def test_partial_directory(self):
directory = path.join(path_to_module, "partial_dir")
res = progress.get_directory_status(directory, ["SampleSheet.csv"])
self.assertEqual(res.status, DirectoryStatus.PARTIAL)
self.assertIsNone(res.message)
def test_inaccessible_directory(self):
directory = path.join(path_to_module, "inaccessible_dir")
res = progress.get_directory_status(directory, ["SampleSheet.csv"])
self.assertEqual(res.status, DirectoryStatus.INVALID)
self.assertIsNotNone(res.message)
def test_complete_directory(self):
directory = path.join(path_to_module, "complete_dir")
res = progress.get_directory_status(directory, ["SampleSheet.csv"])
self.assertEqual(res.status, DirectoryStatus.COMPLETE)
self.assertIsNone(res.message)
def test_new_directory_with_info_file(self):
directory = path.join(path_to_module, "new_dir_with_info_file")
res = progress.get_directory_status(directory, ["SampleSheet.csv"])
self.assertEqual(res.status, DirectoryStatus.NEW)
self.assertIsNone(res.message)
def test_new_directory_one_file_missing(self):
directory = path.join(path_to_module, "new_dir")
res = progress.get_directory_status(
directory, ["SampleSheet.csv", 'not_a_file.txt'])
self.assertEqual(res.status, DirectoryStatus.INVALID)
self.assertIsNotNone(res.message)
def test_new_directory_multiple_files(self):
directory = path.join(path_to_module, "new_dir_two_files")
res = progress.get_directory_status(
directory, ["SampleSheet.csv", 'CompletedJobInfo.xml'])
self.assertEqual(res.status, DirectoryStatus.NEW)
self.assertIsNone(res.message)
def find_single_run(self, directory):
"""
Find a run in the base directory given
:param directory:
:return: DirectoryStatus object
"""
logging.info("looking for run in {}".format(directory))
return progress.get_directory_status(directory, self.get_required_file_list())
def test_has_miseq_complete_file(self):
"""
Tests legacy support to show runs that contain .miseqUploaderComplete as COMPLETE
:return:
"""
directory = path.join(path_to_module, "has_miseq_complete")
res = progress.get_directory_status(directory, ["SampleSheet.csv"])
self.assertEqual(res.status, DirectoryStatus.COMPLETE)
self.assertEqual(
res.message,
"Legacy uploader run. Set to complete to avoid uploading duplicate data."
)
def test_write_to_new_file(self):
# File does not exist yet
self.assertFalse(path.exists(self.status_file))
# Create DirectoryStatus to use for writing
directory_status = DirectoryStatus(self.directory)
# Write to file
directory_status.status = DirectoryStatus.COMPLETE
progress.write_directory_status(directory_status)
# Check that file matches what we wrote
status = progress.get_directory_status(self.directory,
["SampleSheet.csv"])
self.assertEqual(DirectoryStatus.COMPLETE, status.status)
def find_runs(self, directory):
"""
find a list of run directories in the directory given
:param directory:
:return: list of DirectoryStatus objects
"""
logging.info("looking for runs in {}".format(directory))
runs = []
directory_list = common.find_directory_list(directory)
for d in directory_list:
runs.append(progress.get_directory_status(d, self.get_required_file_list()))
return runs
def test_write_with_readonly_is_true_file(self):
# set readonly to True in config
config.set_config_options(readonly=True)
# File does not exist yet
self.assertFalse(path.exists(self.status_file))
# Create DirectoryStatus to use for writing
directory_status = DirectoryStatus(self.directory)
# Try write to file (WRITE COMPLETE)
directory_status.status = DirectoryStatus.COMPLETE
progress.write_directory_status(directory_status)
# Check that file matches what we wrote
# We should find it as NEW as we have readonly=True
status = progress.get_directory_status(self.directory,
["SampleSheet.csv"])
self.assertEqual(DirectoryStatus.NEW, status.status)
