add response parser
Browse files- extractcode.py +30 -0
- responseparser.py +266 -0
extractcode.py
ADDED
@@ -0,0 +1,30 @@
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import urllib.parse
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def extract_code_from_url(url: str) -> str:
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"""Extracts the 'code' parameter from a given URL."""
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parsed_url = urllib.parse.urlparse(url)
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query_params = urllib.parse.parse_qs(parsed_url.query)
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return query_params.get("code", [""])[0] # Return the first code or empty string if not found
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class CallbackManager:
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def __init__(self, redirect_uri: str, client_secret: str = None):
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client_id = os.getenv("APPID")
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if not client_id:
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raise ValueError("APPID environment variable not set.")
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workspace_id = os.getenv("WORKSPACE_URL")
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if not workspace_id:
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raise ValueError("WORKSPACE_URL environment variable not set.")
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self.api = MeldRxAPI(client_id, client_secret, workspace_id, redirect_uri)
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self.auth_code = None
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self.access_token = None
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def handle_callback(self, callback_url: str) -> str:
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"""Handles the callback URL and extracts the code automatically."""
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self.auth_code = extract_code_from_url(callback_url)
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if not self.auth_code:
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return "No authentication code found in URL."
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if self.api.authenticate_with_code(self.auth_code):
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self.access_token = self.api.access_token
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return f"Authentication successful! Access Token: {self.access_token[:10]}... (truncated)"
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return "Authentication failed. Please check the authorization code."
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responseparser.py
ADDED
@@ -0,0 +1,266 @@
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import json
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from datetime import datetime
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from typing import List, Dict, Optional
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class PatientDataExtractor:
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"""Class to extract patient data from a FHIR Bundle response and map it to discharge form fields."""
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def __init__(self, patient_data: str):
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"""Initialize with patient data in JSON string format."""
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self.data = json.loads(patient_data) if isinstance(patient_data, str) else patient_data
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self.patients = self._extract_patients()
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self.current_patient_idx = 0 # Default to first patient
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def _extract_patients(self) -> List[Dict]:
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"""Extract all patient entries from the Bundle."""
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if self.data.get("resourceType") != "Bundle" or "entry" not in self.data:
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raise ValueError("Invalid FHIR Bundle format")
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return [entry["resource"] for entry in self.data["entry"] if entry["resource"]["resourceType"] == "Patient"]
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def set_patient_by_index(self, index: int) -> bool:
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"""Set the current patient by index. Returns True if successful."""
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if 0 <= index < len(self.patients):
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self.current_patient_idx = index
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return True
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return False
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def set_patient_by_id(self, patient_id: str) -> bool:
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"""Set the current patient by FHIR Patient ID. Returns True if successful."""
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for i, patient in enumerate(self.patients):
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if patient["id"] == patient_id:
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self.current_patient_idx = i
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return True
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return False
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def _get_current_patient(self) -> Dict:
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"""Get the currently selected patient resource."""
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return self.patients[self.current_patient_idx]
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def get_first_name(self) -> str:
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"""Extract patient's first name."""
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patient = self._get_current_patient()
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names = patient.get("name", [])
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for name in names:
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if name.get("use") == "official" and "given" in name:
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return name["given"][0] # First given name
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return ""
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def get_last_name(self) -> str:
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"""Extract patient's last name."""
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patient = self._get_current_patient()
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names = patient.get("name", [])
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for name in names:
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if name.get("use") == "official" and "family" in name:
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return name["family"]
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return ""
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def get_middle_initial(self) -> str:
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"""Extract patient's middle initial (second given name initial if present)."""
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patient = self._get_current_patient()
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names = patient.get("name", [])
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for name in names:
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if name.get("use") == "official" and "given" in name and len(name["given"]) > 1:
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return name["given"][1][0] # First letter of second given name
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return ""
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def get_dob(self) -> str:
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"""Extract patient's date of birth."""
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patient = self._get_current_patient()
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return patient.get("birthDate", "")
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def get_age(self) -> str:
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"""Calculate patient's age based on birth date."""
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dob = self.get_dob()
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if not dob:
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return ""
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birth_date = datetime.strptime(dob, "%Y-%m-%d")
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today = datetime.now()
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age = today.year - birth_date.year - ((today.month, today.day) < (birth_date.month, birth_date.day))
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return str(age)
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def get_sex(self) -> str:
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"""Extract patient's sex (gender)."""
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patient = self._get_current_patient()
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return patient.get("gender", "").capitalize()
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def get_address(self) -> str:
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"""Extract patient's street address."""
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patient = self._get_current_patient()
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addresses = patient.get("address", [])
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return addresses[0]["line"][0] if addresses and "line" in addresses[0] else ""
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def get_city(self) -> str:
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"""Extract patient's city."""
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patient = self._get_current_patient()
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addresses = patient.get("address", [])
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return addresses[0]["city"] if addresses and "city" in addresses[0] else ""
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def get_state(self) -> str:
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"""Extract patient's state."""
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patient = self._get_current_patient()
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addresses = patient.get("address", [])
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return addresses[0]["state"] if addresses and "state" in addresses[0] else ""
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def get_zip_code(self) -> str:
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"""Extract patient's postal code."""
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patient = self._get_current_patient()
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addresses = patient.get("address", [])
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return addresses[0]["postalCode"] if addresses and "postalCode" in addresses[0] else ""
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def get_patient_dict(self) -> Dict[str, str]:
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"""Return a dictionary of patient data mapped to discharge form fields."""
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return {
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"first_name": self.get_first_name(),
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"last_name": self.get_last_name(),
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"middle_initial": self.get_middle_initial(),
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"dob": self.get_dob(),
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"age": self.get_age(),
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"sex": self.get_sex(),
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"address": self.get_address(),
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"city": self.get_city(),
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"state": self.get_state(),
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"zip_code": self.get_zip_code(),
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# Fields not directly available in Patient resource can be left blank or populated separately
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"doctor_first_name": "",
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"doctor_last_name": "",
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"doctor_middle_initial": "",
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"hospital_name": "",
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"doctor_address": "",
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"doctor_city": "",
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"doctor_state": "",
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"doctor_zip": "",
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"admission_date": "",
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"referral_source": "",
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"admission_method": "",
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"discharge_date": "",
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"discharge_reason": "",
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"date_of_death": "",
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"diagnosis": "",
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"procedures": "",
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"medications": "",
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"preparer_name": "",
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"preparer_job_title": ""
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}
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def get_all_patients(self) -> List[Dict[str, str]]:
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"""Return a list of dictionaries for all patients."""
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original_idx = self.current_patient_idx
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all_patients = []
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for i in range(len(self.patients)):
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self.set_patient_by_index(i)
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all_patients.append(self.get_patient_dict())
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self.set_patient_by_index(original_idx) # Restore original selection
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return all_patients
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def get_patient_ids(self) -> List[str]:
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"""Return a list of all patient IDs in the Bundle."""
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return [patient["id"] for patient in self.patients]
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# # Example usage with integration into app.py
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# def integrate_with_app(patient_data: str):
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# """Integrate PatientDataExtractor with the Gradio app."""
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# extractor = PatientDataExtractor(patient_data)
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# # Function to populate form with selected patient's data
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# def populate_form(patient_id: str):
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# if extractor.set_patient_by_id(patient_id):
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# patient_dict = extractor.get_patient_dict()
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# return list(patient_dict.values()) # Return values in order expected by display_form
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# return [""] * 28 # Return empty values if patient not found
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# # Modify the Gradio app to include patient selection
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# with gr.Blocks() as demo:
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# gr.Markdown("# Patient Discharge Form with MeldRx Integration")
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# with gr.Tab("Authenticate with MeldRx"):
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# gr.Markdown("## SMART on FHIR Authentication")
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# auth_url_output = gr.Textbox(label="Authorization URL", value=CALLBACK_MANAGER.get_auth_url(), interactive=False)
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# gr.Markdown("Copy the URL above, open it in a browser, log in, and paste the 'code' from the redirect URL below.")
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# auth_code_input = gr.Textbox(label="Authorization Code")
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# auth_submit = gr.Button("Submit Code")
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# auth_result = gr.Textbox(label="Authentication Result")
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# patient_data_button = gr.Button("Fetch Patient Data")
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# patient_data_output = gr.Textbox(label="Patient Data")
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# auth_submit.click(fn=CALLBACK_MANAGER.set_auth_code, inputs=auth_code_input, outputs=auth_result)
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# patient_data_button.click(fn=CALLBACK_MANAGER.get_patient_data, inputs=None, outputs=patient_data_output)
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# with gr.Tab("Discharge Form"):
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# gr.Markdown("## Select Patient")
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# patient_dropdown = gr.Dropdown(choices=extractor.get_patient_ids(), label="Select Patient ID")
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# populate_button = gr.Button("Populate Form with Patient Data")
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# gr.Markdown("## Patient Details")
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# with gr.Row():
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# first_name = gr.Textbox(label="First Name")
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# last_name = gr.Textbox(label="Last Name")
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196 |
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# middle_initial = gr.Textbox(label="Middle Initial")
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197 |
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# with gr.Row():
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# dob = gr.Textbox(label="Date of Birth")
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# age = gr.Textbox(label="Age")
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# sex = gr.Textbox(label="Sex")
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# address = gr.Textbox(label="Address")
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202 |
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# with gr.Row():
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# city = gr.Textbox(label="City")
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# state = gr.Textbox(label="State")
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# zip_code = gr.Textbox(label="Zip Code")
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# gr.Markdown("## Primary Healthcare Professional Details")
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# with gr.Row():
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# doctor_first_name = gr.Textbox(label="Doctor's First Name")
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209 |
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# doctor_last_name = gr.Textbox(label="Doctor's Last Name")
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210 |
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# doctor_middle_initial = gr.Textbox(label="Middle Initial")
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211 |
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# hospital_name = gr.Textbox(label="Hospital/Clinic Name")
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# doctor_address = gr.Textbox(label="Address")
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# with gr.Row():
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# doctor_city = gr.Textbox(label="City")
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# doctor_state = gr.Textbox(label="State")
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# doctor_zip = gr.Textbox(label="Zip Code")
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217 |
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# gr.Markdown("## Admission and Discharge Details")
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218 |
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# with gr.Row():
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219 |
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# admission_date = gr.Textbox(label="Date of Admission")
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220 |
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# referral_source = gr.Textbox(label="Source of Referral")
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221 |
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# admission_method = gr.Textbox(label="Method of Admission")
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222 |
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# with gr.Row():
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223 |
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# discharge_date = gr.Textbox(label="Date of Discharge")
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224 |
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# discharge_reason = gr.Radio(["Treated", "Transferred", "Discharge Against Advice", "Patient Died"], label="Discharge Reason")
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225 |
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# date_of_death = gr.Textbox(label="Date of Death (if applicable)")
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226 |
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# gr.Markdown("## Diagnosis & Procedures")
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227 |
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# diagnosis = gr.Textbox(label="Diagnosis")
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228 |
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# procedures = gr.Textbox(label="Operation & Procedures")
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229 |
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# gr.Markdown("## Medication Details")
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# medications = gr.Textbox(label="Medication on Discharge")
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# gr.Markdown("## Prepared By")
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# with gr.Row():
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# preparer_name = gr.Textbox(label="Name")
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# preparer_job_title = gr.Textbox(label="Job Title")
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# submit = gr.Button("Generate Form")
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# output = gr.Markdown()
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237 |
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# # Inputs list for populate_form and display_form
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239 |
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# inputs_list = [
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# first_name, last_name, middle_initial, dob, age, sex, address, city, state, zip_code,
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241 |
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# doctor_first_name, doctor_last_name, doctor_middle_initial, hospital_name, doctor_address,
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242 |
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# doctor_city, doctor_state, doctor_zip,
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243 |
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# admission_date, referral_source, admission_method, discharge_date, discharge_reason, date_of_death,
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# diagnosis, procedures, medications, preparer_name, preparer_job_title
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# ]
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246 |
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+
# # Populate form with patient data when button is clicked
|
248 |
+
# populate_button.click(
|
249 |
+
# fn=populate_form,
|
250 |
+
# inputs=patient_dropdown,
|
251 |
+
# outputs=inputs_list
|
252 |
+
# )
|
253 |
+
|
254 |
+
# # Generate the form output
|
255 |
+
# submit.click(
|
256 |
+
# display_form,
|
257 |
+
# inputs=inputs_list,
|
258 |
+
# outputs=output
|
259 |
+
# )
|
260 |
+
|
261 |
+
# return demo
|
262 |
+
|
263 |
+
# # Assuming patient_data is the JSON string from your example
|
264 |
+
# # patient_data = <your JSON string here>
|
265 |
+
# # demo = integrate_with_app(patient_data)
|
266 |
+
# # demo.launch()
|