vantage6-algorithm-store 4.3.4__tar.gz → 4.4.0__tar.gz

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vantage6-algorithm-store
-Version: 4.3.4
+Version: 4.4.0
 Summary: Vantage6 algorithm store
 Home-page: https://github.com/vantage6/vantage6
 Requires-Python: >=3.10

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/setup.py

@@ -38,6 +38,7 @@ setup(
         "flask-marshmallow==0.15.0",
         "Flask-RESTful==0.3.10",
         "gevent==23.9.1",
+        "jsonschema==4.21.1",
         "marshmallow==3.19.0",
         "requests==2.31.0",
         "schema==0.7.5",

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/__init__.py

@@ -36,11 +36,12 @@ from pathlib import Path
 from vantage6.common import logger_name
 from vantage6.common.globals import APPNAME
 from vantage6.backend.common.resource.output_schema import BaseHATEOASModelSchema
+from vantage6.backend.common.globals import HOST_URI_ENV
 
 # TODO move this to common, then remove dependency on CLI in algorithm store
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
 from vantage6.algorithm.store._version import __version__
-from vantage6.algorithm.store.globals import API_PATH, HOST_URI_ENV
+from vantage6.algorithm.store.globals import API_PATH
 from vantage6.algorithm.store.globals import RESOURCES, SERVER_MODULE_NAME
 
 # TODO the following are simply copies of the same files in the server - refactor

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/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, 3, 4, "final", __build__, 0)
+version_info = (4, 4, 0, "final", __build__, 0)
 
 # Module version stage suffix map
 _specifier_ = {"alpha": "a", "beta": "b", "candidate": "rc", "final": ""}

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/globals.py

@@ -17,6 +17,3 @@ API_PATH = "/api"
 # Which resources should be initialized. These names correspond to the
 # file-names in the resource directory
 RESOURCES = ["version", "algorithm", "vantage6_server", "role", "rule", "user"]
-
-# environment variable name for host URI
-HOST_URI_ENV = "HOST_URI_ENV_VAR"

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/__init__.py

@@ -13,3 +13,4 @@ from vantage6.algorithm.store.model.developer_algorithm_association import (
     developer_algorithm_association,
 )
 from vantage6.algorithm.store.model.review import Review
+from vantage6.algorithm.store.model.ui_visualization import UIVisualization

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/algorithm.py

@@ -1,4 +1,3 @@
-from __future__ import annotations
 from sqlalchemy import Column, String
 from sqlalchemy.orm import relationship
 
@@ -24,6 +23,10 @@ class Algorithm(Base):
 
     functions : list[:class:`~.model.function.function`]
         List of functions that are available in the algorithm
+    developer : list[:class:`~.model.user.User`]
+        List of users that have developed the algorithm
+    review : :class:`~.model.review.Review`
+        Review of the algorithm
     """
 
     # fields

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/common/enums.py

@@ -19,14 +19,23 @@ class ArgumentType(str, enum.Enum):
     """Enum for argument types"""
 
     COLUMN = "column"
+    COLUMNS = "column_list"
     STRING = "string"
+    STRINGS = "string_list"
     INTEGER = "integer"
+    INTEGERS = "integer_list"
     FLOAT = "float"
+    FLOATS = "float_list"
     BOOLEAN = "boolean"
-    DATE = "date"
     JSON = "json"
-    ORGANIZATIONS = "organizations"
     ORGANIZATION = "organization"
+    ORGANIZATIONS = "organization_list"
+
+
+class VisualizationType(str, enum.Enum):
+    """Enum for visualization types"""
+
+    TABLE = "table"
 
 
 class ReviewStatus(str, enum.Enum):

vantage6-algorithm-store-4.4.0/vantage6/algorithm/store/model/common/ui_visualization_schemas.py

@@ -0,0 +1,62 @@
+"""
+This file describes how the JSON schema for different types of UI visualizations
+should be structured. The schema is used to validate input data.
+"""
+
+from vantage6.algorithm.store.model.common.enums import VisualizationType
+
+
+# To visualize a table in the UI, the algorithm result should contain a table that
+# is structured as follows:
+# [
+#    { "column1": "value1", "column2": "value2", ... },
+#    { "column1": "value3", "column2": "value4", ... },
+# ]
+table_schema = {
+    "type": "object",
+    "properties": {
+        # indicate where in the results the table can be found. E.g. if the table is
+        # in results['data']['table'], the location should be ['data', 'table']. If it
+        # is not specified, the table is assumed to be the root of the results.
+        "location": {
+            "type": "array",
+            "items": {
+                "type": "string",
+            },
+        },
+        # columns of the table. Specify this if you only want to visualize a subset of
+        # the columns in the table. Example value: ["column1", "column2"]
+        "columns": {
+            "type": "array",
+            "items": {
+                "type": "string",
+            },
+        },
+    },
+    "additionalProperties": False,
+}
+
+
+def get_schema_for_visualization(visualization_type: str) -> dict:
+    """
+    Get the schema for a specific visualization type.
+
+    Parameters
+    ----------
+    visualization_type : str
+        Type of the visualization.
+
+    Returns
+    -------
+    dict
+        JSON validation schema for the visualization type.
+
+    Raises
+    ------
+    ValueError
+        If the visualization type is not supported.
+    """
+    if visualization_type == VisualizationType.TABLE.value:
+        return table_schema
+    else:
+        raise ValueError(f"Visualization type '{visualization_type}' is not supported.")

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/function.py

@@ -1,4 +1,3 @@
-from __future__ import annotations
 from sqlalchemy import Column, String, ForeignKey, Integer
 from sqlalchemy.orm import relationship
 
@@ -22,12 +21,14 @@ class Function(Base):
         Type of function
     algorithm_id : int
         ID of the algorithm that this function belongs to
-    algorithm : :class:`~.model.algorithm.algorithm`
+    algorithm : :class:`~.model.algorithm.Algorithm`
         Algorithm that this function belongs to
-    databases : list[:class:`~.model.database.database`]
+    databases : list[:class:`~.model.database.Database`]
         List of databases that this function uses
-    arguments : list[:class:`~.model.argument.argument`]
+    arguments : list[:class:`~.model.argument.Argument`]
         List of arguments that this function uses
+    ui_visualizations : list[:class:`~.model.ui_visualization.UIVisualization`]
+        List of user interface visualizations that this function produces
     """
 
     # fields
@@ -40,4 +41,4 @@ class Function(Base):
     algorithm = relationship("Algorithm", back_populates="functions")
     databases = relationship("Database", back_populates="function")
     arguments = relationship("Argument", back_populates="function")
-    # output = relationship("Output", back_populates='function')
+    ui_visualizations = relationship("UIVisualization", back_populates="function")

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/review.py

@@ -16,6 +16,10 @@ class Review(Base):
         Id of the user appointed as reviewer
     status : str
         Review status
+    reviewers : list[:class:`~.model.user.User`]
+        List of users that have written reviews
+    algorithm : :class:`~.model.algorithm.Algorithm`
+        Algorithm that the review is linked to
     """
 
     # fields

vantage6-algorithm-store-4.4.0/vantage6/algorithm/store/model/ui_visualization.py

@@ -0,0 +1,35 @@
+from sqlalchemy import Column, String, Integer, ForeignKey, JSON
+from sqlalchemy.orm import relationship
+
+from vantage6.algorithm.store.model.base import Base
+
+
+class UIVisualization(Base):
+    """
+    Table that describes how the algorithm should be visualized in the UI.
+
+    Attributes
+    ----------
+    name : str
+        Name of the visualization
+    description: str
+        Description of the visualization
+    type_: str
+        Type of the visualization. Currently available: 'table'
+    schema : dict
+        Schema that describes the visualization, e.g. column names of a table
+    function_id : int
+        Id of the function that the visualization is linked to
+    function : Function
+        Function that the visualization is linked to
+    """
+
+    # fields
+    name = Column(String)
+    description = Column(String)
+    type_ = Column("type", String)
+    schema = Column(JSON)
+    function_id = Column(Integer, ForeignKey("function.id"))
+
+    # relationships
+    function = relationship("Function", back_populates="ui_visualizations")

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/user.py

@@ -17,6 +17,14 @@ class User(Base):
         Username
     v6_server_id : int
         Id of the whitelisted server through which the user is authenticated
+    server : :class:`~.model.vantage6_server.Vantage6Server`
+        Server through which the user is authenticated
+    roles : list[:class:`~.model.role.Role`]
+        List of roles that the user has
+    algorithms : list[:class:`~.model.algorithm.Algorithm`]
+        List of algorithms that the user has developed
+    reviews : list[:class:`~.model.review.Review`]
+        List of reviews that the user has written
     """
 
     # fields

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/vantage6_server.py

@@ -15,6 +15,8 @@ class Vantage6Server(Base):
     ----------
     url : str
         URL of the vantage6 server
+    users : list[:class:`~.model.user.User`]
+        List of known vantage6 users from that server
     """
 
     # fields

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/resource/algorithm.py

@@ -7,6 +7,7 @@ from http import HTTPStatus
 from vantage6.algorithm.store import db
 from vantage6.algorithm.store.model.rule import Operation
 from vantage6.common import logger_name
+from vantage6.algorithm.store.model.ui_visualization import UIVisualization
 from vantage6.algorithm.store.resource.schema.input_schema import AlgorithmInputSchema
 from vantage6.algorithm.store.resource.schema.output_schema import AlgorithmOutputSchema
 from vantage6.algorithm.store.model.algorithm import Algorithm as db_Algorithm
@@ -144,9 +145,19 @@ class Algorithms(AlgorithmStoreResources):
 
         tags: ["Algorithm"]
         """
-        # TODO add filtering
         q = g.session.query(db_Algorithm)
 
+        # filter on properties
+        for field in [
+            "name",
+            "description",
+            "image",
+            "partitioning",
+            "vantage6_version",
+        ]:
+            if (value := request.args.get(field)) is not None:
+                q = q.filter(getattr(db_Algorithm, field).like(f"%{value}%"))
+
         # paginate results
         try:
             page = Pagination.from_query(q, request, db.Algorithm)
@@ -234,6 +245,24 @@ class Algorithms(AlgorithmStoreResources):
                                 description: Type of argument. Can be 'string',
                                   'integer', 'float', 'boolean', 'json',
                                   'column', 'organizations' or 'organization'
+                        ui_visualizations:
+                          type: array
+                          description: List of visualizations that are available in
+                            the algorithm
+                          items:
+                            properties:
+                              name:
+                                type: string
+                                description: Name of the visualization
+                              description:
+                                type: string
+                                description: Description of the visualization
+                              type:
+                                type: string
+                                description: Type of visualization.
+                              schema:
+                                type: object
+                                description: Schema that describes the visualization
 
         responses:
           201:
@@ -279,26 +308,32 @@ class Algorithms(AlgorithmStoreResources):
             )
             func.save()
             # create the arguments
-            arguments = function.get("arguments")
-            if arguments:
-                for argument in arguments:
-                    arg = Argument(
-                        name=argument["name"],
-                        description=argument.get("description", ""),
-                        type_=argument["type"],
-                        function_id=func.id,
-                    )
-                    arg.save()
+            for argument in function.get("arguments", []):
+                arg = Argument(
+                    name=argument["name"],
+                    description=argument.get("description", ""),
+                    type_=argument["type"],
+                    function_id=func.id,
+                )
+                arg.save()
             # create the databases
-            databases = function.get("databases")
-            if databases:
-                for database in databases:
-                    db = Database(
-                        name=database["name"],
-                        description=database.get("description", ""),
-                        function_id=func.id,
-                    )
-                    db.save()
+            for database in function.get("databases", []):
+                db = Database(
+                    name=database["name"],
+                    description=database.get("description", ""),
+                    function_id=func.id,
+                )
+                db.save()
+            # create the visualizations
+            for visualization in function.get("ui_visualizations", []):
+                vis = UIVisualization(
+                    name=visualization["name"],
+                    description=visualization.get("description", ""),
+                    type_=visualization["type"],
+                    schema=visualization.get("schema", {}),
+                    function_id=func.id,
+                )
+                vis.save()
 
         return algorithm_output_schema.dump(algorithm, many=False), HTTPStatus.CREATED
 
@@ -374,6 +409,8 @@ class Algorithm(AlgorithmStoreResources):
                 database.delete()
             for argument in function.arguments:
                 argument.delete()
+            for visualization in function.ui_visualizations:
+                visualization.delete()
             function.delete()
         algorithm.delete()
 
@@ -494,7 +531,7 @@ class Algorithm(AlgorithmStoreResources):
         fields = ["name", "description", "image", "partitioning", "vantage6_version"]
         for field in fields:
             if field in data and data.get(field) is not None:
-                setattr(algorithm, field, data.get("name"))
+                setattr(algorithm, field, data.get(field))
 
         if (functions := data.get("functions")) is not None:
             for function in algorithm.functions:
@@ -502,6 +539,8 @@ class Algorithm(AlgorithmStoreResources):
                     argument.delete()
                 for db in function.databases:
                     db.delete()
+                for visualization in function.ui_visualizations:
+                    visualization.delete()
                 function.delete()
 
             for new_function in functions:
@@ -513,27 +552,30 @@ class Algorithm(AlgorithmStoreResources):
                 )
                 func.save()
 
-                arguments = new_function.get("arguments")
-                if arguments:
-                    for argument in arguments:
-                        arg = Argument(
-                            name=argument["name"],
-                            description=argument.get("description", ""),
-                            type_=argument["type"],
-                            function_id=func.id,
-                        )
-                        arg.save()
-
-                # create the databases
-                databases = new_function.get("databases")
-                if databases:
-                    for database in databases:
-                        db = Database(
-                            name=database["name"],
-                            description=database.get("description", ""),
-                            function_id=func.id,
-                        )
-                        db.save()
+                for argument in new_function.get("arguments", []):
+                    arg = Argument(
+                        name=argument["name"],
+                        description=argument.get("description", ""),
+                        type_=argument["type"],
+                        function_id=func.id,
+                    )
+                    arg.save()
+                for database in new_function.get("databases", []):
+                    db = Database(
+                        name=database["name"],
+                        description=database.get("description", ""),
+                        function_id=func.id,
+                    )
+                    db.save()
+                for visualization in new_function.get("ui_visualizations", []):
+                    vis = UIVisualization(
+                        name=visualization["name"],
+                        description=visualization.get("description", ""),
+                        type_=visualization["type"],
+                        schema=visualization.get("schema", {}),
+                        function_id=func.id,
+                    )
+                    vis.save()
 
         algorithm.save()
 

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/resource/schema/input_schema.py

@@ -1,10 +1,15 @@
-from marshmallow import Schema, fields, ValidationError, validates
+from marshmallow import Schema, fields, ValidationError, validates, validates_schema
 from marshmallow.validate import Range
+from jsonschema import validate as json_validate
 
 from vantage6.algorithm.store.model.common.enums import (
     Partitioning,
     FunctionType,
     ArgumentType,
+    VisualizationType,
+)
+from vantage6.algorithm.store.model.common.ui_visualization_schemas import (
+    get_schema_for_visualization,
 )
 
 
@@ -44,11 +49,12 @@ class FunctionInputSchema(_NameDescriptionSchema):
     Schema for the input of a function.
     """
 
-    type = fields.String(required=True)
+    type_ = fields.String(required=True, data_key="type")
     databases = fields.Nested("DatabaseInputSchema", many=True)
     arguments = fields.Nested("ArgumentInputSchema", many=True)
+    ui_visualizations = fields.Nested("UIVisualizationInputSchema", many=True)
 
-    @validates("type")
+    @validates("type_")
     def validate_type(self, value):
         """
         Validate that the type is one of the allowed values.
@@ -74,9 +80,9 @@ class ArgumentInputSchema(_NameDescriptionSchema):
     Schema for the input of an argument.
     """
 
-    type = fields.String(required=True)
+    type_ = fields.String(required=True, data_key="type")
 
-    @validates("type")
+    @validates("type_")
     def validate_type(self, value):
         """
         Validate that the type is one of the allowed values.
@@ -84,10 +90,47 @@ class ArgumentInputSchema(_NameDescriptionSchema):
         types = [a.value for a in ArgumentType]
         if value not in types:
             raise ValidationError(
-                f"Argument type '{value}' is not one of the allowed values " f"{types}"
+                f"Argument type '{value}' is not one of the allowed values: {types}"
             )
 
 
+class UIVisualizationInputSchema(_NameDescriptionSchema):
+    """
+    Schema for the input of a UI visualization.
+    """
+
+    type_ = fields.String(required=True, data_key="type")
+    schema = fields.Dict()
+
+    @validates("type_")
+    def validate_type(self, value):
+        """
+        Validate that the type is one of the allowed values.
+        """
+        types = [v.value for v in VisualizationType]
+        if value not in types:
+            raise ValidationError(
+                f"UI visualization type '{value}' is not one of the allowed values "
+                f"{types}"
+            )
+
+    @validates_schema
+    def validate_schema(self, data, **kwargs):
+        """
+        Validate that the schema is a valid JSON schema.
+        """
+        schema = data.get("schema")
+        type_ = data.get("type_")
+        if schema and type_:
+            try:
+                json_validate(schema, get_schema_for_visualization(type_))
+            except Exception as exc:
+                raise ValidationError(
+                    "Schema does not match requirements for that visualization type: "
+                    f"{exc}",
+                ) from exc
+
+
 class UserInputSchema(Schema):
     """Schema for validating input for creating a user."""
 

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/resource/schema/output_schema.py

@@ -9,6 +9,7 @@ from vantage6.algorithm.store.model.function import Function
 from vantage6.algorithm.store.model import Base
 from vantage6.algorithm.store.model.role import Role
 from vantage6.algorithm.store.model.rule import Rule
+from vantage6.algorithm.store.model.ui_visualization import UIVisualization
 from vantage6.algorithm.store.model.user import User
 from vantage6.algorithm.store.model.review import Review
 from vantage6.algorithm.store.model.vantage6_server import Vantage6Server
@@ -80,12 +81,14 @@ class FunctionOutputSchema(HATEOASModelSchema):
 
     class Meta:
         model = Function
-        exclude = ["type_"]
 
-    type = fields.String(attribute="type_")
+    type_ = fields.String(data_key="type")
 
     databases = fields.Nested("DatabaseOutputSchema", many=True, exclude=["id"])
     arguments = fields.Nested("ArgumentOutputSchema", many=True, exclude=["id"])
+    ui_visualizations = fields.Nested(
+        "UIVisualizationOutputSchema", many=True, exclude=["id"]
+    )
 
 
 class DatabaseOutputSchema(HATEOASModelSchema):
@@ -100,9 +103,17 @@ class ArgumentOutputSchema(HATEOASModelSchema):
 
     class Meta:
         model = Argument
-        exclude = ["type_"]
 
-    type = fields.String(attribute="type_")
+    type_ = fields.String(data_key="type")
+
+
+class UIVisualizationOutputSchema(HATEOASModelSchema):
+    """Marshmallow output schema to serialize the UIVisualization model"""
+
+    class Meta:
+        model = UIVisualization
+
+    type_ = fields.String(data_key="type")
 
 
 class Vantage6ServerOutputSchema(HATEOASModelSchema):

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6_algorithm_store.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vantage6-algorithm-store
-Version: 4.3.4
+Version: 4.4.0
 Summary: Vantage6 algorithm store
 Home-page: https://github.com/vantage6/vantage6
 Requires-Python: >=3.10

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6_algorithm_store.egg-info/SOURCES.txt

@@ -19,9 +19,11 @@ vantage6/algorithm/store/model/review.py
 vantage6/algorithm/store/model/role.py
 vantage6/algorithm/store/model/role_rule_association.py
 vantage6/algorithm/store/model/rule.py
+vantage6/algorithm/store/model/ui_visualization.py
 vantage6/algorithm/store/model/user.py
 vantage6/algorithm/store/model/vantage6_server.py
 vantage6/algorithm/store/model/common/enums.py
+vantage6/algorithm/store/model/common/ui_visualization_schemas.py
 vantage6/algorithm/store/resource/__init__.py
 vantage6/algorithm/store/resource/algorithm.py
 vantage6/algorithm/store/resource/role.py

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6_algorithm_store.egg-info/requires.txt

@@ -5,13 +5,14 @@ Flask-Principal==0.4.0
 flask-marshmallow==0.15.0
 Flask-RESTful==0.3.10
 gevent==23.9.1
+jsonschema==4.21.1
 marshmallow==3.19.0
 requests==2.31.0
 schema==0.7.5
 SQLAlchemy==1.4.46
 werkzeug==3.0.1
-vantage6==4.3.4
-vantage6-common==4.3.4
+vantage6==4.4.0
+vantage6-common==4.4.0
 
 [dev]
 coverage==6.4.4

{vantage6-algorithm-store-4.3.4 → vantage6-algorithm-store-4.4.0}/vantage6/algorithm/store/model/argument.py

@@ -20,10 +20,10 @@ class Argument(Base):
         Description of the argument
     function_id : int
         ID of the algorithm that this function belongs to
-    function : :class:`~.model.algorithm.algorithm`
-        Algorithm function that this argument belongs to
     type_ : str
         Type of the argument
+    function : :class:`~.model.algorithm.algorithm`
+        Algorithm function that this argument belongs to
     """
 
     # fields