113 lines
4.5 KiB
Python
113 lines
4.5 KiB
Python
from pathlib import Path
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import pandas as pd
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import shlex
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import subprocess
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from zipfile import ZipFile
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import json
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from django.conf import settings
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from uuid import uuid4
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def available_states():
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"""This method will return a sorted list of available states based on the 'geography/demographics.csv' in the `settings.SYNTHEA_RESOURCE_DIR` folder.
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Returns:
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List: Sorted list on state name with dicts holding the id and name of the state.
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"""
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states = []
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# Read the demographics.csv file from the Synthea resources and get all the unique state names
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# Important, the state name for synthea is case sensitive (field id)
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df = pd.read_csv(settings.SYNTHEA_RESOURCE_DIR / 'geography/demographics.csv', index_col=False)
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for state in df.STNAME.unique():
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states.append({'id' : state , 'name' : state})
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# Sort on name
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states = sorted(states, key=lambda s: s['name'].lower())
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return states
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def available_modules():
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"""This method will load all the available modules that are in the folder `settings.SYNTHEA_MODULE_DIR`. Only files ending on .json will be loaded.
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Returns:
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List: Sorted list on module name with dicts holding the id and name of the module.
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"""
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# Assumption here: Only .json files in the main folder are modules. The rest are submodules...
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modules = []
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for module in settings.SYNTHEA_MODULE_DIR.iterdir():
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if module.is_file() and module.suffix == '.json':
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data = json.loads(module.read_text())
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modules.append({'id' : module.name.replace('.json',''), 'name' : data['name']})
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modules = sorted(modules, key=lambda m: m['name'].lower())
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return modules
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def run_synthea(state, population = 50, gender = None, age = None, module = None):
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"""This module will run the Synthea application on the background. This method expects Synthea to be installed on the `settings.SYNTHEA_BASE_DIR` location.
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The output will be written to a unique folder in `settings.SYNTHEA_OUTPUT_DIR` that will be zipped and returned.
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It will return the log and the zipfile location for futher processing. The zip file will not be deleted afterwards. So cleanup needs to be done manually.
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Args:
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state (str, required): The state where to generate synthetic patient data for.
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population (int, optional): The amount of patients to generate. Defaults to 50.
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gender (str, optional): Either generate only male(m), only female(f), or None for both. Defaults to None.
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age (str, optional): This is the age range of the generated patients. Input is always like [min_age]-[max_age]. Defaults to None.
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module (str, optional): The module to use for generating patient data When None, all modules are used. Defaults to None.
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Raises:
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Exception: When the Synthea run fails it will return an Exception witht he Java error in it.
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Returns:
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(str,Path): The returning zipfile has the enabled options in the file name.
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"""
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# Add a unique dir to the output, so multiple Synthea processes can run parallel
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temp_id = uuid4().hex
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output_folder = settings.SYNTHEA_OUTPUT_DIR / temp_id
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synthea_cmd = [settings.SYNTHEA_BASE_DIR / 'run_synthea','--exporter.baseDirectory',output_folder]
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zip_file = 'Synthea_'
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if population:
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synthea_cmd.append('-p')
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synthea_cmd.append(str(population))
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zip_file += f'population_{population}_'
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if gender:
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synthea_cmd.append('-g')
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synthea_cmd.append(gender.upper())
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zip_file += f'gender_{gender}_'
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if age:
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synthea_cmd.append('-a')
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synthea_cmd.append(age)
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zip_file += f'age_{age}_'
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if module:
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synthea_cmd.append('-m')
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synthea_cmd.append(module)
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zip_file += f'module_{module}_'
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if state:
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synthea_cmd.append(state)
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zip_file += f'state_{state}'
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process_ok = False
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log = ''
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with subprocess.Popen(synthea_cmd,cwd=settings.SYNTHEA_BASE_DIR, stdout=subprocess.PIPE,stderr=subprocess.PIPE) as process:
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for line in process.stdout:
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line = line.decode('utf8')
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log += line
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if not process_ok:
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process_ok = line.find('BUILD SUCCESSFUL') >= 0
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if process_ok:
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with ZipFile(f'{output_folder}/{zip_file}_{temp_id}.zip', 'w') as export:
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for file in (output_folder / settings.SYNTHEA_EXPORT_TYPE).iterdir():
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export.write(file,file.name)
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return (log,Path(f'{output_folder}/{zip_file}_{temp_id}.zip'))
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else:
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raise Exception(log) |