Adding extra example

migrations/example/versions/add_identifier.py

@@ -21,37 +21,53 @@
 
 def upgrade():
     # Defines upgrading function ran on upgrade command
-    response = requests.get(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS)
-    if response.status_code == 200:
-        patient_resource = response.json()
-        if 'identifier' not in patient_resource:
-            patient_resource['identifier'] = []
-        patient_resource['identifier'].append({
-            "use": "usual",
-            "system": "http://hospital.smarthealthit.org",
-            "value": "12345"
-        })
-        update_response = requests.put(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS, data=json.dumps(patient_resource))
-        if update_response.status_code == 200:
-            logging.info('Identifier appended successfully.')
-        else:
-            logging.error(f'Failed to append identifier: {update_response.status_code} {update_response.text}')
+    patient_resource = {
+        "resourceType": "Patient",
+        "id": PATIENT_ID,
+        "name": [
+            {
+                "use": "official",
+                "family": "Doe",
+                "given": [
+                    "John",
+                    "A"
+                ]
+            }
+        ],
+        "identifier": [
+            {
+                "system": "uwDAL_Clarity",
+                "value": "12345"
+            }
+        ],
+        "gender": "male",
+        "birthDate": "1980-01-01",
+        "telecom": [
+            {
+                "system": "phone",
+                "value": "555-555-5555",
+                "use": "home"
+            }
+        ]
+    }
+    response = requests.put(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS, data=json.dumps(patient_resource))
+    if response.status_code == 200 or response.status_code == 201:
+        logging.info('Patient updated successfully with phone number.')
     else:
-        logging.error(f'Failed to retrieve patient for updating: {response.status_code} {response.text}')
+        logging.error(f'Failed to update patient: {response.status_code} {response.text}')
 
 def downgrade():
     # Defines downgrading function ran on downgrade command
     response = requests.get(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS)
     if response.status_code == 200:
         patient_resource = response.json()
-        if 'identifier' in patient_resource:
-            patient_resource['identifier'] = [id for id in patient_resource['identifier'] if id['value'] != '12345']
-            update_response = requests.put(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS, data=json.dumps(patient_resource))
-            if update_response.status_code == 200:
-                logging.info('Identifier deleted successfully.')
-            else:
-                logging.error(f'Failed to delete identifier: {update_response.status_code} {update_response.text}')
+        # Remove the phone number if it exists
+        if 'telecom' in patient_resource:
+            patient_resource['telecom'] = [entry for entry in patient_resource['telecom'] if entry['system'] != 'phone' or entry['value'] != '555-555-5555']
+        response = requests.put(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS, data=json.dumps(patient_resource))
+        if response.status_code == 200 or response.status_code == 201:
+            logging.info('Patient phone number removed successfully.')
         else:
-            logging.info('No identifier to delete.')
+            logging.error(f'Failed to update patient: {response.status_code} {response.text}')
     else:
-        logging.error(f'Failed to retrieve patient for updating: {response.status_code} {response.text}')
+        logging.error(f'Failed to fetch patient: {response.status_code} {response.text}')

migrations/example/versions/add_mrn.py

@@ -0,0 +1,92 @@
+import requests
+import json
+import logging
+import os
+import sys
+
+# Migration script generated for adding MRNs to Patient resources
+revision = 'c5a1c49e-8efb-4610-b9d3-f59f98541f16'
+down_revision = 'd5a1c49e-8efb-4610-b9d3-f59f98541f16'
+
+# Configure logging
+logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
+
+# Define the FHIR server base URL
+FHIR_SERVER_URL = os.getenv('FHIR_URL')
+
+# Headers for FHIR requests
+HEADERS = {
+    'Content-Type': 'application/fhir+json'
+}
+
+# Mock patient to MRN map
+patient_mrn_map = [
+    {"PAT_ID": "12345", "MRN": "U6789012"},
+    {"PAT_ID": "67890", "MRN": "U3456789"}
+]
+
+def upgrade():
+    for record in patient_mrn_map:
+        pat_id = record['PAT_ID']
+        mrn = record['MRN']
+        add_mrn_to_patient(pat_id, mrn)
+
+def add_mrn_to_patient(pat_id, mrn):
+    # Fetch the existing patient resource
+    response = requests.get(f'{FHIR_SERVER_URL}/Patient',params={"identifier": f'uwDAL_Clarity|{pat_id}'}, headers=HEADERS)
+
+    if response.status_code == 200:
+        patients = response.json().get('entry', [])
+        if len(patients) > 1:
+            logging.error(f'Multiple patients found with PAT_ID {pat_id}. Halting the upgrade process.')
+            sys.exit(1)
+        elif len(patients) == 1:
+            patient_resource = patients[0]['resource']
+            # Add the new MRN identifier
+            patient_resource['identifier'].append({
+                "system": "urn:oid:1.2.3.4.5.6.7.8.9.10.11.12.13",
+                "value": mrn
+            })
+            # Update the patient resource
+            update_response = requests.put(f"{FHIR_SERVER_URL}/Patient/{patient_resource['id']}", headers=HEADERS, data=json.dumps(patient_resource))
+            if update_response.status_code in [200, 201]:
+                logging.info(f'Successfully updated Patient {pat_id} with MRN {mrn}.')
+            else:
+                logging.error(f'Failed to update Patient {pat_id}: {update_response.status_code} {update_response.text}')
+        else:
+            logging.error(f'No patient found with PAT_ID {pat_id}.')
+    else:
+        logging.error(f'Failed to fetch patient {pat_id}: {response.status_code} {response.text}')
+
+def downgrade():
+    for record in patient_mrn_map:
+        pat_id = record['PAT_ID']
+        mrn = record['MRN']
+        remove_mrn_from_patient(pat_id, mrn)
+
+def remove_mrn_from_patient(pat_id, mrn):
+    # Fetch the existing patient resource
+    response = requests.get(f'{FHIR_SERVER_URL}/Patient?identifier=uwDAL_Clarity|{pat_id}', headers=HEADERS)
+    if response.status_code == 200:
+        patients = response.json().get('entry', [])
+        if len(patients) > 1:
+            logging.error(f'Multiple patients found with PAT_ID {pat_id}. Halting the downgrade process.')
+            sys.exit(1)
+        elif len(patients) == 1:
+            patient_resource = patients[0]['resource']
+            # Remove the MRN identifier
+            patient_resource['identifier'] = [id for id in patient_resource['identifier'] if id['value'] != mrn]
+            # Update the patient resource
+            update_response = requests.put(f"{FHIR_SERVER_URL}/Patient/{patient_resource['id']}", headers=HEADERS, data=json.dumps(patient_resource))
+            if update_response.status_code in [200, 201]:
+                logging.info(f'Successfully removed MRN {mrn} from Patient {pat_id}.')
+            else:
+                logging.error(f'Failed to update Patient {pat_id}: {update_response.status_code} {update_response.text}')
+        else:
+            logging.error(f'No patient found with PAT_ID {pat_id}.')
+    else:
+        logging.error(f'Failed to fetch patient {pat_id}: {response.status_code} {response.text}')
+
+if __name__ == "__main__":
+    # Run the upgrade function
+    upgrade()

migrations/example/versions/create_patient.py

@@ -24,6 +24,12 @@ def upgrade():
     patient_resource = {
         "resourceType": "Patient",
         "id": PATIENT_ID,
+        "identifier": [
+            {
+                "system": "uwDAL_Clarity",
+                "value": "12345"
+            }
+        ],
         "name": [
             {
                 "use": "official",
@@ -37,16 +43,16 @@ def upgrade():
         "gender": "male",
         "birthDate": "1980-01-01"
     }
-    response = requests.put(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS, data=json.dumps(patient_resource))
+    response = requests.put(f'{FHIR_SERVER_URL}/Patient/examples', headers=HEADERS, data=json.dumps(patient_resource))
     if response.status_code == 200 or response.status_code == 201:
         logging.info('Patient created successfully.')
     else:
         logging.error(f'Failed to create patient: {response.status_code} {response.text}')
 
 def downgrade():
     # Defines downgrading function ran on downgrade command
-    response = requests.delete(f'{FHIR_SERVER_URL}/Patient/{PATIENT_ID}', headers=HEADERS)
+    response = requests.delete(f'{FHIR_SERVER_URL}/Patient/examples', headers=HEADERS)
     if response.status_code == 200 or response.status_code == 204:
         logging.info('Patient deleted successfully.')
     else:
-        logging.error(f'Failed to delete patient: {response.status_code} {response.text}')
+        logging.error(f'Failed to delete patient: {response.status_code} {response.text}')