def test_operations_errors(self):
gs = Geneset(MagicMock(),
genes=["FHIT"],
source="UCSC",
species="H**o sapiens")
gs_source_err = Geneset(
MagicMock(),
genes=["BRCA2"],
source="Wrong source",
species="H**o sapiens",
)
message = "Cannot compare Genesets with different sources"
with self.assertRaisesRegex(ValueError, message):
gs | gs_source_err
gs_species_err = Geneset(
MagicMock(),
genes=["BRCA2"],
source="UCSC",
species="Wrong species",
)
message = "Cannot compare Genesets with different species"
with self.assertRaisesRegex(ValueError, message):
gs | gs_species_err
not_implemented = gs.__or__({"BRCA2"})
self.assertEqual(not_implemented, NotImplemented)
def test_create(self, geneset_mock):
collection_mock = MagicMock(id=1)
geneset_mock.configure_mock(
id=None,
name="Test name",
collection=collection_mock,
genes=["FHIT", "MYC"],
source="UCSC",
species="H**o sapiens",
)
geneset_mock.api = MagicMock(
**{"post.return_value": {
"id": 1,
"slug": "test"
}})
Geneset.save(geneset_mock)
geneset_mock.api.post.assert_called_once_with({
"process": {
"slug": "create-geneset"
},
"input": {
"genes": ["FHIT", "MYC"],
"source": "UCSC",
"species": "H**o sapiens",
},
"name": "Test name",
"collection": {
"id": collection_mock
},
})
def test_update_fields(self, geneset_mock):
geneset_mock.configure_mock(id=1,
slug="test",
_original_values={"slug": "test-old"})
geneset_mock.WRITABLE_FIELDS = ("slug", )
geneset_mock.api = MagicMock(
**{"patch.return_value": {
"id": 1,
"slug": "test"
}})
Geneset.save(geneset_mock)
self.assertEqual(geneset_mock._update_fields.call_count, 1)
def test_dont_override_genes(self):
gs = Geneset(MagicMock(),
genes=["FHIT", "MYC"],
source="UCSC",
species="H**o sapiens")
gs2 = Geneset(
MagicMock(),
genes=["BRCA2", "MYC", "ABC"],
source="UCSC",
species="H**o sapiens",
)
gs | gs2
# the original genesets should not change when performing set operations on them
self.assertCountEqual(gs.genes, ["FHIT", "MYC"])
self.assertCountEqual(gs2.genes, ["BRCA2", "MYC", "ABC"])
def test_arguments(self):
gs = Geneset(MagicMock(),
genes=["FHIT", "MYC"],
source="UCSC",
species="H**o sapiens")
# test all geneset attributes
self.assertCountEqual(gs.genes, ["FHIT", "MYC"])
self.assertEqual(len(gs._genes), 2)
self.assertEqual(gs.source, "UCSC")
self.assertEqual(gs.species, "H**o sapiens")
def test_fetch_data(self):
gs = Geneset(
MagicMock(),
output={
"geneset_json": 1,
"source": "UCSC",
"species": "H**o sapiens"
},
id=1,
)
response = MagicMock()
response.content = '{"json": {"genes": ["FHIT", "MYC"]}}'.encode(
"utf-8")
gs.resolwe = MagicMock(**{
"session.get.return_value": response,
"url": ""
})
# test all geneset attributes
self.assertCountEqual(gs.genes, ["FHIT", "MYC"])
self.assertEqual(gs.source, "UCSC")
self.assertEqual(gs.species, "H**o sapiens")
def test_setters(self):
gs = Geneset(MagicMock())
gs.genes = ["FHIT"]
self.assertCountEqual(gs.genes, ["FHIT"])
gs.species = "Test species"
self.assertEqual(gs.species, "Test species")
gs.source = "Test source"
self.assertEqual(gs.source, "Test source")
# saved geneset should not allow to change genes/species/source values
gs_saved = Geneset(MagicMock(), id=1)
message = "Not allowed to change field source after geneset is saved"
with self.assertRaisesRegex(ValueError, message):
gs_saved.source = "Test source"
def test_set_operations(self):
gs = Geneset(MagicMock(),
genes=["FHIT", "MYC"],
source="UCSC",
species="H**o sapiens")
gs2 = Geneset(
MagicMock(),
genes=["BRCA2", "MYC", "ABC"],
source="UCSC",
species="H**o sapiens",
)
gs_union = gs | gs2
gs_intersection = gs & gs2
gs_difference = gs - gs2
gs_rsub = gs.__rsub__(gs2)
gs_symmetric_difference = gs ^ gs2
# test set operations
self.assertCountEqual(gs_union.genes, ["FHIT", "MYC", "BRCA2", "ABC"])
self.assertCountEqual(gs_intersection.genes, ["MYC"])
self.assertCountEqual(gs_difference.genes, ["FHIT"])
self.assertCountEqual(gs_rsub.genes, ["BRCA2", "ABC"])
self.assertCountEqual(gs_symmetric_difference.genes,
["FHIT", "BRCA2", "ABC"])
def test_empty_set(self):
# test creating empty geneset
gs = Geneset(MagicMock(), genes=[])
self.assertCountEqual(gs.genes, [])
def test_create_errors(self):
gs = Geneset(MagicMock(), genes=["FHIT"], source="UCSC")
message = "Fields species must not be none"
with self.assertRaisesRegex(ValueError, message):
gs.save()