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 test_dataset_check(self, mock_request):
ds = pyrefinebio.Dataset(id="test-dataset")
is_done = ds.check()
self.assertTrue(is_done)
self.assertTrue(ds.is_processing)
self.assertTrue(ds.is_processed)
def test_dataset_skip_quantile_normalization(self, mock_post_by_endpoint):
"""
Test skipping quantile normalization
Test the corner case brought up by Steven where we set
quantile_normalize False. We used to check if quantile_normalize was
truthy before adding it to the request, which caused it to always be
true.
"""
pyrefinebio.Dataset(
data={
"GSE68833": ["ALL"]
},
aggregate_by="EXPERIMENT",
email_address="*****@*****.**",
quantile_normalize=False,
).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("quantile_normalize", None),
False)
def test_dataset_extract(self, mock_unpack):
ds = pyrefinebio.Dataset()
ds._downloaded_path = "foo"
ds.extract()
mock_unpack.assert_called_with("foo")
def test_dataset_process(self, mock_request):
ds = pyrefinebio.Dataset(
data={"test-experiment": ["sample-1", "sample-2"]},
email_address="test-email")
ds.process()
self.assertTrue(ds.start)
self.assertTrue(ds.is_processing)
def test_dataset_download_no_url(self, mock_request):
ds = pyrefinebio.Dataset(id="non-processed-dataset", download_url=None)
with self.assertRaises(pyrefinebio.exceptions.DownloadError) as de:
ds.download("test")
self.assertEqual(
str(de.exception),
"Unable to download Dataset\nDownload url not found - you must process the Dataset before downloading.",
)
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_process_bad_token(self):
pyrefinebio.config.Config().token = "this-is-a-bad-token"
data = {}
exs = pyrefinebio.Experiment.search(num_downloadable_samples=1)
ex = next(exs)
data[ex.accession_code] = ["ALL"]
ds = pyrefinebio.Dataset(data=data)
with self.assertRaises(pyrefinebio.exceptions.BadRequest) as br:
ds.process()
self.assertEqual(
br.exception.base_message,
"Bad Request: You must provide an active API token ID")
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_dataset_process_no_email(self):
try:
token = pyrefinebio.Token(
id="42240c84-b3d9-4f41-8001-6f40abce9d7d")
token.agree_to_terms_and_conditions()
except pyrefinebio.exceptions.NotFound:
token = pyrefinebio.Token()
token.agree_to_terms_and_conditions()
data = {}
exs = pyrefinebio.Experiment.search(num_downloadable_samples=1)
ex = next(exs)
data[ex.accession_code] = ["ALL"]
ds = pyrefinebio.Dataset(data=data)
with self.assertRaises(pyrefinebio.exceptions.BadRequest) as br:
ds.process()
self.assertEqual(br.exception.base_message,
"Bad Request: You must provide an email address.")
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 test_add_samples(self):
dataset = pyrefinebio.Dataset()
dataset.add_samples("test-experiment-1")
experiment2 = pyrefinebio.Experiment(
accession_code="test-experiment-2")
dataset.add_samples(experiment2)
sample1 = pyrefinebio.Sample(accession_code="sample1")
sample2 = pyrefinebio.Sample(accession_code="sample2")
dataset.add_samples("test-experiment-3",
samples=[sample1, sample2, "sample3"])
self.assertDictEqual(
dataset.data,
{
"test-experiment-1": ["ALL"],
"test-experiment-2": ["ALL"],
"test-experiment-3": ["sample1", "sample2", "sample3"],
},
)
def test_dataset_save_bad_data(self):
with self.assertRaises(pyrefinebio.exceptions.InvalidData):
pyrefinebio.Dataset(data={"lol": ["not-good"]}).save()