Move models into submodule

nerdd_backend/actions/save_module_to_db.py

@@ -2,7 +2,8 @@
 
 from nerdd_link import Action, Channel, ModuleMessage
 
-from ..data import Module, Repository
+from ..data import Repository
+from ..models import Module
 
 __all__ = ["SaveModuleToDb"]
 

nerdd_backend/actions/save_result_to_db.py

@@ -2,7 +2,8 @@
 
 from nerdd_link import Action, Channel, ResultMessage
 
-from ..data import Repository, Result
+from ..data import Repository
+from ..models import Result
 
 __all__ = ["SaveResultToDb"]
 

nerdd_backend/data/__init__.py

@@ -1,8 +1,4 @@
 from .exceptions import *
-from .job import *
 from .memory_repository import *
-from .module import *
 from .repository import *
-from .result import *
 from .rethinkdb_repository import *
-from .source import *

nerdd_backend/data/memory_repository.py

@@ -2,12 +2,9 @@
 
 from nerdd_link.utils import ObservableList
 
+from ..models import Job, Module, Result, Source
 from .exceptions import RecordNotFoundError
-from .job import Job
-from .module import Module
 from .repository import Repository
-from .result import Result
-from .source import Source
 
 __all__ = ["MemoryRepository"]
 

nerdd_backend/data/repository.py

@@ -1,10 +1,7 @@
 from abc import ABC, abstractmethod
 from typing import AsyncIterable, List, Optional, Tuple
 
-from .job import Job
-from .module import Module
-from .result import Result
-from .source import Source
+from ..models import Job, Module, Result, Source
 
 __all__ = ["Repository"]
 
@@ -48,9 +45,7 @@ async def upsert_module(self, module: Module) -> None:
     # JOBS
     #
     @abstractmethod
-    def get_job_changes(
-        self, job_id: str
-    ) -> AsyncIterable[Tuple[Optional[Job], Optional[Job]]]:
+    def get_job_changes(self, job_id: str) -> AsyncIterable[Tuple[Optional[Job], Optional[Job]]]:
         pass
 
     @abstractmethod

nerdd_backend/data/rethinkdb_repository.py

@@ -5,12 +5,9 @@
 from rethinkdb import RethinkDB
 from rethinkdb.errors import ReqlOpFailedError
 
+from ..models import Job, Module, Result, Source
 from .exceptions import RecordNotFoundError
-from .job import Job
-from .module import Module
 from .repository import Repository
-from .result import Result
-from .source import Source
 
 __all__ = ["RethinkDbRepository"]
 
@@ -74,17 +71,12 @@ async def get_module_changes(
             yield old_module, new_module
 
     async def get_all_modules(self) -> List[Module]:
-        cursor = (
-            await self.r.db(self.database_name).table("modules").run(self.connection)
-        )
+        cursor = await self.r.db(self.database_name).table("modules").run(self.connection)
         return [Module(**item) async for item in cursor]
 
     async def get_module_by_id(self, module_id: str) -> Module:
         result = (
-            await self.r.db(self.database_name)
-            .table("modules")
-            .get(module_id)
-            .run(self.connection)
+            await self.r.db(self.database_name).table("modules").get(module_id).run(self.connection)
         )
 
         if result is None:
@@ -94,11 +86,7 @@ async def get_module_by_id(self, module_id: str) -> Module:
 
     async def create_module_table(self) -> None:
         try:
-            await (
-                self.r.db(self.database_name)
-                .table_create("modules")
-                .run(self.connection)
-            )
+            await self.r.db(self.database_name).table_create("modules").run(self.connection)
         except ReqlOpFailedError:
             pass
 
@@ -146,26 +134,15 @@ async def upsert_job(self, job: Job) -> None:
         )
 
     async def get_job_by_id(self, job_id: str) -> Job:
-        result = (
-            await self.r.db(self.database_name)
-            .table("jobs")
-            .get(job_id)
-            .run(self.connection)
-        )
+        result = await self.r.db(self.database_name).table("jobs").get(job_id).run(self.connection)
 
         if result is None:
             raise RecordNotFoundError(Job, job_id)
 
         return Job(**result)
 
     async def delete_job_by_id(self, job_id: str) -> None:
-        await (
-            self.r.db(self.database_name)
-            .table("jobs")
-            .get(job_id)
-            .delete()
-            .run(self.connection)
-        )
+        await self.r.db(self.database_name).table("jobs").get(job_id).delete().run(self.connection)
 
     #
     # SOURCES
@@ -190,10 +167,7 @@ async def upsert_source(self, source: Source) -> None:
 
     async def get_source_by_id(self, source_id: str) -> Source:
         result = (
-            await self.r.db(self.database_name)
-            .table("sources")
-            .get(source_id)
-            .run(self.connection)
+            await self.r.db(self.database_name).table("sources").get(source_id).run(self.connection)
         )
 
         if result is None:

nerdd_backend/models/__init__.py

@@ -0,0 +1,4 @@
+from .job import *
+from .module import *
+from .result import *
+from .source import *

nerdd_backend/routers/dynamic.py

@@ -5,7 +5,7 @@
 from fastapi import APIRouter, Body, Depends, HTTPException, Query, Request, UploadFile
 from pydantic import create_model, model_validator
 
-from ..data import Module
+from ..models import Module
 from .jobs import CreateJobRequest, create_job, delete_job, get_job
 from .results import get_results
 from .sources import put_multiple_sources
@@ -63,9 +63,7 @@ def get_dynamic_router(module: Module):
     )
     QueryModelPost = create_model(
         "QueryModelForm",
-        __validators__={
-            "validate_to_json": model_validator(mode="before")(validate_to_json)
-        },
+        __validators__={"validate_to_json": model_validator(mode="before")(validate_to_json)},
         inputs=(List[str], []),
         sources=(List[str], []),
         **field_definitions,
@@ -154,11 +152,7 @@ async def create_complex_job(
     router.websocket(f"/websocket/{module.name}" "/jobs/{job_id}")(get_job_ws)
     router.websocket(f"/websocket/{module.name}" "/jobs/{job_id}/")(get_job_ws)
 
-    router.websocket(f"/websocket/{module.name}" "/jobs/{job_id}/results")(
-        get_results_ws
-    )
-    router.websocket(f"/websocket/{module.name}" "/jobs/{job_id}/results/")(
-        get_results_ws
-    )
+    router.websocket(f"/websocket/{module.name}" "/jobs/{job_id}/results")(get_results_ws)
+    router.websocket(f"/websocket/{module.name}" "/jobs/{job_id}/results/")(get_results_ws)
 
     return router

nerdd_backend/routers/sources.py

@@ -9,7 +9,8 @@
 from fastapi import APIRouter, HTTPException, Request, UploadFile
 from fastapi.encoders import jsonable_encoder
 
-from ..data import RecordNotFoundError, Repository, Source
+from ..data import RecordNotFoundError, Repository
+from ..models import Source
 
 sources_router = APIRouter(prefix="/sources")
 
@@ -33,9 +34,7 @@ async def _put_input(input: str):
             file = UploadFile(file_stream)
             return await put_source(request, file=file)
 
-        sources_from_inputs = await asyncio.gather(
-            *[_put_input(input) for input in inputs]
-        )
+        sources_from_inputs = await asyncio.gather(*[_put_input(input) for input in inputs])
         all_sources += sources_from_inputs
 
     for source_id in sources:
@@ -44,17 +43,13 @@ async def _put_input(input: str):
             all_sources.append(source)
 
     # create one json file referencing all sources
-    sources_from_files = await asyncio.gather(
-        *[put_source(request, file=file) for file in files]
-    )
+    sources_from_files = await asyncio.gather(*[put_source(request, file=file) for file in files])
     all_sources += sources_from_files
 
     all_sources_objects = [source.model_dump() for source in all_sources]
 
     # create a merged file with all sources
-    file_stream = BytesIO(
-        json.dumps(jsonable_encoder(all_sources_objects)).encode("utf-8")
-    )
+    file_stream = BytesIO(json.dumps(jsonable_encoder(all_sources_objects)).encode("utf-8"))
     file = UploadFile(file_stream, filename="input.json")
     result_source = await put_source(request, file=file, format="json")
 

tests/steps/repository.py

@@ -1,8 +1,10 @@
 import pytest_asyncio
-from nerdd_backend.data import MemoryRepository, Module
 from nerdd_module.tests import MolWeightModel
 from pytest_bdd import given
 
+from nerdd_backend.data import MemoryRepository
+from nerdd_backend.models import Module
+
 from .async_step import async_step