def finish(project):
log = task.logger
conf = task.conf
project_id = project["id"]
log.info("Cleaning project {0} ...".format(project_id))
projres = ProjectResults(project)
projres.clean(conf)
# save project.conf
projres.save_def()
def make_project(log, conf, project, base_path=None):
project_id = project["id"]
project_path = get_project_path(conf, project_id)
if not os.path.exists(project_path):
os.makedirs(project_path)
temp_path = get_temp_path(conf, project_id)
if not os.path.exists(temp_path):
os.makedirs(temp_path)
projdb_path = os.path.join(project_path, "project.db")
if "annotations" in project:
annotations = project["annotations"]
if not isinstance(annotations, dict):
log.warn("Overriding project annotations field with an empty dictionary")
project["annotations"] = annotations = {}
else:
project["annotations"] = annotations = {}
for key in project.keys():
if key not in ["id", "assembly", "files", "annotations", "oncodriveclust", "oncodrivefm"]:
value = project[key]
del project[key]
annotations[key] = value
project["path"] = project_path
project["temp_path"] = temp_path
project["db"] = projdb_path
if "assembly" not in project:
project["assembly"] = "hg19"
files = project["files"]
# make absolute paths if necessary
if base_path is not None:
for i, file in enumerate(files):
if not os.path.isabs(file):
files[i] = os.path.join(base_path, file)
missing_files = []
# copy variants files into project path
for i, file in enumerate(files):
file_base_name = os.path.basename(file)
if not os.path.dirname(file).startswith(project_path):
dst_name = "{0:02d}-{1}".format(i, file_base_name)
dst_path = os.path.join(project_path, dst_name)
log.info(" {0} --> {1}".format(file_base_name, dst_name))
if os.path.exists(file):
shutil.copy(file, dst_path)
files[i] = dst_path
else:
missing_files += [file]
else:
log.info(" {0}".format(file_base_name))
if len(missing_files) > 0:
raise Exception("Project {0} references some missing files:\n{1}".format(project_id, "\n".join(missing_files)))
# save project.conf
projres = ProjectResults(project)
projres.save_def()
