File size: 12,252 Bytes
03b34b8 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 |
import json
from datetime import datetime
from typing import List, Dict, Optional
class PatientDataExtractor:
"""Class to extract patient data from a FHIR Bundle response and map it to discharge form fields."""
def __init__(self, patient_data: str):
"""Initialize with patient data in JSON string format."""
self.data = json.loads(patient_data) if isinstance(patient_data, str) else patient_data
self.patients = self._extract_patients()
self.current_patient_idx = 0 # Default to first patient
def _extract_patients(self) -> List[Dict]:
"""Extract all patient entries from the Bundle."""
if self.data.get("resourceType") != "Bundle" or "entry" not in self.data:
raise ValueError("Invalid FHIR Bundle format")
return [entry["resource"] for entry in self.data["entry"] if entry["resource"]["resourceType"] == "Patient"]
def set_patient_by_index(self, index: int) -> bool:
"""Set the current patient by index. Returns True if successful."""
if 0 <= index < len(self.patients):
self.current_patient_idx = index
return True
return False
def set_patient_by_id(self, patient_id: str) -> bool:
"""Set the current patient by FHIR Patient ID. Returns True if successful."""
for i, patient in enumerate(self.patients):
if patient["id"] == patient_id:
self.current_patient_idx = i
return True
return False
def _get_current_patient(self) -> Dict:
"""Get the currently selected patient resource."""
return self.patients[self.current_patient_idx]
def get_first_name(self) -> str:
"""Extract patient's first name."""
patient = self._get_current_patient()
names = patient.get("name", [])
for name in names:
if name.get("use") == "official" and "given" in name:
return name["given"][0] # First given name
return ""
def get_last_name(self) -> str:
"""Extract patient's last name."""
patient = self._get_current_patient()
names = patient.get("name", [])
for name in names:
if name.get("use") == "official" and "family" in name:
return name["family"]
return ""
def get_middle_initial(self) -> str:
"""Extract patient's middle initial (second given name initial if present)."""
patient = self._get_current_patient()
names = patient.get("name", [])
for name in names:
if name.get("use") == "official" and "given" in name and len(name["given"]) > 1:
return name["given"][1][0] # First letter of second given name
return ""
def get_dob(self) -> str:
"""Extract patient's date of birth."""
patient = self._get_current_patient()
return patient.get("birthDate", "")
def get_age(self) -> str:
"""Calculate patient's age based on birth date."""
dob = self.get_dob()
if not dob:
return ""
birth_date = datetime.strptime(dob, "%Y-%m-%d")
today = datetime.now()
age = today.year - birth_date.year - ((today.month, today.day) < (birth_date.month, birth_date.day))
return str(age)
def get_sex(self) -> str:
"""Extract patient's sex (gender)."""
patient = self._get_current_patient()
return patient.get("gender", "").capitalize()
def get_address(self) -> str:
"""Extract patient's street address."""
patient = self._get_current_patient()
addresses = patient.get("address", [])
return addresses[0]["line"][0] if addresses and "line" in addresses[0] else ""
def get_city(self) -> str:
"""Extract patient's city."""
patient = self._get_current_patient()
addresses = patient.get("address", [])
return addresses[0]["city"] if addresses and "city" in addresses[0] else ""
def get_state(self) -> str:
"""Extract patient's state."""
patient = self._get_current_patient()
addresses = patient.get("address", [])
return addresses[0]["state"] if addresses and "state" in addresses[0] else ""
def get_zip_code(self) -> str:
"""Extract patient's postal code."""
patient = self._get_current_patient()
addresses = patient.get("address", [])
return addresses[0]["postalCode"] if addresses and "postalCode" in addresses[0] else ""
def get_patient_dict(self) -> Dict[str, str]:
"""Return a dictionary of patient data mapped to discharge form fields."""
return {
"first_name": self.get_first_name(),
"last_name": self.get_last_name(),
"middle_initial": self.get_middle_initial(),
"dob": self.get_dob(),
"age": self.get_age(),
"sex": self.get_sex(),
"address": self.get_address(),
"city": self.get_city(),
"state": self.get_state(),
"zip_code": self.get_zip_code(),
# Fields not directly available in Patient resource can be left blank or populated separately
"doctor_first_name": "",
"doctor_last_name": "",
"doctor_middle_initial": "",
"hospital_name": "",
"doctor_address": "",
"doctor_city": "",
"doctor_state": "",
"doctor_zip": "",
"admission_date": "",
"referral_source": "",
"admission_method": "",
"discharge_date": "",
"discharge_reason": "",
"date_of_death": "",
"diagnosis": "",
"procedures": "",
"medications": "",
"preparer_name": "",
"preparer_job_title": ""
}
def get_all_patients(self) -> List[Dict[str, str]]:
"""Return a list of dictionaries for all patients."""
original_idx = self.current_patient_idx
all_patients = []
for i in range(len(self.patients)):
self.set_patient_by_index(i)
all_patients.append(self.get_patient_dict())
self.set_patient_by_index(original_idx) # Restore original selection
return all_patients
def get_patient_ids(self) -> List[str]:
"""Return a list of all patient IDs in the Bundle."""
return [patient["id"] for patient in self.patients]
# # Example usage with integration into app.py
# def integrate_with_app(patient_data: str):
# """Integrate PatientDataExtractor with the Gradio app."""
# extractor = PatientDataExtractor(patient_data)
# # Function to populate form with selected patient's data
# def populate_form(patient_id: str):
# if extractor.set_patient_by_id(patient_id):
# patient_dict = extractor.get_patient_dict()
# return list(patient_dict.values()) # Return values in order expected by display_form
# return [""] * 28 # Return empty values if patient not found
# # Modify the Gradio app to include patient selection
# with gr.Blocks() as demo:
# gr.Markdown("# Patient Discharge Form with MeldRx Integration")
# with gr.Tab("Authenticate with MeldRx"):
# gr.Markdown("## SMART on FHIR Authentication")
# auth_url_output = gr.Textbox(label="Authorization URL", value=CALLBACK_MANAGER.get_auth_url(), interactive=False)
# gr.Markdown("Copy the URL above, open it in a browser, log in, and paste the 'code' from the redirect URL below.")
# auth_code_input = gr.Textbox(label="Authorization Code")
# auth_submit = gr.Button("Submit Code")
# auth_result = gr.Textbox(label="Authentication Result")
# patient_data_button = gr.Button("Fetch Patient Data")
# patient_data_output = gr.Textbox(label="Patient Data")
# auth_submit.click(fn=CALLBACK_MANAGER.set_auth_code, inputs=auth_code_input, outputs=auth_result)
# patient_data_button.click(fn=CALLBACK_MANAGER.get_patient_data, inputs=None, outputs=patient_data_output)
# with gr.Tab("Discharge Form"):
# gr.Markdown("## Select Patient")
# patient_dropdown = gr.Dropdown(choices=extractor.get_patient_ids(), label="Select Patient ID")
# populate_button = gr.Button("Populate Form with Patient Data")
# gr.Markdown("## Patient Details")
# with gr.Row():
# first_name = gr.Textbox(label="First Name")
# last_name = gr.Textbox(label="Last Name")
# middle_initial = gr.Textbox(label="Middle Initial")
# with gr.Row():
# dob = gr.Textbox(label="Date of Birth")
# age = gr.Textbox(label="Age")
# sex = gr.Textbox(label="Sex")
# address = gr.Textbox(label="Address")
# with gr.Row():
# city = gr.Textbox(label="City")
# state = gr.Textbox(label="State")
# zip_code = gr.Textbox(label="Zip Code")
# gr.Markdown("## Primary Healthcare Professional Details")
# with gr.Row():
# doctor_first_name = gr.Textbox(label="Doctor's First Name")
# doctor_last_name = gr.Textbox(label="Doctor's Last Name")
# doctor_middle_initial = gr.Textbox(label="Middle Initial")
# hospital_name = gr.Textbox(label="Hospital/Clinic Name")
# doctor_address = gr.Textbox(label="Address")
# with gr.Row():
# doctor_city = gr.Textbox(label="City")
# doctor_state = gr.Textbox(label="State")
# doctor_zip = gr.Textbox(label="Zip Code")
# gr.Markdown("## Admission and Discharge Details")
# with gr.Row():
# admission_date = gr.Textbox(label="Date of Admission")
# referral_source = gr.Textbox(label="Source of Referral")
# admission_method = gr.Textbox(label="Method of Admission")
# with gr.Row():
# discharge_date = gr.Textbox(label="Date of Discharge")
# discharge_reason = gr.Radio(["Treated", "Transferred", "Discharge Against Advice", "Patient Died"], label="Discharge Reason")
# date_of_death = gr.Textbox(label="Date of Death (if applicable)")
# gr.Markdown("## Diagnosis & Procedures")
# diagnosis = gr.Textbox(label="Diagnosis")
# procedures = gr.Textbox(label="Operation & Procedures")
# gr.Markdown("## Medication Details")
# medications = gr.Textbox(label="Medication on Discharge")
# gr.Markdown("## Prepared By")
# with gr.Row():
# preparer_name = gr.Textbox(label="Name")
# preparer_job_title = gr.Textbox(label="Job Title")
# submit = gr.Button("Generate Form")
# output = gr.Markdown()
# # Inputs list for populate_form and display_form
# inputs_list = [
# first_name, last_name, middle_initial, dob, age, sex, address, city, state, zip_code,
# doctor_first_name, doctor_last_name, doctor_middle_initial, hospital_name, doctor_address,
# doctor_city, doctor_state, doctor_zip,
# admission_date, referral_source, admission_method, discharge_date, discharge_reason, date_of_death,
# diagnosis, procedures, medications, preparer_name, preparer_job_title
# ]
# # Populate form with patient data when button is clicked
# populate_button.click(
# fn=populate_form,
# inputs=patient_dropdown,
# outputs=inputs_list
# )
# # Generate the form output
# submit.click(
# display_form,
# inputs=inputs_list,
# outputs=output
# )
# return demo
# # Assuming patient_data is the JSON string from your example
# # patient_data = <your JSON string here>
# # demo = integrate_with_app(patient_data)
# # demo.launch() |