def zip_simulation(project_id: str) -> Optional[str]:
project_zip_path = server.get_project_file(project_id, ProjectFile.SIMULATION_ZIP)
if server.simulation_files_exist(project_id):
(pdb_file_path, xtc_file_path) = server.get_simulation_file_paths(project_id)
with ZipFile(project_zip_path, 'w') as archive:
archive.write(pdb_file_path, 'trajectory.pdb')
archive.write(xtc_file_path, 'trajectory.xtc')
return project_zip_path
return None
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 parse_input_file(project_id: str) -> Union[str, Dict]:
input_file_path = server.get_project_file(project_id, ProjectFile.INPUT)
if not os.path.isfile(input_file_path):
return messages.MISSING_PROJECT_FILES
input_file = open(file=input_file_path, mode='r')
input_dictionary = {}
for line in input_file.readlines():
if line[len(line) - 1] == '\n':
line = line[:-1]
key_and_value = line.split(' = ')
input_dictionary[key_and_value[0]] = key_and_value[1]
return input_dictionary
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_sim_files(project_id: str) -> bool:
# Firstly, convert the 'trajectory.dat' file to 'trajectory.pdb'
if not convert_dat_to_pdb(project_id):
return False
# If the 'server-sims' directory doesn't exist, make it here
os.makedirs(server.get_simulation_folder_path(), exist_ok=True)
# Get the file paths for the output simulation PDB and XTC files
(pdb_file_path, xtc_file_path) = server.get_simulation_file_paths(project_id)
# The original 'trajectory.pdb' that will be converted to simulation files
original_pdb_path = server.get_project_file(project_id, ProjectFile.TRAJECTORY_PDB)
try:
os.remove(pdb_file_path)
os.remove(xtc_file_path)
except OSError:
pass
convert_pdb_to_xtc(input_file_path=original_pdb_path, output_file_path=xtc_file_path)
convert_pdb_to_single_frame(input_file_path=original_pdb_path, output_file_path=pdb_file_path)
return True
def is_executable(project_id: str, regenerate: bool) -> bool:
input_file = server.get_project_file(project_id, ProjectFile.INPUT)
if not os.path.isfile(input_file):
return False
project_settings = get_project_settings(project_id)
generation_method = project_settings.generation.method
if generation_method == 'generate-sa' or generation_method == 'generate-folded':
if regenerate:
sequence_file = server.get_project_file(project_id, ProjectFile.SEQUENCE)
if os.path.isfile(sequence_file):
return True
else:
return False
else:
generated_top = server.get_project_file(project_id, ProjectFile.GENERATED_TOP)
generated_dat = server.get_project_file(project_id, ProjectFile.GENERATED_DAT)
if os.path.isfile(generated_dat) and os.path.isfile(generated_top):
return True
else:
return False
elif generation_method == 'cadnano-interface':
if regenerate:
cadnano_project_file = server.get_project_file(project_id, ProjectFile.CADNANO)
if os.path.isfile(cadnano_project_file):
return True
else:
return False
else:
generated_top = server.get_project_file(project_id, ProjectFile.GENERATED_TOP)
generated_dat = server.get_project_file(project_id, ProjectFile.GENERATED_DAT)
if os.path.isfile(generated_dat) and os.path.isfile(generated_top):
return True
else:
return False
else:
return False
def save_project_settings(project_id: str, project_settings: ProjectSettings):
project_settings_file_path = server.get_project_file(project_id, ProjectFile.SETTINGS)
file_util.write_string_to_file(jsonpickle.encode(project_settings), project_settings_file_path)
def get_project_settings(project_id: str) -> ProjectSettings:
project_settings_file_path = server.get_project_file(project_id, ProjectFile.SETTINGS)
return jsonpickle.decode(file_util.get_file_contents_as_string(project_settings_file_path))