Merge pull request #22 from prefeitura-rio/development

Expansão da Cobertura de Testes, Melhorias na Validação e Modelo de Dados

api/app/main.py

@@ -47,7 +47,6 @@
 app.include_router(entities_mrg.router)
 app.include_router(entities.router)
 app.include_router(auth.router)
-# app.include_router(users.router)
 
 register_tortoise(
     app,

api/app/models.py

@@ -3,14 +3,14 @@
 from tortoise.models import Model
 
 from app.enums import RaceEnum, GenderEnum, NationalityEnum, ConditionCodeTypeEnum, CategoryEnum, ClinicalStatusEnum, SystemEnum
-
+from app.validators import CPFValidator
 
 
 class RawPatientRecord(Model):
-    id          = fields.UUIDField(pk=True)
-    patient_cpf = fields.CharField(max_length=11)
-    data        = fields.JSONField()
-    creator     = fields.ForeignKeyField("app.User", related_name="raw_record_creator", null=False)
+    id              = fields.UUIDField(pk=True)
+    patient_cpf     = fields.CharField(max_length=11, validators=[CPFValidator()])
+    data            = fields.JSONField()
+    data_source     = fields.ForeignKeyField("app.DataSource", related_name="raw_record_creator", null=False)
 
     created_at  = fields.DatetimeField(auto_now_add=True)
     updated_at  = fields.DatetimeField(auto_now=True)
@@ -21,9 +21,9 @@ class Meta:
 
 class RawPatientCondition(Model):
     id          = fields.UUIDField(pk=True)
-    patient_cpf = fields.CharField(max_length=11)
+    patient_cpf = fields.CharField(max_length=11, validators=[CPFValidator()])
     data        = fields.JSONField()
-    creator     = fields.ForeignKeyField("app.User", related_name="raw_condition_creator", null=False)
+    data_source = fields.ForeignKeyField("app.DataSource", related_name="raw_condition_creator", null=False)
 
     created_at  = fields.DatetimeField(auto_now_add=True)
     updated_at  = fields.DatetimeField(auto_now=True)
@@ -34,10 +34,10 @@ class Meta:
 
 class StandardizedPatientRecord(Model):
     id                  = fields.UUIDField(pk=True)
-    patient_cpf         = fields.CharField(max_length=11)
-    birth_city          = fields.CharField(max_length=32)
-    birth_state         = fields.CharField(max_length=32)
-    birth_country       = fields.CharField(max_length=32)
+    patient_cpf         = fields.CharField(max_length=11, validators=[CPFValidator()])
+    birth_city          = fields.ForeignKeyField("app.City", related_name="birthcity_stdpatients", null=True)
+    birth_state         = fields.ForeignKeyField("app.State", related_name="birthstate_stdpatients", null=True)
+    birth_country       = fields.ForeignKeyField("app.Country", related_name="birthcountry_stdpatients", null=True)
     birth_date          = fields.DateField()
     active              = fields.BooleanField(default=True,null=True)
     protected_person    = fields.BooleanField(null=True)
@@ -48,7 +48,7 @@ class StandardizedPatientRecord(Model):
     name                = fields.CharField(max_length=512)
     race                = fields.CharEnumField(enum_type=RaceEnum)
     gender              = fields.CharEnumField(enum_type=GenderEnum)
-    nationality         = fields.CharEnumField(enum_type=NationalityEnum)
+    nationality         = fields.CharEnumField(enum_type=NationalityEnum, null=True)
     raw_source          = fields.ForeignKeyField("app.RawPatientRecord", related_name="std_record_raw", null=False)
     cns_list            = fields.JSONField(null=True)
     address_list        = fields.JSONField(null=True)
@@ -62,11 +62,11 @@ class Meta:
 
 class StandardizedPatientCondition(Model):
     id              = fields.UUIDField(pk=True)
-    patient_cpf     = fields.CharField(max_length=11)
+    patient_cpf     = fields.CharField(max_length=11, validators=[CPFValidator()])
     cid             = fields.CharField(max_length=4)
     ciap            = fields.CharField(max_length=4, null=True)
-    clinical_status = fields.CharEnumField(enum_type=ClinicalStatusEnum, max_length=32)
-    category        = fields.CharEnumField(enum_type=CategoryEnum, max_length=32)
+    clinical_status = fields.CharEnumField(enum_type=ClinicalStatusEnum, null=True)
+    category        = fields.CharEnumField(enum_type=CategoryEnum, null=True)
     date            = fields.DatetimeField()
     raw_source      = fields.ForeignKeyField("app.RawPatientCondition", related_name="std_condition_raw", null=False)
     created_at      = fields.DatetimeField(auto_now_add=True)
@@ -77,9 +77,8 @@ class Meta:
 
 
 class DataSource(Model):
-    id          = fields.UUIDField(pk=True)
+    cnes        = fields.CharField(max_length=50, unique=True, pk=True)
     system      = fields.CharEnumField(SystemEnum)
-    cnes        = fields.CharField(max_length=50, unique=True)
     description = fields.CharField(max_length=512)
 
 
@@ -91,21 +90,18 @@ class ConditionCode(Model):
 
 
 class City(Model):
-    id      = fields.UUIDField(pk=True)
-    code    = fields.CharField(max_length=10, unique=True)
+    code    = fields.CharField(max_length=10, pk=True)
     name    = fields.CharField(max_length=512)
     state   = fields.ForeignKeyField("app.State", related_name="cities")
 
 
 class Country(Model):
-    id      = fields.UUIDField(pk=True)
-    code    = fields.CharField(max_length=10, unique=True)
+    code    = fields.CharField(max_length=10, pk=True)
     name    = fields.CharField(max_length=512)
 
 
 class State(Model):
-    id      = fields.UUIDField(pk=True)
-    code    = fields.CharField(max_length=10, unique=True)
+    code    = fields.CharField(max_length=10, pk=True)
     name    = fields.CharField(max_length=512)
     country = fields.ForeignKeyField("app.Country", related_name="states")
 
@@ -160,7 +156,7 @@ class PatientCns(Model):
 
 class Patient(Model):
     id                  = fields.UUIDField(pk=True)
-    patient_cpf         = fields.CharField(max_length=11, unique=True)
+    patient_cpf         = fields.CharField(max_length=11, unique=True, validators=[CPFValidator()])
     birth_date          = fields.DateField()
     active              = fields.BooleanField(default=True)
     protected_person    = fields.BooleanField(null=True)
@@ -171,17 +167,18 @@ class Patient(Model):
     name                = fields.CharField(max_length=512)
     race                = fields.ForeignKeyField("app.Race", related_name="patient_race")
     gender              = fields.ForeignKeyField("app.Gender", related_name="patient_gender")
-    nationality         = fields.ForeignKeyField("app.Nationality", related_name="patient_nationality")
+    nationality         = fields.ForeignKeyField("app.Nationality", related_name="patient_nationality", null=True)
     birth_city          = fields.ForeignKeyField("app.City", related_name="birth_patients", null=True)
     created_at          = fields.DatetimeField(auto_now_add=True)
+    updated_at          = fields.DatetimeField(auto_now=True)
 
 
 class PatientCondition(Model):
     id              = fields.UUIDField(pk=True)
     patient         = fields.ForeignKeyField("app.Patient", related_name="patientconditions")
     condition_code  = fields.ForeignKeyField("app.ConditionCode", related_name="codes")
-    clinical_status = fields.CharEnumField(enum_type=ClinicalStatusEnum, max_length=32)
-    category        = fields.CharEnumField(enum_type=CategoryEnum, max_length=32)
+    clinical_status = fields.CharEnumField(enum_type=ClinicalStatusEnum, null=True)
+    category        = fields.CharEnumField(enum_type=CategoryEnum, null=True)
     date            = fields.DatetimeField()
     created_at      = fields.DatetimeField(auto_now_add=True)
     updated_at      = fields.DatetimeField(auto_now=True)

api/app/pydantic_models.py

@@ -60,10 +60,23 @@ class TokenData(BaseModel):
     username: Optional[str]
 
 
+class RawDataModel(BaseModel):
+    patient_cpf: str
+    data: dict
+
+
+class RawDataListModel(BaseModel):
+    data_list: List[RawDataModel]
+    cnes: str
+
+class BulkInsertOutputModel(BaseModel):
+    count: int
+
+
 class ConditionListModel(BaseModel):
     code: str
-    clinical_status: str
-    category: str
+    clinical_status: Optional[str]
+    category: Optional[str]
     date: datetime
 
 
@@ -73,13 +86,13 @@ class PatientConditionListModel(BaseModel):
 
 
 class PatientModel(BaseModel):
-    active: Optional[bool]
+    active: Optional[bool] = True
     birth_city: Optional[str]
     birth_state: Optional[str]
     birth_country: Optional[str]
     birth_date: date
     patient_cpf: str
-    deceased: Optional[bool]
+    deceased: Optional[bool] = False
     deceased_date: Optional[date]
     father_name: Optional[str]
     gender: str
@@ -102,11 +115,11 @@ class CompletePatientModel(BaseModel):
     telecom_list: List[TelecomModel]
     address_list: List[AddressModel]
     condition_list: List[ConditionListModel]
-    active: Optional[bool]
+    active: Optional[bool] = True
     birth_city: Optional[str]
     birth_state: Optional[str]
     birth_country: Optional[str]
-    deceased: Optional[bool]
+    deceased: Optional[bool] = False
     deceased_date: Optional[date]
     father_name: Optional[str]
     mother_name: Optional[str]
@@ -138,9 +151,9 @@ class StandardizedTelecomModel(BaseModel):
 
 class StandardizedPatientRecordModel(BaseModel):
     active: Optional[bool] = True
-    birth_city: Optional[str]
-    birth_state: Optional[str]
-    birth_country: Optional[str]
+    birth_city_cod: Optional[str]
+    birth_state_cod: Optional[str]
+    birth_country_cod: Optional[str]
     birth_date: date
     patient_cpf: str
     deceased: Optional[bool] = False
@@ -162,7 +175,15 @@ class StandardizedPatientConditionModel(BaseModel):
     patient_cpf : str
     cid : str
     ciap: Optional[str]
-    clinical_status: str
-    category: str
+    clinical_status: Optional[str]
+    category: Optional[str]
     date: datetime
-    raw_source_id: Optional[str]
+    raw_source_id: Optional[str]
+
+
+class StandardizedPatientRecordListModel(BaseModel):
+    records: List[StandardizedPatientRecordModel]
+
+
+class StandardizedPatientConditionListModel(BaseModel):
+    conditions: List[StandardizedPatientConditionModel]

api/app/routers/auth.py

@@ -10,20 +10,34 @@
 from app.pydantic_models import Token
 from app.utils import authenticate_user, create_access_token
 
+
 router = APIRouter(prefix="/auth", tags=["Autenticação"])
 
 
-@router.post("/token", response_model=Token)
-async def login_for_access_token(form_data: Annotated[OAuth2PasswordRequestForm, Depends()]):
+@router.post("/token")
+async def login_for_access_token(
+    form_data: Annotated[OAuth2PasswordRequestForm, Depends()]
+) -> Token:
+
     user: User = await authenticate_user(form_data.username, form_data.password)
+
     if not user:
         raise HTTPException(
-            status_code=status.HTTP_401_UNAUTHORIZED,
-            detail="Incorrect username or password",
-            headers={"WWW-Authenticate": "Bearer"},
+            status_code = status.HTTP_401_UNAUTHORIZED,
+            detail      = "Incorrect username or password",
+            headers     = {"WWW-Authenticate": "Bearer"},
         )
-    access_token_expires = timedelta(minutes=config.JWT_ACCESS_TOKEN_EXPIRE_MINUTES)
+
+    access_token_expires = timedelta(
+        minutes = config.JWT_ACCESS_TOKEN_EXPIRE_MINUTES
+    )
+
     access_token = create_access_token(
-        data={"sub": user.username}, expires_delta=access_token_expires
+        data            = {"sub": user.username},
+        expires_delta   = access_token_expires
     )
-    return {"access_token": access_token, "token_type": "bearer"}
+
+    return {
+        "access_token": access_token,
+        "token_type": "bearer"
+    }

api/app/routers/entities.py

@@ -18,11 +18,12 @@
 router = APIRouter(prefix="/outros", tags=["Outras Entidades"])
 
 
-@router.post("/user", response_model=UserRegisterOutputModel, status_code=200)
+@router.post("/user", status_code=201)
 async def create_user(
-    _: Annotated[User, Depends(get_current_active_user)],
-    user: UserRegisterInputModel,
+    _       : Annotated[User, Depends(get_current_active_user)],
+    user    : UserRegisterInputModel,
 ) -> UserRegisterOutputModel:
+
     user_data = user.dict()
     datasource_data = user_data.pop('data_source')
 
@@ -32,16 +33,14 @@ async def create_user(
         description = datasource_data['description']
     )
 
-    user_data['password'] = password_hash(user_data['password'])
-    user_data['data_source'] = datasource_instance
+    user_data['password']       = password_hash(user_data['password'])
+    user_data['data_source']    = datasource_instance
 
-    user_instance = await User.create(
-        **user_data
-    )
+    user_instance = await User.create(**user_data)
 
     output = {
         **dict(user_instance),
         'data_source': dict(datasource_instance)
     }
 
-    return output
+    return output