Initial commit

webservice/apps/synthea/lib/utils.py

@@ -0,0 +1,83 @@
+from pathlib import Path
+import pandas as pd
+import shlex
+import subprocess
+from zipfile import ZipFile
+import json
+
+def available_states():
+    #TODO: Make a setting for this path
+    location = Path('/opt/development/synthea_webservice/synthea/src/main/resources/geography/')
+
+    df = pd.read_csv(location / 'timezones.csv', index_col=False)
+    # The state information is expected in the first column
+    states = df[df.columns[0]].to_list()
+    states.sort()
+    return states
+
+def available_modules():
+    #TODO: Make a setting for this path
+    location = Path('/opt/development/synthea_webservice/synthea/src/main/resources/modules/')
+
+    # Assumption here: A folder is a single module. And all .json in the main modules folder is a module.
+    modules = []
+    for module in location.iterdir():
+        if module.is_file() and module.suffix == '.json':
+            data = json.loads(module.read_text())
+            modules.append({'module' : 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):
+    # TODO: Make synthea setting(s)
+    location = '/opt/development/synthea_webservice/synthea/'
+    synthea_cmd = ['/opt/development/synthea_webservice/synthea/run_synthea']
+    zip_file = 'Synthea_'
+    zip_export = location
+
+    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=location, 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'{zip_export}/{zip_file}.zip', 'w') as export:
+            for file in Path(location + 'output/fhir_stu3').iterdir():
+                export.write(file,file.name)
+
+        return Path(f'{zip_export}/{zip_file}.zip')
+    else:
+        raise Exception(log)
+
+
+
+