Initial support for file metadata.

entities/api/core/gql_loaders.py

@@ -1,22 +1,23 @@
-import uuid
 import typing
-import strawberry
-import database.models as db
+import uuid
 from collections import defaultdict
-from typing import Any, Mapping, Tuple, Optional
-from sqlalchemy import ColumnElement, ColumnExpressionArgument, tuple_
-from sqlalchemy.orm import RelationshipProperty
-from sqlalchemy.ext.asyncio import AsyncSession
-from strawberry.type import StrawberryType
-from strawberry.dataloader import DataLoader
-from strawberry.arguments import StrawberryArgument
+from typing import Any, Mapping, Optional, Tuple
+
+import database.models as db
+import strawberry
+from api.core.deps import get_cerbos_client, get_db_session, require_auth_principal
+from api.core.strawberry_extensions import DependencyExtension
 from cerbos.sdk.client import CerbosClient
 from cerbos.sdk.model import Principal, Resource, ResourceDesc
-from fastapi import Depends
 from database.models import Base
+from fastapi import Depends
+from sqlalchemy import ColumnElement, ColumnExpressionArgument, tuple_
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.orm import RelationshipProperty
+from strawberry.arguments import StrawberryArgument
+from strawberry.dataloader import DataLoader
+from strawberry.type import StrawberryType
 from thirdparty.cerbos_sqlalchemy.query import get_query
-from api.core.deps import require_auth_principal, get_cerbos_client, get_db_session
-from api.core.strawberry_extensions import DependencyExtension
 
 CERBOS_ACTION_VIEW = "view"
 CERBOS_ACTION_CREATE = "create"
@@ -50,6 +51,33 @@ async def get_entities(
     return result.scalars().all()
 
 
+async def get_files(
+    model: db.File,
+    session: AsyncSession,
+    cerbos_client: CerbosClient,
+    principal: Principal,
+    filters: Optional[list[ColumnExpressionArgument]] = [],
+    order_by: Optional[list[tuple[ColumnElement[Any], ...]]] = [],
+):
+    rd = ResourceDesc(model.__tablename__)
+    plan = cerbos_client.plan_resources(CERBOS_ACTION_VIEW, principal, rd)
+    query = get_query(
+        plan,
+        model,
+        {
+            "request.resource.attr.owner_user_id": db.Entity.owner_user_id,
+            "request.resource.attr.collection_id": db.Entity.collection_id,
+        },
+        [(db.Entity, model.entity_id == db.Entity.id)],
+    )
+    if filters:
+        query = query.filter(*filters)
+    if order_by:
+        query = query.order_by(*order_by)
+    result = await session.execute(query)
+    return result.scalars().all()
+
+
 class EntityLoader:
     """
     Creates DataLoader instances on-the-fly for SQLAlchemy relationships
@@ -72,6 +100,11 @@ def loader_for(self, relationship: RelationshipProperty) -> DataLoader:
         except KeyError:
             related_model = relationship.entity.entity
 
+            if type(related_model) == db.File:
+                load_method = get_files
+            else:
+                load_method = get_entities
+
             async def load_fn(keys: list[Tuple]) -> list[Any]:
                 if not relationship.local_remote_pairs:
                     raise Exception("invalid relationship")
@@ -80,7 +113,7 @@ async def load_fn(keys: list[Tuple]) -> list[Any]:
                 if relationship.order_by:
                     order_by = [relationship.order_by]
                 db_session = self.engine.session()
-                rows = await get_entities(
+                rows = await load_method(
                     related_model,
                     db_session,
                     self.cerbos_client,
@@ -125,6 +158,22 @@ async def resolve_entity(
     return resolve_entity
 
 
+def get_file_loader(sql_model, gql_type):
+    @strawberry.field(extensions=[DependencyExtension()])
+    async def resolve_file(
+        id: typing.Optional[uuid.UUID] = None,
+        session: AsyncSession = Depends(get_db_session, use_cache=False),
+        cerbos_client: CerbosClient = Depends(get_cerbos_client),
+        principal: Principal = Depends(require_auth_principal),
+    ) -> list[Base]:
+        filters = []
+        if id:
+            filters.append(sql_model.entity_id == id)
+        return await get_files(sql_model, session, cerbos_client, principal, filters, [])
+
+    return resolve_file
+
+
 def get_base_creator(sql_model, gql_type):
     @strawberry.mutation(extensions=[DependencyExtension()])
     async def create(

entities/api/main.py

@@ -1,15 +1,23 @@
 import typing
+
+import database.models as db
 import strawberry
 import uvicorn
-import database.models as db
 from cerbos.sdk.client import CerbosClient
 from cerbos.sdk.model import Principal
+from database.connect import AsyncDB
 from fastapi import Depends, FastAPI
 from strawberry.fastapi import GraphQLRouter
-from database.connect import AsyncDB
 from thirdparty.strawberry_sqlalchemy_mapper import StrawberrySQLAlchemyMapper
-from api.core.gql_loaders import EntityLoader, get_base_loader, get_base_updater, get_base_creator
+
 from api.core.deps import get_auth_principal, get_cerbos_client, get_engine
+from api.core.gql_loaders import (
+    EntityLoader,
+    get_base_creator,
+    get_base_loader,
+    get_base_updater,
+    get_file_loader,
+)
 from api.core.settings import APISettings
 
 ######################
@@ -24,6 +32,11 @@ class EntityInterface:
     pass
 
 
+@strawberry_sqlalchemy_mapper.type(db.Entity)
+class Entity:
+    pass
+
+
 @strawberry_sqlalchemy_mapper.type(db.Sample)
 class Sample:
     pass
@@ -34,15 +47,22 @@ class SequencingRead:
     pass
 
 
+@strawberry_sqlalchemy_mapper.type(db.File)
+class File:
+    pass
+
+
 # --------------------
 # Queries
 # --------------------
 
 
 @strawberry.type
 class Query:
+    entity: typing.List[Sample] = get_base_loader(db.Entity, EntityInterface)
     samples: typing.List[Sample] = get_base_loader(db.Sample, Sample)
     sequencing_reads: typing.List[SequencingRead] = get_base_loader(db.SequencingRead, SequencingRead)
+    files: typing.List[File] = get_file_loader(db.File, File)
 
 
 # --------------------

entities/cerbos/policies/file.yaml

@@ -0,0 +1,20 @@
+# yaml-language-server: $schema=https://api.cerbos.dev/latest/cerbos/policy/v1/Policy.schema.json
+apiVersion: api.cerbos.dev/v1
+resourcePolicy:
+  version: "default"
+  importDerivedRoles:
+    - common_roles
+  resource: "file"
+  rules:
+    - actions: ['*']
+      effect: EFFECT_ALLOW
+      derivedRoles:
+        - project_member
+
+    - actions: ['download']
+      effect: EFFECT_ALLOW
+      derivedRoles:
+        - owner
+  schemas:
+    principalSchema:
+      ref: cerbos:///principal.json

entities/database/models/__init__.py

@@ -3,5 +3,6 @@
 
 from database.models.base import Base, meta, Entity  # noqa: F401
 from database.models.samples import Sample, SequencingRead  # noqa: F401
+from database.models.files import File  # noqa: F401
 
 # configure_mappers()

entities/database/models/base.py

@@ -1,8 +1,14 @@
-from sqlalchemy.orm import DeclarativeBase, Mapped
-from sqlalchemy import MetaData, Column, Integer
+from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column, relationship
+from sqlalchemy import MetaData, Column, Integer, String
 import uuid6
 import uuid
 from sqlalchemy.dialects.postgresql import UUID
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from database.models.files import File
+else:
+    File = "File"
 
 meta = MetaData(
     naming_convention={
@@ -27,9 +33,10 @@ class Entity(Base):
 
     # The "type" field distinguishes between subclasses (e.g. sample,
     # sequencing_read, etc)
-    type: Mapped[str]
+    type: Mapped[str] = mapped_column(String, nullable=False)
 
     # Attributes for each entity
-    producing_run_id = Column(Integer, nullable=True)
-    owner_user_id = Column(Integer, nullable=False)
-    collection_id = Column(Integer, nullable=False)
+    producing_run_id: Mapped[uuid.UUID] = mapped_column(Integer, nullable=True)
+    owner_user_id: Mapped[int] = mapped_column(Integer, nullable=False)
+    collection_id: Mapped[int] = mapped_column(Integer, nullable=False)
+    files: Mapped[list[File]] = relationship(File, back_populates="entity", foreign_keys="File.entity_id")

entities/database/models/files.py

@@ -0,0 +1,31 @@
+import uuid
+
+import uuid6
+from database.models.base import Base, Entity
+from sqlalchemy import Column, ForeignKey, Integer, String
+from sqlalchemy.dialects.postgresql import UUID
+from sqlalchemy.orm import mapped_column, Mapped, relationship
+
+
+class File(Base):
+    __tablename__ = "file"
+
+    id: Column[uuid.UUID] = Column(UUID(as_uuid=True), primary_key=True, default=uuid6.uuid7)
+
+    # TODO - the relationship between Entities and Files is currently being
+    # configured in both directions: entities have {fieldname}_file_id fields,
+    # *and* files have {entity_id, field_name} fields to map back to
+    # entities. We'll probably deprecate one side of this relationship in
+    # the future, but I'm not sure yet which one is going to prove to be
+    # more useful.
+    entity_id = mapped_column(ForeignKey("entity.id"))
+    entity_field_name = Column(String)
+    entity: Mapped[Entity] = relationship(Entity, back_populates="files", foreign_keys=entity_id)
+
+    status = mapped_column(String, nullable=False)
+    protocol = mapped_column(String, nullable=False)
+    namespace = Column(String, nullable=False)
+    path = Column(String, nullable=False)
+    file_format = Column(String, nullable=False)
+    compression_type = Column(String, nullable=False)
+    size = Column(Integer, nullable=False)

entities/database/models/samples.py

@@ -1,16 +1,23 @@
 from database.models.base import Entity
-from sqlalchemy import Column, ForeignKey, String
+from sqlalchemy import ForeignKey, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.dialects.postgresql import UUID
+from typing import TYPE_CHECKING
+import uuid
+
+if TYPE_CHECKING:
+    from database.models.files import File
+else:
+    File = "File"
 
 
 class Sample(Entity):
     __tablename__ = "sample"
     __mapper_args__ = {"polymorphic_identity": __tablename__}
 
-    entity_id = mapped_column(ForeignKey("entity.id"), primary_key=True)
-    name = Column(String, nullable=False)
-    location = Column(String, nullable=False)
+    entity_id: Mapped[uuid.UUID] = mapped_column(ForeignKey("entity.id"), primary_key=True)
+    name: Mapped[str] = mapped_column(String, nullable=False)
+    location: Mapped[str] = mapped_column(String, nullable=False)
 
     sequencing_reads: Mapped[list["SequencingRead"]] = relationship(
         "SequencingRead",
@@ -23,10 +30,12 @@ class SequencingRead(Entity):
     __tablename__ = "sequencing_read"
     __mapper_args__ = {"polymorphic_identity": __tablename__}
 
-    entity_id = mapped_column(ForeignKey("entity.id"), primary_key=True)
-    nucleotide = Column(String, nullable=False)
-    sequence = Column(String, nullable=False)
-    protocol = Column(String, nullable=False)
+    entity_id: Mapped[uuid.UUID] = mapped_column(ForeignKey("entity.id"), primary_key=True)
+    nucleotide: Mapped[str] = mapped_column(String, nullable=False)
+    sequence: Mapped[str] = mapped_column(String, nullable=False)
+    protocol: Mapped[str] = mapped_column(String, nullable=False)
+    sequence_file_id: Mapped[uuid.UUID] = mapped_column(ForeignKey("file.id"), nullable=True)
+    sequence_file: Mapped[File] = relationship("File", foreign_keys=sequence_file_id)
 
-    sample_id = Column(UUID, ForeignKey("sample.entity_id"), nullable=False)
+    sample_id: Mapped[uuid.UUID] = mapped_column(UUID, ForeignKey("sample.entity_id"), nullable=False)
     sample: Mapped[Sample] = relationship("Sample", back_populates="sequencing_reads", foreign_keys=sample_id)

entities/database_migrations/versions/20230828_131743_create_files_table.py

@@ -0,0 +1,44 @@
+"""create files table
+
+Create Date: 2023-08-28 20:17:44.359982
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "20230828_131743"
+down_revision = "20230809_181634"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "file",
+        sa.Column("id", sa.UUID(), nullable=False),
+        sa.Column("entity_id", sa.UUID(), nullable=True),
+        sa.Column("entity_field_name", sa.String(), nullable=True),
+        sa.Column("protocol", sa.String(), nullable=False),
+        sa.Column("namespace", sa.String(), nullable=False),
+        sa.Column("path", sa.String(), nullable=False),
+        sa.Column("file_format", sa.String(), nullable=False),
+        sa.Column("compression_type", sa.String(), nullable=False),
+        sa.Column("size", sa.Integer(), nullable=False),
+        sa.ForeignKeyConstraint(["entity_id"], ["entity.id"], name=op.f("fk_file_entity_id_entity")),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_file")),
+    )
+    op.add_column("sequencing_read", sa.Column("sequence_file_id", sa.UUID(), nullable=True))
+    op.create_foreign_key(
+        op.f("fk_sequencing_read_sequence_file_id_file"), "sequencing_read", "file", ["sequence_file_id"], ["id"]
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_constraint(op.f("fk_sequencing_read_sequence_file_id_file"), "sequencing_read", type_="foreignkey")
+    op.drop_column("sequencing_read", "sequence_file_id")
+    op.drop_table("file")
+    # ### end Alembic commands ###

entities/database_migrations/versions/20230828_141240_add_file_status.py

@@ -0,0 +1,25 @@
+"""add file status
+
+Create Date: 2023-08-28 21:12:41.448938
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "20230828_141240"
+down_revision = "20230828_131743"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("file", sa.Column("status", sa.String(), nullable=False))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("file", "status")
+    # ### end Alembic commands ###