def unorganised_runfolder(name="180124_A00181_0019_BH72M5DMXX",
root_path="/foo"):
sample_indexes = sample_index_generator()
lane_numbers = lane_generator()
runfolder = Runfolder(name=name, path=os.path.join(root_path, name))
runfolder.projects = [
runfolder_project(runfolder,
project_name=p,
sample_indexes=sample_indexes,
lane_numbers=lane_numbers) for p in fake_projects
]
# add another project with missing files
project = runfolder_project(runfolder,
project_name="JKL_123",
sample_indexes=sample_indexes,
lane_numbers=lane_numbers)
project.project_files = []
runfolder.projects.append(project)
checksums = {}
for project in runfolder.projects:
for sample in project.samples:
for sample_file in sample.sample_files:
checksums[os.path.relpath(
sample_file.file_path,
os.path.dirname(runfolder.path))] = sample_file.checksum
for project_file in project.project_files:
checksums[os.path.relpath(
project_file.file_path,
os.path.dirname(runfolder.path))] = project_file.checksum
runfolder.checksums = checksums
return runfolder
def _get_runfolders(self):
# TODO Filter based on expression for runfolders...
runfolder_expression = r"^\d+_"
directories = self.file_system_service.find_runfolder_directories(
self._base_path)
for directory in directories:
if re.match(runfolder_expression, os.path.basename(directory)):
name = os.path.basename(directory)
path = os.path.join(self._base_path, directory)
projects_base_dir = os.path.join(path, "Projects")
project_directories = self.file_system_service.find_project_directories(
projects_base_dir)
runfolder = Runfolder(name=name, path=path, projects=None)
def project_from_dir(d):
return Project(name=os.path.basename(d),
path=os.path.join(projects_base_dir, d),
runfolder_path=path)
# There are scenarios where there are no project directories in the runfolder,
# i.e. when fastq files have not yet been divided into projects
if project_directories:
runfolder.projects = map(project_from_dir,
project_directories)
yield runfolder
def _get_runfolder_object(self, directory, ignore_errors=False):
name = os.path.basename(directory)
path = os.path.join(self._base_path, directory)
runfolder = Runfolder(name=name, path=path, projects=None)
self._add_checksums_for_runfolder(runfolder, ignore_errors=ignore_errors)
self._add_projects_to_runfolder(runfolder)
return runfolder
def _get_runfolders(self):
# TODO Filter based on expression for runfolders...
runfolder_expression = r"^\d+_"
directories = self.file_system_service.find_runfolder_directories(
self._base_path)
for directory in directories:
if re.match(runfolder_expression, os.path.basename(directory)):
name = os.path.basename(directory)
path = os.path.join(self._base_path, directory)
runfolder = Runfolder(name=name, path=path, projects=None)
self._add_projects_to_runfolder(runfolder)
yield runfolder
def organise_runfolder(self, runfolder_id, lanes, projects, force):
"""
Organise a runfolder in preparation for delivery. This will create separate subdirectories for each of the
projects and symlink all files belonging to the project to be delivered under this directory.
:param runfolder_id: the name of the runfolder to be organised
:param lanes: if not None, only samples on any of the specified lanes will be organised
:param projects: if not None, only projects in this list will be organised
:param force: if True, a previously organised project will be renamed with a unique suffix
:raises ProjectAlreadyOrganisedException: if a project has already been organised and force is False
:return: a Runfolder instance representing the runfolder after organisation
"""
# retrieve a runfolder object and project objects to be organised
runfolder = self.runfolder_service.find_runfolder(runfolder_id)
projects_on_runfolder = list(
self.runfolder_service.find_projects_on_runfolder(
runfolder, only_these_projects=projects))
# handle previously organised projects
organised_projects_path = os.path.join(runfolder.path, "Projects")
for project in projects_on_runfolder:
self.check_previously_organised_project(project,
organised_projects_path,
force)
# organise the projects and return a new Runfolder instance
organised_projects = []
for project in projects_on_runfolder:
organised_projects.append(
self.organise_project(runfolder, project,
organised_projects_path, lanes))
return Runfolder(runfolder.name,
runfolder.path,
projects=organised_projects,
checksums=runfolder.checksums)
fake_directories = [
"160930_ST-E00216_0111_BH37CWALXX", "160930_ST-E00216_0112_BH37CWALXX"
]
fake_projects = ["ABC_123", "DEF_456"]
def mock_file_system_service(directories, projects):
mock_file_system_service_instance = MagicMock()
mock_file_system_service_instance.find_runfolder_directories.return_value = directories
mock_file_system_service_instance.find_project_directories.return_value = projects
return mock_file_system_service_instance
_runfolder1 = Runfolder(name="160930_ST-E00216_0111_BH37CWALXX",
path="/foo/160930_ST-E00216_0111_BH37CWALXX")
_runfolder1.projects = [
RunfolderProject(
name="ABC_123",
path="/foo/160930_ST-E00216_0111_BH37CWALXX/Projects/ABC_123",
runfolder_path=_runfolder1.path),
RunfolderProject(
name="DEF_456",
path="/foo/160930_ST-E00216_0111_BH37CWALXX/Projects/DEF_456",
runfolder_path=_runfolder1.path)
]
_runfolder2 = Runfolder(name="160930_ST-E00216_0112_BH37CWALXX",
path="/foo/160930_ST-E00216_0112_BH37CWALXX")