Initial commit

src/api.py

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+from datetime import timedelta
+
+from fastapi import Depends, FastAPI, HTTPException, status
+from fastapi.security import OAuth2PasswordRequestForm
+
+from sqlmodel import select
+from sqlmodel.ext.asyncio.session import AsyncSession
+
+from sqlalchemy.orm import selectinload, joinedload
+
+from .models.authentication import (
+  User, UserRead,
+  Role, RoleRead,
+  UserRoleLink
+)
+from .models.category import (
+  CategoryGroup, CategoryModelType,
+  Category, CategoryRead
+)
+from .database import get_db_session, pandas_query
+from .security import (
+    User, Token,
+    authenticate_user, get_current_active_user, create_access_token,
+    )
+from .config import conf
+
+api = FastAPI()
+
+
+@api.get("/nothing")
+async def get_nothing() -> str:
+    return ''
+
+@api.post("/token", response_model=Token)
+async def login_for_access_token(form_data: OAuth2PasswordRequestForm = Depends()):
+    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"},
+        )
+    access_token_expires = timedelta(
+        minutes=conf.security['access_token_expire_minutes'])
+    access_token = create_access_token(
+        data={"sub": user.username},
+        expires_delta=access_token_expires)
+    return {"access_token": access_token, "token_type": "bearer"}
+
+@api.get("/users")
+async def get_users(
+    *, db_session: AsyncSession = Depends(get_db_session)
+    ) -> list[UserRead]:
+    query = select(User).options(selectinload(User.roles))
+    data = await db_session.exec(query)
+    return data.all()
+
+@api.get("/roles")
+async def get_roles(
+    *, db_session: AsyncSession = Depends(get_db_session)
+    ) -> list[RoleRead]:
+    query = select(Role).options(selectinload(Role.users))
+    data = await db_session.exec(query)
+    return data.all()
+
+@api.get("/categories")
+async def get_categories(
+    *, db_session: AsyncSession = Depends(get_db_session)
+    ) -> list[CategoryRead]:
+    query = select(Category)
+    data = await db_session.exec(query)
+    return data.all()
+
+
+@api.get("/categories_p")
+async def get_categories_p(
+    *, db_session: AsyncSession = Depends(get_db_session)
+    ) -> list[CategoryRead]:
+    query = select(Category)
+    df = await db_session.run_sync(pandas_query, query)
+    return df.to_dict(orient="records")
+
+# @api.get("/user-role")
+# async def get_user_role_relation(
+#     *, db_session: AsyncSession = Depends(get_db_session)
+#     ) -> list[UserRoleLink]:
+#     roles = await db_session.exec(select(UserRoleLink))
+#     return roles.all()

src/application.py

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+from fastapi import Depends, FastAPI
+from .api import api
+
+app = FastAPI()
+app.mount('/v2', api)

src/config.py

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+from os import environ
+import logging
+from pathlib import Path
+import yaml
+
+from sqlalchemy.ext.asyncio.engine import AsyncEngine
+from sqlalchemy.orm.session import sessionmaker
+
+logger = logging.getLogger(__name__)
+ENV = environ.get('env', 'prod')
+
+
+class Config:
+    app: dict
+    postgres: dict
+    storage: dict
+    map: dict
+    security: dict
+    version: str
+    engine: AsyncEngine
+    session_maker: sessionmaker
+
+    def __init__(self) -> None:
+        from ._version import __version__
+        self.version = __version__
+
+
+conf = Config()
+
+
+def set_app_config(app) -> None:
+    raw_configs = []
+    with open(Path(__file__).parent / 'defaults.yml') as cf:
+        raw_configs.append(cf.read())
+    for cf_path in (
+        Path(Path.cwd().root) / 'etc' / 'gisaf' / ENV,
+        Path.home() / '.local' / 'gisaf' / ENV
+    ):
+        try:
+            with open(cf_path.with_suffix('.yml')) as cf:
+                raw_configs.append(cf.read())
+        except FileNotFoundError:
+            pass
+
+    yaml_config = yaml.safe_load('\n'.join(raw_configs))
+
+    conf.app = yaml_config['app']
+    conf.postgres = yaml_config['postgres']
+    conf.storage = yaml_config['storage']
+    conf.map = yaml_config['map']
+    conf.security = yaml_config['security']
+    # create_dirs()
+
+
+# def create_dirs():
+#     """
+#     Create the directories needed for a proper functioning of the app
+#     """
+#     ## Avoid circular imports
+#     from treetrail.api_v1 import attachment_types
+#     for type in attachment_types:
+#         base_dir = Path(conf.storage['root_attachment_path']) / type
+#         base_dir.mkdir(parents=True, exist_ok=True)
+#     logger.info(f'Cache dir: {get_cache_dir()}')
+#     get_cache_dir().mkdir(parents=True, exist_ok=True)
+
+
+def get_cache_dir() -> Path:
+    return Path(conf.storage['root_cache_path'])

src/database.py

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+from sqlalchemy.ext.asyncio import create_async_engine
+from sqlmodel.ext.asyncio.session import AsyncSession
+
+import pandas as pd
+
+echo = False
+pg_url = "postgresql+asyncpg://avgis@localhost/avgis"
+
+engine = create_async_engine(pg_url, echo=echo)
+
+async def get_db_session():
+    async with AsyncSession(engine) as session:
+        yield session
+
+def pandas_query(session, query):
+    return pd.read_sql_query(query, session.connection())

src/models/authentication.py

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+from sqlmodel import Field, SQLModel, MetaData, Relationship
+
+schema = 'gisaf_admin'
+metadata = MetaData(schema=schema)
+
+class UserRoleLink(SQLModel, table=True):
+    metadata = metadata
+    __tablename__: str = 'roles_users'
+    user_id: int | None = Field(
+        default=None, foreign_key="user.id", primary_key=True
+    )
+    role_id: int | None = Field(
+        default=None, foreign_key="role.id", primary_key=True
+    )
+
+
+class UserBase(SQLModel):
+    username: str
+    email: str
+
+
+class User(UserBase, table=True):
+    metadata = metadata
+    id: int | None = Field(default=None, primary_key=True)
+    roles: list["Role"] = Relationship(back_populates="users",
+                                       link_model=UserRoleLink)
+    password: str | None = None
+
+
+class RoleBase(SQLModel):
+    name: str = Field(unique=True)
+
+class RoleWithDescription(RoleBase):
+    description: str | None
+
+class Role(RoleWithDescription, table=True):
+    metadata = metadata
+    id: int | None = Field(default=None, primary_key=True)
+    users: list[User] = Relationship(back_populates="roles",
+                                     link_model=UserRoleLink)
+
+
+class UserReadNoRoles(UserBase):
+    id: int
+    email: str | None
+
+
+class RoleRead(RoleBase):
+    id: int
+    users: list[UserReadNoRoles] = []
+
+
+class RoleReadNoUsers(RoleBase):
+    id: int
+
+
+class UserRead(UserBase):
+    id: int
+    email: str | None
+    roles: list[RoleReadNoUsers] = []

src/models/category.py

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+from typing import Any
+from sqlmodel import Field, SQLModel, MetaData, JSON, TEXT, Relationship, Column
+
+schema = 'gisaf_survey'
+metadata = MetaData(schema=schema)
+
+mapbox_type_mapping = {
+    'Point': 'symbol',
+    'Line': 'line',
+    'Polygon': 'fill',
+}
+
+class CategoryGroup(SQLModel, table=True):
+    metadata = metadata
+    name: str = Field(min_length=4, max_length=4,
+                      default=None, primary_key=True)
+    major: str
+    long_name: str
+
+    class Admin:
+        menu = 'Other'
+        flask_admin_model_view = 'CategoryGroupModelView'
+
+
+class CategoryModelType(SQLModel, table=True):
+    metadata = metadata
+    name: str = Field(default=None, primary_key=True)
+
+    class Admin:
+        menu = 'Other'
+        flask_admin_model_view = 'MyModelViewWithPrimaryKey'
+
+
+class CategoryBase(SQLModel):
+    metadata = metadata
+
+    class Admin:
+        menu = 'Other'
+        flask_admin_model_view = 'CategoryModelView'
+
+    name: str | None = Field(default=None, primary_key=True)
+    description: str | None
+    group: str = Field(min_length=4, max_length=4,
+                       foreign_key="CategoryGroup.name", index=True)
+    #group_: CategoryGroup = Relationship()
+    minor_group_1: str = Field(min_length=4, max_length=4, default='----')
+    minor_group_2: str = Field(min_length=4, max_length=4, default='----')
+    status: str = Field(min_length=1, max_length=1)
+    custom: bool | None
+    auto_import: bool = True
+    model_type: str = Field(max_length=50,
+                            foreign_key='CategoryModelType.name', default='Point')
+    long_name: str | None = Field(max_length=50)
+    style: str | None = Field(sa_column=Column(TEXT))
+    symbol: str | None = Field(max_length=1)
+    mapbox_type_custom: str | None = Field(max_length=32)
+    mapbox_paint: dict[str, Any] | None = Field(sa_column=Column(JSON, none_as_null=True))
+    mapbox_layout: dict[str, Any] | None = Field(sa_column=Column(JSON, none_as_null=True))
+    viewable_role: str | None
+    extra: dict[str, Any] | None = Field(sa_column=Column(JSON, none_as_null=True))
+
+
+class Category(CategoryBase, table=True):
+    name: str = Field(default=None, primary_key=True)
+
+
+class CategoryRead(CategoryBase):
+    name: str
+    domain = 'V'  # Survey
+
+    @property
+    def layer_name(self):
+        """
+        ISO compliant layer name (see ISO 13567)
+        :return: str
+        """
+        return '{self.domain}-{self.group:4s}-{self.minor_group_1:4s}-{self.minor_group_2:4s}-{self.status:1s}'.format(self=self)
+
+    @property
+    def table_name(self):
+        """
+        Table name
+        :return:
+        """
+        if self.minor_group_2 == '----':
+            return '{self.domain}_{self.group:4s}_{self.minor_group_1:4s}'.format(self=self)
+        else:
+            return '{self.domain}_{self.group:4s}_{self.minor_group_1:4s}_{self.minor_group_2:4s}'.format(self=self)
+
+    @property
+    def raw_survey_table_name(self):
+        """
+        Table name
+        :return:
+        """
+        if self.minor_group_2 == '----':
+            return 'RAW_{self.domain}_{self.group:4s}_{self.minor_group_1:4s}'.format(self=self)
+        else:
+            return 'RAW_{self.domain}_{self.group:4s}_{self.minor_group_1:4s}_{self.minor_group_2:4s}'.format(self=self)
+
+    @property
+    def mapbox_type(self):
+        return self.mapbox_type_custom or mapbox_type_mapping[self.model_type]

src/security.py

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+from datetime import datetime, timedelta
+from passlib.context import CryptContext
+
+from fastapi import Depends, HTTPException, status
+from fastapi.security import OAuth2PasswordBearer
+from pydantic import BaseModel
+from jose import JWTError, jwt
+
+from sqlalchemy.future import select
+
+from .config import conf
+from .models.authentication import User as UserInDB
+
+
+# openssl rand -hex 32
+# import secrets
+# SECRET_KEY = secrets.token_hex(32)
+ALGORITHM: str = "HS256"
+
+
+class Token(BaseModel):
+    access_token: str
+    token_type: str
+
+
+class TokenData(BaseModel):
+    username: str | None = None
+
+
+class User(BaseModel):
+    username: str
+    email: str | None = None
+    full_name: str | None = None
+    disabled: bool | None = None
+
+
+oauth2_scheme = OAuth2PasswordBearer(tokenUrl="token")
+
+pwd_context = CryptContext(schemes=["bcrypt"], deprecated="auto")
+
+
+def get_password_hash(password: str):
+    return pwd_context.hash(password)
+
+
+async def delete_user(username):
+    async with conf.session_maker.begin() as session:
+        user_in_db: UserInDB | None = await get_user(username)
+        if user_in_db is None:
+            raise SystemExit(f'User {username} does not exist in the database')
+        await session.delete(user_in_db)
+
+
+async def enable_user(username, enable=True):
+    async with conf.session_maker.begin() as session:
+        user_in_db: UserInDB | None = await get_user(username)
+        if user_in_db is None:
+            raise SystemExit(f'User {username} does not exist in the database')
+        user_in_db.disabled = not enable # type: ignore
+        session.add(user_in_db)
+        await session.commit()
+
+
+async def create_user(username: str, password: str, full_name: str,
+                      email: str, **kwargs):
+    async with conf.session_maker.begin() as session:
+        user_in_db: UserInDB | None = await get_user(username)
+        if user_in_db is None:
+            user = UserInDB(
+                username=username,
+                password=get_password_hash(password),
+                full_name=full_name,
+                email=email,
+                disabled=False
+            )
+            session.add(user)
+        else:
+            user_in_db.full_name = full_name # type: ignore
+            user_in_db.email = email # type: ignore
+            user_in_db.password = get_password_hash(password) # type: ignore
+        await session.commit()
+
+
+async def get_user(username: str) -> (UserInDB | None):
+    async with conf.session_maker.begin() as session:
+        req = await session.execute(select(UserInDB).where(UserInDB.username==username))
+        return req.scalar()
+
+
+def verify_password(plain_password, hashed_password):
+    return pwd_context.verify(plain_password, hashed_password)
+
+
+async def get_current_user(token: str = Depends(oauth2_scheme)) -> User:
+    credentials_exception = HTTPException(
+        status_code=status.HTTP_401_UNAUTHORIZED,
+        detail="Could not validate credentials",
+        headers={"WWW-Authenticate": "Bearer"},
+    )
+    try:
+        payload = jwt.decode(token, conf.security['secret_key'], algorithms=[ALGORITHM])
+        username: str = payload.get("sub", '')
+        if username == '':
+            raise credentials_exception
+        token_data = TokenData(username=username)
+    except JWTError:
+        raise credentials_exception
+    user = await get_user(username=token_data.username) # type: ignore
+    if user is None:
+        raise credentials_exception
+    return User(username=user.username, # type: ignore
+                email=user.email, # type: ignore
+                full_name=user.full_name) # type: ignore
+
+
+async def authenticate_user(username: str, password: str):
+    user = await get_user(username)
+    if not user:
+        return False
+    if not verify_password(password, user.password):
+        return False
+    return user
+
+
+async def get_current_active_user(current_user: User = Depends(get_current_user)):
+    if current_user.disabled:
+        raise HTTPException(status_code=400, detail="Inactive user")
+    return current_user
+
+
+def create_access_token(data: dict, expires_delta: timedelta):
+    to_encode = data.copy()
+    expire = datetime.utcnow() + expires_delta
+    to_encode.update({"exp": expire})
+    encoded_jwt = jwt.encode(to_encode,
+                             conf.security['secret_key'],
+                             algorithm=ALGORITHM)
+    return encoded_jwt