Add standard format

.flake8

@@ -1,3 +1,4 @@
 [flake8]
 max-line-length=120
 exclude = docs/*,.tox/*
+ignore = E203, W503, W504, E704

.git-blame-ignore-revs

@@ -0,0 +1,5 @@
+# Initial commit to format the codebase with black
+e454428fdf5b3d32f8ffbe9bded3878a80e7b169
+# Initial commit to sort import on the codebase
+2d69e4fb6daf037cb2f4358fde0c6c96e3f7ca16
+

.github/workflows/format.yml

@@ -0,0 +1,19 @@
+name: Check format
+
+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-dev.txt
+      - name: Run black
+        run: black --check opentaxii/ tests/
+      - name: Run isort
+        run: isort --check-only opentaxii/ tests/

docs/conf.py

@@ -13,8 +13,9 @@
 # serve to show the default.
 
 import datetime
-import sys
 import os
+import sys
+
 import sphinx_rtd_theme
 
 # If extensions (or modules to document with autodoc) are in another directory,

docs/update_db_schema_diagram.py

@@ -5,9 +5,10 @@
 current_dir = os.path.dirname(__file__)
 sys.path.append(os.path.abspath(os.path.join(current_dir, "..")))
 
-from opentaxii.persistence.sqldb.models import Base
 from sqla_graphs import TableGrapher
 
+from opentaxii.persistence.sqldb.models import Base
+
 grapher = TableGrapher(
     style={"node_table_header": {"bgcolor": "#000080"}},
     graph_options={"size": "30,30!"},  # inches, this maps to 2880px

examples/hooks.py

@@ -1,6 +1,8 @@
 
 from opentaxii.signals import (
-    CONTENT_BLOCK_CREATED, INBOX_MESSAGE_CREATED, SUBSCRIPTION_CREATED
+    CONTENT_BLOCK_CREATED,
+    INBOX_MESSAGE_CREATED,
+    SUBSCRIPTION_CREATED,
 )
 
 

opentaxii/__init__.py

@@ -1,11 +1,11 @@
 '''
-    OpenTAXII, TAXII server implementation from EclecticIQ.
+OpenTAXII, TAXII server implementation from EclecticIQ.
 '''
+
 # flake8: noqa
 
 from ._version import __version__
-from .server import TAXIIServer
 from .config import ServerConfig
 from .entities import Account
-
 from .local import context
+from .server import TAXIIServer

opentaxii/auth/api.py

@@ -1,4 +1,3 @@
-
 class OpenTAXIIAuthAPI:
     '''Abstract class that represents OpenTAXII Authentication API.
 

opentaxii/auth/manager.py

@@ -47,9 +47,7 @@ def update_account(self, account, password):
         for colname, permission in list(account.permissions.items()):
             collection = self.server.servers.taxii1.persistence.get_collection(colname)
             if not collection:
-                log.warning(
-                    "update_account.unknown_collection",
-                    collection=colname)
+                log.warning("update_account.unknown_collection", collection=colname)
                 account.permissions.pop(colname)
         account = self.api.update_account(account, password)
         return account

opentaxii/auth/sqldb/api.py

@@ -2,10 +2,11 @@
 
 import jwt
 import structlog
+from sqlalchemy.orm import exc
+
 from opentaxii.auth import OpenTAXIIAuthAPI
 from opentaxii.common.sqldb import BaseSQLDatabaseAPI
 from opentaxii.entities import Account as AccountEntity
-from sqlalchemy.orm import exc
 
 from .models import Account, Base
 
@@ -32,16 +33,19 @@ class SQLDatabaseAPI(BaseSQLDatabaseAPI, OpenTAXIIAuthAPI):
     BASEMODEL = Base
 
     def __init__(
-            self,
-            db_connection,
-            create_tables=False,
-            secret=None,
-            token_ttl_secs=None,
-            **engine_parameters):
+        self,
+        db_connection,
+        create_tables=False,
+        secret=None,
+        token_ttl_secs=None,
+        **engine_parameters,
+    ):
         super().__init__(db_connection, create_tables, **engine_parameters)
         if not secret:
-            raise ValueError('Secret is not defined for %s.%s' % (
-                self.__module__, self.__class__.__name__))
+            raise ValueError(
+                'Secret is not defined for %s.%s'
+                % (self.__module__, self.__class__.__name__)
+            )
         self.secret = secret
         self.token_ttl_secs = token_ttl_secs or 60 * 60  # 60min
 
@@ -71,18 +75,25 @@ def get_account(self, token):
         return account_to_account_entity(account)
 
     def delete_account(self, username):
-        account = self.db.session.query(Account).filter_by(username=username).one_or_none()
+        account = (
+            self.db.session.query(Account).filter_by(username=username).one_or_none()
+        )
         if account:
             self.db.session.delete(account)
             self.db.session.commit()
 
     def get_accounts(self):
         return [
             account_to_account_entity(account)
-            for account in self.db.session.query(Account).all()]
+            for account in self.db.session.query(Account).all()
+        ]
 
     def update_account(self, obj, password=None):
-        account = self.db.session.query(Account).filter_by(username=obj.username).one_or_none()
+        account = (
+            self.db.session.query(Account)
+            .filter_by(username=obj.username)
+            .one_or_none()
+        )
         if not account:
             account = Account(username=obj.username)
             self.db.session.add(account)
@@ -120,4 +131,5 @@ def account_to_account_entity(account):
         id=account.id,
         username=account.username,
         is_admin=account.is_admin,
-        permissions=account.permissions)
+        permissions=account.permissions,
+    )

opentaxii/auth/sqldb/models.py

@@ -2,10 +2,7 @@
 
 from sqlalchemy import schema, types
 from sqlalchemy.ext.declarative import declarative_base
-
-from werkzeug.security import (
-    check_password_hash, generate_password_hash
-)
+from werkzeug.security import check_password_hash, generate_password_hash
 
 __all__ = ['Base', 'Account']
 
@@ -42,6 +39,8 @@ def permissions(self, permissions):
         for collection_name, permission in permissions.items():
             if permission not in ALL_PERMISSIONS:
                 raise ValueError(
-                    "Unknown permission '{}' specified for collection '{}'"
-                    .format(permission, collection_name))
+                    "Unknown permission '{}' specified for collection '{}'".format(
+                        permission, collection_name
+                    )
+                )
         self._permissions = json.dumps(permissions)

opentaxii/cli/__init__.py

@@ -1,9 +1,8 @@
-from opentaxii.server import TAXIIServer
 from opentaxii.config import ServerConfig
 from opentaxii.middleware import create_app
+from opentaxii.server import TAXIIServer
 from opentaxii.utils import configure_logging
 
-
 config = ServerConfig()
 configure_logging(config['logging'], plain=True)
 

opentaxii/cli/auth.py

@@ -7,7 +7,7 @@
 def create_account(argv=None):
     parser = argparse.ArgumentParser(
         description="Create Account via OpenTAXII Auth API",
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     parser.add_argument("-u", "--username", required=True)
     parser.add_argument("-p", "--password", required=True)
@@ -38,7 +38,7 @@ def is_truely(text):
 def update_account(argv=None):
     parser = argparse.ArgumentParser(
         description="Update Account via OpenTAXII Auth API",
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     fields = ("password", "admin")
     parser.add_argument("-u", "--username", required=True)

opentaxii/cli/run.py

@@ -1,4 +1,3 @@
-
 from opentaxii.cli import app
 
 

opentaxii/common/sqldb.py

@@ -20,7 +20,7 @@ def __init__(self, db_connection, create_tables=False, **engine_parameters):
                 "autocommit": False,
                 "autoflush": True,
             },
-            **engine_parameters
+            **engine_parameters,
         )
         if create_tables:
             self.db.create_all_tables()

opentaxii/config.py

@@ -99,7 +99,7 @@ def _get_env_config(env=os.environ, optional_env_var=None):
                 continue
             if key == optional_env_var:
                 continue
-            key = key[len(ENV_VAR_PREFIX):].lstrip("_").lower()
+            key = key[len(ENV_VAR_PREFIX) :].lstrip("_").lower()
             value = yaml.safe_load(value)
 
             container = result

opentaxii/entities.py

@@ -1,4 +1,3 @@
-
 class Account:
     '''Represents Account entity.
 
@@ -9,25 +8,21 @@ class Account:
     :param dict details: additional details of an account
     '''
 
-    def __init__(
-            self, id, username, permissions, is_admin=False, **details):
+    def __init__(self, id, username, permissions, is_admin=False, **details):
         self.id = id
         self.username = username
         self.permissions = permissions
         self.is_admin = is_admin
         self.details = details
 
     def can_read(self, collection_name):
-        return (
-            self.is_admin or
-            self.permissions.get(collection_name) in ('read', 'modify'))
+        return self.is_admin or self.permissions.get(collection_name) in (
+            'read',
+            'modify',
+        )
 
     def can_modify(self, collection_name):
-        return (
-            self.is_admin or
-            self.permissions.get(collection_name) == 'modify')
+        return self.is_admin or self.permissions.get(collection_name) == 'modify'
 
     def __repr__(self):
-        return (
-            'Account(username={}, is_admin={})'
-            .format(self.username, self.is_admin))
+        return 'Account(username={}, is_admin={})'.format(self.username, self.is_admin)

opentaxii/exceptions.py

@@ -1,4 +1,3 @@
-
 from .taxii.exceptions import UnauthorizedStatus
 
 

opentaxii/http.py

@@ -1,10 +1,8 @@
-
-from .middleware import create_app
 from .config import ServerConfig
+from .middleware import create_app
 from .server import TAXIIServer
 from .utils import configure_logging
 
-
 # This module is also used as a Gunicorn configuration module, i.e. passed
 # as ``--config python:opentaxii.http``. ``logconfig_dict`` module-level
 # variable is recognised by Gunicorn >= 19.8.  The desired effect is to
@@ -15,12 +13,7 @@
     'version': 1,
     'disable_existing_loggers': False,
     'root': {},
-    'loggers': {
-        'gunicorn.error': {
-            'level': 'INFO',
-            'propagate': True
-        }
-    }
+    'loggers': {'gunicorn.error': {'level': 'INFO', 'propagate': True}},
 }
 
 config_obj = ServerConfig()

opentaxii/middleware.py

@@ -2,8 +2,7 @@
 
 import structlog
 from flask import Flask, request
-from marshmallow.exceptions import \
-    ValidationError as MarshmallowValidationError
+from marshmallow.exceptions import ValidationError as MarshmallowValidationError
 from werkzeug.exceptions import HTTPException
 
 from .exceptions import InvalidAuthHeader
@@ -42,7 +41,9 @@ def create_app(server):
     app.register_error_handler(500, server.handle_internal_error)
     app.register_error_handler(StatusMessageException, server.handle_status_exception)
     app.register_error_handler(HTTPException, server.handle_http_exception)
-    app.register_error_handler(MarshmallowValidationError, server.handle_validation_exception)
+    app.register_error_handler(
+        MarshmallowValidationError, server.handle_validation_exception
+    )
     app.before_request(functools.partial(create_context_before_request, server))
     app.after_request(cleanup_context)
     return app

opentaxii/persistence/__init__.py

@@ -1,4 +1,7 @@
 # flake8: noqa
 from .api import OpenTAXII2PersistenceAPI, OpenTAXIIPersistenceAPI
-from .manager import (BasePersistenceManager, Taxii1PersistenceManager,
-                      Taxii2PersistenceManager)
+from .manager import (
+    BasePersistenceManager,
+    Taxii1PersistenceManager,
+    Taxii2PersistenceManager,
+)

opentaxii/persistence/api.py

@@ -1,9 +1,14 @@
 import datetime
 from typing import Dict, List, Optional, Tuple
 
-from opentaxii.taxii2.entities import (ApiRoot, Collection, Job,
-                                       ManifestRecord, STIXObject,
-                                       VersionRecord)
+from opentaxii.taxii2.entities import (
+    ApiRoot,
+    Collection,
+    Job,
+    ManifestRecord,
+    STIXObject,
+    VersionRecord,
+)
 
 
 class OpenTAXIIPersistenceAPI:
@@ -267,6 +272,7 @@ class OpenTAXII2PersistenceAPI:
 
     Stub, pending implementation.
     """
+
     @staticmethod
     def get_next_param(self, kwargs: Dict) -> str:
         """
@@ -295,9 +301,7 @@ def get_api_roots(self) -> List[ApiRoot]:
     def get_api_root(self, api_root_id: str) -> 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: str, job_id: str) -> Optional[Job]:
         raise NotImplementedError
 
     def get_collections(self, api_root_id: str) -> List[Collection]:
@@ -334,7 +338,9 @@ def get_objects(
     ) -> Tuple[List[STIXObject], bool, Optional[str]]:
         raise NotImplementedError
 
-    def add_objects(self, api_root_id: str, collection_id: str, objects: List[Dict]) -> Job:
+    def add_objects(
+        self, api_root_id: str, collection_id: str, objects: List[Dict]
+    ) -> Job:
         raise NotImplementedError
 
     def get_object(