def project_from_dir(d):
project = RunfolderProject(name=os.path.basename(d),
path=os.path.join(projects_base_dir, d),
runfolder_path=runfolder.path,
runfolder_name=runfolder.name)
project.project_files = self.get_report_files(
project, checksums=runfolder.checksums)
project.samples = self.sample_repository.get_samples(
project, runfolder)
return project
def project_from_dir(d):
project = RunfolderProject(name=os.path.basename(d),
path=os.path.join(projects_base_dir, d),
runfolder_path=runfolder.path,
runfolder_name=runfolder.name)
try:
project.project_files = self.get_report_files(
project, checksums=runfolder.checksums)
except ProjectReportNotFoundException as e:
log.warning(e)
project.samples = self.sample_repository.get_samples(
project, runfolder)
return project
def organise_project(self, runfolder, project, organised_projects_path,
lanes):
"""
Organise a project on a runfolder into its own directory and into a standard structure. If the project has
already been organised, a ProjectAlreadyOrganisedException will be raised, unless force is True. If force is
True, the existing project path will be renamed with a unique suffix.
:param runfolder: a Runfolder instance representing the runfolder on which the project belongs
:param project: a Project instance representing the project to be organised
:param lanes: if not None, only samples on any of the specified lanes will be organised
:param force: if True, a previously organised project will be renamed with a unique suffix
:raises ProjectAlreadyOrganisedException: if project has already been organised and force is False
:return: a Project instance representing the project after organisation
"""
# symlink the samples
organised_project_path = os.path.join(organised_projects_path,
project.name)
organised_project_runfolder_path = os.path.join(
organised_project_path, runfolder.name)
organised_samples = []
for sample in project.samples:
organised_samples.append(
self.organise_sample(sample, organised_project_runfolder_path,
lanes))
# symlink the project files
organised_project_files = []
if project.project_files:
project_file_base = self.file_system_service.dirname(
project.project_files[0].file_path)
for project_file in project.project_files:
organised_project_files.append(
self.organise_project_file(
project_file,
organised_project_runfolder_path,
project_file_base=project_file_base))
organised_project = RunfolderProject(project.name,
organised_project_path,
runfolder.path,
runfolder.name,
samples=organised_samples)
organised_project_files.append(
self.runfolder_service.dump_project_samplesheet(
runfolder, organised_project))
organised_project.project_files = organised_project_files
self.runfolder_service.dump_project_checksums(organised_project)
return organised_project
def runfolder_project(runfolder,
project_name="ABC_123",
sample_indexes=sample_index_generator(),
lane_numbers=lane_generator(),
project_root="Unaligned",
report_type=report_type_generator()):
project = RunfolderProject(name=project_name,
path=os.path.join(runfolder.path, project_root,
project_name),
runfolder_path=runfolder.path,
runfolder_name=runfolder.name)
project.project_files = project_report_files(project, next(report_type))
sample_names = sample_name_generator()
# a straight-forward sample with files on one lane
lane_number = next(lane_numbers)
samples = [
project_sample(project, next(sample_names), next(sample_indexes),
lane_number)
]
# a sample with files on two lanes
sample_name = next(sample_names)
sample_index = next(sample_indexes)
sample = project_sample(project, sample_name, sample_index, lane_number)
lane_number = next(lane_numbers)
t_sample = project_sample(project, sample_name, sample_index, lane_number)
sample.sample_files.extend(t_sample.sample_files)
samples.append(sample)
# a sample with two preps on two lanes and sample files in subdirectories
sample_name = next(sample_names)
t_samples = [
project_sample(project,
sample_name=sample_name,
sample_index=si,
lane_no=l,
sample_id="{}-{}-{}".format(sample_name, si, l))
for si in [next(sample_indexes),
next(sample_indexes)]
for l in [next(lane_numbers), next(lane_numbers)]
]
samples.extend(t_samples)
project.samples = samples
return project