def test_bad_location(self):
with self.assertRaisesRegex(ValueError, "end must be greater"):
structures.ProtoclusterAnnotation(10, 5, "product", dummy_tool(),
{})
with self.assertRaisesRegex(ValueError, "absolute distance"):
structures.ProtoclusterAnnotation(5,
10,
"product",
dummy_tool(), {},
neighbourhood_left=-1)
with self.assertRaisesRegex(ValueError, "absolute distance"):
structures.ProtoclusterAnnotation(5,
10,
"product",
dummy_tool(), {},
neighbourhood_right=-1)
with self.assertRaisesRegex(ValueError,
"cannot extend out of a record"):
structures.ProtoclusterAnnotation(5,
10,
"product",
dummy_tool(), {},
neighbourhood_left=7)
def test_equality(self):
first = structures.ProtoclusterAnnotation(5, 50, "product",
dummy_tool(),
{"a": ["first"]})
second = structures.ProtoclusterAnnotation(5, 50, "product",
dummy_tool(),
{"a": ["first"]})
assert first == second
assert first != second.details
second.details["a"][0] = "irst"
assert first != second
def test_attributes(self):
cluster = structures.ProtoclusterAnnotation(25,
50,
"product",
dummy_tool(), {
"a": ["first"],
"b": ["second"]
},
neighbourhood_left=10,
neighbourhood_right=5)
assert cluster.start == 15
cluster.neighbourhood_left += 3
assert cluster.start == 12
assert cluster.end == 55
cluster.neighbourhood_right += 3
assert cluster.end == 58
assert len(cluster) == cluster.end - cluster.start
assert cluster.label == cluster.product == "product"
cluster.product = "something else"
assert cluster.label == cluster.product == "something else"
assert isinstance(cluster.tool, structures.Tool)
assert cluster.tool.name == dummy_tool().name
def test_areas(self):
assert self.results.get_areas() == [self.sub, self.cluster]
self.sub.start = 6
assert self.results.get_areas() == [self.cluster, self.sub]
extra = structures.ProtoclusterAnnotation(2, 50, "product",
dummy_tool(), {})
self.results.protoclusters.append(extra)
assert self.results.get_areas() == [extra, self.cluster, self.sub]
def setUp(self):
self.sub = structures.SubRegionAnnotation(5, 50, "label", dummy_tool(),
{
"a": ["first"],
"b": ["and", "second"]
})
self.cluster = structures.ProtoclusterAnnotation(
5, 40, "product", dummy_tool(), {"a": ["first"]})
self.results = structures.SideloadedResults("rec_name", [self.sub],
[self.cluster])
def test_secmet_conversion(self):
source = structures.ProtoclusterAnnotation(25,
50,
"product",
dummy_tool(), {
"a": ["first"],
"b": ["second"]
},
neighbourhood_left=10,
neighbourhood_right=5)
dest = source.to_secmet()
assert isinstance(dest, SideloadedProtocluster)
assert dest.product == "product"
assert dest.tool == source.tool.name
assert dest.core_location.start == 25
assert dest.core_location.end == 50
assert dest.location.start == 15
assert dest.location.end == 55
assert dest.neighbourhood_range == 10
def test_json_conversion(self):
cluster = structures.ProtoclusterAnnotation(5, 50, "product",
dummy_tool(), {
"a": ["first"],
"b": ["and", "second"]
})
as_json = json.loads(json.dumps(
cluster.to_json())) # string conversion to match real use
regenerated = structures.ProtoclusterAnnotation.from_json(as_json)
assert cluster == regenerated
as_json["details"] = {"a": "first", "b": ["and", "second"]}
regenerated = structures.ProtoclusterAnnotation.from_json(as_json)
assert regenerated.details["a"] == [
"first"
] # single strings should be listified
as_json.pop("tool")
regenerated = structures.ProtoclusterAnnotation.from_schema_json(
as_json, dummy_tool())
assert cluster == regenerated