Tests on permissions

src/biodm/components/controllers/controller.py

@@ -80,10 +80,9 @@ def validate(cls, data: bytes) -> (Any | list | dict | None):
         :param data: some request body
         :type data: bytes
         """
-        try:
+        try: 
             json_data = json.load(io.BytesIO(data))
-            cls.schema.many = isinstance(json_data, list)
-            return cls.schema.loads(json_data=data)
+            return cls.schema.loads(json_data=json_data, many=isinstance(json_data, list))
 
         except ValidationError as e:
             raise PayloadValidationError() from e

src/biodm/components/table.py

@@ -1,13 +1,16 @@
 from __future__ import annotations
-from typing import TYPE_CHECKING, List
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, Any, List, Dict
 import datetime
 
 from sqlalchemy import (
     inspect, Column, Integer, text, String, TIMESTAMP, ForeignKey, UUID
 )
+import sqlalchemy
 from sqlalchemy.ext.asyncio import AsyncAttrs
 from sqlalchemy.ext.declarative import declared_attr
 from sqlalchemy.orm import DeclarativeBase, relationship, Mapped
+import sqlalchemy.orm
 from sqlalchemy.orm.relationships import Relationship
 
 if TYPE_CHECKING:
@@ -16,10 +19,34 @@
 
 
 class Base(DeclarativeBase, AsyncAttrs):
-    """Base class for ORM declarative Tables."""
-    # Enable entity - service linkage.
+    """Base class for ORM declarative Tables.
+ 
+    :param svc: Enable entity - service linkage
+    :type svc: DatabaseService
+    :param __permissions: Stores rules for user defined permissions on hierarchical entities
+    :type __permissions: Dict
+    """
     svc: DatabaseService
-    # perm: Permission
+    __permissions: Dict = {}
+
+    def __init_subclass__(cls, **kw: Any) -> None:
+        """Sets up the rules according to permissions objects set on tables."""
+        if hasattr(cls, "permissions"):
+            Base.__permissions[cls.__name__] = Base.__permissions.get(cls.__name__, (cls, []))
+            Base.__permissions[cls.__name__][1].append(cls.permissions)
+
+            for table in cls.permissions.propagates_to or []:
+                Base.__permissions[table.__name__][1].append(cls.permissions)
+        return super().__init_subclass__(**kw)
+
+    @classmethod
+    def setup_permissions(cls):
+        """After tables have been added to Base, you may call this method to factor in changes. 
+        -- Temporary for dev mode --."""
+        d = {}
+        for name, (table, permission) in Base.__permissions.items():
+            print(name, table, permission)
+        Base.__permissions = d
 
     @declared_attr
     def __tablename__(cls) -> str:
@@ -79,10 +106,26 @@ def user(cls) -> Mapped["User"]:
     )
     validated_at = Column(TIMESTAMP(timezone=True))
 
-
+@dataclass
 class Permission:
-    def __init__(self, propagates_to: List[Base]) -> None:
-        pass
+    """Holds permissions for a given entity's attributes."""
+    field: Column
+    # Verbs.
+    create: bool=False
+    read: bool=False
+    update: bool=False
+    download: bool=False
+    visualize: bool=False
+    # Flags.
+    # propagates: bool=True # ? 
+    use_same: bool=True
+
+    # TODO: check inputs
+    # def __init__(
+    #     self,
+
+    # ) -> None:
+    #     pass
 
 """"""
 """Class that produces necessary fields to declare ressource permissions for an entity.

src/biodm/managers/dbmanager.py

@@ -61,6 +61,7 @@ async def session(self) -> AsyncGenerator[AsyncSession, None]:
 
     async def init_db(self) -> None:
         """Drop all tables and create them."""
+        Base.setup_permissions()
         async with self.engine.begin() as conn:
             await conn.run_sync(Base.metadata.drop_all)
             await conn.run_sync(Base.metadata.create_all)

src/biodm/tests/conftest.py

@@ -137,14 +137,9 @@ def __init__(self, app):
 
 @pytest.fixture()
 def client():
-    with TestClient(**
-        {
-            "app": app, 
-            'backend_options': {
-                "use_uvloop": True
-            }
-        }
-    ) as c:
+    with TestClient(app=app, backend_options={
+        "use_uvloop": True
+    }) as c:
         yield c
 
 

src/biodm/tests/test_resource.py

@@ -19,7 +19,8 @@ def test_resource_schema(client):
 
 def test_create_unary_resource(client):
     """"""
-    response = client.post('/bs/', content=json_bytes({'name': 'test'}))
+    item = {'name': 'test'}
+    response = client.post('/bs/', content=json_bytes(item))
 
     assert response.status_code == 201
     assert "id" in response.text
@@ -59,11 +60,7 @@ def test_create_wrong_data(client):
 
 
 def test_read_resource(client):
-    item = {
-        'x': 1,
-        'y': 2,
-        'c': {'data': '1234'},
-    }
+    item = {'x': 1, 'y': 2, 'c': {'data': '1234'},}
 
     _ = client.post('/as/', content=json_bytes(item))
     response = client.get('/cs/1')
@@ -84,16 +81,8 @@ def test_missing_resource(client):
 
 
 def test_readall_resource(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    item2 = {
-        'x': 3,
-        'y': 4,
-        'bs': [{'name': 'tit'},{'name': 'tat'},]
-    }
+    item1 = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'},{'name': 'bap'},]}
+    item2 = {'x': 3, 'y': 4, 'bs': [{'name': 'tit'},{'name': 'tat'},]}
 
     _ = client.post('/as/', content=json_bytes([item1, item2]))
     response = client.get('/bs/')
@@ -106,16 +95,8 @@ def test_readall_resource(client):
 
 
 def test_filter_resource_wildcard(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    item2 = {
-        'x': 3,
-        'y': 4,
-        'bs': [{'name': 'tit'},{'name': 'tat'},]
-    }
+    item1 = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'},{'name': 'bap'},]}
+    item2 = {'x': 3, 'y': 4, 'bs': [{'name': 'tit'},{'name': 'tat'},]}
 
     _ = client.post('/as/', content=json_bytes([item1, item2]))
     response = client.get('/bs?name=b*')
@@ -130,16 +111,8 @@ def test_filter_resource_wildcard(client):
 
 
 def test_filter_resource_values(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    item2 = {
-        'x': 3,
-        'y': 4,
-        'bs': [{'name': 'tit'},{'name': 'tat'},]
-    }
+    item1 = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'},{'name': 'bap'},]}
+    item2 = {'x': 3, 'y': 4, 'bs': [{'name': 'tit'},{'name': 'tat'},]}
 
     _ = client.post('/as/', content=json_bytes([item1, item2]))
     response = client.get('/bs?name=bip,tat')
@@ -152,16 +125,8 @@ def test_filter_resource_values(client):
 
 
 def test_filter_resource_op(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    item2 = {
-        'x': 3,
-        'y': 4,
-        'bs': [{'name': 'tit'},{'name': 'tat'},]
-    }
+    item1 = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'},{'name': 'bap'},]}
+    item2 = {'x': 3, 'y': 4, 'bs': [{'name': 'tit'},{'name': 'tat'},]}
 
     _ = client.post('/as/', content=json_bytes([item1, item2]))
     response = client.get('/as?x.lt(2)')
@@ -201,42 +166,30 @@ def test_filter_resource_with_fields(client):
 
 @pytest.mark.xfail(raises=ValueError)
 def test_filter_wrong_op(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    client.post('/as/', content=json_bytes(item1))
+    item = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'}, {'name': 'bap'},]}
+
+    client.post('/as/', content=json_bytes(item))
     client.get('/as?x.lt=2')
 
 
 @pytest.mark.xfail(raises=ValueError)
 def test_filter_wrong_wildcard(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    client.post('/as/', content=json_bytes(item1))
+    item = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'}, {'name': 'bap'},]}
+
+    client.post('/as/', content=json_bytes(item))
     client.get('/as?y=2*')
 
 
 @pytest.mark.xfail(raises=ValueError)
 def test_filter_op_on_string(client):
-    item1 = {
-        'x': 1,
-        'y': 2,
-        'bs': [{'name': 'bip'},{'name': 'bap'},]
-    }
-    client.post('/as/', content=json_bytes(item1))
+    item = {'x': 1, 'y': 2, 'bs': [{'name': 'bip'}, {'name': 'bap'},]}
+
+    client.post('/as/', content=json_bytes(item))
     client.get('/bs?name.gt(2)')
 
 
 def test_delete_resource(client):
-    item = {
-        'x': 1,
-        'y': 2,
-    }
+    item = {'x': 1, 'y': 2,}
 
     _ = client.post('/as/', content=json_bytes(item))
     response = client.delete('/as/1')

src/example/app.py

@@ -3,16 +3,16 @@
 
 from biodm.api import Api
 
-from entities.controllers import CONTROLLERS
 from entities import tables, schemas
+from entities import controllers 
 # from example import manifests
 import config
 
 
 def main():
     app = Api(
         debug=config.DEBUG, 
-        controllers=CONTROLLERS,
+        controllers=controllers.CONTROLLERS,
         instance={
             'config': config,
             'tables': tables,

src/example/entities/controllers/__init__.py

@@ -1,8 +1,9 @@
 from .tag import TagController
+from .project import ProjectController
 from .file import FileController
 from .dataset import DatasetController
 
 
 
 
-CONTROLLERS = [TagController, FileController, DatasetController]
+CONTROLLERS = [TagController, FileController, ProjectController, DatasetController]

src/example/entities/controllers/project.py

@@ -0,0 +1,5 @@
+from biodm.components.controllers import ResourceController
+
+
+class ProjectController(ResourceController):
+    pass

src/example/entities/schemas/__init__.py

@@ -1,3 +1,4 @@
+from .project import ProjectSchema
 from .tag import TagSchema
 from .dataset import DatasetSchema
-from .file import FileSchema
+from .file import FileSchema

src/example/entities/schemas/dataset.py

@@ -1,19 +1,8 @@
 from marshmallow import Schema, validate, pre_load, ValidationError
 from marshmallow.fields import String, Date, List, Nested, Integer, UUID
 
-from biodm.tables import User, Group, ListGroup
-from biodm.schemas import UserSchema, GroupSchema, ListGroupSchema
-from entities.tables import Dataset
-# from controllers import schemas
-# from .group import GroupSchema
-# from .user import UserSchema
-# from .tag import TagSchema
-
 
 class DatasetSchema(Schema):
-    class Meta:
-        model = Dataset
-
     id = Integer()
     version = Integer()
     name = String(required=True)
@@ -30,9 +19,11 @@ class Meta:
         #     [u.id for u in User]
         # )
     )
+    id_project = Integer()
 
-    owner_group = Nested('GroupSchema') # , only=('name', 'n_members',)
-    contact = Nested('UserSchema', only=('username', ))
+    # owner_group = Nested('GroupSchema')
+    contact = Nested('UserSchema')
+    project = Nested('ProjectSchema')
     tags = List(Nested('TagSchema'))
 
     id_ls_download = Integer()
@@ -52,13 +43,13 @@ def pre_load_process(self, data, many, **kwargs):
         elif not id_uc:
             raise ValidationError("Need one of username_user_contact or contact fields.")
 
-        name_group = data.get('name_owner_group')
-        group_name = data.get('owner_group', {}).get('name')
-        if name_group and group_name:
-            assert(name_group == group_name)
-        elif group_name and not name_group:
-            ret["name_owner_group"] = group_name
-        elif not name_group:
-            raise ValidationError("Need one of name_owner_group or group fields.")
+        # name_group = data.get('name_owner_group')
+        # group_name = data.get('owner_group', {}).get('name')
+        # if name_group and group_name:
+        #     assert(name_group == group_name)
+        # elif group_name and not name_group:
+        #     ret["name_owner_group"] = group_name
+        # elif not name_group:
+        #     raise ValidationError("Need one of name_owner_group or group fields.")
 
-        return ret
+        # return ret

src/example/entities/schemas/file.py

@@ -1,18 +1,12 @@
 from marshmallow import Schema, validate
 from marshmallow.fields import String, List, Nested, Integer, Bool
 
-from entities.tables import File
-from .dataset import DatasetSchema
-
 
 class FileSchema(Schema):
-    class Meta:
-        model = File
-
     id = Integer()
     filename = String(required=True)
     url = String(required=False)
     ready = Bool(required=False)
     id_dataset = Integer(required=True)
     version_dataset = Integer(required=True)
-    dataset = Nested(DatasetSchema, required=True, load_only=True)
+    dataset = Nested('DatasetSchema', required=True, load_only=True)