def test_get_bytes_no_file(self):
e = DataFileElement("/not/a/valid/path.txt", readonly=True)
# We currently expect, in the case where the filepath doesn't exist, to
# get the same bytes as if the file existed and were empty.
self.assertEqual(e.get_bytes(), six.b(""))
# read-only status should have no effect.
e = DataFileElement("/not/a/valid/path.txt", readonly=True)
self.assertEqual(e.get_bytes(), six.b(""))
def test_get_bytes_no_file(self):
e = DataFileElement("/not/a/valid/path.txt", readonly=True)
# We currently expect, in the case where the filepath doesn't exist, to
# get the same bytes as if the file existed and were empty.
self.assertEqual(e.get_bytes(), six.b(""))
# read-only status should have no effect.
e = DataFileElement("/not/a/valid/path.txt", readonly=True)
self.assertEqual(e.get_bytes(), six.b(""))
def test_load_dataset_tempfile(self):
"""
Test DataElement temporary file based context loader.
"""
# Creating separate element from global so we can mock it up.
e = DataFileElement(GH_IMAGE_FP, readonly=True)
e.write_temp = mock.MagicMock(wraps=e.write_temp)
e.clean_temp = mock.MagicMock(wraps=e.clean_temp)
e.get_bytes = mock.MagicMock(wraps=e.get_bytes)
# Using explicit patcher start/stop in order to avoid using ``patch``
# as a decorator because ``osgeo`` might not be defined when
# decorating the method.
patcher_gdal_open = mock.patch('smqtk.algorithms.image_io.gdal_io.gdal'
'.Open', wraps=osgeo.gdal.Open)
self.addCleanup(patcher_gdal_open.stop)
m_gdal_open = patcher_gdal_open.start()
with load_dataset_tempfile(e) as gdal_ds:
# noinspection PyUnresolvedReferences
e.write_temp.assert_called_once_with()
# noinspection PyUnresolvedReferences
e.get_bytes.assert_not_called()
m_gdal_open.assert_called_once()
assert gdal_ds.RasterCount == 3
assert gdal_ds.RasterXSize == 512
assert gdal_ds.RasterYSize == 600
# noinspection PyUnresolvedReferences
e.clean_temp.assert_called_once_with()
assert len(e._temp_filepath_stack) == 0
def test_load_dataset_vsimem(self):
"""
Test that VSIMEM loading context
"""
if LooseVersion(osgeo.__version__).version[0] < 2:
pytest.skip("Skipping VSIMEM test because GDAL version < 2")
# Creating separate element from global so we can mock it up.
e = DataFileElement(GH_IMAGE_FP, readonly=True)
e.write_temp = mock.MagicMock(wraps=e.write_temp)
e.clean_temp = mock.MagicMock(wraps=e.clean_temp)
e.get_bytes = mock.MagicMock(wraps=e.get_bytes)
vsimem_path_re = re.compile(r'^/vsimem/\w+$')
# Using explicit patcher start/stop in order to avoid using ``patch``
# as a *decorator* because ``osgeo`` might not be defined when
# decorating the method.
patcher_gdal_open = mock.patch(
'smqtk.algorithms.image_io.gdal_io.gdal.Open',
wraps=osgeo.gdal.Open,
)
self.addCleanup(patcher_gdal_open.stop)
patcher_gdal_unlink = mock.patch(
'smqtk.algorithms.image_io.gdal_io.gdal.Unlink',
wraps=osgeo.gdal.Unlink,
)
self.addCleanup(patcher_gdal_unlink.stop)
m_gdal_open = patcher_gdal_open.start()
m_gdal_unlink = patcher_gdal_unlink.start()
with load_dataset_vsimem(e) as gdal_ds:
# noinspection PyUnresolvedReferences
e.write_temp.assert_not_called()
# noinspection PyUnresolvedReferences
e.get_bytes.assert_called_once_with()
m_gdal_open.assert_called_once()
ds_path = gdal_ds.GetDescription()
assert vsimem_path_re.match(ds_path)
assert gdal_ds.RasterCount == 3
assert gdal_ds.RasterXSize == 512
assert gdal_ds.RasterYSize == 600
m_gdal_unlink.assert_called_once_with(ds_path)
# noinspection PyUnresolvedReferences
e.clean_temp.assert_not_called()
assert len(e._temp_filepath_stack) == 0
def iqr_ingest_file():
"""
Ingest the file with the given UID, getting the path from the
uploader.
:return: string of data/descriptor element's UUID
:rtype: str
"""
# TODO: Add status dict with a "GET" method branch for getting that
# status information.
fid = flask.request.form['fid']
sid = self.get_current_iqr_session()
self._log.debug(
"[%s::%s] Getting temporary filepath from "
"uploader module", sid, fid)
upload_filepath = self.mod_upload.get_path_for_id(fid)
self.mod_upload.clear_completed(fid)
self._log.debug("[%s::%s] Moving uploaded file", sid, fid)
sess_upload = osp.join(self._iqr_work_dirs[sid],
osp.basename(upload_filepath))
os.rename(upload_filepath, sess_upload)
# Record uploaded data as user example data for this session.
upload_data = DataFileElement(sess_upload)
uuid = upload_data.uuid()
self._iqr_example_data[sid][uuid] = upload_data
# Extend session ingest -- modifying
self._log.debug(
"[%s::%s] Adding new data to session "
"external positives", sid, fid)
data_b64 = base64.b64encode(upload_data.get_bytes())
data_ct = upload_data.content_type()
r = self._iqr_service.post('add_external_pos',
sid=sid,
base64=data_b64,
content_type=data_ct)
r.raise_for_status()
return str(uuid)
def iqr_ingest_file():
"""
Ingest the file with the given UID, getting the path from the
uploader.
:return: string of data/descriptor element's UUID
:rtype: str
"""
# TODO: Add status dict with a "GET" method branch for getting that
# status information.
fid = flask.request.form['fid']
sid = self.get_current_iqr_session()
self._log.debug("[%s::%s] Getting temporary filepath from "
"uploader module", sid, fid)
upload_filepath = self.mod_upload.get_path_for_id(fid)
self.mod_upload.clear_completed(fid)
self._log.debug("[%s::%s] Moving uploaded file",
sid, fid)
sess_upload = osp.join(self._iqr_work_dirs[sid],
osp.basename(upload_filepath))
os.rename(upload_filepath, sess_upload)
# Record uploaded data as user example data for this session.
upload_data = DataFileElement(sess_upload)
uuid = upload_data.uuid()
self._iqr_example_data[sid][uuid] = upload_data
# Extend session ingest -- modifying
self._log.debug("[%s::%s] Adding new data to session "
"external positives", sid, fid)
data_b64 = base64.b64encode(upload_data.get_bytes())
data_ct = upload_data.content_type()
r = self._iqr_service.post('add_external_pos', sid=sid,
base64=data_b64, content_type=data_ct)
r.raise_for_status()
return str(uuid)
def test_get_bytes(self):
# Test with a known real file.
test_file_path = os.path.join(TEST_DATA_DIR, 'text_file')
e = DataFileElement(test_file_path)
self.assertEqual(e.get_bytes(), six.b("Some text content.\n"))
def test_get_bytes(self):
# Test with a known real file.
test_file_path = os.path.join(TEST_DATA_DIR, 'text_file')
e = DataFileElement(test_file_path)
self.assertEqual(e.get_bytes(), six.b("Some text content.\n"))
