User Interface Backend

app.main

User Interface Backend - FastAPI interface

FastAPI app

User Interface Backend - FastAPI interface

class Token(**data)[source]

Bases: BaseModel

Token for accessing the UI backend service after user authentication.

access_token: str

token_type: str

class TokenData(**data)[source]

Bases: BaseModel

Additional data for user access token

username: Optional[str]

class User(**data)[source]

Bases: BaseModel

Website user for authentication

disabled: Optional[bool]

email: Optional[str]

full_name: Optional[str]

username: str

class UserInDB(**data)[source]

Bases: User

User in database

hashed_password: str

authenticate_user(db, username, password)[source]

Retrieve a user from the user database using username and password.

Parameters:

db (Dict) – User database
username (str) – Username
password (str) – Plaintext password

Return type:

Union[bool, User]

Returns: User object if username exists and password is correct, false otherwise

create_access_token(data, expires_delta=None)[source]

Create an access token for user authentication-

Parameters:

data (dict) – Data encoded by the token
expires_delta (Optional[timedelta]) – timedelta object specifying the expiration time (default: 15 minutes)

Return type:

str

Returns: Access token

async get_current_active_user(current_user=Depends(get_current_user))[source]

Ensure current user is active (non-disabled)

Parameters:: current_user (User) – Current user
Return type:: User

Returns: current_user if user is not disabled

async get_current_user(token=Depends(OAuth2PasswordBearer))[source]

Retrieve user from database by access token.

Parameters:: token (str) – Access token provided by user
Return type:: User

Returns: User if access token is valid.

get_password_hash(password)[source]

Hash plaintext password.

Parameters:: password (str) – Plaintext password
Return type:: str

Returns: Hashed password

async get_patient_info(patient_id, recommendation_id, current_user=Depends(get_current_active_user))[source]

Get patient data of a specific patient

Parameters:

patient_id (str) – Patient identifier
recommendation_id (str) – Guideline recommendation identifier.
current_user (User) – Authenticated user

Return type:

Dict

Returns: Patient data of a specific patient.

get_patients_from_recommendation(recommendation_id)[source]

Retrieve list of patients that were evaluated for a specific guideline recommendation.

Parameters:: recommendation_id (str) – Guideline recommendation identifier.
Return type:: List

Returns: List of patients

get_recommendation_ids()[source]

Retrieve all available guideline recommendation identifier from the guideline interface.

Returns: List of available guideline recommendation identifier

Return type:: Dict

async get_recommendation_list(current_user=Depends(get_current_active_user))[source]

Lists identifiers of available guideline recommendations.

Parameters:: current_user (User) – Authenticated user
Return type:: Dict

Returns: List of available guideline recommendation identifier

async get_recommendation_results(recommendation_id, current_user=Depends(get_current_active_user))[source]

Get results (summary + detailed) of the guideline recommendation evaluation on clinical data.

Parameters:

recommendation_id (str) – Guideline recommendation identifier.
current_user (User) – Authenticated user

Return type:

Dict

Returns: Results (summary + detailed) of the guideline recommendation evaluation

get_recommendation_results_details(recommendation_id)[source]

Retrieves the details of the guideline recommendation adherence evaluation.

The detailed results include all clinical data that was used to evaluated the guideline recommendation adherence.

Parameters:: recommendation_id (str) – Guideline recommendation identifier.
Return type:: DataFrame

Returns: Details of the guideline recommendation adherence evaluation.

get_recommendation_results_summary(recommendation_id)[source]

Retrieves the summary of the guideline recommendation adherence evaluation.

The summary includes patient identifier, ward, birth date, time on ICU and whether the guideline recommendation is applicable and implemented.

Parameters:: recommendation_id (str) – Guideline recommendation identifier.
Return type:: DataFrame

Returns: Summary of the guideline recommendation adherence evaluation

async get_recommendation_variable_names(recommendation_id, current_user=Depends(get_current_active_user))[source]

Lists clinical variable names required to evaluate a specific guideline recommendation.

Parameters:

recommendation_id (str) – Guideline recommendation identifier.
current_user (User) – Authenticated user

Return type:

Dict

Returns: Clinical variable names

get_recommendation_variables(recommendation_id)[source]

Retrieve the clinical variables names that are required to evaluate guideline recommendation adherence of the given recommendation.

Parameters:: recommendation_id (str) – Guideline recommendation identifier.
Return type:: DataFrame

Returns: List of clinical variables names

get_user(db, username)[source]

Retrieve a user from the user database

Parameters:

db (Dict) – User database
username (str) – Username

Return type:

Optional[User]

Returns: User entry from user database

async list_patient_by_recommendation(recommendation_id, current_user=Depends(get_current_active_user))[source]

List current patients for a specific guideline recommendation.

Parameters:

recommendation_id (str) – Guideline recommendation identifier.
current_user (User) – Authenticated user

Return type:

List

Returns: Current patients for specific guideline recommendation.

async list_patients(current_user=Depends(get_current_active_user))[source]

List current patients

Parameters:: current_user (User) – Authenticated user
Return type:: Dict

Returns: Current patients

load_user_db()[source]

Read the user database from yaml file

Returns: User database as dictionary

Return type:: Dict

async login_for_access_token(form_data=Depends(OAuth2PasswordRequestForm))[source]

Login form to retrieve access token.

Parameters:: form_data (OAuth2PasswordRequestForm) – Formulat data with “username” and “password” fields.
Return type:: Dict

Returns: Access token if the provided username and password are valid.

request_patient_data(patient_id, variable_name)[source]

Get clinical data for a specific patient.

Parameters:

patient_id (str) – Patient identifier
variable_name (List[str]) – List of clinical variable names to return for the patients.

Return type:

DataFrame

Returns: List of all available values for the requested variables for the specified patient.

async root()[source]

Server greeting.

Returns: Server greeting.

Return type:: Dict

verify_password(plain_password, hashed_password)[source]

Verify user provided password against hashed database password.

Parameters:

plain_password (str) – User provided plaintext password
hashed_password (str) – Hashed password from user database.

Return type:

bool

Returns: True if passwords match, False otherwise