Fix UUID json serialization

.github/workflows/mypy.yml

@@ -0,0 +1,17 @@
+name: Check mypy
+
+on:
+  - pull_request
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install deps
+        run: pip install -r requirements.txt -r requirements-dev.txt
+      - name: Run mypy
+        run: mypy

docs/installation/docker.rst

@@ -120,11 +120,12 @@ TAXII 2 instance with Compose
 
 Checkout the configuration at: :github-file:`examples/docker-compose-taxii2.yml <examples/docker-compose-taxii2.yml>`.
 
-To add dummy data, you can execute:
-
 .. code-block:: shell
 
-    # while the compose project is running
+    # Start
+    docker compose -f examples/docker-compose-taxii2.yml up
+
+    # To add dummy data, run this while the compose project is running
     docker exec -i examples-opentaxii-1 bash < examples/taxii2/data-setup.sh
 
 Full Example with Compose

opentaxii/auth/__init__.py

@@ -1,3 +1,8 @@
 # flake8: noqa
 from .api import OpenTAXIIAuthAPI
 from .manager import AuthManager
+
+__all__ = (
+    "AuthManager",
+    "OpenTAXIIAuthAPI",
+)

opentaxii/auth/sqldb/api.py

@@ -1,4 +1,5 @@
 from datetime import datetime, timedelta
+from typing import Optional
 
 import jwt
 import structlog
@@ -10,40 +11,41 @@
 
 from .models import Account, Base
 
-__all__ = ['SQLDatabaseAPI']
+__all__ = ["SQLDatabaseAPI"]
 
 
 log = structlog.getLogger(__name__)
 
 
 class SQLDatabaseAPI(BaseSQLDatabaseAPI, OpenTAXIIAuthAPI):
-    """Naive SQL database implementation of OpenTAXII Auth API.
-
-    Implementation will work with any DB supported by SQLAlchemy package.
-
-    :param str db_connection: a string that indicates database dialect and
-                          connection arguments that will be passed directly
-                          to :func:`~sqlalchemy.engine.create_engine` method.
-    :param bool create_tables=False: if True, tables will be created in the DB.
-    :param str secret: secret string used for token generation
-    :param int token_ttl_secs: TTL for JWT token, in seconds.
-    :param engine_parameters=None: if defined, these arguments would be passed to sqlalchemy.create_engine
-    """
 
     BASEMODEL = Base
 
     def __init__(
         self,
-        db_connection,
-        create_tables=False,
-        secret=None,
-        token_ttl_secs=None,
+        db_connection: str,
+        create_tables: bool = False,
+        secret: Optional[str] = None,
+        token_ttl_secs: Optional[int] = None,
         **engine_parameters,
     ):
+        """Naive SQL database implementation of OpenTAXII Auth API.
+
+        Implementation will work with any DB supported by SQLAlchemy package.
+
+        :param db_connection: a string that indicates database dialect and
+                            connection arguments that will be passed directly to
+                            :func:`~sqlalchemy.engine.create_engine` method.
+        :param create_tables=False: if True, tables will be created in the DB.
+        :param secret: secret string used for token generation
+        :param token_ttl_secs: TTL for JWT token, in seconds.
+        :param engine_parameters=None: if defined, these arguments would be passed
+            to sqlalchemy.create_engine
+        """
         super().__init__(db_connection, create_tables, **engine_parameters)
         if not secret:
             raise ValueError(
-                'Secret is not defined for %s.%s'
+                "Secret is not defined for %s.%s"
                 % (self.__module__, self.__class__.__name__)
             )
         self.secret = secret
@@ -59,7 +61,9 @@ def authenticate(self, username, password):
         return self._generate_token(account.id, ttl=self.token_ttl_secs)
 
     def create_account(self, username, password, is_admin=False):
-        account = Account(username=username, is_admin=is_admin, permissions={})
+        account = Account(  # type: ignore[misc]
+            username=username, is_admin=is_admin, permissions={}
+        )
         account.set_password(password)
         self.db.session.add(account)
         self.db.session.commit()

opentaxii/auth/sqldb/models.py

@@ -28,6 +28,7 @@ def set_password(self, password):
         self.password_hash = generate_password_hash(password)
 
     def is_password_valid(self, password):
+        assert self.password_hash is not None
         return check_password_hash(self.password_hash, password)
 
     @property

opentaxii/common/sqldb.py

@@ -3,7 +3,7 @@
 from opentaxii.sqldb_helper import SQLAlchemyDB
 
 try:
-    from sqlalchemy.orm import DeclarativeMeta
+    from sqlalchemy.orm import DeclarativeMeta  # type: ignore[attr-defined]
 except ImportError:
     from sqlalchemy.ext.declarative import DeclarativeMeta
 

opentaxii/config.py

@@ -112,7 +112,7 @@ def _get_env_config(env=os.environ, optional_env_var=None):
 
     @classmethod
     def _load_configs(cls, *configs):
-        result = dict()
+        result: dict = dict()
         for config in configs:
             # read content from path-like object
             if not isinstance(config, dict):

opentaxii/middleware.py

@@ -25,7 +25,7 @@ def create_app(server):
     """
 
     app = Flask(__name__)
-    app.taxii_server = server
+    app.taxii_server = server  # type: ignore[attr-defined]
 
     server.init_app(app)
 

opentaxii/persistence/__init__.py

@@ -1,7 +1,10 @@
 # flake8: noqa
 from .api import OpenTAXII2PersistenceAPI, OpenTAXIIPersistenceAPI
-from .manager import (
-    BasePersistenceManager,
-    Taxii1PersistenceManager,
-    Taxii2PersistenceManager,
+from .manager import Taxii1PersistenceManager, Taxii2PersistenceManager
+
+__all__ = (
+    "OpenTAXII2PersistenceAPI",
+    "OpenTAXIIPersistenceAPI",
+    "Taxii1PersistenceManager",
+    "Taxii2PersistenceManager",
 )

opentaxii/persistence/api.py

@@ -1,4 +1,5 @@
 import datetime
+import uuid
 from typing import Dict, List, Optional, Tuple
 
 from opentaxii.taxii2.entities import (
@@ -34,6 +35,18 @@ def create_service(self, service_entity):
         """
         raise NotImplementedError()
 
+    def update_service(self, obj):
+        """Update service. To implement in subclass"""
+        raise NotImplementedError()
+
+    def delete_service(self, service_id):
+        """Delete service. To implement in subclass"""
+        raise NotImplementedError()
+
+    def set_collection_services(self, collection_id, service_ids):
+        """Set collection's services. To implement in subclass"""
+        raise NotImplementedError()
+
     def create_collection(self, collection_entity):
         """Create a collection.
 
@@ -273,8 +286,11 @@ class OpenTAXII2PersistenceAPI:
     Stub, pending implementation.
     """
 
+    def init_app(self, app):
+        pass
+
     @staticmethod
-    def get_next_param(self, kwargs: Dict) -> str:
+    def get_next_param(kwargs: Dict) -> str:
         """
         Get value for `next` based on :class:`Dict` instance.
 
@@ -298,23 +314,25 @@ def get_api_roots(self) -> List[ApiRoot]:
         """
         raise NotImplementedError
 
-    def get_api_root(self, api_root_id: str) -> Optional[ApiRoot]:
+    def get_api_root(self, api_root_id: uuid.UUID) -> Optional[ApiRoot]:
         raise NotImplementedError
 
-    def get_job_and_details(self, api_root_id: str, job_id: str) -> Optional[Job]:
+    def get_job_and_details(
+        self, api_root_id: uuid.UUID, job_id: uuid.UUID
+    ) -> Optional[Job]:
         raise NotImplementedError
 
-    def get_collections(self, api_root_id: str) -> List[Collection]:
+    def get_collections(self, api_root_id: uuid.UUID) -> List[Collection]:
         raise NotImplementedError
 
     def get_collection(
-        self, api_root_id: str, collection_id_or_alias: str
+        self, api_root_id: uuid.UUID, collection_id_or_alias: str
     ) -> Optional[Collection]:
         raise NotImplementedError
 
     def get_manifest(
         self,
-        collection_id: str,
+        collection_id: uuid.UUID,
         limit: Optional[int] = None,
         added_after: Optional[datetime.datetime] = None,
         next_kwargs: Optional[Dict] = None,
@@ -327,7 +345,7 @@ def get_manifest(
 
     def get_objects(
         self,
-        collection_id: str,
+        collection_id: uuid.UUID,
         limit: Optional[int] = None,
         added_after: Optional[datetime.datetime] = None,
         next_kwargs: Optional[Dict] = None,
@@ -339,13 +357,13 @@ def get_objects(
         raise NotImplementedError
 
     def add_objects(
-        self, api_root_id: str, collection_id: str, objects: List[Dict]
+        self, api_root_id: uuid.UUID, collection_id: uuid.UUID, objects: List[Dict]
     ) -> Job:
         raise NotImplementedError
 
     def get_object(
         self,
-        collection_id: str,
+        collection_id: uuid.UUID,
         object_id: str,
         limit: Optional[int] = None,
         added_after: Optional[datetime.datetime] = None,
@@ -362,7 +380,7 @@ def get_object(
 
     def delete_object(
         self,
-        collection_id: str,
+        collection_id: uuid.UUID,
         object_id: str,
         match_version: Optional[List[str]] = None,
         match_spec_version: Optional[List[str]] = None,
@@ -371,13 +389,13 @@ def delete_object(
 
     def get_versions(
         self,
-        collection_id: str,
+        collection_id: uuid.UUID,
         object_id: str,
         limit: Optional[int] = None,
         added_after: Optional[datetime.datetime] = None,
         next_kwargs: Optional[Dict] = None,
         match_spec_version: Optional[List[str]] = None,
-    ) -> Tuple[List[VersionRecord], bool]:
+    ) -> Tuple[Optional[List[VersionRecord]], bool]:
         """
         Get all versions of single object from database.