Mongo persistence #7

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Merged

rosesyrett merged 11 commits into master from mongoPersistence

Jul 29, 2022

Pipfile.lock

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setup.cfg

-Original file line number
+Diff line change
@@ Expand Up / @@ -27,6 +27,8 @@ install_requires = @@
         diffcalc-core
         fastapi
         uvicorn
+        pymongo
+        motor
     [options.extras_require]
     # For development tests/docs
@@ Expand Down @@

src/diffcalc_API/__init__.py

-Original file line number
+Diff line change
@@ -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/config.py

-Original file line number
+Diff line change
@@ -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",
@@ Expand Down @@

src/diffcalc_API/database.py

-Original file line number
+Diff line change
@@ -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/errors/constraints.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -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:
@@ Expand Down @@

src/diffcalc_API/errors/definitions.py

-Original file line number
+Diff line change
@@ -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
@@ Expand All / @@ -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]
     #######################################################################################
@@ Expand Down @@

src/diffcalc_API/errors/hkl.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -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:
@@ Expand Down @@

src/diffcalc_API/errors/ub.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -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:
@@ Expand Down @@

src/diffcalc_API/routes/constraints.py

-Original file line number
+Diff line change
@@ -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}. "
+            )
+        }

src/diffcalc_API/routes/hkl.py

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -3,10 +3,9 @@
  
    from fastapi import APIRouter, Depends, Query, Response

    from diffcalc_API.services import hkl 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="/calculate", tags=["hkl"])

    router = APIRouter(prefix="/hkl", tags=["hkl"])

    SingleConstraint = Union[Tuple[str, float], str]

    @@ -19,8 +18,9 @@ async def calculate_ub(
  
        first_tag: Optional[Union[int, str]] = Query(default=None, example="refl1"),

        second_tag: Optional[Union[int, str]] = Query(default=None, example="plane"),

        store: HklCalcStore = Depends(get_store),

        collection: Optional[str] = Query(default=None, example="B07"),

    ):

        content = await service.calculate_ub(name, first_tag, second_tag, store)

        content = await service.calculate_ub(name, first_tag, second_tag, store, collection)

        return Response(content=content, media_type="application/text")

    @@ -30,9 +30,10 @@ async def lab_position_from_miller_indices(
  
        miller_indices: Tuple[float, float, float] = Query(example=[0, 0, 1]),

        wavelength: float = Query(..., example=1.0),

        store: HklCalcStore = Depends(get_store),

        collection: Optional[str] = Query(default=None, example="B07"),

    ):

        positions = await service.lab_position_from_miller_indices(

            name, miller_indices, wavelength, store

            name, miller_indices, wavelength, store, collection

        )

        return {"payload": positions}

    @@ -46,8 +47,11 @@ async def miller_indices_from_lab_position(
  
        ),

        wavelength: float = Query(..., example=1.0),

        store: HklCalcStore = Depends(get_store),

        collection: Optional[str] = Query(default=None, example="B07"),

    ):

        hkl = await service.miller_indices_from_lab_position(name, pos, wavelength, store)

        hkl = await service.miller_indices_from_lab_position(

            name, pos, wavelength, store, collection

        )

        return {"payload": hkl}

    @@ -59,8 +63,11 @@ async def scan_hkl(
  
        inc: PositionType = Query(..., example=(0.1, 0, 0.1)),

        wavelength: float = Query(..., example=1),

        store: HklCalcStore = Depends(get_store),

        collection: Optional[str] = Query(default=None, example="B07"),

    ):

        scan_results = await service.scan_hkl(name, start, stop, inc, wavelength, store)

        scan_results = await service.scan_hkl(

            name, start, stop, inc, wavelength, store, collection

        )

        return {"payload": scan_results}

    @@ -72,8 +79,11 @@ async def scan_wavelength(
  
        inc: float = Query(..., example=0.2),

        hkl: PositionType = Query(..., example=(1, 0, 1)),

        store: HklCalcStore = Depends(get_store),

        collection: Optional[str] = Query(default=None, example="B07"),

    ):

        scan_results = await service.scan_wavelength(name, start, stop, inc, hkl, store)

        scan_results = await service.scan_wavelength(

            name, start, stop, inc, hkl, store, collection

        )

        return {"payload": scan_results}

    @@ -87,9 +97,10 @@ async def scan_constraint(
  
        hkl: PositionType = Query(..., example=(1, 0, 1)),

        wavelength: float = Query(..., example=1.0),

        store: HklCalcStore = Depends(get_store),

        collection: Optional[str] = Query(default=None, example="B07"),

    ):

        scan_results = await service.scan_constraint(

            name, constraint, start, stop, inc, hkl, wavelength, store

            name, constraint, start, stop, inc, hkl, wavelength, store, collection

        )

        return {"payload": scan_results}

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