Mongo persistence (#7)

* removed errorDefinitions file, and placed into errors folder instead. Added class variable in stores/protocol to allow specifying error responses related directly to loading/unloading the Hkl object store

* changed all file, variable and class names. Updated dev packages to include pep8-naming

* added typed-ast package to setup.cfg to pass lint check

* relocked pipfile and fixed issues to make lint pass

* made constants all caps (including enum members), more explicit return types from services

* added mongodb store, changed how objects are persisted so they can fall under a collection, eg several samples may relate to one beamline for example

* modified files to pass pre-commit checks and tests

* using motor to make store calls non blocking

* abstracted the get_store functionality, took out side effects from store creation. Seperate PR to follow to take all side effects out

* updated pipfile lock to include motor

Author: rosesyrett

Pipfile.lock

@@ -27,6 +27,8 @@ install_requires =
     diffcalc-core
     fastapi
     uvicorn
+    pymongo
+    motor
 
 [options.extras_require]
 # For development tests/docs

setup.cfg

@@ -1,10 +1,7 @@
-from . import config, server
+from . import config, database, server
 from ._version_git import __version__
 
 # __all__ defines the public API for the package.
 # Each module also defines its own __all__.
-__all__ = [
-    "__version__",
-    "server",
-    "config",
-]
+
+__all__ = ["__version__", "server", "config", "database"]

src/diffcalc_API/__init__.py

@@ -1,9 +1,8 @@
-# this file is for defining constants
-
-SAVE_PICKLES_FOLDER = "/dls/tmp/ton99817/diffcalc_pickles"
+SAVE_PICKLES_FOLDER = "/"
 VECTOR_PROPERTIES = ["n_hkl", "n_phi", "surf_nhkl", "surf_nphi"]
 CONSTRAINTS_WITH_NO_VALUE = {"a_eq_b", "bin_eq_bout", "mu_is_gam", "bisect"}
 
+
 ALL_CONSTRAINTS = {
     "delta",
     "gam" "qaz",

src/diffcalc_API/config.py

@@ -0,0 +1,5 @@
+import motor.motor_asyncio
+from motor.motor_asyncio import AsyncIOMotorClient, AsyncIOMotorDatabase
+
+client: AsyncIOMotorClient = motor.motor_asyncio.AsyncIOMotorClient()
+database: AsyncIOMotorDatabase = client.test_db

src/diffcalc_API/database.py

@@ -12,7 +12,7 @@ class Codes(ErrorCodes):
     CHECK_CONSTRAINT_EXISTS = 400
 
 
-responses = {code: ALL_RESPONSES[code] for code in np.unique(Codes().all_codes())}
+responses = {code: ALL_RESPONSES[code] for code in np.unique(Codes.all_codes())}
 
 
 def check_constraint_exists(constraint: str) -> None:

src/diffcalc_API/errors/constraints.py

@@ -1,4 +1,5 @@
-from typing import Any, Dict, Union
+from enum import IntEnum
+from typing import Any, Dict, List, Union
 
 from diffcalc.util import DiffcalcException
 from pydantic import BaseModel
@@ -25,14 +26,10 @@ class DiffcalcExceptionModel(BaseModel):
     detail: str
 
 
-class ErrorCodes:
-    def all_codes(self):
-        attributes = [
-            attr
-            for attr in dir(self)
-            if (not attr.startswith("__")) and (not attr == "all_codes")
-        ]
-        return [getattr(self, attr) for attr in attributes]
+class ErrorCodes(IntEnum):
+    @classmethod
+    def all_codes(cls) -> List[int]:
+        return [val.value for val in cls]
 
 
 #######################################################################################

src/diffcalc_API/errors/definitions.py

@@ -16,7 +16,7 @@ class Codes(ErrorCodes):
     CALCULATE_UB_MATRIX = 400
 
 
-responses = {code: ALL_RESPONSES[code] for code in np.unique(Codes().all_codes())}
+responses = {code: ALL_RESPONSES[code] for code in np.unique(Codes.all_codes())}
 
 
 def check_valid_miller_indices(miller_indices: Tuple[float, float, float]) -> None:

src/diffcalc_API/errors/hkl.py

@@ -20,7 +20,7 @@ class Codes(ErrorCodes):
     CHECK_PROPERTY_IS_VALID = 400
 
 
-responses = {code: ALL_RESPONSES[code] for code in np.unique(Codes().all_codes())}
+responses = {code: ALL_RESPONSES[code] for code in np.unique(Codes.all_codes())}
 
 
 def check_params_not_empty(params: SetLatticeParams) -> None:

src/diffcalc_API/errors/ub.py

@@ -1,52 +1,72 @@
-from typing import Dict, Union
+from typing import Dict, Optional, Union
 
-from fastapi import APIRouter, Body, Depends, Response
+from fastapi import APIRouter, Body, Depends, Query, Response
 
 from diffcalc_API.services import constraints as service
-from diffcalc_API.stores.pickling import get_store
-from diffcalc_API.stores.protocol import HklCalcStore
+from diffcalc_API.stores.protocol import HklCalcStore, get_store
 
 router = APIRouter(prefix="/constraints", tags=["constraints"])
 
 
 @router.get("/{name}")
-async def get_constraints(name: str, store: HklCalcStore = Depends(get_store)):
-    content = await service.get_constraints(name, store)
-
+async def get_constraints(
+    name: str,
+    store: HklCalcStore = Depends(get_store),
+    collection: Optional[str] = Query(default=None, example="B07"),
+):
+    content = await service.get_constraints(name, store, collection)
     return Response(content=content, media_type="application/text")
 
 
-@router.put("/{name}/set")
+@router.post("/{name}")
 async def set_constraints(
     name: str,
     constraints: Dict[str, Union[float, bool]] = Body(
         example={"qaz": 0, "alpha": 0, "eta": 0}
     ),
     store: HklCalcStore = Depends(get_store),
+    collection: Optional[str] = Query(default=None, example="B07"),
 ):
-    await service.set_constraints(name, constraints, store)
+    await service.set_constraints(name, constraints, store, collection)
 
-    return {"message": f"constraints updated (replaced) for crystal {name}"}
+    return {
+        "message": (
+            f"constraints updated (replaced) for crystal {name} in "
+            + f"collection {collection}"
+        )
+    }
 
 
-@router.patch("/{name}/unconstrain/{property}")
+@router.delete("/{name}/{property}")
 async def remove_constraint(
     name: str,
     property: str,
     store: HklCalcStore = Depends(get_store),
+    collection: Optional[str] = Query(default=None, example="B07"),
 ):
-    await service.remove_constraint(name, property, store)
+    await service.remove_constraint(name, property, store, collection)
 
-    return {"message": f"unconstrained {property} for crystal {name}. "}
+    return {
+        "message": (
+            f"unconstrained {property} for crystal {name} in "
+            + f"collection {collection}. "
+        )
+    }
 
 
-@router.patch("/{name}/constrain/{property}")
+@router.patch("/{name}/{property}")
 async def set_constraint(
     name: str,
     property: str,
     value: Union[float, bool] = Body(...),
     store: HklCalcStore = Depends(get_store),
+    collection: Optional[str] = Query(default=None, example="B07"),
 ):
-    await service.set_constraint(name, property, value, store)
+    await service.set_constraint(name, property, value, store, collection)
 
-    return {"message": f"constrained {property} for crystal {name}. "}
+    return {
+        "message": (
+            f"constrained {property} for crystal {name} in collection "
+            + f"{collection}. "
+        )
+    }