def test_download(self):
"""Test that all files in a dataset can be downloaded with one command."""
storage_client = GoogleCloudStorageClient()
dataset_name = "another-dataset"
storage_client.upload_from_string(
string=json.dumps([1, 2, 3]),
cloud_path=storage.path.generate_gs_path(TEST_BUCKET_NAME,
dataset_name,
"file_0.txt"),
)
storage_client.upload_from_string(
string=json.dumps([4, 5, 6]),
cloud_path=storage.path.generate_gs_path(TEST_BUCKET_NAME,
dataset_name,
"file_1.txt"),
)
dataset = Dataset(path=f"gs://{TEST_BUCKET_NAME}/{dataset_name}")
with tempfile.TemporaryDirectory() as temporary_directory:
dataset.download(local_directory=temporary_directory)
with open(os.path.join(temporary_directory, "file_0.txt")) as f:
self.assertEqual(f.read(), "[1, 2, 3]")
with open(os.path.join(temporary_directory, "file_1.txt")) as f:
self.assertEqual(f.read(), "[4, 5, 6]")
def test_download_from_nested_dataset(self):
"""Test that all files in a nested dataset can be downloaded with one command."""
dataset_path = self._create_nested_cloud_dataset()
dataset = Dataset(path=dataset_path, recursive=True)
with tempfile.TemporaryDirectory() as temporary_directory:
dataset.download(local_directory=temporary_directory)
with open(os.path.join(temporary_directory, "file_0.txt")) as f:
self.assertEqual(f.read(), "[1, 2, 3]")
with open(os.path.join(temporary_directory, "file_1.txt")) as f:
self.assertEqual(f.read(), "[4, 5, 6]")
with open(
os.path.join(temporary_directory, "sub-directory",
"sub_file.txt")) as f:
self.assertEqual(f.read(), "['a', 'b', 'c']")
with open(
os.path.join(temporary_directory, "sub-directory",
"sub-sub-directory",
"sub_sub_file.txt")) as f:
self.assertEqual(f.read(), "['blah', 'b', 'c']")
def test_upload_with_nested_dataset_preserves_nested_structure(self):
"""Test that uploading a dataset containing datafiles in a nested directory structure to the cloud preserves
this structure in the cloud.
"""
with tempfile.TemporaryDirectory() as temporary_directory:
local_paths = self._create_files_and_nested_subdirectories(
temporary_directory)
dataset = Dataset(path=temporary_directory, recursive=True)
upload_path = storage.path.generate_gs_path(
TEST_BUCKET_NAME, "my-dataset")
dataset.upload(cloud_path=upload_path)
cloud_datafile_relative_paths = {
blob.name.split(dataset.name)[-1].strip("/")
for blob in GoogleCloudStorageClient().scandir(
upload_path,
filter=lambda blob: not blob.name.endswith(".octue") and
SIGNED_METADATA_DIRECTORY not in blob.name,
)
}
# Check that the paths relative to the dataset directory are the same in the cloud as they are locally.
local_datafile_relative_paths = {
path.split(temporary_directory)[-1].strip(os.path.sep).replace(
os.path.sep, "/")
for path in local_paths
}
self.assertEqual(cloud_datafile_relative_paths,
local_datafile_relative_paths)
def test_download_from_nested_dataset_with_no_local_directory_given(self):
"""Test that, when downloading all files from a nested dataset and no local directory is given, the dataset
structure is preserved in the temporary directory used.
"""
dataset_path = self._create_nested_cloud_dataset()
dataset = Dataset(path=dataset_path, recursive=True)
# Mock the temporary directory created in `Dataset.download_all_files` so we can access it for the test.
temporary_directory = tempfile.TemporaryDirectory()
with patch("tempfile.TemporaryDirectory",
return_value=temporary_directory):
dataset.download()
with open(os.path.join(temporary_directory.name, "file_0.txt")) as f:
self.assertEqual(f.read(), "[1, 2, 3]")
with open(os.path.join(temporary_directory.name, "file_1.txt")) as f:
self.assertEqual(f.read(), "[4, 5, 6]")
with open(
os.path.join(temporary_directory.name, "sub-directory",
"sub_file.txt")) as f:
self.assertEqual(f.read(), "['a', 'b', 'c']")
with open(
os.path.join(temporary_directory.name, "sub-directory",
"sub-sub-directory", "sub_sub_file.txt")) as f:
self.assertEqual(f.read(), "['blah', 'b', 'c']")
def test_serialisation_and_deserialisation(self):
"""Test that manifests can be serialised and deserialised."""
with tempfile.TemporaryDirectory() as temporary_directory:
datasets = {
"my_dataset_0":
Dataset(
path=os.path.join(temporary_directory, "my_dataset_0"),
files=[
Datafile(
path=os.path.join(temporary_directory,
"my_dataset_0", "my_file_0.txt"))
],
),
"my_dataset_1":
Dataset(
path=os.path.join(temporary_directory, "my_dataset_1"),
files=[
Datafile(
path=os.path.join(temporary_directory,
"my_dataset_1", "my_file_1.txt"))
],
),
}
for dataset in datasets.values():
dataset.update_local_metadata()
manifest = Manifest(datasets=datasets,
id="7e0025cd-bd68-4de6-b48d-2643ebd5effd",
name="my-manifest")
serialised_manifest = manifest.to_primitive()
self.assertEqual(
serialised_manifest,
{
"id": manifest.id,
"name": "my-manifest",
"datasets": {
"my_dataset_0":
os.path.join(temporary_directory, "my_dataset_0"),
"my_dataset_1":
os.path.join(temporary_directory, "my_dataset_1"),
},
},
)
deserialised_manifest = Manifest.deserialise(serialised_manifest)
self.assertEqual(manifest.name, deserialised_manifest.name)
self.assertEqual(manifest.id, deserialised_manifest.id)
for key in manifest.datasets.keys():
self.assertEqual(manifest.datasets[key].name,
deserialised_manifest.datasets[key].name)
self.assertEqual(manifest.datasets[key].id,
deserialised_manifest.datasets[key].id)
self.assertEqual(manifest.datasets[key].path,
deserialised_manifest.datasets[key].path)
def test_upload_works_with_implicit_cloud_location_if_cloud_location_previously_provided(
self):
"""Test `Dataset.to_cloud` works with an implicit cloud location if the cloud location has previously been
provided.
"""
dataset_path = self._create_nested_cloud_dataset()
dataset = Dataset(path=dataset_path, recursive=True)
dataset.upload()
def test_cannot_add_non_datafiles(self):
"""Ensures that exception will be raised if adding a non-datafile object"""
class NotADatafile:
pass
resource = Dataset()
with self.assertRaises(exceptions.InvalidInputException):
resource.add(NotADatafile())
def test_error_raised_if_attempting_to_generate_signed_url_for_local_dataset(
self):
"""Test that an error is raised if trying to generate a signed URL for a local dataset."""
with tempfile.TemporaryDirectory() as temporary_directory:
dataset = Dataset(path=temporary_directory,
tags={"hello": "world"})
with self.assertRaises(exceptions.CloudLocationNotSpecified):
dataset.generate_signed_url()
def test_metadata_hash_is_same_for_different_datasets_with_the_same_metadata(
self):
"""Test that the metadata hash is the same for datasets with different files but the same metadata."""
first_dataset = Dataset(labels={"a", "b", "c"})
second_dataset = Dataset(
files={Datafile(path="blah", hypothetical=True)},
labels={"a", "b", "c"})
self.assertEqual(first_dataset.metadata_hash_value,
second_dataset.metadata_hash_value)
def test_exists_in_cloud(self):
"""Test whether all files of a dataset are in the cloud or not can be determined."""
self.assertFalse(self.create_valid_dataset().all_files_are_in_cloud)
with tempfile.TemporaryDirectory() as temporary_directory:
self.assertTrue(
Dataset(path=temporary_directory).all_files_are_in_cloud)
files = [
Datafile(path="gs://hello/file.txt"),
Datafile(path="gs://goodbye/file.csv")
]
self.assertTrue(Dataset(files=files).all_files_are_in_cloud)
def test_exiting_context_manager_of_cloud_dataset_updates_cloud_metadata(
self):
"""Test that cloud metadata for a cloud dataset is updated on exit of the dataset context manager."""
dataset_path = self._create_nested_cloud_dataset()
dataset = Dataset(path=dataset_path, recursive=True)
with dataset:
dataset.tags = {"cat": "dog"}
dataset.labels = {"animals"}
reloaded_dataset = Dataset(path=dataset_path)
self.assertEqual(reloaded_dataset.id, dataset.id)
self.assertEqual(reloaded_dataset.tags, {"cat": "dog"})
self.assertEqual(reloaded_dataset.labels, {"animals"})
def test_stored_metadata_ignored_if_hypothetical_is_true(self):
"""Test that instantiation metadata is used instead of stored metadata if `hypothetical` is `True`."""
cloud_path = storage.path.generate_gs_path(TEST_BUCKET_NAME,
"existing_dataset")
# Create a dataset in the cloud and set some metadata on it.
with Dataset(path=cloud_path) as dataset:
dataset.tags = {"existing": True}
# Load it separately from the cloud object and check that the instantiation metadata is used instead of the
# stored metadata.
reloaded_datafile = Dataset(path=cloud_path,
tags={"new": "tag"},
hypothetical=True)
self.assertEqual(reloaded_datafile.tags, {"new": "tag"})
def test_instantiation_metadata_used_if_not_hypothetical_but_no_stored_metadata(
self):
"""Test that instantiation metadata is used if `hypothetical` is `False` but there's no stored metadata."""
cloud_path = storage.path.generate_gs_path(TEST_BUCKET_NAME,
"non_existing_dataset")
dataset = Dataset(path=cloud_path, tags={"new": "tag"})
self.assertEqual(dataset.tags, {"new": "tag"})
def test_from_cloud(self):
"""Test that a Dataset in cloud storage can be accessed via a cloud path."""
with tempfile.TemporaryDirectory() as temporary_directory:
dataset = create_dataset_with_two_files(temporary_directory)
dataset.tags = {"a": "b", "c": 1}
cloud_path = storage.path.generate_gs_path(TEST_BUCKET_NAME,
"a_directory",
dataset.name)
dataset.upload(cloud_path)
persisted_dataset = Dataset(path=cloud_path)
self.assertEqual(
persisted_dataset.path,
f"gs://{TEST_BUCKET_NAME}/a_directory/{dataset.name}")
self.assertEqual(persisted_dataset.id, dataset.id)
self.assertEqual(persisted_dataset.name, dataset.name)
self.assertEqual(persisted_dataset.hash_value, dataset.hash_value)
self.assertEqual(persisted_dataset.tags, dataset.tags)
self.assertEqual(persisted_dataset.labels, dataset.labels)
self.assertEqual({file.name
for file in persisted_dataset.files},
{file.name
for file in dataset.files})
for file in persisted_dataset:
self.assertEqual(
file.cloud_path,
f"gs://{TEST_BUCKET_NAME}/a_directory/{dataset.name}/{file.name}"
)
def test_instantiating_from_serialised_cloud_datasets_with_no_dataset_json_file(
self):
"""Test that a Manifest can be instantiated from a serialized cloud dataset with no `dataset.json` file. This
simulates what happens when such a cloud dataset is referred to in a manifest received by a child service.
"""
GoogleCloudStorageClient().upload_from_string(
"[1, 2, 3]",
cloud_path=storage.path.generate_gs_path(TEST_BUCKET_NAME,
"my_dataset",
"file_0.txt"),
)
GoogleCloudStorageClient().upload_from_string(
"[4, 5, 6]",
cloud_path=storage.path.generate_gs_path(TEST_BUCKET_NAME,
"my_dataset",
"file_1.txt"),
)
serialised_cloud_dataset = Dataset(
path=f"gs://{TEST_BUCKET_NAME}/my_dataset").to_primitive()
manifest = Manifest(datasets={"my_dataset": serialised_cloud_dataset})
self.assertEqual(len(manifest.datasets), 1)
self.assertEqual(manifest.datasets["my_dataset"].path,
f"gs://{TEST_BUCKET_NAME}/my_dataset")
self.assertEqual(len(manifest.datasets["my_dataset"].files), 2)
def test_finalise_with_upload(self):
"""Test that the `finalise` method can be used to upload the output manifest's datasets to a cloud location
and that it updates the manifest with signed URLs for accessing them.
"""
with tempfile.TemporaryDirectory() as temporary_directory:
dataset_path = os.path.join(temporary_directory, "the_dataset")
with Datafile(path=os.path.join(dataset_path, "my_file.dat"), mode="w") as (datafile, f):
f.write("hello")
output_manifest = Manifest(
datasets={
"the_dataset": Dataset(
path=dataset_path, files={datafile.local_path}, labels={"one", "two", "three"}
)
}
)
analysis = Analysis(
twine={
"output_values_schema": {"type": "object", "properties": {"blah": {"type": "integer"}}},
"output_manifest": {"datasets": {"the_dataset": {"purpose": "testing"}}},
},
output_values={"blah": 3},
output_manifest=output_manifest,
)
with patch("google.cloud.storage.blob.Blob.generate_signed_url", new=mock_generate_signed_url):
analysis.finalise(upload_output_datasets_to=f"gs://{TEST_BUCKET_NAME}/datasets")
signed_url_for_dataset = analysis.output_manifest.datasets["the_dataset"].path
self.assertTrue(storage.path.is_url(signed_url_for_dataset))
self.assertTrue(
signed_url_for_dataset.startswith(
f"{self.test_result_modifier.storage_emulator_host}/{TEST_BUCKET_NAME}/datasets/the_dataset"
)
)
downloaded_dataset = Dataset(path=signed_url_for_dataset)
self.assertEqual(downloaded_dataset.name, "the_dataset")
self.assertEqual(len(downloaded_dataset.files), 1)
self.assertEqual(downloaded_dataset.labels, {"one", "two", "three"})
with downloaded_dataset.files.one() as (downloaded_datafile, f):
self.assertEqual(f.read(), "hello")
def test_filter_name_filters_exclude_path(self):
"""Ensures that filters applied to the name will not catch terms in the extension"""
resource = Dataset(files=[
Datafile(path="first-path-within-dataset/a_test_file.csv"),
Datafile(path="second-path-within-dataset/a_test_file.txt"),
])
files = resource.files.filter(name__icontains="second")
self.assertEqual(0, len(files))
def test_exiting_context_manager_of_local_dataset_updates_local_metadata(
self):
"""Test that local metadata for a local dataset is updated on exit of the dataset context manager."""
with tempfile.TemporaryDirectory() as temporary_directory:
self._create_files_and_nested_subdirectories(temporary_directory)
dataset = Dataset(path=temporary_directory, recursive=True)
with dataset:
dataset.tags = {"cat": "dog"}
dataset.labels = {"animals"}
reloaded_dataset = Dataset(path=temporary_directory,
recursive=True)
self.assertEqual(reloaded_dataset.id, dataset.id)
self.assertEqual(reloaded_dataset.tags, {"cat": "dog"})
self.assertEqual(reloaded_dataset.labels, {"animals"})
def test_serialisation_and_deserialisation(self):
"""Test that a dataset can be serialised and deserialised."""
dataset_id = "e376fb31-8f66-414d-b99f-b43395cebbf1"
dataset = self.create_valid_dataset(id=dataset_id,
labels=["b", "a"],
tags={
"a": 1,
"b": 2
})
serialised_dataset = dataset.to_primitive()
self.assertEqual(
serialised_dataset,
{
"name":
"test-dataset",
"labels": ["a", "b"],
"tags": {
"a": 1,
"b": 2
},
"id":
dataset_id,
"path":
os.path.join(REPOSITORY_ROOT, "tests", "data", "basic_files",
"configuration", "test-dataset"),
"files": [
os.path.join(
REPOSITORY_ROOT,
"tests",
"data",
"basic_files",
"configuration",
"test-dataset",
"path-within-dataset",
"a_test_file.csv",
),
os.path.join(
REPOSITORY_ROOT,
"tests",
"data",
"basic_files",
"configuration",
"test-dataset",
"path-within-dataset",
"another_test_file.csv",
),
],
},
)
deserialised_dataset = Dataset.deserialise(serialised_dataset)
self.assertEqual(dataset.id, deserialised_dataset.id)
self.assertEqual(dataset.path, deserialised_dataset.path)
self.assertEqual(dataset.name, deserialised_dataset.name)
self.assertEqual(dataset.labels, deserialised_dataset.labels)
self.assertEqual(dataset.tags, deserialised_dataset.tags)
def test_get_file_by_label(self):
"""Ensure files can be accessed by label from the dataset."""
files = [
Datafile(path="path-within-dataset/a_my_file.csv",
labels="one a b3 all"),
Datafile(path="path-within-dataset/a_your_file.csv",
labels="two a2 b3 all"),
Datafile(path="path-within-dataset/a_your_file.csv",
labels="three all"),
]
resource = Dataset(files=files)
# Check working for single result
self.assertEqual(
resource.get_file_by_label("three").labels, files[2].labels)
# Check raises for too many results
with self.assertRaises(
exceptions.UnexpectedNumberOfResultsException) as e:
resource.get_file_by_label("all")
self.assertIn("More than one result found", e.exception.args[0])
# Check raises for no result
with self.assertRaises(
exceptions.UnexpectedNumberOfResultsException) as e:
resource.get_file_by_label("billyjeanisnotmylover")
self.assertIn(
"No results found for filters {'labels__contains': 'billyjeanisnotmylover'}",
e.exception.args[0])
def test_adding_cloud_datafile_to_local_dataset(self):
"""Test that when a cloud datafile is added to a local dataset, it is downloaded to the root of the dataset."""
with Datafile(path=storage.path.generate_gs_path(
TEST_BUCKET_NAME, "path", "to", "datafile.dat"),
mode="w") as (
datafile,
f,
):
f.write("hello")
with tempfile.TemporaryDirectory() as temporary_directory:
dataset = Dataset(path=os.path.join(temporary_directory, "path",
"to", "dataset"))
dataset.add(datafile)
self.assertIn(datafile, dataset)
self.assertEqual(datafile.local_path,
os.path.join(dataset.path, "datafile.dat"))
def test_stored_metadata_has_priority_over_instantiation_metadata_if_not_hypothetical(
self):
"""Test that stored metadata is used instead of instantiation metadata if `hypothetical` is `False`."""
cloud_path = storage.path.generate_gs_path(TEST_BUCKET_NAME,
"existing_dataset")
# Create a dataset in the cloud and set some metadata on it.
with Dataset(path=cloud_path) as dataset:
dataset.tags = {"existing": True}
# Load it separately from the cloud object and check that the stored metadata is used instead of the
# instantiation metadata.
with self.assertLogs() as logging_context:
reloaded_dataset = Dataset(path=cloud_path, tags={"new": "tag"})
self.assertEqual(reloaded_dataset.tags, {"existing": True})
self.assertIn(
"Overriding metadata given at instantiation with stored metadata",
logging_context.output[0])
def test_adding_cloud_datafile_to_cloud_dataset_when_file_is_already_in_dataset_directory(
self):
"""Test that a cloud datafile's path is kept as-is when adding it to a cloud dataset if it is already in the
dataset directory and no `path_in_dataset` is provided.
"""
dataset = Dataset(path=storage.path.generate_gs_path(
TEST_BUCKET_NAME, "path", "to", "dataset"))
with Datafile(path=storage.path.join(dataset.path, "subfolder",
"datafile.dat"),
mode="w") as (datafile, f):
f.write("hello")
dataset.add(datafile)
self.assertIn(datafile, dataset)
self.assertEqual(
datafile.cloud_path,
storage.path.join(dataset.path, "subfolder", "datafile.dat"))
def test_from_cloud_with_no_metadata_file(self):
"""Test that any cloud directory can be accessed as a dataset if it has no `.octue` metadata file in it, the
cloud dataset doesn't lose any information during serialization, and a metadata file is uploaded afterwards.
"""
cloud_storage_client = GoogleCloudStorageClient()
cloud_storage_client.upload_from_string(
"[1, 2, 3]",
cloud_path=storage.path.generate_gs_path(TEST_BUCKET_NAME,
"my_dataset",
"file_0.txt"),
)
cloud_storage_client.upload_from_string(
"[4, 5, 6]",
cloud_path=storage.path.generate_gs_path(TEST_BUCKET_NAME,
"my_dataset",
"file_1.txt"),
)
cloud_dataset = Dataset(path=f"gs://{TEST_BUCKET_NAME}/my_dataset")
self.assertEqual(cloud_dataset.path,
f"gs://{TEST_BUCKET_NAME}/my_dataset")
self.assertEqual(cloud_dataset.name, "my_dataset")
self.assertEqual({file.name
for file in cloud_dataset.files},
{"file_0.txt", "file_1.txt"})
for file in cloud_dataset:
self.assertEqual(
file.cloud_path,
f"gs://{TEST_BUCKET_NAME}/my_dataset/{file.name}")
# Test serialisation doesn't lose any information.
deserialised_dataset = Dataset.deserialise(
cloud_dataset.to_primitive())
self.assertEqual(deserialised_dataset.id, cloud_dataset.id)
self.assertEqual(deserialised_dataset.name, cloud_dataset.name)
self.assertEqual(deserialised_dataset.path, cloud_dataset.path)
self.assertEqual(deserialised_dataset.hash_value,
cloud_dataset.hash_value)
def test_adding_local_datafile_to_local_dataset_when_file_is_already_in_dataset_directory(
self):
"""Test that a local datafile's path is kept as-is when adding it to a local dataset if it is already in the
dataset directory.
"""
with tempfile.TemporaryDirectory() as temporary_directory:
dataset = Dataset(path=os.path.join(temporary_directory, "path",
"to", "dataset"))
with Datafile(path=os.path.join(dataset.path, "subfolder",
"datafile.dat"),
mode="w") as (datafile, f):
f.write("hello")
dataset.add(datafile)
self.assertIn(datafile, dataset)
self.assertEqual(
datafile.local_path,
os.path.join(dataset.path, "subfolder", "datafile.dat"))
def test_adding_cloud_datafile_to_cloud_dataset(self):
"""Test that a cloud datafile can be added to a cloud dataset and that it's copied into the dataset root if no
`path_within_dataset` is provided.
"""
dataset = Dataset(path=storage.path.generate_gs_path(
TEST_BUCKET_NAME, "path", "to", "dataset"))
with Datafile(path=storage.path.generate_gs_path(
TEST_BUCKET_NAME, "path", "to", "datafile.dat"),
mode="w") as (
datafile,
f,
):
f.write("hello")
dataset.add(datafile)
self.assertIn(datafile, dataset)
self.assertEqual(datafile.cloud_path,
storage.path.join(dataset.path, "datafile.dat"))
def test_filter_name_filters_include_extension(self):
"""Ensures that filters applied to the name will catch terms in the extension"""
files = [
Datafile(path="path-within-dataset/a_test_file.csv"),
Datafile(path="path-within-dataset/a_test_file.txt"),
]
self.assertEqual(
Dataset(files=files).files.filter(
name__icontains="txt").pop().path,
FilterSet({files[1]}).pop().local_path)
def test_all_datasets_are_in_cloud(self):
"""Test whether all files of all datasets in a manifest are in the cloud or not can be determined."""
self.assertFalse(
self.create_valid_manifest().all_datasets_are_in_cloud)
self.assertTrue(Manifest().all_datasets_are_in_cloud)
files = [
Datafile(path="gs://hello/file.txt"),
Datafile(path="gs://goodbye/file.csv")
]
manifest = Manifest(datasets={"my_dataset": Dataset(files=files)})
self.assertTrue(manifest.all_datasets_are_in_cloud)
def create_valid_dataset(self, **kwargs):
"""Create a valid dataset with two valid datafiles (they're the same file in this case)."""
path = os.path.join(self.data_path, "basic_files", "configuration", "test-dataset")
return Dataset(
path=path,
files=[
Datafile(path=os.path.join(path, "path-within-dataset", "a_test_file.csv")),
Datafile(path=os.path.join(path, "path-within-dataset", "another_test_file.csv")),
],
**kwargs
)
def test_adding_local_datafile_to_local_dataset(self):
"""Test that a local datafile can be added to a local dataset and that it is copied to the root of the dataset
if no `path_within_dataset` is provided.
"""
with tempfile.TemporaryDirectory() as temporary_directory:
dataset = Dataset(path=os.path.join(temporary_directory, "path",
"to", "dataset"))
with Datafile(path=os.path.join(temporary_directory, "path", "to",
"datafile.dat"),
mode="w") as (
datafile,
f,
):
f.write("hello")
dataset.add(datafile)
self.assertIn(datafile, dataset)
self.assertEqual(datafile.local_path,
os.path.join(dataset.path, "datafile.dat"))