def run_task(self, fw_spec):
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec)
wf = lp.get_wf_by_fw_id(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
database = fw_spec['mongo_database']
if self.criteria is not None:
entry = database.get_entry(criteria=self.criteria)
else:
entry = {}
inserted = []
for root_key, method_name in self.insertion_data.items():
get_results_method = getattr(wf_class, method_name)
results = get_results_method(wf)
for key, val in results.items():
entry[key] = jsanitize(val)
inserted.append(key)
if self.criteria is not None:
database.save_entry(entry=entry)
else:
database.insert_entry(entry=entry)
logging.info("Inserted data:\n{}".format('- {}\n'.join(inserted)))
return FWAction()
def run_task(self, fw_spec):
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec)
wf = lp.get_wf_by_fw_id(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
database = fw_spec['mongo_database']
if self.criteria is not None:
entry = database.get_entry(criteria=self.criteria)
else:
entry = {}
inserted = []
for root_key, method_name in self.insertion_data.items():
get_results_method = getattr(wf_class, method_name)
results = get_results_method(wf)
for key, val in results.items():
entry[key] = jsanitize(val)
inserted.append(key)
if self.criteria is not None:
database.save_entry(entry=entry)
else:
database.insert_entry(entry=entry)
logging.info("Inserted data:\n{}".format('- {}\n'.join(inserted)))
return FWAction()
def run_task(self, fw_spec):
self.db_data.connect_mongoengine()
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec)
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
get_results_method = getattr(wf_class, 'get_mongoengine_results')
#TODO extend for multiple documents?
document = get_results_method(wf)
with self.db_data.switch_collection(document.__class__) as document.__class__:
#TODO it would be better to try to remove automatically the FileFields already saved if the save of
# the document fails.
document.save()
def run_task(self, fw_spec):
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec)
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
deleted_files = []
# iterate over all the fws and launches
for fw_id, fw in wf.id_fw.items():
for l in fw.launches+fw.archived_launches:
l_dir = l.launch_dir
deleted_files.extend(self.delete_files(os.path.join(l_dir, TMPDIR_NAME)))
deleted_files.extend(self.delete_files(os.path.join(l_dir, INDIR_NAME)))
deleted_files.extend(self.delete_files(os.path.join(l_dir, OUTDIR_NAME), self.out_exts))
logging.info("Deleted files:\n {}".format("\n".join(deleted_files)))
return FWAction(stored_data={'deleted_files': deleted_files})
def run_task(self, fw_spec):
self.db_data.connect_mongoengine()
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec)
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
wf_module = importlib.import_module(wf.metadata['workflow_module'])
wf_class = getattr(wf_module, wf.metadata['workflow_class'])
get_results_method = getattr(wf_class, 'get_mongoengine_results')
#TODO extend for multiple documents?
document = get_results_method(wf)
with self.db_data.switch_collection(
document.__class__) as document.__class__:
#TODO it would be better to try to remove automatically the FileFields already saved if the save of
# the document fails.
document.save()
def run_task(self, fw_spec):
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec)
wf = lp.get_wf_by_fw_id_lzyfw(fw_id)
deleted_files = []
# iterate over all the fws and launches
for fw_id, fw in wf.id_fw.items():
for l in fw.launches + fw.archived_launches:
l_dir = l.launch_dir
deleted_files.extend(
self.delete_files(os.path.join(l_dir, TMPDIR_NAME)))
deleted_files.extend(
self.delete_files(os.path.join(l_dir, INDIR_NAME)))
deleted_files.extend(
self.delete_files(os.path.join(l_dir, OUTDIR_NAME),
self.out_exts))
logging.info("Deleted files:\n {}".format("\n".join(deleted_files)))
return FWAction(stored_data={'deleted_files': deleted_files})
def run_task(self, fw_spec):
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec=fw_spec)
def run_task(self, fw_spec):
lp, fw_id = get_lp_and_fw_id_from_task(self, fw_spec=fw_spec)