Node post methods

.pre-commit-config.yaml

@@ -58,6 +58,7 @@ repos:
  - passlib
  - pytest~=3.6,<5.0.0
  - sphinx<4
+ - importlib_metadata~=4.3
  exclude: >
  (?x)^(
  docs/.*|

aiida_restapi/main.py

@@ -3,11 +3,12 @@
 from fastapi import FastAPI
 
 from aiida_restapi.graphql import main
-from aiida_restapi.routers import auth, computers, groups, users
+from aiida_restapi.routers import auth, computers, groups, nodes, users
 
 app = FastAPI()
 app.include_router(auth.router)
 app.include_router(computers.router)
+app.include_router(nodes.router)
 app.include_router(groups.router)
 app.include_router(users.router)
 app.add_route("/graphql", main.app, name="graphql")

aiida_restapi/models.py

@@ -6,17 +6,47 @@
 """
 # pylint: disable=too-few-public-methods
 
+import inspect
+import io
 from datetime import datetime
 from typing import ClassVar, Dict, List, Optional, Type, TypeVar
 from uuid import UUID
 
 from aiida import orm
+from aiida.restapi.common.identifiers import load_entry_point_from_full_type
+from fastapi import Form
 from pydantic import BaseModel, Field
 
 # Template type for subclasses of `AiidaModel`
 ModelType = TypeVar("ModelType", bound="AiidaModel")
 
 
+def as_form(cls: Type[BaseModel]) -> Type[BaseModel]:
+ """
+ Adds an as_form class method to decorated models. The as_form class method
+ can be used with FastAPI endpoints
+
+ Note: Taken from https://github.com/tiangolo/fastapi/issues/2387
+ """
+ new_params = [
+ inspect.Parameter(
+ field.alias,
+ inspect.Parameter.POSITIONAL_ONLY,
+ default=(Form(field.default) if not field.required else Form(...)),
+ )
+ for field in cls.__fields__.values()
+ ]
+
+ async def _as_form(**data: Dict) -> BaseModel:
+ return cls(**data)
+
+ sig = inspect.signature(_as_form)
+ sig = sig.replace(parameters=new_params)
+ _as_form.__signature__ = sig # type: ignore
+ setattr(cls, "as_form", _as_form)
+ return cls
+
+
 class AiidaModel(BaseModel):
  """A mapping of an AiiDA entity to a pydantic model."""
 
@@ -26,6 +56,7 @@ class Config:
  """The models configuration."""
 
  orm_mode = True
+ extra = "forbid"
 
  @classmethod
  def get_projectable_properties(cls) -> List[str]:
@@ -88,6 +119,11 @@ class User(AiidaModel):
 
  _orm_entity = orm.User
 
+ class Config:
+ """The models configuration."""
+
+ extra = "allow"
+
  id: Optional[int] = Field(description="Unique user id (pk)")
  email: str = Field(description="Email address of the user")
  first_name: Optional[str] = Field(description="First name of the user")
@@ -119,6 +155,107 @@ class Computer(AiidaModel):
  description="General settings for these communication and management protocols"
  )
 
+ description: Optional[str] = Field(description="Description of node")
+
+
+class Node(AiidaModel):
+ """AiiDA Node Model."""
+
+ _orm_entity = orm.Node
+
+ id: Optional[int] = Field(description="Unique id (pk)")
+ uuid: Optional[UUID] = Field(description="Unique uuid")
+ node_type: Optional[str] = Field(description="Node type")
+ process_type: Optional[str] = Field(description="Process type")
+ label: str = Field(description="Label of node")
+ description: Optional[str] = Field(description="Description of node")
+ ctime: Optional[datetime] = Field(description="Creation time")
+ mtime: Optional[datetime] = Field(description="Last modification time")
+ user_id: Optional[int] = Field(description="Created by user id (pk)")
+ dbcomputer_id: Optional[int] = Field(description="Associated computer id (pk)")
+ attributes: Optional[Dict] = Field(
+ description="Variable attributes of the node",
+ )
+ extras: Optional[Dict] = Field(
+ description="Variable extras (unsealed) of the node",
+ )
+
+
+@as_form
+class Node_Post(AiidaModel):
+ """AiiDA model for posting Nodes."""
+
+ node_type: Optional[str] = Field(description="Node type")
+ process_type: Optional[str] = Field(description="Process type")
+ label: str = Field(description="Label of node")
+ description: Optional[str] = Field(description="Description of node")
+ user_id: Optional[int] = Field(description="Created by user id (pk)")
+ dbcomputer_id: Optional[int] = Field(description="Associated computer id (pk)")
+ attributes: Optional[Dict] = Field(
+ description="Variable attributes of the node",
+ )
+ extras: Optional[Dict] = Field(
+ description="Variable extras (unsealed) of the node",
+ )
+
+ @classmethod
+ def create_new_node(
+ cls: Type[ModelType],
+ node_type: str,
+ node_dict: dict,
+ ) -> orm.Node:
+ "Create and Store new Node"
+
+ orm_class = load_entry_point_from_full_type(node_type)
+ attributes = node_dict.pop("attributes", {})
+ extras = node_dict.pop("extras", {})
+
+ if issubclass(orm_class, orm.BaseType):
+ orm_object = orm_class(
+ attributes["value"],
+ **node_dict,
+ )
+ elif issubclass(orm_class, orm.Dict):
+ orm_object = orm_class(
+ dict=attributes,
+ **node_dict,
+ )
+ elif issubclass(orm_class, orm.Code):
+ orm_object = orm_class()
+ orm_object.set_remote_computer_exec(
+ (
+ orm.Computer.get(id=node_dict.get("dbcomputer_id")),
+ attributes["remote_exec_path"],
+ )
+ )
+ orm_object.label = node_dict.get("label")
+ else:
+ orm_object = load_entry_point_from_full_type(node_type)(**node_dict)
+ orm_object.set_attribute_many(attributes)
+
+ orm_object.set_extra_many(extras)
+ orm_object.store()
+ return orm_object
+
+ @classmethod
+ def create_new_node_with_file(
+ cls: Type[ModelType],
+ node_type: str,
+ node_dict: dict,
+ file: bytes,
+ ) -> orm.Node:
+ "Create and Store new Node with file"
+ attributes = node_dict.pop("attributes", {})
+ extras = node_dict.pop("extras", {})
+
+ orm_object = load_entry_point_from_full_type(node_type)(
+ file=io.BytesIO(file), **node_dict, **attributes
+ )
+
+ orm_object.set_extra_many(extras)
+ orm_object.store()
+ return orm_object
+
 
 class Group(AiidaModel):
  """AiiDA Group model."""

aiida_restapi/routers/groups.py

@@ -41,6 +41,7 @@ async def read_group(group_id: int) -> Optional[Group]:
 
 
 @router.post("/groups", response_model=Group)
+@with_dbenv()
 async def create_group(
  group: Group_Post,
  current_user: User = Depends(

aiida_restapi/routers/nodes.py

@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+"""Declaration of FastAPI application."""
+from typing import List, Optional
+
+from aiida import orm
+from aiida.cmdline.utils.decorators import with_dbenv
+from fastapi import APIRouter, Depends, File, HTTPException
+from importlib_metadata import entry_points
+
+from aiida_restapi import models
+
+from .auth import get_current_active_user
+
+router = APIRouter()
+
+ENTRY_POINTS = entry_points()
+
+
+@router.get("/nodes", response_model=List[models.Node])
+@with_dbenv()
+async def read_nodes() -> List[models.Node]:
+ """Get list of all nodes"""
+ return models.Node.get_entities()
+
+
+@router.get("/nodes/projectable_properties", response_model=List[str])
+async def get_nodes_projectable_properties() -> List[str]:
+ """Get projectable properties for nodes endpoint"""
+
+ return models.Node.get_projectable_properties()
+
+
+@router.get("/nodes/{nodes_id}", response_model=models.Node)
+@with_dbenv()
+async def read_node(nodes_id: int) -> Optional[models.Node]:
+ """Get nodes by id."""
+ qbobj = orm.QueryBuilder()
+
+ qbobj.append(orm.Node, filters={"id": nodes_id}, project=["**"], tag="node").limit(
+ 1
+ )
+ return qbobj.dict()[0]["node"]
+
+
+@router.post("/nodes", response_model=models.Node)
+@with_dbenv()
+async def create_node(
+ node: models.Node_Post,
+ current_user: models.User = Depends(
+ get_current_active_user
+ ), # pylint: disable=unused-argument
+) -> models.Node:
+ """Create new AiiDA node."""
+
+ node_dict = node.dict(exclude_unset=True)
+ node_type = node_dict.pop("node_type", None)
+
+ try:
+ (entry_point_node,) = ENTRY_POINTS.select(
+ group="aiida.rest.post", name=node_type
+ )
+ except ValueError as exc:
+ raise HTTPException(
+ status_code=404, detail="Entry point '{}' not recognized.".format(node_type)
+ ) from exc
+
+ try:
+ orm_object = entry_point_node.load().create_new_node(node_type, node_dict)
+ except (TypeError, ValueError, KeyError) as err:
+ raise HTTPException(status_code=400, detail="Error: {0}".format(err)) from err
+
+ return models.Node.from_orm(orm_object)
+
+
+@router.post("/nodes/singlefile", response_model=models.Node)
+@with_dbenv()
+async def create_upload_file(
+ upload_file: bytes = File(...),
+ params: models.Node_Post = Depends(models.Node_Post.as_form), # type: ignore # pylint: disable=maybe-no-member
+ current_user: models.User = Depends(
+ get_current_active_user
+ ), # pylint: disable=unused-argument
+) -> models.Node:
+ """Endpoint for uploading file data"""
+ node_dict = params.dict(exclude_unset=True, exclude_none=True)
+ node_type = node_dict.pop("node_type", None)
+
+ try:
+ (entry_point_node,) = entry_points(group="aiida.rest.post", name=node_type)
+ except KeyError as exc:
+ raise KeyError("Entry point '{}' not recognized.".format(node_type)) from exc
+
+ orm_object = entry_point_node.load().create_new_node_with_file(
+ node_type, node_dict, upload_file
+ )
+
+ return models.Node.from_orm(orm_object)

aiida_restapi/routers/users.py

@@ -39,6 +39,7 @@ async def read_user(user_id: int) -> Optional[User]:
 
 
 @router.post("/users", response_model=User)
+@with_dbenv()
 async def create_user(
  user: User,
  current_user: User = Depends(

conftest.py

@@ -67,6 +67,17 @@ def default_groups():
  return [group_1.id, group_2.id]
 
 
+@pytest.fixture(scope="function")
+def default_nodes():
+ """Populate database with some nodes."""
+ node_1 = orm.Int(1).store()
+ node_2 = orm.Float(1.1).store()
+ node_3 = orm.Str("test_string").store()
+ node_4 = orm.Bool(False).store()
+
+ return [node_1.id, node_2.id, node_3.id, node_4.id]
+
+
 @pytest.fixture(scope="function")
 def authenticate():
  """Authenticate user.

setup.json

@@ -19,6 +19,18 @@
  ],
  "aiida.cmdline.data": [
  "restapi = aiida_restapi.cli:data_cli"
+ ],
+ "aiida.rest.post": [
+ "data.str.Str.| = aiida_restapi.models:Node_Post",
+ "data.float.Float.| = aiida_restapi.models:Node_Post",
+ "data.int.Int.| = aiida_restapi.models:Node_Post",
+ "data.bool.Bool.| = aiida_restapi.models:Node_Post",
+ "data.structure.StructureData.| = aiida_restapi.models:Node_Post",
+ "data.orbital.OrbitalData.| = aiida_restapi.models:Node_Post",
+ "data.list.List.| = aiida_restapi.models:Node_Post",
+ "data.dict.Dict.| = aiida_restapi.models:Node_Post",
+ "data.singlefile.SingleFileData.| = aiida_restapi.models:Node_Post",
+ "data.code.Code.| = aiida_restapi.models:Node_Post"
  ]
  },
  "include_package_data": true,
@@ -36,7 +48,8 @@
  "pydantic~=1.8.2",
  "graphene~=2.0",
  "python-dateutil~=2.0",
- "lark~=0.11.0"
+ "lark~=0.11.0",
+ "importlib_metadata~=4.3"
  ],
  "extras_require": {
  "testing": [

tests/test_computers.py

@@ -23,6 +23,7 @@ def test_get_computers_projectable(client):
  "scheduler_type",
  "transport_type",
  "metadata",
+ "description",
  ]
 
 

tests/test_graphql/test_full/test_full.yml

@@ -1,4 +1,4 @@
 data:
- aiidaVersion: 1.6.4
+ aiidaVersion: 1.6.5
  node:
  label: node 1

tests/test_models/test_computer_get_entities.yml

@@ -1,4 +1,5 @@
-- hostname: localhost_1
+- description: ''
+ hostname: localhost_1
  id: int
  metadata: {}
  name: test_comp_1