vantage6-algorithm-store 5.0.2rc2__tar.gz → 5.0.3__tar.gz

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: vantage6-algorithm-store
-Version: 5.0.2rc2
+Version: 5.0.3
 Summary: Vantage6 algorithm store
 Author: Vantage6 Team
 Maintainer-email: Frank Martin <f.martin@iknl.nl>, Bart van Beusekom <b.vanbeusekom@iknl.nl>
@@ -18,8 +18,8 @@ Requires-Dist: python-keycloak==5.5.0
 Requires-Dist: requests==2.33.1
 Requires-Dist: schema==0.7.5
 Requires-Dist: sqlalchemy==2.0.37
-Requires-Dist: vantage6-common==5.0.2rc2
-Requires-Dist: vantage6==5.0.2rc2
+Requires-Dist: vantage6-common==5.0.3
+Requires-Dist: vantage6==5.0.3
 Provides-Extra: dev
 Requires-Dist: black; extra == 'dev'
 Requires-Dist: coverage==7.10.2; extra == 'dev'

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vantage6-algorithm-store"
-version = "5.0.2rc2"
+version = "5.0.3"
 description = "Vantage6 algorithm store"
 readme = "README.md"
 license = {text = "MIT"}
@@ -30,8 +30,8 @@ dependencies = [
     "requests==2.33.1",
     "schema==0.7.5",
     "sqlalchemy==2.0.37",
-    "vantage6-common==5.0.2rc2",
-    "vantage6==5.0.2rc2",
+    "vantage6-common==5.0.3",
+    "vantage6==5.0.3",
 ]
 
 [project.optional-dependencies]

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/tests_store/base/unittest_base.py

@@ -2,7 +2,9 @@ import os
 import unittest
 from http import HTTPStatus
 from unittest.mock import Mock, patch
+from uuid import uuid1
 
+import jwt
 from cryptography.hazmat.backends import default_backend
 from cryptography.hazmat.primitives import serialization
 from cryptography.hazmat.primitives.asymmetric import rsa
@@ -107,10 +109,10 @@ class TestResources(unittest.TestCase):
     def register_user(
         self,
         username: str = "test_user",
-        user_roles: list[Role] = None,
-        user_rules: list[Rule] = None,
+        user_roles: list[Role] | None = None,
+        user_rules: list[Rule] | None = None,
         organization_id: int = 1,
-        authenticate_mock: Mock = None,
+        authenticate_mock: Mock | None = None,
         auth: bool = True,
     ) -> User:
         user = User(username=username, organization_id=organization_id)
@@ -147,3 +149,23 @@ class TestResources(unittest.TestCase):
                 rules=role["rules"],
             )
             new_role.save()
+
+    def login_node(self) -> dict:
+        """
+        Build headers with a real node JWT (mirrors vantage6-hq's `login_node` test
+        helper), for testing endpoints that recognize nodes via the
+        `vantage6_client_type` claim rather than a registered store `User`.
+
+        Returns
+        -------
+        dict
+            Authorization header with a valid node bearer token.
+        """
+        mock_claims = {
+            "sub": str(uuid1()),
+            "vantage6_client_type": "node",
+            "exp": 9999999999,
+            "iat": 0,
+        }
+        mock_token = jwt.encode(mock_claims, MOCK_PRIVATE_KEY_PEM, algorithm="RS256")
+        return {"Authorization": f"Bearer {mock_token}"}

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/tests_store/resources/test_algorithm.py

@@ -136,6 +136,63 @@ class TestAlgorithmResources(TestResources):
         policy.delete()
         user.delete()
 
+    def test_view_algorithm_decorator_node(self):
+        """
+        Test that a node JWT is always allowed to list approved algorithms
+        (`allow_node=True` on the decorator), even under the store's most
+        restrictive algorithm_view policy - and that this does not extend to
+        non-approved algorithms.
+        """
+        # even the most restrictive policy should not block a node
+        policy = Policy(
+            key=StorePolicies.ALGORITHM_VIEW.value,
+            value=AlgorithmViewPolicies.ONLY_WITH_EXPLICIT_PERMISSION.value,
+        )
+        policy.save()
+
+        node_headers = self.login_node()
+
+        # a node with a valid token can list approved algorithms
+        rv = self.app.get("/api/algorithm", headers=node_headers)
+        self.assertEqual(rv.status_code, HTTPStatus.OK)
+
+        # a node cannot use this to see non-approved algorithms
+        for arg in [
+            "awaiting_reviewer_assignment",
+            "under_review",
+            "in_review_process",
+            "invalidated",
+        ]:
+            rv = self.app.get(f"/api/algorithm?{arg}=1", headers=node_headers)
+            self.assertEqual(rv.status_code, HTTPStatus.UNAUTHORIZED)
+
+        # this is not a blanket bypass: a request without a token is still governed
+        # by the normal policy
+        rv = self.app.get("/api/algorithm")
+        self.assertEqual(rv.status_code, HTTPStatus.UNAUTHORIZED)
+
+        # cleanup
+        policy.delete()
+
+    def test_view_algorithm_single_not_affected_by_node_bypass(self):
+        """
+        Test that the node bypass on the algorithm list endpoint does not extend to
+        /api/algorithm/<id>, which was deliberately left on the un-modified
+        decorator.
+        """
+        algorithm = Algorithm(
+            name="test_algorithm", status=AlgorithmStatus.APPROVED.value
+        )
+        algorithm.save()
+
+        # no policy is defined, so the default (AUTHENTICATED) applies - and a node
+        # token is not looked up as a store User, so it is rejected here
+        rv = self.app.get(f"/api/algorithm/{algorithm.id}", headers=self.login_node())
+        self.assertEqual(rv.status_code, HTTPStatus.UNAUTHORIZED)
+
+        # cleanup
+        algorithm.delete()
+
     @patch("vantage6.algorithm.store.resource._authenticate")
     def test_algorithm_view_multi(self, authenticate_mock):
         """Test GET /api/algorithm"""
@@ -544,9 +601,24 @@ class TestAlgorithmResources(TestResources):
         self.assertEqual(response.status_code, HTTPStatus.OK)
         self.assertEqual(response.json["description"], "new_description")
 
+        # check that another developer cannot update this algorithm - they are
+        # not its owner
+        self.register_user(
+            username="other_developer",
+            user_rules=[Rule.get_by_("algorithm", Operation.EDIT)],
+            authenticate_mock=authenticate_mock,
+        )
+        response = self.app.patch(
+            f"/api/algorithm/{algorithm.id}", json={"description": "other_description"}
+        )
+        self.assertEqual(response.status_code, HTTPStatus.FORBIDDEN)
+
+        # switch back to the algorithm's own developer for the remaining checks
+        self._mock_auth(user, authenticate_mock, True)
+
         # check that algorithm cannot be updated if it is approved
         algorithm.status = AlgorithmStatus.APPROVED.value
-        algorithm.approved_at = datetime.datetime.now(datetime.timezone.utc)
+        algorithm.approved_at = datetime.datetime.now(datetime.UTC)
         algorithm.save()
         response = self.app.patch(
             f"/api/algorithm/{algorithm.id}", json={"description": "new_description"}
@@ -554,7 +626,7 @@ class TestAlgorithmResources(TestResources):
         self.assertEqual(response.status_code, HTTPStatus.FORBIDDEN)
 
         # check that algorithm cannot be updated if it is invalidated
-        algorithm.invalidated_at = datetime.datetime.now(datetime.timezone.utc)
+        algorithm.invalidated_at = datetime.datetime.now(datetime.UTC)
         algorithm.save()
         response = self.app.patch(
             f"/api/algorithm/{algorithm.id}", json={"description": "new_description"}

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/__init__.py

@@ -26,6 +26,7 @@ from flask_principal import Identity, identity_changed
 
 from vantage6.common import logger_name
 from vantage6.common.enum import StorePolicies
+from vantage6.common.exceptions import AuthenticationException
 from vantage6.common.globals import DEFAULT_API_PATH
 
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
@@ -100,7 +101,7 @@ class AlgorithmStoreApp(Vantage6App):
         """Configure JWT authentication."""
 
         @self.jwt.user_lookup_loader
-        def user_lookup_loader(jwt_payload: dict, jwt_headers: dict) -> db.User:
+        def user_lookup_loader(jwt_payload: dict, jwt_headers: dict) -> db.User | str:
             """
             Load the user, node or container instance from the JWT payload.
 
@@ -113,15 +114,27 @@ class AlgorithmStoreApp(Vantage6App):
 
             Returns
             -------
-            db.User:
-                The user identity.
+            db.User | str:
+                The user identity, or the keycloak id if it is a node that is
+                authenticating.
+
+            Raises
+            ------
+            AuthenticationException
+                If no store `User` is registered for this (non-node) identity.
             """
             identity = jwt_headers["sub"]
+
+            if jwt_headers.get("vantage6_client_type") == "node":
+                return identity
+
             auth_identity = Identity(identity)
 
             user = db.User.get_by_keycloak_id(identity)
             if not user:
-                raise Exception("No user found for keycloak id %s", identity)
+                raise AuthenticationException(
+                    f"No user found for keycloak id {identity}"
+                )
 
             # add role permissions
             for role in user.roles:

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/link_algorithms.py

@@ -213,7 +213,7 @@ def link_algorithms_from_config(config: dict) -> None:
         developer = db.User.get_first_user()
     if not developer:
         log.warning(
-            "link_algorithms: No users found; skipping seeding",
+            "link_algorithms: No users found (root_username=%s); skipping seeding",
             root_username,
         )
         return

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/model/algorithm.py

@@ -60,9 +60,7 @@ class Algorithm(Base):
     partitioning = Column(String)
     vantage6_version = Column(String)
     digest = Column(String)
-    submitted_at = Column(
-        DateTime, default=datetime.datetime.now(datetime.timezone.utc)
-    )
+    submitted_at = Column(DateTime, default=datetime.datetime.now(datetime.UTC))
     approved_at = Column(DateTime)
     invalidated_at = Column(DateTime)
     developer_id = Column(Integer, ForeignKey("user.id"))
@@ -96,14 +94,14 @@ class Algorithm(Base):
         bool
             True if all reviews are approved, False otherwise
         """
-        return all([review.status == ReviewStatus.APPROVED for review in self.reviews])
+        return all(review.status == ReviewStatus.APPROVED for review in self.reviews)
 
     def approve(self) -> None:
         """
         Approve the algorithm, and invalidate all other algorithms with the same image.
         """
         self.status = AlgorithmStatus.APPROVED.value
-        self.approved_at = datetime.datetime.now(datetime.timezone.utc)
+        self.approved_at = datetime.datetime.now(datetime.UTC)
         self.save()
 
         for other_version in self.get_by_image(self.image):

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/model/base.py

@@ -109,7 +109,7 @@ class ModelBase(BaseModelBase):
     """
 
     @classmethod
-    def get(cls, id_: int = None):
+    def get(cls, id_: int | None = None):
         """
         Get a single object by its id, or a list of objects when no id is
         specified.

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/model/policy.py

@@ -130,6 +130,4 @@ class Policy(Base):
                 None,
             )
 
-        if result is None:
-            return False
-        return True
+        return result is not None

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/model/review.py

@@ -32,9 +32,7 @@ class Review(Base):
     algorithm_id = Column(Integer, ForeignKey("algorithm.id"))
     reviewer_id = Column(Integer, ForeignKey("user.id"))
     requested_by_id = Column(Integer, ForeignKey("user.id"))
-    requested_at = Column(
-        DateTime, default=datetime.datetime.now(datetime.timezone.utc)
-    )
+    requested_at = Column(DateTime, default=datetime.datetime.now(datetime.UTC))
     submitted_at = Column(DateTime)
     status = Column(Text, default=ReviewStatus.UNDER_REVIEW.value)
     comment = Column(Text)

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/permission.py

@@ -36,10 +36,7 @@ class RuleCollection(RuleCollectionBase):
         """
         perm = getattr(self, operation, None)
 
-        if perm and perm.can():
-            return True
-
-        return False
+        return bool(perm and perm.can())
 
 
 class PermissionManager(PermissionManagerBase):

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/__init__.py

@@ -7,7 +7,7 @@ from http import HTTPStatus
 from typing import TYPE_CHECKING
 
 from flask import g, request
-from flask_jwt_extended import get_jwt_identity, verify_jwt_in_request
+from flask_jwt_extended import get_jwt, get_jwt_identity, verify_jwt_in_request
 from flask_mail import Mail
 from flask_restful import Api
 
@@ -105,6 +105,26 @@ def _authorize_user(
     return None, None
 
 
+def _is_node_request() -> bool:
+    """
+    Check whether the current request carries a valid node JWT.
+
+    Nodes are never registered as a store `User` - unlike `_authenticate`, this does
+    not do a database lookup. It only relies on the `vantage6_client_type` claim set
+    by the shared vantage6 Keycloak realm.
+
+    Note that this function does not raise if no token is present at all, so it is safe
+    to call unconditionally before any policy-based access checks.
+
+    Returns
+    -------
+    bool
+        Whether the request is authenticated as a node.
+    """
+    verify_jwt_in_request(optional=True)
+    return get_jwt().get("vantage6_client_type") == "node"
+
+
 def with_authentication() -> Callable:
     """
     Decorator to verify that the user is authenticated from the linked Keycloak service.
@@ -169,10 +189,21 @@ def with_permission(resource: str, operation: Operation) -> Callable:
     return protection_decorator
 
 
-def with_permission_to_view_algorithms() -> Callable:
+def with_permission_to_view_algorithms(allow_node: bool = False) -> Callable:
     """
     Decorator to verify that the user has as a permission on a resource.
 
+    Parameters
+    ----------
+    allow_node : bool, optional
+        If True, also allow requests authenticated as a node (see `_is_node_request`)
+        to view approved algorithms, regardless of the store's `algorithm_view` policy.
+        This lets nodes independently re-verify - for their own
+        `allowed_algorithm_stores` policy - that an image is a registered, approved
+        algorithm in this store, without requiring the node to be registered as a
+        store `User`. Node access is still restricted to approved algorithms only.
+        Default is False.
+
     Returns
     -------
     Callable
@@ -183,13 +214,6 @@ def with_permission_to_view_algorithms() -> Callable:
     def protection_decorator(fn):
         @wraps(fn)
         def decorator(self, *args, **kwargs):
-            policies = Policy.get_as_dict()
-            # check if everyone has permission to view algorithms
-            algorithm_view_policy = policies.get(
-                StorePolicies.ALGORITHM_VIEW.value,
-                DefaultStorePolicies.ALGORITHM_VIEW.value,
-            )
-
             # check if user is trying to view algorithms that are not approved by review
             # or have been invalidated - these algorithms always require authentication
             # even when algorithms are open to all
@@ -201,6 +225,20 @@ def with_permission_to_view_algorithms() -> Callable:
                 or request_args.get("invalidated")
             )
 
+            # nodes re-verifying an image against this store's catalog are always
+            # allowed to see approved algorithms, independent of the store's
+            # algorithm_view policy - they are never allowed to see non-approved ones
+            if allow_node and request_approved and _is_node_request():
+                g.node = True
+                return fn(self, *args, **kwargs)
+
+            policies = Policy.get_as_dict()
+            # check if everyone has permission to view algorithms
+            algorithm_view_policy = policies.get(
+                StorePolicies.ALGORITHM_VIEW.value,
+                DefaultStorePolicies.ALGORITHM_VIEW.value,
+            )
+
             # if the algorithm is public and approved, allow access
             if (
                 algorithm_view_policy == AlgorithmViewPolicies.PUBLIC

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/algorithm.py

@@ -67,7 +67,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
     services : dict
         Dictionary with services required for the resource endpoints
     """
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info('Setting up "%s" and subdirectories', path)
 
     api.add_resource(
@@ -148,7 +148,7 @@ class AlgorithmBaseResource(AlgorithmStoreResources):
 class Algorithms(AlgorithmBaseResource):
     """Resource for /algorithm"""
 
-    @with_permission_to_view_algorithms()
+    @with_permission_to_view_algorithms(allow_node=True)
     def get(self):
         """List algorithms
         ---
@@ -159,6 +159,12 @@ class Algorithms(AlgorithmBaseResource):
           algorithms, set the 'awaiting_reviewer_assignment', 'under_review' or
           'invalidated' parameter to True.
 
+          Nodes are always allowed to list approved algorithms (e.g. filtered by
+          'image'), regardless of this store's algorithm_view policy - this lets a node
+          independently verify that an image is a registered, approved algorithm for
+          its own allowed_algorithm_stores policy. Nodes cannot use the non-approved
+          filters.
+
         parameters:
           - in: query
             name: name
@@ -863,6 +869,12 @@ class Algorithm(AlgorithmBaseResource):
         if not algorithm:
             return {"msg": "Algorithm not found"}, HTTPStatus.NOT_FOUND
 
+        # only the algorithm's own developer may edit it
+        if algorithm.developer_id != g.user.id:
+            return {
+                "msg": "You can only edit algorithms you submitted yourself."
+            }, HTTPStatus.FORBIDDEN
+
         data = request.get_json(silent=True)
 
         # validate the request body
@@ -887,7 +899,7 @@ class Algorithm(AlgorithmBaseResource):
                 "algorithm and go through the review process if you want to update it."
             }, HTTPStatus.FORBIDDEN
         elif algorithm.reviews and any(
-            [r.is_review_finished() for r in algorithm.reviews]
+            r.is_review_finished() for r in algorithm.reviews
         ):
             return {
                 "msg": "This algorithm has at least one submitted review, and can "
@@ -1043,7 +1055,7 @@ class AlgorithmInvalidate(AlgorithmStoreResources):
             return {"msg": "Algorithm not found"}, HTTPStatus.NOT_FOUND
 
         # invalidate the algorithm
-        algorithm.invalidated_at = datetime.datetime.now(datetime.timezone.utc)
+        algorithm.invalidated_at = datetime.datetime.now(datetime.UTC)
         algorithm.status = AlgorithmStatus.REMOVED.value
         algorithm.save()
 

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/policy.py

@@ -38,7 +38,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
     services : dict
         Dictionary with services required for the resource endpoints
     """
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info('Setting up "%s" and subdirectories', path)
 
     api.add_resource(

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/review.py

@@ -52,7 +52,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
         Dictionary with services required for the resource endpoints
     """
 
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info(f'Setting up "{path}" and subdirectories')
 
     api.add_resource(
@@ -138,7 +138,7 @@ class ReviewBase(AlgorithmStoreResources):
             True if the reviewers assignment is finished, False otherwise
         """
         # get the number of unique organizations assigned to review the algorithm.
-        current_orgs = len(set([(rev.reviewer.organization_id) for rev in reviews]))
+        current_orgs = len({(rev.reviewer.organization_id) for rev in reviews})
 
         return (
             current_orgs >= Policy.get_minimum_reviewing_orgs()
@@ -565,12 +565,12 @@ class Review(ReviewBase):
         if not algorithm.is_review_finished():
             # if number of reviews after deletion is less than the minium,
             # new reviewers should be assigned
-            other_reviews = [r for r in algorithm.reviews if not r.id == review.id]
+            other_reviews = [r for r in algorithm.reviews if r.id != review.id]
             if not other_reviews or not self._is_reviewers_assignment_finished(
                 other_reviews
             ):
                 algorithm.status = AlgorithmStatus.AWAITING_REVIEWER_ASSIGNMENT.value
-            elif all([r.status == ReviewStatus.APPROVED for r in other_reviews]):
+            elif all(r.status == ReviewStatus.APPROVED for r in other_reviews):
                 # if this was the last remaining review that needed to be approved, but
                 # it is now deleted, the algorithm should be approved
                 algorithm.status = AlgorithmStatus.APPROVED.value
@@ -747,7 +747,7 @@ class ReviewApprove(ReviewUpdateResources):
 
         # update the review status to 'approved'
         review.status = ReviewStatus.APPROVED.value
-        review.submitted_at = datetime.datetime.now(datetime.timezone.utc)
+        review.submitted_at = datetime.datetime.now(datetime.UTC)
         if comment := data.get("comment"):
             review.comment = comment
         review.save()
@@ -842,7 +842,7 @@ class ReviewReject(ReviewUpdateResources):
 
         # update the review status to 'rejected'
         review.status = ReviewStatus.REJECTED.value
-        review.submitted_at = datetime.datetime.now(datetime.timezone.utc)
+        review.submitted_at = datetime.datetime.now(datetime.UTC)
         if comment := data.get("comment"):
             review.comment = comment
         review.save()
@@ -850,7 +850,7 @@ class ReviewReject(ReviewUpdateResources):
         # also update the algorithm status to 'rejected'
         algorithm: db.Algorithm = review.algorithm
         algorithm.status = AlgorithmStatus.REJECTED.value
-        algorithm.invalidated_at = datetime.datetime.now(datetime.timezone.utc)
+        algorithm.invalidated_at = datetime.datetime.now(datetime.UTC)
         algorithm.save()
 
         # the other reviews of this algorithm are dropped as they are no longer required

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/role.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import logging
 from http import HTTPStatus
 
@@ -50,7 +49,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
     services : dict
         Dictionary with services required for the resource endpoints
     """
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info(f'Setting up "{path}" and subdirectories')
 
     api.add_resource(

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/rule.py

@@ -35,7 +35,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
     services : dict
         Dictionary with services required for the resource endpoints
     """
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info(f'Setting up "{path}" and subdirectories')
 
     api.add_resource(

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/schema/input_schema.py

@@ -4,9 +4,8 @@ Marshmallow schemas for validating input data for the API.
 
 import json
 
-import marshmallow.validate as validate
 from jsonschema import validate as json_validate
-from marshmallow import Schema, ValidationError, fields, validates_schema
+from marshmallow import Schema, ValidationError, fields, validate, validates_schema
 
 from vantage6.common.enum import (
     AlgorithmArgumentType,
@@ -177,14 +176,16 @@ class FunctionInputSchema(_NameDescriptionSchema):
                             f"float, while the conditional argument '{conditional_on}' "
                             "requires a float"
                         ) from exc
-                elif conditional_type == AlgorithmArgumentType.BOOLEAN:
-                    if conditional_value.lower() not in ["true", "false", "1", "0"]:
-                        raise ValidationError(
-                            f"Conditional value '{conditional_value}' is not a valid "
-                            "boolean, while the conditional argument "
-                            f"'{conditional_on}' requires a boolean. Please use 'true',"
-                            " 'false', '1', or '0'"
-                        )
+                elif (
+                    conditional_type == AlgorithmArgumentType.BOOLEAN
+                    and conditional_value.lower() not in ["true", "false", "1", "0"]
+                ):
+                    raise ValidationError(
+                        f"Conditional value '{conditional_value}' is not a valid "
+                        "boolean, while the conditional argument "
+                        f"'{conditional_on}' requires a boolean. Please use 'true',"
+                        " 'false', '1', or '0'"
+                    )
 
     @staticmethod
     def _check_circular_conditions(arguments: list[dict]) -> None:
@@ -244,7 +245,7 @@ class _MixedBaseTypeField(fields.Field):
     """
 
     def _deserialize(self, value, attr, data, **kwargs):
-        if isinstance(value, str) or isinstance(value, int) or isinstance(value, float):
+        if isinstance(value, (str, int, float)):
             return value
         else:
             raise ValidationError("Values should be str, int or float")
@@ -381,8 +382,8 @@ class ArgumentInputSchema(_NameDescriptionSchema):
                 try:
                     json_list = json.loads(default)
                     if not isinstance(json_list, list):
-                        raise ValueError(f"Not a list: {json_list}")
-                except ValueError as exc:
+                        raise TypeError(f"Not a list: {json_list}")
+                except (ValueError, TypeError) as exc:
                     raise ValidationError(
                         f"Default value '{default}' is not a valid JSON array, while "
                         f"the argument type {type_} requires a JSON array"
@@ -394,10 +395,10 @@ class ArgumentInputSchema(_NameDescriptionSchema):
                 try:
                     json_list = json.loads(default)
                     if not isinstance(json_list, list):
-                        raise ValueError(f"Not a list: {json_list}")
+                        raise TypeError(f"Not a list: {json_list}")
                     for value in json_list:
                         int(value)
-                except ValueError as exc:
+                except (ValueError, TypeError) as exc:
                     raise ValidationError(
                         f"Default value '{default}' is not a valid JSON array of "
                         f"integers, while the argument type {type_} requires a JSON "
@@ -407,10 +408,10 @@ class ArgumentInputSchema(_NameDescriptionSchema):
                 try:
                     json_list = json.loads(default)
                     if not isinstance(json_list, list):
-                        raise ValueError(f"Not a list: {json_list}")
+                        raise TypeError(f"Not a list: {json_list}")
                     for value in json_list:
                         float(value)
-                except ValueError as exc:
+                except (ValueError, TypeError) as exc:
                     raise ValidationError(
                         f"Default value '{default}' is not a valid JSON array of "
                         f"floats, while the argument type {type_} requires a JSON array"
@@ -436,9 +437,12 @@ class ArgumentInputSchema(_NameDescriptionSchema):
 
         # if there are both allowed values and a default value, validate that the
         # default value is one of the allowed values
-        if data.get("default_value") and data.get("allowed_values"):
-            if data.get("default_value") not in data.get("allowed_values"):
-                raise ValidationError("Default value is not one of the allowed values")
+        if (
+            data.get("default_value")
+            and data.get("allowed_values")
+            and data.get("default_value") not in data.get("allowed_values")
+        ):
+            raise ValidationError("Default value is not one of the allowed values")
 
 
 class UIVisualizationInputSchema(_NameDescriptionSchema):

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/schema/output_schema.py

@@ -27,15 +27,15 @@ class HATEOASModelSchema(BaseHATEOASModelSchema):
     def __init__(self, *args, **kwargs) -> None:
         # set lambda functions to create links for one to one relationship
         # TODO check if all below are used
-        setattr(self, "algorithm", lambda obj: self.create_hateoas("algorithm", obj))
-        setattr(self, "function", lambda obj: self.create_hateoas("function", obj))
-        setattr(self, "database", lambda obj: self.create_hateoas("database", obj))
-        setattr(self, "argument", lambda obj: self.create_hateoas("argument", obj))
-        setattr(self, "rule", lambda obj: self.create_hateoas("rule", obj))
-        setattr(self, "role", lambda obj: self.create_hateoas("role", obj))
-        setattr(self, "user", lambda obj: self.create_hateoas("user", obj))
-        setattr(self, "review", lambda obj: self.create_hateoas("review", obj))
-        setattr(self, "hq", lambda obj: self.create_hateoas("hq", obj))
+        self.algorithm = lambda obj: self.create_hateoas("algorithm", obj)
+        self.function = lambda obj: self.create_hateoas("function", obj)
+        self.database = lambda obj: self.create_hateoas("database", obj)
+        self.argument = lambda obj: self.create_hateoas("argument", obj)
+        self.rule = lambda obj: self.create_hateoas("rule", obj)
+        self.role = lambda obj: self.create_hateoas("role", obj)
+        self.user = lambda obj: self.create_hateoas("user", obj)
+        self.review = lambda obj: self.create_hateoas("review", obj)
+        self.hq = lambda obj: self.create_hateoas("hq", obj)
 
         # call super class. Do this after setting the attributes above, because
         # the super class initializer will call the attributes.

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/user.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 import logging
 from http import HTTPStatus
 
@@ -49,7 +48,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
         Dictionary with services required for the resource endpoints
     """
 
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info(f'Setting up "{path}" and subdirectories')
 
     api.add_resource(

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/resource/version.py

@@ -31,7 +31,7 @@ def setup(api: Api, api_base: str, services: dict) -> None:
     services : dict
         Dictionary with services required for the resource endpoints
     """
-    path = "/".join([api_base, module_name])
+    path = f"{api_base}/{module_name}"
     log.info('Setting up "%s" and subdirectories', path)
 
     api.add_resource(

{vantage6_algorithm_store-5.0.2rc2 → vantage6_algorithm_store-5.0.3}/vantage6/algorithm/store/wsgi.py

@@ -11,7 +11,7 @@ from vantage6.algorithm.store import run_store
 
 if len(sys.argv) < 2:
     error("No config file provided from WSGI! Exiting...")
-    exit(1)
+    sys.exit(1)
 config_file = sys.argv[1]
 
 store_app = run_store(config_file, system_folders=False)