def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/test/" and not kwargs:
return MockResponse(page1, url)
if url == "https://api.refine.bio/v1/test/" and kwargs["params"] == {"offset": 2, "limit": 2}:
return MockResponse(page2, url)
if url == "https://api.refine.bio/v1/processors/" and kwargs["params"] == {"limit": 10}:
return MockResponse(
{
"count": 20,
"next": "foo",
"previous": None,
"results": [processor(i) for i in range(10)],
},
url,
)
if url == "https://api.refine.bio/v1/processors/" and kwargs["params"] == {
"offset": 10,
"limit": 10,
}:
return MockResponse(
{
"count": 20,
"next": "foo",
"previous": None,
"results": [processor(i) for i in range(10, 20)],
},
url,
)
def mocked_success_requests(*args, **kwargs):
if args[0] == 'https://pi-test.sagepay.com/api/v1/merchant-session-keys':
return MockResponse({
'merchantSessionKey': 'unique-key',
'expiry': '2015-08-11T11:45:16.285+01:00'
}, 201)
else:
return MockResponse({}, 201)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/token/":
return MockResponse(token, url)
if url == "https://api.refine.bio/v1/token/123456789/":
return MockResponse(token, url)
if url == "https://api.refine.bio/v1/token/test/":
return MockResponse(token2, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/samples/SRR5445147/":
return MockResponse(sample_1, url)
if url == "https://api.refine.bio/v1/samples/GSM1562009/":
return MockResponse(sample_2, url)
# this request needs to exist because the result's organism index is None for both test samples
# so a request will be made to make sure that that value should actually be None
if url == "https://api.refine.bio/v1/computational_results/1339595/":
return MockResponse(result, url)
if url == "https://api.refine.bio/v1/samples/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/samples/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/samples/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
if url == "https://api.refine.bio/v1/search/":
return MockResponse(e_search_1, "e_search_2")
if url == "e_search_2":
return MockResponse(e_search_2, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/qn_targets/MUSTELA_PUTORIUS_FURO/":
return MockResponse(qn_target, url)
if url == "https://api.refine.bio/v1/qn_targets/HUMAN/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/qn_targets/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/qn_targets/":
return MockResponse(qn_target_organisms, url)
def test_download_compendium_extract(self, mock_get, mock_download,
mock_unpack):
mock_get.return_value = MockResponse(
{
"count":
1,
"next":
None,
"previous":
None,
"results": [{
"id": 123,
"computed_file": {
"download_url": "test_url"
}
}],
},
"url",
)
pyrefinebio.download_compendium("./", "test_organism", extract=True)
expected_path = os.path.abspath("compendium-123.zip")
mock_download.assert_called_with("test_url", expected_path, True)
mock_unpack.assert_called_with(expected_path)
def test_download_compendium(self, mock_get, mock_download):
mock_get.return_value = MockResponse(
{
"count": 1,
"next": None,
"previous": None,
"results": [{
"computed_file": {
"download_url": "test_url"
}
}],
},
"url",
)
pyrefinebio.download_compendium("test", "test_organism")
mock_get.assert_called_with(
"compendia",
params={
"primary_organism__name": "test_organism",
"quant_sf_only": False,
"latest_version": True,
},
)
mock_download.assert_called_with("test_url", os.path.abspath("test"),
True)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/transcriptome_indices/1/":
return MockResponse(index_1, url)
if url == "https://api.refine.bio/v1/transcriptome_indices/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/transcriptome_indices/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/transcriptome_indices/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/processors/1/":
return MockResponse(processor_1, url)
if url == "https://api.refine.bio/v1/processors/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/processors/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/processors/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def test_download_dataset_notify_me(self, mock_post, mock_get,
mock_download):
mr = MockResponse(
{
"id": "test_dataset",
"is_processed": True,
"download_url": "test_url"
}, "url")
mock_get.return_value = mr
mock_post.return_value = mr
dataset_dict = {"test": ["foo", "bar"]}
pyrefinebio.download_dataset("test",
"*****@*****.**",
dataset_dict=dataset_dict,
notify_me=True)
mock_post.assert_called_with(
"dataset",
payload={
"data": dataset_dict,
"aggregate_by": "EXPERIMENT",
"email_address": "*****@*****.**",
"start": True,
"quantile_normalize": True,
"quant_sf_only": False,
"notify_me": True,
},
)
mock_download.assert_called_with("test_url", os.path.abspath("test"),
True)
def test_dataset_notify_me(self, mock_put_by_endpoint,
mock_post_by_endpoint):
"""
Test requesting to be notified
"""
mock_post_by_endpoint.return_value = MockResponse(dataset, "")
# First test that notify_me is false by default
ds = pyrefinebio.Dataset(
data={"GSE68833": ["ALL"]},
aggregate_by="EXPERIMENT",
email_address="*****@*****.**",
)
ds.save()
self.assertEqual(mock_post_by_endpoint.call_count, 1)
# We need to use assertEqual here because None is False-y
args, kwargs = mock_post_by_endpoint.call_args
self.assertEqual(kwargs["payload"].get("notify_me", None), False)
self.assertIsNotNone(ds.id)
# Now set notify_me true
ds.notify_me = True
ds.save()
self.assertEqual(mock_put_by_endpoint.call_count, 1)
args, kwargs = mock_put_by_endpoint.call_args
self.assertTrue(kwargs["payload"].get("notify_me", None))
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/organisms/GORILLA/":
return MockResponse(gorilla, url)
if url == "https://api.refine.bio/v1/organisms/HUMAN/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/organisms/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/organisms/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/experiments/SRP150473/":
return MockResponse(experiment, url)
if url == "https://api.refine.bio/v1/experiments/bad-accession-code/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/experiments/force-500-error/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/search/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def test_host_and_ip(self, mock_get: MagicMock):
mock_get.return_value = MockResponse({'data': [
{
'ip': '192.168.99.99',
'machine_type': 'unknown',
'name': 'something'
}
]}, 200)
haip = self.host.get_host_and_ip(name='pi-garage')
print(haip)
def test_download_compendium_no_token(self, mock_compendia_get,
mock_computed_file_get):
mock_compendia_get.return_value = MockResponse(
{
"count": 1,
"next": None,
"previous": None,
"results": [{
"computed_file": {
"download_url": None
}
}],
},
"url",
)
mock_computed_file_get.return_value = MockResponse(
{"download_url": None}, "url")
with self.assertRaises(pyrefinebio.exceptions.DownloadError):
pyrefinebio.download_compendium("test", "test_organism")
def test_iteration(self, mock_request):
T = pyrefinebio.Processor
response = MockResponse(page1, "https://api.refine.bio/v1/test/")
paginatedList = pyrefinebio.util.create_paginated_list(T, response)
actual = [item0, item1, item2, item3]
i = 0
for processor in paginatedList:
self.assertObject(processor, actual[i])
i += 1
def test_dataset_save(self, mock_put, mock_post):
mock_post.return_value = MockResponse(dataset, "")
mock_put.return_value = MockResponse(dataset, "")
ds = pyrefinebio.Dataset(
data={"test-experiment": ["sample-1", "sample-2"]},
email_address="test-email")
ds = ds.save()
mock_post.assert_called_with(
"dataset",
payload={
"data": {
"test-experiment": ["sample-1", "sample-2"]
},
"email_address": "test-email",
"notify_me": False,
},
)
ds.email_address = "changed-email"
ds.save()
mock_put.assert_called_with(
"dataset/test-dataset",
payload={
"data": {
"test-experiment": ["sample-1", "sample-2"]
},
"aggregate_by": "EXPERIMENT",
"scale_by": "NONE",
"email_address": "changed-email",
"quantile_normalize": True,
"quant_sf_only": False,
"svd_algorithm": "NONE",
# We want email notifications to be opt-out
"notify_me": False,
},
)
def mock_request(method, url, data, **kwargs):
if method == "POST":
data = json.loads(data)
ds = {}
for key, value in dataset.items():
if data.get(key):
ds[key] = data.get(key)
else:
ds[key] = value
return MockResponse(ds, url)
if url == "https://api.refine.bio/v1/dataset/test-dataset/":
return MockResponse(dataset, url)
if url == "https://api.refine.bio/v1/dataset/non-processed-dataset/":
return MockResponse(non_processed_dataset, url)
if url == "https://api.refine.bio/v1/dataset/":
return MockResponse(dataset, url)
if url == "https://api.refine.bio/v1/dataset/500/":
return MockResponse(dataset, url, status=500)
def test_dataset_download_no_size_header(self, mock_get, mock_input,
mock_copy):
ds = pyrefinebio.Dataset(download_url="test_download_url")
mr = MockResponse(None, "test_download_url", headers={})
setattr(mr, "raw", "raw")
mock_get.return_value.__enter__.return_value = mr
mock_input.return_value = "n"
ds.download("test_path")
mock_get.assert_called_with("test_download_url", stream=True)
mock_copy.assert_not_called()
def test_dataset_download(self, mock_get, mock_open, mock_copy):
ds = pyrefinebio.Dataset(download_url="test_download_url")
mr = MockResponse(None,
"test_download_url",
headers={"content-length": 3})
setattr(mr, "raw", "raw")
mock_get.return_value.__enter__.return_value = mr
mock_open.return_value.__enter__.return_value = "file"
ds.download("test_path")
mock_get.assert_called_with("test_download_url", stream=True)
mock_open.assert_called_with(os.path.abspath("test_path"), "wb")
mock_copy.assert_called_with("raw", "file")
def test_indexing(self, mock_request):
T = pyrefinebio.Processor
response = MockResponse(page1, "https://api.refine.bio/v1/test/")
paginatedList = pyrefinebio.util.create_paginated_list(T, response)
self.assertObject(paginatedList[0], item0)
self.assertObject(paginatedList[1], item1)
self.assertObject(paginatedList[2], item2)
self.assertObject(paginatedList[3], item3)
self.assertObject(paginatedList[-1], item3)
self.assertObject(paginatedList[-2], item2)
with self.assertRaises(IndexError):
paginatedList[4]
with self.assertRaises(IndexError):
paginatedList[-5]
def test_download_dataset_experiments(self, mock_post, mock_get,
mock_download):
mr = MockResponse(
{
"id": "test_dataset",
"is_processed": True,
"download_url": "test_url"
}, "url")
mock_get.return_value = mr
mock_post.return_value = mr
experiment2 = pyrefinebio.Experiment(
accession_code="test-experiment-2")
pyrefinebio.download_dataset(
"test",
"*****@*****.**",
experiments=["test-experiment-1", experiment2])
mock_post.assert_called_with(
"dataset",
payload={
"data": {
"test-experiment-1": ["ALL"],
"test-experiment-2": ["ALL"]
},
"aggregate_by": "EXPERIMENT",
"email_address": "*****@*****.**",
"start": True,
"quantile_normalize": True,
"quant_sf_only": False,
"notify_me": False,
},
)
mock_download.assert_called_with("test_url", os.path.abspath("test"),
True)
def test_download_dataset_extract(self, mock_post, mock_get, mock_download,
mock_unpack):
mr = MockResponse(
{
"id": "test_dataset",
"is_processed": True,
"download_url": "test_url"
}, "url")
mock_get.return_value = mr
mock_post.return_value = mr
dataset_dict = {"test": ["foo", "bar"]}
pyrefinebio.download_dataset("./",
"*****@*****.**",
dataset_dict=dataset_dict,
extract=True)
expected_path = os.path.abspath("dataset-test_dataset.zip")
mock_download.assert_called_with("test_url", expected_path, True)
mock_unpack.assert_called_with(expected_path)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/original_files/1/":
return MockResponse(og_file_1, url)
if url == "https://api.refine.bio/v1/original_files/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/original_files/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/jobs/processor/29708302/":
return MockResponse(processor_job, url)
if url == "https://api.refine.bio/v1/jobs/downloader/7381811/":
return MockResponse(downloader_job, url)
if url == "https://api.refine.bio/v1/original_files/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/computed_files/1/":
return MockResponse(computed_file_1, url)
if url == "https://api.refine.bio/v1/computed_files/2/":
return MockResponse(computed_file_2, url)
if url == "https://api.refine.bio/v1/computed_files/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/computed_files/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/computed_files/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
if url == "https://api.refine.bio/v1/computational_results/2784485/":
return MockResponse(result, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/compendia/1/":
return MockResponse(compendium_object_1, url)
if url == "https://api.refine.bio/v1/compendia/42/":
return MockResponse(compendium_object_2, url)
if url == "https://api.refine.bio/v1/compendia/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/compendia/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/compendia/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def mock_request(method, url, **kwargs):
if url == "https://api.refine.bio/v1/jobs/downloader/1/":
return MockResponse(job_1, url)
if url == "https://api.refine.bio/v1/jobs/downloader/2/":
return MockResponse(job_2, url)
if url == "https://api.refine.bio/v1/jobs/downloader/0/":
return MockResponse(None, url, status=404)
if url == "https://api.refine.bio/v1/jobs/downloader/500/":
return MockResponse(None, url, status=500)
if url == "https://api.refine.bio/v1/jobs/downloader/":
return MockResponse(search_1, "search_2")
if url == "search_2":
return MockResponse(search_2, url)
def mock_get(*args: Any, **kwargs: Any) -> MockResponse:
return MockResponse(OIDCConfig)
def mock_get(*args: Any, **kwargs: Any) -> MockResponse:
return MockResponse({}, DummyExc)
def mock_get(args: Any, **kwargs: Any) -> MockResponse:
nonlocal call_count
call_count += 1
return MockResponse(OIDCConfig)