84 lines
2.8 KiB
Python
84 lines
2.8 KiB
Python
from pathlib import Path
|
|
import pandas as pd
|
|
import shlex
|
|
import subprocess
|
|
from zipfile import ZipFile
|
|
import json
|
|
|
|
from django.conf import settings
|
|
from uuid import uuid4
|
|
|
|
|
|
def available_states():
|
|
states = []
|
|
# Read the timezones.csv file from the Synthea resources. This should give us all the 'state' on the first column
|
|
df = pd.read_csv(settings.SYNTHEA_STATES_DIR / 'timezones.csv', index_col=False)
|
|
for state in df[df.columns[0]].to_list():
|
|
states.append({'id' : state , 'name' : state})
|
|
|
|
#states = df[df.columns[0]].to_list()
|
|
# Sort on name
|
|
states = sorted(states, key=lambda k: k['name'].lower())
|
|
#states.sort()
|
|
return states
|
|
|
|
def available_modules():
|
|
# Assumption here: Only .json files in the main folder are modules. The rest are submodules...
|
|
modules = []
|
|
for module in settings.SYNTHEA_MODULE_DIR.iterdir():
|
|
if module.is_file() and module.suffix == '.json':
|
|
data = json.loads(module.read_text())
|
|
modules.append({'id' : module.name.replace('.json',''), 'name' : data['name']})
|
|
|
|
modules = sorted(modules, key=lambda k: k['name'].lower())
|
|
return modules
|
|
|
|
def run_synthea(state = None, population = None, gender = None, age = None, module = None):
|
|
# Add a unique dir to the output, so multiple Synthea processes can run parallel
|
|
temp_id = uuid4().hex
|
|
output_folder = settings.SYNTHEA_OUTPUT_DIR / temp_id
|
|
|
|
synthea_cmd = [settings.SYNTHEA_BASE_DIR / 'run_synthea','--exporter.baseDirectory',output_folder]
|
|
zip_file = 'Synthea_'
|
|
|
|
if population:
|
|
synthea_cmd.append('-p')
|
|
synthea_cmd.append(str(population))
|
|
zip_file += f'population_{population}_'
|
|
|
|
if gender:
|
|
synthea_cmd.append('-g')
|
|
synthea_cmd.append(gender.upper())
|
|
zip_file += f'gender_{gender}_'
|
|
|
|
if age:
|
|
synthea_cmd.append('-a')
|
|
synthea_cmd.append(age)
|
|
zip_file += f'age_{age}_'
|
|
|
|
if module:
|
|
synthea_cmd.append('-m')
|
|
synthea_cmd.append(module)
|
|
zip_file += f'module_{module}_'
|
|
|
|
if state:
|
|
synthea_cmd.append(state)
|
|
zip_file += f'state_{state}'
|
|
|
|
process_ok = False
|
|
log = ''
|
|
with subprocess.Popen(synthea_cmd,cwd=settings.SYNTHEA_BASE_DIR, stdout=subprocess.PIPE,stderr=subprocess.PIPE) as process:
|
|
for line in process.stdout:
|
|
line = line.decode('utf8')
|
|
log += line
|
|
if not process_ok:
|
|
process_ok = line.find('BUILD SUCCESSFUL') >= 0
|
|
|
|
if process_ok:
|
|
with ZipFile(f'{output_folder}/{zip_file}_{temp_id}.zip', 'w') as export:
|
|
for file in (output_folder / settings.SYNTHEA_EXPORT_TYPE).iterdir():
|
|
export.write(file,file.name)
|
|
|
|
return (log,Path(f'{output_folder}/{zip_file}_{temp_id}.zip'))
|
|
else:
|
|
raise Exception(log) |