class BestPracticeAnalysisService(object):
def __init__(self, general_project_repo):
self.general_project_repo = general_project_repo
self.file_system_service = FileSystemService()
def get_samples(self, project_name):
project = self.general_project_repo.get_project(
project_name=project_name)
for directory in self.file_system_service.list_directories(
project.path):
if self.file_system_service.isfile("{}.lst".format(directory)) and \
self.file_system_service.isfile("{}.md5".format(directory)):
yield self.file_system_service.basename(directory)
def __init__(self, base_path, file_system_service=FileSystemService()):
"""
Instantiate a new FileSystemBasedRunfolderRepository
:param base_path: the directory where runfolders are stored
:param file_system_service: a service which can access the file system.
"""
self._base_path = base_path
self.file_system_service = file_system_service
def __init__(self, root_directory, filesystem_service=FileSystemService()):
"""
Instantiate a `GeneralProjectRepository` instance
:param root_directory: directory in which to look for projects
:param filesystem_service: a file system service used to interact with the file system, defaults to
`FileSystemService`
"""
self.root_directory = root_directory
self.filesystem_service = filesystem_service
def __init__(self,
runfolder_service,
file_system_service=FileSystemService()):
"""
Instantiate a new OrganiseService
:param runfolder_service: an instance of a RunfolderService
:param file_system_service: an instance of FileSystemService
"""
self.runfolder_service = runfolder_service
self.file_system_service = file_system_service
def __init__(self,
session_factory,
file_system_service=FileSystemService()):
"""
Instantiate a new DatabaseBasedStagingRepository
:param session_factory: factory method which can produce new sqlalchemy Session objects
:param file_system_service: a service for accessing the file system. Mostly shadows normal
stdlib methods for accessing the file system, but this allows for easier mocking
in tests.
"""
self.session = session_factory()
self.file_system_service = file_system_service
def __init__(self,
sample_repository,
filesystem_service=FileSystemService(),
metadata_service=MetadataService()):
"""
Instantiate a new UnorganisedRunfolderProjectRepository object
:param sample_repository: a RunfolderProjectBasedSampleRepository instance
:param filesystem_service: a FileSystemService instance for accessing the file system
"""
self.filesystem_service = filesystem_service
self.sample_repository = sample_repository
self.metadata_service = metadata_service
def __init__(self,
delivery_sources_repo,
general_project_repo,
runfolder_service,
staging_service,
mover_service,
project_links_directory,
file_system_service=FileSystemService()):
self.delivery_sources_repo = delivery_sources_repo
self.staging_service = staging_service
self.mover_service = mover_service
self.general_project_repo = general_project_repo
self.runfolder_service = runfolder_service
self.project_links_directory = project_links_directory
self.file_system_service = file_system_service
def __init__(
self,
base_path,
project_repository,
file_system_service=FileSystemService(),
metadata_service=MetadataService()):
"""
Instantiate a new `FileSystemBasedUnorganisedRunfolderRepository` object.
:param base_path: the directory where runfolders are stored
:param project_repository: an instance of UnorganisedRunfolderProjectRepository
:param file_system_service: a service which can access the file system
"""
super(FileSystemBasedUnorganisedRunfolderRepository, self).__init__(
base_path,
file_system_service=file_system_service,
metadata_service=metadata_service)
self.project_repository = project_repository
def _assert_is_dir(directory):
if not FileSystemService.isdir(directory):
raise AssertionError("{} is not a directory".format(
os.path.abspath(directory)))
def __init__(self, general_project_repo):
self.general_project_repo = general_project_repo
self.file_system_service = FileSystemService()
def __init__(self, file_system_service=FileSystemService()):
self.file_system_service = file_system_service
def test_list_files_recursively(self):
self.assertListEqual(
sorted(self.files),
sorted(
list(FileSystemService().list_files_recursively(
self.rootdir))))