def initialize_project(project: Project):
project_folder_path = server.get_project_folder_path(project.id)
os.makedirs(project_folder_path, exist_ok=True)
analysis_folder_path = server.get_analysis_folder_path(project.id)
os.makedirs(analysis_folder_path, exist_ok=True)
default_project_settings = ProjectSettings(name=project.name, generation=None)
save_project_settings(project.id, default_project_settings)
def convert_dat_to_pdb(project_id: str) -> bool:
if not server.project_file_exists(project_id, ProjectFile.TRAJECTORY_DAT) \
or not server.project_file_exists(project_id, ProjectFile.GENERATED_TOP):
return False
project_folder_path = server.get_project_folder_path(project_id)
process = subprocess.Popen(["traj2pdb.py", "trajectory.dat", "generated.top", "trajectory.pdb"],
cwd=project_folder_path)
process.wait()
return True
def execute_sim(job_id: str,
project_id: str,
user_id: str,
should_regenerate: bool,
fresh_execution=True,
execution_time=None):
job = Job(id=job_id,
process_name=execute_sim.request.id,
start_time=timezone.now(),
finish_time=None,
terminated=False)
job.save(update_fields=[
'process_name', 'start_time', 'finish_time', 'terminated'
])
# Clean the previous execution files
if should_regenerate or fresh_execution:
server.clean_project(project_id)
project_folder_path = server.get_project_folder_path(project_id)
stdout_file_path = server.get_project_file(project_id, ProjectFile.STDOUT)
if should_regenerate:
print("Regenerating topology for project: " + project_id)
generate_initial_configuration(project_id, stdout_file_path)
print("Received new execution for project: " + project_id)
stdout_log_file = open(file=stdout_file_path, mode='w')
process = subprocess.Popen(['oxDNA', 'input.txt'],
cwd=project_folder_path,
stdout=stdout_log_file)
try:
process.wait(timeout=execution_time)
except TimeoutExpired as ex:
process.terminate()
print("Simulation wall time of " + str(execution_time) +
"s reached for project: " + project_id)
stdout_log_file.close()
print("Simulation completed, generating pdb file for project: " +
project_id)
if not project_util.generate_sim_files(project_id):
print('Unable to convert simulation to visualizer output.')
execute_output_analysis(project_id, user_id)
job = Job(id=job_id, finish_time=timezone.now(), process_name=None)
job.save(update_fields=['process_name', 'finish_time'])
def convert_dat_to_pdb(project_id: str) -> bool:
if not server.project_file_exists(project_id, ProjectFile.TRAJECTORY_DAT) \
or not server.project_file_exists(project_id, ProjectFile.GENERATED_TOP):
return False
project_folder_path = server.get_project_folder_path(project_id)
process = subprocess.Popen([
'traj2pdb.py', ProjectFile.TRAJECTORY_DAT.value,
ProjectFile.GENERATED_TOP.value, ProjectFile.TRAJECTORY_PDB.value
],
cwd=project_folder_path)
process.wait()
return True
def zip_project(project_id: str) -> Optional[str]:
project_folder_path = server.get_project_folder_path(project_id)
project_zip_path = server.get_project_file(project_id, ProjectFile.PROJECT_ZIP)
if server.project_folder_exists(project_id):
if os.path.exists(project_zip_path):
os.remove(project_zip_path)
with ZipFile(project_zip_path, 'w') as archive:
for (dir_path, dir_names, file_names) in os.walk(project_folder_path):
file_names_len = len(file_names)
for i in range(0, file_names_len):
if '.zip' in file_names[i]:
continue
archive.write(os.path.join(dir_path, file_names[i]), file_names[i])
return project_zip_path
return None
def generate_input_file(project_id: str, data: Union[Dict, object]):
project_folder_path = server.get_project_folder_path(project_id)
input_path = os.path.join(project_folder_path,
defaults.DEFAULT_INPUT_FILE_NAME)
os.makedirs(project_folder_path, exist_ok=True)
input_file = open(file=input_path, mode='w')
for key, value in data.items():
if key == 'output_prefix' and value == '':
continue
if key == 'project_id':
continue
if key == 'T':
value = value + ' K'
input_file.write(key + ' = ' + str(value) + '\n')
input_file.close()
return messages.INPUT_GENERATED
def generate_sa(project_id: str, generation: Generation,
log_file_path: str) -> bool:
log = None
project_folder_path = server.get_project_folder_path(project_id)
if log_file_path is not None:
log = open(file=log_file_path, mode='w')
process = subprocess.Popen(args=generation.arguments,
cwd=os.path.join(os.getcwd(),
project_folder_path),
stderr=log)
else:
process = subprocess.Popen(args=generation.arguments,
cwd=os.path.join(os.getcwd(),
project_folder_path))
result_code = process.wait()
if log_file_path is not None:
log.close()
return result_code == 0
def generate_cadnano_interface(project_id: str, generation: Generation,
log_file_path: str) -> bool:
log = None
project_folder_path = server.get_project_folder_path(project_id)
if log_file_path is not None:
log = open(file=log_file_path, mode='w')
process = subprocess.Popen(args=generation.arguments,
cwd=os.path.join(os.getcwd(),
project_folder_path),
stderr=log)
else:
process = subprocess.Popen(args=generation.arguments,
cwd=os.path.join(os.getcwd(),
project_folder_path))
process.wait()
if log_file_path is not None:
log.close()
if os.path.isfile(os.path.join(project_folder_path, 'prova.top')):
os.rename(os.path.join(project_folder_path, 'prova.top'),
os.path.join(project_folder_path, 'generated.top'))
else:
return False
if os.path.isfile(os.path.join(project_folder_path, 'prova.conf')):
os.rename(os.path.join(project_folder_path, 'prova.conf'),
os.path.join(project_folder_path, 'generated.dat'))
else:
return False
if os.path.isfile(os.path.join(project_folder_path, 'virt2nuc')):
os.remove(os.path.join(project_folder_path, 'virt2nuc'))
return True
