def _new_request_file(request: flask.Request) -> str:
"""
Process an incoming Flask request and
return path to temporary request file.
"""
request_files = request.files
if request_files:
# Multipart PUT request:
# We expect two files: a JSON file "body"
# and a binary file "user_code".
# "body" contains the generator request and
request_storage = request_files.get('body')
request_dict = json.load(request_storage.stream)
# "user_code" is a ZIP archive with the user code.
user_code_storage = request_files.get('user_code')
_, user_code_path = new_temp_file(suffix=user_code_storage.filename)
user_code_storage.save(user_code_path)
print(f' * User code file: {user_code_path}')
else:
# Not a multipart PUT request: Expect JSON request in
# body content:
request_dict = request.json
user_code_path = None
if not isinstance(request_dict, dict):
print(f'Error: received invalid request: {request_dict}')
raise werkzeug.exceptions.BadRequest('request data must be JSON')
try:
CubeGeneratorRequest.get_schema().validate_instance(request_dict)
except jsonschema.ValidationError as e:
print(f'Error: received invalid request: {request_dict}')
raise werkzeug.exceptions.BadRequest('request is no valid JSON') from e
if user_code_path:
# If we have user code, alter the "code_config"
# part of the generator request so it points to
# the temporary ZIP archive.
code_config = request_dict.get('code_config')
if isinstance(code_config, dict):
file_set = code_config.get('file_set')
if isinstance(file_set, dict):
file_set['path'] = user_code_path
# Write the request to a temporary file
_, request_path = new_temp_file(suffix='_request.yaml')
with open(request_path, 'w') as stream:
yaml.dump(request_dict, stream)
print(f' * Request: {request_path}')
return request_path
def test_output(self):
_, output_path = new_temp_file(suffix='.json')
result = self.invoke_cli(['versions', '-o', output_path])
self.assertEqual(0, result.exit_code)
with open(output_path) as fp:
text = fp.read()
self.assertJson(text)
_, output_path = new_temp_file(suffix='.yml')
result = self.invoke_cli(['versions', '-o', output_path])
self.assertEqual(0, result.exit_code)
with open(output_path) as fp:
text = fp.read()
self.assertYaml(text)
def test_new_temp_file(self):
fd, file_path = new_temp_file()
self.assertIsInstance(fd, int)
self.assertIsInstance(file_path, str)
self.assertTrue(os.path.basename(file_path).startswith('xcube-'))
self.assertTrue(os.path.isabs(file_path))
self.assertTrue(os.path.isfile(file_path))
fd, file_path = new_temp_file(prefix='bibo.', suffix='.zip')
self.assertIsInstance(fd, int)
self.assertIsInstance(file_path, str)
self.assertTrue(os.path.basename(file_path).startswith('bibo.'))
self.assertTrue(os.path.basename(file_path).endswith('.zip'))
self.assertTrue(os.path.isabs(file_path))
self.assertTrue(os.path.isfile(file_path))
def _init_local_store():
"""
Initialize a "directory" data store with test datasets.
"""
from xcube.core.new import new_cube
local_base_dir = new_temp_dir(suffix='_local_store')
dataset_1 = new_cube(width=36, height=18, variables={'A': 0.1, 'B': 0.2})
dataset_2 = new_cube(width=36, height=18, variables={'C': 0.2, 'D': 0.3})
dataset_1.to_zarr(os.path.join(local_base_dir, 'DATASET-1.zarr'))
dataset_2.to_zarr(os.path.join(local_base_dir, 'DATASET-2.zarr'))
global STORES_CONFIG_PATH
_, STORES_CONFIG_PATH = new_temp_file(suffix='_stores.yaml')
with open(STORES_CONFIG_PATH, 'w') as stream:
yaml.dump(
{
'test': {
'title': 'Local test store',
'store_id': 'file',
'store_params': {
'root': local_base_dir
}
}
}, stream)
print(f' * Store base directory: {local_base_dir}')
print(f' * Store configuration: {STORES_CONFIG_PATH}')
def to_local(self) -> 'FileSet':
"""
Turn this file set into an existing, local file set.
"""
if self.is_local():
return self
details = self._get_details()
fs, root = details.fs, details.root
url_path = fsspec.core.strip_protocol(self.path)
suffix = ''
for suffix in reversed(url_path.split('/')):
if suffix != '':
break
if root.endswith('/'):
temp_dir = new_temp_dir(prefix=TEMP_FILE_PREFIX, suffix=suffix)
# TODO: replace by loop so we can apply includes/excludes
# before downloading actual files. See impl of fs.get().
fs.get(root, temp_dir + "/", recursive=True)
return FileSet(temp_dir,
sub_path=self.sub_path,
includes=self.includes,
excludes=self.excludes)
else:
_, temp_file = new_temp_file(prefix=TEMP_FILE_PREFIX,
suffix=suffix)
fs.get_file(root, temp_file)
return FileSet(temp_file,
sub_path=self.sub_path,
includes=self.includes,
excludes=self.excludes)
def write_data(self,
data: xr.Dataset,
data_id: str,
replace=False,
**write_params) -> str:
assert_instance(data, xr.Dataset, name='data')
assert_instance(data_id, str, name='data_id')
fs, root, write_params = self.load_fs(write_params)
if not replace and fs.exists(data_id):
raise DataStoreError(f'Data resource {data_id} already exists')
# This doesn't yet work as expected with fsspec and netcdf:
# engine = write_params.pop('engine', 'scipy')
# with fs.open(data_id, 'wb') as file:
# data.to_netcdf(file, engine=engine, **write_params)
is_local = is_local_fs(fs)
if is_local:
file_path = data_id
else:
_, file_path = new_temp_file(suffix='.nc')
engine = write_params.pop('engine', 'netcdf4')
data.to_netcdf(file_path, engine=engine, **write_params)
if not is_local:
fs.put_file(file_path, data_id)
return data_id
def open_data(self, data_id: str, **open_params) -> gpd.GeoDataFrame:
# TODO: implement me correctly,
# this is not valid for shapefile AND geojson
fs, root, open_params = self.load_fs(open_params)
is_local = is_local_fs(fs)
if is_local:
file_path = data_id
else:
_, file_path = new_temp_file()
fs.get_file(data_id, file_path)
return gpd.read_file(file_path,
driver=self.get_driver_name(),
**open_params)
def write_data(self, data: gpd.GeoDataFrame, data_id: str,
**write_params) -> str:
# TODO: implement me correctly,
# this is not valid for shapefile AND geojson
assert_instance(data, (gpd.GeoDataFrame, pd.DataFrame), 'data')
fs, root, write_params = self.load_fs(write_params)
is_local = is_local_fs(fs)
if is_local:
file_path = data_id
else:
_, file_path = new_temp_file()
data.to_file(file_path, driver=self.get_driver_name(), **write_params)
if not is_local:
fs.put_file(file_path, data_id)
return data_id
def _write_local_zip(self, zip_path: Optional[str]) -> 'FileSet':
"""Write file set into local ZIP archive."""
local_dir_path = self.get_local_path()
if not zip_path:
_, zip_path = new_temp_file(prefix=TEMP_FILE_PREFIX, suffix='.zip')
sub_path = _normalize_sub_path(self.sub_path)
with zipfile.ZipFile(zip_path, 'w') as zip_file:
for key in self.keys():
file_path = os.path.join(local_dir_path, key)
zip_file.write(file_path,
arcname=_strip_sub_path_from_key(key, sub_path))
return FileSet(zip_path, sub_path=self.sub_path)
def open_data(self, data_id: str, **open_params) -> xr.Dataset:
assert_instance(data_id, str, name='data_id')
fs, root, open_params = self.load_fs(open_params)
# This doesn't yet work as expected with fsspec and netcdf:
# engine = open_params.pop('engine', 'scipy')
# with fs.open(data_id, 'rb') as file:
# return xr.open_dataset(file, engine=engine, **open_params)
is_local = is_local_fs(fs)
if is_local:
file_path = data_id
else:
_, file_path = new_temp_file(suffix='.nc')
fs.get_file(data_id, file_path)
engine = open_params.pop('engine', 'netcdf4')
return xr.open_dataset(file_path, engine=engine, **open_params)
def _new_result_file() -> str:
_, file_path = new_temp_file(prefix='xcube-gen2-', suffix='-result.json')
return file_path