vantage6-algorithm-store 4.14.0__tar.gz → 4.15.0__tar.gz

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: vantage6_algorithm_store
-Version: 4.14.0
+Version: 4.15.0
 Summary: Vantage6 algorithm store
 Home-page: https://github.com/vantage6/vantage6
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Requires-Dist: flask==3.1.1
+Requires-Dist: flask==3.1.3
 Requires-Dist: flask-cors==6.0.0
 Requires-Dist: Flask-Principal==0.4.0
 Requires-Dist: flask-marshmallow==0.15.0
@@ -13,12 +13,12 @@ Requires-Dist: Flask-RESTful==0.3.10
 Requires-Dist: gevent==25.4.2
 Requires-Dist: jsonschema==4.21.1
 Requires-Dist: marshmallow==3.26.2
-Requires-Dist: requests==2.32.4
+Requires-Dist: requests==2.33.1
 Requires-Dist: schema==0.7.5
 Requires-Dist: SQLAlchemy==1.4.46
-Requires-Dist: werkzeug==3.1.5
-Requires-Dist: vantage6==4.14.0
-Requires-Dist: vantage6-common==4.14.0
+Requires-Dist: werkzeug==3.1.8
+Requires-Dist: vantage6==4.15.0
+Requires-Dist: vantage6-common==4.15.0
 Provides-Extra: dev
 Requires-Dist: coverage==6.4.4; extra == "dev"
 Dynamic: description
@@ -175,36 +175,36 @@ easily.
 ### Docker images
 
 The vantage6 infrastructure is delivered in Docker images. All Docker images are stored
-in our private [Harbor](https://goharbor.io/) registry. The most important images are:
+in the vantage6 GitHub Container Registry. The most important images are:
 
-- `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
-- `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
-- `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
-- `harbor2.vantage6.ai/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
+- `ghcr.io/vantage6/infrastructure/node:VERSION` -> _Node application Docker image_
+- `ghcr.io/vantage6/infrastructure/server:VERSION` -> _Server application Docker image_
+- `ghcr.io/vantage6/infrastructure/ui:VERSION` -> _User interface Docker image_
+- `ghcr.io/vantage6/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
 
 with `VERSION` being the full semantic version of the vantage6 infrastructure, e.g.
 `4.0.0` or `4.1.0rc0`.
 
 Several other images are used to support the infrastructure:
 
-- `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
-- `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
-- `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
-- `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
-- `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
-- `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
+- `ghcr.io/vantage6/infrastructure-base:VERSION` -> _Base image for the infrastructure_
+- `ghcr.io/vantage6/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
+- `ghcr.io/vantage6/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
+- `ghcr.io/vantage6/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
+- `ghcr.io/vantage6/infrastructure/vpn-configurator` -> _VPN image used for initialization_
+- `ghcr.io/vantage6/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
 
 And finally there are some images released for algorithm development:
 
-- `harbor2.vantage6.ai/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
-- `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
+- `ghcr.io/vantage6/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
+- `ghcr.io/vantage6/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
 
 ## :gift_heart: Join the community!
 
-We hope to continue developing, improving, and supporting **vantage6** with the help of 
-the federated learning community. If you are interested in contributing, first of all, 
-thank you! Second, please take a look at our 
-[contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html) 
+We hope to continue developing, improving, and supporting **vantage6** with the help of
+the federated learning community. If you are interested in contributing, first of all,
+thank you! Second, please take a look at our
+[contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html)
 and our [code of conduct](CODE_OF_CONDUCT.md).
 
 <a href="https://github.com/vantage6/vantage6/graphs/contributors">

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/setup.py

@@ -31,7 +31,7 @@ setup(
     packages=find_namespace_packages(),
     python_requires=">=3.10",
     install_requires=[
-        "flask==3.1.1",
+        "flask==3.1.3",
         "flask-cors==6.0.0",
         "Flask-Principal==0.4.0",
         "flask-marshmallow==0.15.0",
@@ -39,10 +39,10 @@ setup(
         "gevent==25.4.2",
         "jsonschema==4.21.1",
         "marshmallow==3.26.2",
-        "requests==2.32.4",
+        "requests==2.33.1",
         "schema==0.7.5",
         "SQLAlchemy==1.4.46",
-        "werkzeug==3.1.5",
+        "werkzeug==3.1.8",
         f"vantage6 == {version_ns['__version__']}",
         f"vantage6-common == {version_ns['__version__']}",
     ],

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/tests_store/resources/test_algorithm.py

@@ -448,8 +448,36 @@ class TestAlgorithmResources(TestResources):
             rv.json["functions"][0]["arguments"][0]["conditional_value"], "test"
         )
 
+        # explicit null values for optional fields should be accepted
+        json_data["functions"][0]["arguments"] = [
+            {
+                "name": "nullable-arg",
+                "type": ArgumentType.STRING,
+                "has_default_value": False,
+                "default_value": None,
+                "conditional_operator": None,
+                "conditional_value": None,
+            }
+        ]
+        rv = self.app.post("/api/algorithm", json=json_data, headers=HEADERS)
+        self.assertEqual(rv.status_code, 201)
+
         # test that there is an error if argument with conditional does not have a
         # default value
+        json_data["functions"][0]["arguments"] = [
+            {
+                "name": "dependent",
+                "type": ArgumentType.STRING,
+                "has_default_value": True,
+                "conditional_on": "conditional",
+                "conditional_operator": "==",
+                "conditional_value": "test",
+            },
+            {
+                "name": "conditional",
+                "type": ArgumentType.STRING,
+            },
+        ]
         json_data["functions"][0]["arguments"][0]["has_default_value"] = False
         rv = self.app.post("/api/algorithm", json=json_data, headers=HEADERS)
         self.assertEqual(rv.status_code, 400)

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6/algorithm/store/_version.py

@@ -7,7 +7,7 @@ with open(os.path.join(here, "__build__")) as fp:
     __build__ = json.load(fp)
 
 # Module version
-version_info = (4, 14, 0, "final", __build__, 0)
+version_info = (4, 15, 0, "final", __build__, 0)
 
 # Module version stage suffix map
 _specifier_ = {"alpha": "a", "beta": "b", "candidate": "rc", "final": ""}

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6/algorithm/store/model/permission.py

@@ -13,7 +13,6 @@ from sqlalchemy import Column, Integer, ForeignKey, Table
 
 from vantage6.algorithm.store.model.base import Base
 
-
 Permission = Table(
     "Permission",
     Base.metadata,

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6/algorithm/store/resource/rule.py

@@ -15,7 +15,6 @@ from vantage6.algorithm.store.resource import (
 from vantage6.algorithm.store.resource.schema.output_schema import RuleOutputSchema
 from vantage6.backend.common.resource.pagination import Pagination
 
-
 module_name = logger_name(__name__)
 log = logging.getLogger(module_name)
 rule_schema = RuleOutputSchema()
@@ -44,13 +43,6 @@ def setup(api: Api, api_base: str, services: dict) -> None:
         methods=("GET",),
         resource_class_kwargs=services,
     )
-    # api.add_resource(
-    #     Rule,
-    #     path + "/<int:id>",
-    #     endpoint="rule_with_id",
-    #     methods=("GET",),
-    #     resource_class_kwargs=services,
-    # )
 
 
 # ------------------------------------------------------------------------------
@@ -143,7 +135,7 @@ class Rules(AlgorithmStoreResources):
             role = db.Role.get(args["role_id"])
             if not role:
                 return {
-                    "msg": f'Role with id={args["role_id"]} does not exist!'
+                    "msg": f"Role with id={args['role_id']} does not exist!"
                 }, HTTPStatus.BAD_REQUEST
             q = (
                 q.join(db.role_rule_association)
@@ -203,41 +195,3 @@ class Rules(AlgorithmStoreResources):
 
         # model serialization
         return self.response(page, rule_schema)
-
-
-# class Rule(ServicesResources):
-#     @with_user
-#     def get(self, id):
-#         """Returns a specific rule
-#         ---
-#         description: >-
-#             Get a rule by it's id. The user must be authenticated, but does
-#             not require any additional permissions to view rules.\n
-
-#             Accesible to users.
-
-#         parameters:
-#         - in: path
-#           name: id
-#           schema:
-#               type: integer
-#           minimum: 1
-#           description: rule_id
-#           required: true
-
-#         responses:
-#           200:
-#             description: Ok
-#           404:
-#             description: Rule not found
-
-#         security:
-#             - bearerAuth: []
-
-#         tags: ["Rule"]
-#         """
-#         rule = db.Rule.get(id)
-#         if not rule:
-#             return {"msg": f"Rule id={id} not found!"}, HTTPStatus.NOT_FOUND
-
-#         return rule_schema.dump(rule, many=False), HTTPStatus.OK

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6/algorithm/store/resource/schema/input_schema.py

@@ -272,10 +272,10 @@ class ArgumentInputSchema(_NameDescriptionSchema):
     type_ = fields.String(required=True, data_key="type")
     allowed_values = fields.List(_MixedBaseTypeField())
     has_default_value = fields.Boolean()
-    default_value = fields.String()
+    default_value = fields.String(allow_none=True)
     conditional_on = fields.String()
-    conditional_operator = fields.String()
-    conditional_value = fields.String()
+    conditional_operator = fields.String(allow_none=True)
+    conditional_value = fields.String(allow_none=True)
     is_frontend_only = fields.Boolean()
 
     @validates("type_")
@@ -294,6 +294,8 @@ class ArgumentInputSchema(_NameDescriptionSchema):
         """
         Validate that the conditional comparator is one of the allowed values.
         """
+        if value is None:
+            return
         comparators = [c.value for c in ConditionalArgComparator]
         if value not in comparators:
             raise ValidationError(

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6/algorithm/store/resource/vantage6_server.py

@@ -28,7 +28,6 @@ from vantage6.algorithm.store.resource import (
 from vantage6.algorithm.store.resource import AlgorithmStoreResources
 from vantage6.algorithm.store.default_roles import DefaultRole
 
-
 module_name = __name__.split(".")[-1]
 log = logging.getLogger(logger_name(__name__))
 

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6/algorithm/store/resource/version.py

@@ -12,7 +12,6 @@ from vantage6.algorithm.store._version import __version__
 # TODO move to common / refactor
 from vantage6.algorithm.store.resource import AlgorithmStoreResources
 
-
 module_name = logger_name(__name__)
 log = logging.getLogger(module_name)
 

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6_algorithm_store.egg-info/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: vantage6_algorithm_store
-Version: 4.14.0
+Version: 4.15.0
 Summary: Vantage6 algorithm store
 Home-page: https://github.com/vantage6/vantage6
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Requires-Dist: flask==3.1.1
+Requires-Dist: flask==3.1.3
 Requires-Dist: flask-cors==6.0.0
 Requires-Dist: Flask-Principal==0.4.0
 Requires-Dist: flask-marshmallow==0.15.0
@@ -13,12 +13,12 @@ Requires-Dist: Flask-RESTful==0.3.10
 Requires-Dist: gevent==25.4.2
 Requires-Dist: jsonschema==4.21.1
 Requires-Dist: marshmallow==3.26.2
-Requires-Dist: requests==2.32.4
+Requires-Dist: requests==2.33.1
 Requires-Dist: schema==0.7.5
 Requires-Dist: SQLAlchemy==1.4.46
-Requires-Dist: werkzeug==3.1.5
-Requires-Dist: vantage6==4.14.0
-Requires-Dist: vantage6-common==4.14.0
+Requires-Dist: werkzeug==3.1.8
+Requires-Dist: vantage6==4.15.0
+Requires-Dist: vantage6-common==4.15.0
 Provides-Extra: dev
 Requires-Dist: coverage==6.4.4; extra == "dev"
 Dynamic: description
@@ -175,36 +175,36 @@ easily.
 ### Docker images
 
 The vantage6 infrastructure is delivered in Docker images. All Docker images are stored
-in our private [Harbor](https://goharbor.io/) registry. The most important images are:
+in the vantage6 GitHub Container Registry. The most important images are:
 
-- `harbor2.vantage6.ai/infrastructure/node:VERSION` -> _Node application Docker image_
-- `harbor2.vantage6.ai/infrastructure/server:VERSION` -> _Server application Docker image_
-- `harbor2.vantage6.ai/infrastructure/ui:VERSION` -> _User interface Docker image_
-- `harbor2.vantage6.ai/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
+- `ghcr.io/vantage6/infrastructure/node:VERSION` -> _Node application Docker image_
+- `ghcr.io/vantage6/infrastructure/server:VERSION` -> _Server application Docker image_
+- `ghcr.io/vantage6/infrastructure/ui:VERSION` -> _User interface Docker image_
+- `ghcr.io/vantage6/infrastructure/algorithm-store:VERSION` -> _Algorithm store Docker image_
 
 with `VERSION` being the full semantic version of the vantage6 infrastructure, e.g.
 `4.0.0` or `4.1.0rc0`.
 
 Several other images are used to support the infrastructure:
 
-- `harbor2.vantage6.ai/infrastructure/infrastructure-base:VERSION` -> _Base image for the infrastructure_
-- `harbor2.vantage6.ai/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
-- `harbor2.vantage6.ai/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
-- `harbor2.vantage6.ai/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
-- `harbor2.vantage6.ai/infrastructure/vpn-configurator` -> _VPN image used for initialization_
-- `harbor2.vantage6.ai/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
+- `ghcr.io/vantage6/infrastructure-base:VERSION` -> _Base image for the infrastructure_
+- `ghcr.io/vantage6/infrastructure/squid:VERSION` -> _Squid proxy image used for the whitelisting service_
+- `ghcr.io/vantage6/infrastructure/alpine` -> _Alpine image used for vpn traffic forwarding_
+- `ghcr.io/vantage6/infrastructure/vpn-client` -> _VPN image used to connect to the VPN_
+- `ghcr.io/vantage6/infrastructure/vpn-configurator` -> _VPN image used for initialization_
+- `ghcr.io/vantage6/infrastructure/ssh-tunnel` -> _SSH tunnel image used for connecting algorithms to external services_
 
 And finally there are some images released for algorithm development:
 
-- `harbor2.vantage6.ai/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
-- `harbor2.vantage6.ai/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
+- `ghcr.io/vantage6/infrastructure/algorithm-base:MAJOR.MINOR` -> _Base image for algorithm development_
+- `ghcr.io/vantage6/infrastructure/algorithm-ohdsi-base:MAJOR.MINOR` -> _Extended algorithm base image for OHDSI algorithm development_
 
 ## :gift_heart: Join the community!
 
-We hope to continue developing, improving, and supporting **vantage6** with the help of 
-the federated learning community. If you are interested in contributing, first of all, 
-thank you! Second, please take a look at our 
-[contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html) 
+We hope to continue developing, improving, and supporting **vantage6** with the help of
+the federated learning community. If you are interested in contributing, first of all,
+thank you! Second, please take a look at our
+[contributing guidelines](https://docs.vantage6.ai/en/main/devops/contribute.html)
 and our [code of conduct](CODE_OF_CONDUCT.md).
 
 <a href="https://github.com/vantage6/vantage6/graphs/contributors">

{vantage6_algorithm_store-4.14.0 → vantage6_algorithm_store-4.15.0}/vantage6_algorithm_store.egg-info/requires.txt

@@ -1,4 +1,4 @@
-flask==3.1.1
+flask==3.1.3
 flask-cors==6.0.0
 Flask-Principal==0.4.0
 flask-marshmallow==0.15.0
@@ -6,12 +6,12 @@ Flask-RESTful==0.3.10
 gevent==25.4.2
 jsonschema==4.21.1
 marshmallow==3.26.2
-requests==2.32.4
+requests==2.33.1
 schema==0.7.5
 SQLAlchemy==1.4.46
-werkzeug==3.1.5
-vantage6==4.14.0
-vantage6-common==4.14.0
+werkzeug==3.1.8
+vantage6==4.15.0
+vantage6-common==4.15.0
 
 [dev]
 coverage==6.4.4