def test_update_coords_metadata_only(self):
ds1 = zarr.open(TEST_CUBE_ZARR_COORDS)
delete_list = [
'geospatial_lat_max', 'geospatial_lat_min', 'geospatial_lat_units',
'geospatial_lon_max', 'geospatial_lon_min', 'geospatial_lon_units',
'time_coverage_end', 'time_coverage_start'
]
for attr in ds1.attrs.keys():
if attr in delete_list:
ds1.attrs.__delitem__(attr)
edit_metadata(TEST_CUBE_ZARR_COORDS,
update_coords=True,
in_place=False,
output_path=TEST_CUBE_ZARR_EDIT,
monitor=print)
ds1 = zarr.open(TEST_CUBE_ZARR_COORDS)
ds2 = zarr.open(TEST_CUBE_ZARR_EDIT)
for attr in delete_list:
self.assertNotIn(attr, ds1.attrs.keys())
self.assertEqual(ds1.__len__(), ds2.__len__())
self.assertIn('geospatial_lat_max', ds2.attrs.keys())
self.assertIn('geospatial_lat_min', ds2.attrs.keys())
self.assertIn('geospatial_lat_resolution', ds2.attrs.keys())
self.assertIn('geospatial_lat_units', ds2.attrs.keys())
self.assertIn('geospatial_lon_max', ds2.attrs.keys())
self.assertEqual(180.0, ds2.attrs.__getitem__('geospatial_lon_max'))
self.assertEqual(-180.0, ds2.attrs.__getitem__('geospatial_lon_min'))
self.assertEqual('2010-01-04T00:00:00.000000000',
ds2.attrs.__getitem__('time_coverage_end'))
self.assertEqual('2010-01-01T00:00:00.000000000',
ds2.attrs.__getitem__('time_coverage_start'))
self.assertEqual('degrees_east',
ds2.attrs.__getitem__('geospatial_lon_units'))
def test_edit_metadata(self):
edit_metadata(TEST_CUBE_ZARR, metadata_path=TEST_NEW_META_YML, in_place=False,
output_path=TEST_CUBE_ZARR_EDIT, monitor=print)
ds1 = zarr.open(TEST_CUBE_ZARR)
ds2 = zarr.open(TEST_CUBE_ZARR_EDIT)
self.assertEqual(ds1.__len__(), ds2.__len__())
self.assertEqual(ds1.attrs.__getitem__('start_date'), ds2.attrs.__getitem__('start_date'))
self.assertEqual('happiness', ds2['conc_chl'].attrs.__getitem__('units'))
self.assertNotIn('creator_name', ds1.attrs.keys())
self.assertIn('creator_name', ds2.attrs.keys())
def test_edit_metadata_in_place(self):
edit_metadata(TEST_CUBE_ZARR, metadata_path=TEST_NEW_META_YML, in_place=True, monitor=print)
ds1 = zarr.open(TEST_CUBE_ZARR)
self.assertEqual(36, ds1.__len__())
self.assertEqual('14-APR-2017 10:27:50.183264', ds1.attrs.__getitem__('start_date'))
self.assertEqual('happiness', ds1['conc_chl'].attrs.__getitem__('units'))
self.assertIn('creator_name', ds1.attrs.keys())
self.assertIn('creator_url', ds1.attrs.keys())
self.assertEqual('Brockmann Consult GmbH with love', ds1.attrs.__getitem__('creator_name'))
self.assertEqual('www.some_very_nice_url.com', ds1.attrs.__getitem__('creator_url'))
def test_edit_zmetadata(self):
optimize_dataset(TEST_CUBE_ZARR, unchunk_coords=True, output_path=TEST_CUBE_ZARR_OPTIMIZED)
edit_metadata(TEST_CUBE_ZARR_OPTIMIZED, metadata_path=TEST_NEW_META_YML, in_place=False,
output_path=TEST_CUBE_ZARR_OPTIMIZED_EDIT, monitor=print)
ds1 = zarr.open(TEST_CUBE_ZARR)
ds2 = zarr.convenience.open_consolidated(TEST_CUBE_ZARR_OPTIMIZED_EDIT)
self.assertEqual(ds1.__len__(), ds2.__len__())
self.assertEqual(ds1.attrs.__getitem__('start_date'), ds2.attrs.__getitem__('start_date'))
self.assertEqual('happiness', ds2['conc_chl'].attrs.__getitem__('units'))
self.assertNotIn('creator_name', ds1.attrs.keys())
self.assertIn('creator_name', ds2.attrs.keys())
def test_update_coords_metadata(self):
edit_metadata(TEST_CUBE_ZARR, metadata_path=TEST_NEW_META_YML, update_coords=True, in_place=False,
output_path=TEST_CUBE_ZARR_EDIT, monitor=print)
ds1 = zarr.open(TEST_CUBE_ZARR)
ds2 = zarr.open(TEST_CUBE_ZARR_EDIT)
self.assertEqual(ds1.__len__(), ds2.__len__())
self.assertEqual(ds1.attrs.__getitem__('start_date'), ds2.attrs.__getitem__('start_date'))
self.assertEqual(ds1.attrs.__getitem__('start_date'), ds2.attrs.__getitem__('start_date'))
self.assertEqual('happiness', ds2['conc_chl'].attrs.__getitem__('units'))
self.assertIn('geospatial_lon_units', ds2.attrs.keys())
self.assertEqual('degrees_east', ds2.attrs.__getitem__('geospatial_lon_units'))
self.assertNotIn('geospatial_lat_max', ds1.attrs.keys())
self.assertNotIn('geospatial_lat_max', ds2.attrs.keys())
def edit(cube, output, metadata, coords, in_place):
"""
Edit the metadata of an xcube dataset.
Edits the metadata of a given CUBE.
The command currently works only for data cubes using ZARR format.
"""
from xcube.core.edit import edit_metadata
edit_metadata(cube,
output_path=output,
metadata_path=metadata,
update_coords=coords,
in_place=in_place,
monitor=print)
def test_failures(self):
with self.assertRaises(RuntimeError) as cm:
edit_metadata('pippo',
in_place=True,
exception_type=RuntimeError,
metadata_path=TEST_NEW_META_YML)
self.assertEqual('Input path must point to ZARR dataset directory.',
f'{cm.exception}')
with self.assertRaises(RuntimeError) as cm:
edit_metadata(TEST_CUBE_ZARR,
exception_type=RuntimeError,
metadata_path=TEST_NEW_META_YML)
self.assertEqual('Output path must be given.', f'{cm.exception}')
with self.assertRaises(RuntimeError) as cm:
edit_metadata(TEST_CUBE_ZARR,
output_path=TEST_CUBE_ZARR,
exception_type=RuntimeError,
metadata_path=TEST_NEW_META_YML)
self.assertEqual('Output path already exists.', f'{cm.exception}')
with self.assertRaises(RuntimeError) as cm:
edit_metadata(TEST_CUBE_ZARR,
output_path='./' + TEST_CUBE_ZARR,
exception_type=RuntimeError,
metadata_path=TEST_NEW_META_YML)
self.assertEqual('Output path already exists.', f'{cm.exception}')