def test_get_resource_collection(self):
collection = Collection(id=1, resolwe=MagicMock())
collection.id = 1 # this is overriden when initialized
self.assertEqual(get_resource_collection(collection), 1)
relation = Relation(id=1, resolwe=MagicMock())
relation._hydrated_collection = Collection(id=2, resolwe=MagicMock())
relation._hydrated_collection.id = 2 # this is overriden when initialized
self.assertEqual(get_resource_collection(relation), 2)
data = Data(id=1, resolwe=MagicMock())
data._collections = [Collection(id=3, resolwe=MagicMock())]
data._collections[0].id = 3 # this is overriden when initialized
self.assertEqual(get_resource_collection(data), 3)
sample = Sample(id=1, resolwe=MagicMock())
sample._collections = [Collection(id=4, resolwe=MagicMock())]
sample._collections[0].id = 4 # this is overriden when initialized
self.assertEqual(get_resource_collection(sample), 4)
sample = Sample(id=1, resolwe=MagicMock())
sample._collections = [
Collection(id=5, resolwe=MagicMock()),
Collection(id=6, resolwe=MagicMock())
]
sample._collections[0].id = 5 # this is overriden when initialized
sample._collections[1].id = 6 # this is overriden when initialized
self.assertEqual(get_resource_collection(sample), None)
with self.assertRaises(LookupError):
get_resource_collection(sample, fail_silently=False)
def test_get_resource_collection(self):
collection = Collection(id=1, resolwe=MagicMock())
collection.id = 1 # this is overriden when initialized
self.assertEqual(get_resource_collection(collection), 1)
relation = Relation(id=1, resolwe=MagicMock())
relation._hydrated_collection = Collection(id=2, resolwe=MagicMock())
relation._hydrated_collection.id = 2 # this is overriden when initialized
self.assertEqual(get_resource_collection(relation), 2)
data = Data(id=1, resolwe=MagicMock())
data._collections = [Collection(id=3, resolwe=MagicMock())]
data._collections[0].id = 3 # this is overriden when initialized
self.assertEqual(get_resource_collection(data), 3)
sample = Sample(id=1, resolwe=MagicMock())
sample._collections = [Collection(id=4, resolwe=MagicMock())]
sample._collections[0].id = 4 # this is overriden when initialized
self.assertEqual(get_resource_collection(sample), 4)
sample = Sample(id=1, resolwe=MagicMock())
sample._collections = [
Collection(id=5, resolwe=MagicMock()),
Collection(id=6, resolwe=MagicMock())
]
sample._collections[0].id = 5 # this is overriden when initialized
sample._collections[1].id = 6 # this is overriden when initialized
self.assertEqual(get_resource_collection(sample), None)
with self.assertRaises(LookupError):
get_resource_collection(sample, fail_silently=False)
def test_dehydrate_data(self, resolwe_mock):
data_obj = Data(id=1, resolwe=MagicMock())
data_obj.id = 1 # this is overriden when initialized
process = self.process_mock
result = Resolwe._process_inputs(resolwe_mock, {"genome": data_obj}, process)
self.assertEqual(result, {'genome': 1})
result = Resolwe._process_inputs(resolwe_mock, {"reads": [data_obj]}, process)
self.assertEqual(result, {'reads': [1]})
def test_dehydrate_data(self, resolwe_mock):
data_obj = Data(id=1, resolwe=MagicMock())
data_obj.id = 1 # this is overriden when initialized
process = self.process_json[0]
result = Resolwe._process_inputs(resolwe_mock, {"genome": data_obj}, process)
self.assertEqual(result, {'genome': 1})
result = Resolwe._process_inputs(resolwe_mock, {"reads": [data_obj]}, process)
self.assertEqual(result, {'reads': [1]})
def test_dehydrate_data(self, resolwe_mock, copy_mock):
data_obj = Data(id=1, resolwe=MagicMock())
data_obj.id = 1 # this is overriden when initialized
process = self.process_mock
# I appears it is not possible to deepcopy MagicMocks so we just patch
# the deepcopy functionality:
copy_mock.deepcopy = MagicMock(return_value={"genome": data_obj})
result = Resolwe._process_inputs(resolwe_mock, {"genome": data_obj}, process)
self.assertEqual(result, {'genome': 1})
# I appears it is not possible to deepcopy MagicMocks so we just patch
# the deepcopy functionality:
copy_mock.deepcopy = MagicMock(return_value={"reads": data_obj})
result = Resolwe._process_inputs(resolwe_mock, {"reads": [data_obj]}, process)
self.assertEqual(result, {'reads': [1]})
def test_dehydrate_data(self, resolwe_mock, copy_mock):
data_obj = Data(id=1, resolwe=MagicMock())
data_obj.id = 1 # this is overriden when initialized
process = self.process_mock
# I appears it is not possible to deepcopy MagicMocks so we just patch
# the deepcopy functionality:
copy_mock.deepcopy = MagicMock(return_value={"genome": data_obj})
result = Resolwe._process_inputs(resolwe_mock, {"genome": data_obj},
process)
self.assertEqual(result, {'genome': 1})
# I appears it is not possible to deepcopy MagicMocks so we just patch
# the deepcopy functionality:
copy_mock.deepcopy = MagicMock(return_value={"reads": data_obj})
result = Resolwe._process_inputs(resolwe_mock, {"reads": [data_obj]},
process)
self.assertEqual(result, {'reads': [1]})
def _get_data_uri(self, data: Data, data_type: str) -> str:
field_name = self.data_type_to_field_name[data_type]
files = data.files(field_name=field_name)
if not files:
raise LookupError(
f"Data {data.slug} has no files named {field_name}!")
elif len(files) > 1:
raise LookupError(
f"Data {data.slug} has multiple files named {field_name}!")
return f"{data.id}/{files[0]}"
def test_get_samples(self):
collection = Collection(id=1, resolwe=MagicMock())
collection._samples = ['sample_1', 'sample_2']
self.assertEqual(get_samples(collection), ['sample_1', 'sample_2'])
collection_1 = Collection(id=1, resolwe=MagicMock())
collection_1._samples = ['sample_1']
collection_2 = Collection(id=2, resolwe=MagicMock())
collection_2._samples = ['sample_2']
self.assertEqual(get_samples([collection_1, collection_2]), ['sample_1', 'sample_2'])
data = Data(id=1, resolwe=MagicMock())
data.api(data.id).get = MagicMock(return_value={'entities': [7]})
data.resolwe.sample.get = MagicMock(return_value='sample_1')
self.assertEqual(get_samples(data), ['sample_1'])
data1 = Data(id=1, resolwe=MagicMock())
data1.api(data.id).get = MagicMock(return_value={'entities': [7]})
data1.resolwe.sample.get = MagicMock(return_value='sample1')
data2 = Data(id=2, resolwe=MagicMock())
data2.api(data.id).get = MagicMock(return_value={'entities': [8]})
data2.resolwe.sample.get = MagicMock(return_value='sample2')
self.assertEqual(get_samples([data1, data2]), ['sample1', 'sample2'])
data = Data(id=1, resolwe=MagicMock(**{'sample.get.return_value': None}))
data._sample = None
with self.assertRaises(TypeError):
get_samples(data)
sample = Sample(id=1, resolwe=MagicMock())
self.assertEqual(get_samples(sample), [sample])
sample_1 = Sample(id=1, resolwe=MagicMock())
sample_2 = Sample(id=3, resolwe=MagicMock())
self.assertEqual(get_samples([sample_1, sample_2]), [sample_1, sample_2])
def test_get_data_id(self):
data = Data(id=1, resolwe=MagicMock())
data.id = 1 # this is overriden when initialized
self.assertEqual(get_data_id(data), 1)
self.assertEqual(get_data_id(2), 2)
def test_get_samples(self):
collection = Collection(id=1, resolwe=MagicMock())
collection._samples = ['sample_1', 'sample_2']
self.assertEqual(get_samples(collection), ['sample_1', 'sample_2'])
collection_1 = Collection(id=1, resolwe=MagicMock())
collection_1._samples = ['sample_1']
collection_2 = Collection(id=2, resolwe=MagicMock())
collection_2._samples = ['sample_2']
self.assertEqual(get_samples([collection_1, collection_2]),
['sample_1', 'sample_2'])
data = Data(id=1, resolwe=MagicMock())
data._sample = 'sample_1'
self.assertEqual(get_samples(data), ['sample_1'])
data1 = Data(id=1, resolwe=MagicMock())
data1._sample = 'sample1'
data2 = Data(id=2, resolwe=MagicMock())
data2._sample = 'sample2'
self.assertEqual(get_samples([data1, data2]), ['sample1', 'sample2'])
data = Data(id=1,
resolwe=MagicMock(**{'sample.filter.return_value': None}))
data._sample = None
with self.assertRaises(TypeError):
get_samples(data)
sample = Sample(id=1, resolwe=MagicMock())
self.assertEqual(get_samples(sample), [sample])
sample_1 = Sample(id=1, resolwe=MagicMock())
sample_2 = Sample(id=3, resolwe=MagicMock())
self.assertEqual(get_samples([sample_1, sample_2]),
[sample_1, sample_2])
def test_get_data_id(self):
data = Data(id=1, resolwe=MagicMock())
data.id = 1 # this is overriden when initialized
self.assertEqual(get_data_id(data), 1)
self.assertEqual(get_data_id(2), 2)
def test_get_samples(self):
collection = Collection(id=1, resolwe=MagicMock())
collection._samples = ['sample_1', 'sample_2']
self.assertEqual(get_samples(collection), ['sample_1', 'sample_2'])
collection_1 = Collection(id=1, resolwe=MagicMock())
collection_1._samples = ['sample_1']
collection_2 = Collection(id=2, resolwe=MagicMock())
collection_2._samples = ['sample_2']
self.assertEqual(get_samples([collection_1, collection_2]),
['sample_1', 'sample_2'])
data = Data(id=1, resolwe=MagicMock())
data.api(data.id).get = MagicMock(return_value={'entities': [7]})
data.resolwe.sample.get = MagicMock(return_value='sample_1')
self.assertEqual(get_samples(data), ['sample_1'])
data1 = Data(id=1, resolwe=MagicMock())
data1.api(data.id).get = MagicMock(return_value={'entities': [7]})
data1.resolwe.sample.get = MagicMock(return_value='sample1')
data2 = Data(id=2, resolwe=MagicMock())
data2.api(data.id).get = MagicMock(return_value={'entities': [8]})
data2.resolwe.sample.get = MagicMock(return_value='sample2')
self.assertEqual(get_samples([data1, data2]), ['sample1', 'sample2'])
data = Data(id=1,
resolwe=MagicMock(**{'sample.get.return_value': None}))
data._sample = None
with self.assertRaises(TypeError):
get_samples(data)
sample = Sample(id=1, resolwe=MagicMock())
self.assertEqual(get_samples(sample), [sample])
sample_1 = Sample(id=1, resolwe=MagicMock())
sample_2 = Sample(id=3, resolwe=MagicMock())
self.assertEqual(get_samples([sample_1, sample_2]),
[sample_1, sample_2])