(
'Will eventually write test to check if phenotype sextuples' +
'are mapped to ZP ids')
def test_allZPAvailable(self):
"""
This test will identify if there are
any missing ZP terms in the mapping file
:return:
"""
# TODO add this test to check if all phenotype sextuples
# are mapped to ZP ids
return
class ZFINTestCase(SourceTestCase):
def setUp(self):
self.source = ZFIN('rdf_graph', True)
self.source.settestonly(True)
self._setDirToSource()
def tearDown(self):
self.source = None
def test_mapping_of_phenotypes_to_zp_ids(self):
"""
test that code correctly uses zp_map to map phenotypes to zp ids
:return:
"""
mapping_file = "./tests/resources/zfin/zp-mapping-test-map.txt"
pheno_file = "./tests/resources/zfin/zp-mapping-test-phenotype.txt"
self.source.zp_map = self.source._load_zp_mappings(mapping_file)
pheno_dat = open(pheno_file).read().split('\t')
(fish_num, fish_name, start_stage_id, start_stage_name, end_stage_id,
end_stage_name, subterm1_id, subterm1_name, postcomp1_rel_id,
postcomp1_rel_name, superterm1_id, superterm1_name, quality_id,
quality_name, modifier, subterm2_id, subterm2_name, postcomp2_rel_id,
postcomp2_rel_name, superterm2_id, superterm2_name, pub_id, env_id) = \
pheno_dat
self.assertEqual(
self.source._map_octuple_to_phenotype(
subterm1_id, postcomp1_rel_id, superterm1_id, quality_id,
subterm2_id, postcomp2_rel_id, superterm2_id, "abnormal"),
'ZP:0022140')
def test_load_zp_mappings(self):
"""
test correct loading of zp mappings file and construction of zp_map
"""
if self.source is not None:
try:
zp_map = self.source._load_zp_mappings(
"./tests/resources/zfin/zp-mapping-test.txt")
self.assertIsInstance(
zp_map, dict, "_load_zp_mappings() didn't return dict!")
self.assertTrue(
len(zp_map) == 1,
"_load_zp_mappings() didn't return exactly one thing!")
self.assertDictEqual(
zp_map, {
'MONARCH:b308a8f1c67793a56d16': {
'post_composed_relationship_id_1': 'BFO:0000050',
'post_composed_relationship_id_2': 'BFO:0000050',
'quality_id': 'PATO:0001453',
'subterm1_id': 'ZFA:0009114',
'subterm2_id': 'GO:0005927',
'superterm1_id': 'ZFA:0001056',
'superterm2_id': 'ZFA:0001056',
'zp_id': 'ZP:0002959',
'modifier': 'PATO:0000460'
}
},
"_load_zp_mappings() " + "didn't return what I expected!")
except Exception as t_except:
LOGGER.error(t_except)
def test_make_zpkey(self):
"""
test that _make_zpkey returns correct id
"""
if self.source is not None:
try:
dummy_args = list(map(str, list(range(1,
9)))) # 1 - 8 as strings
expected_key = self.source.make_id("_".join(dummy_args))
self.assertEqual(self.source._make_zpkey(*dummy_args),
expected_key)
self.assertEqual(
self.source._make_zpkey(['0'] * 8),
self.source._make_zpkey([''] * 8),
"_make_zpkey() doesn't seem to be replacing empty " +
"strings with zeros before making key," +
"this might cause zp_map lookup issues")
except Exception as t_except:
LOGGER.error(t_except)
def test_genotype_labels(self):
"""
test that genotype label is set correctly after parse()
"""
if self.source is not None:
test_resource_dir = "../../tests/resources/zfin/"
self.source.files['fish_components']['file'] = test_resource_dir + \
"genotype-label-test-fish_components_fish.txt"
self.source.files['backgrounds']['file'] = test_resource_dir + \
"genotype-label-test-genotype_backgrounds.txt"
self.source.files['geno']['file'] = test_resource_dir + \
"genotype-label-test-genotype_features.txt"
self.source.parse()
this_iri = URIRef("http://zfin.org/ZDB-GENO-070228-3")
expect_genotype_label = "shha<sup>tbx392/tbx392</sup> (AB)"
self.assertEqual(str(self.source.testgraph.label(this_iri, None)),
expect_genotype_label)
