wip rebase on remote branch & add wip work for actually saving data

.dockerignore

@@ -0,0 +1,4 @@
+**/.share
+**/.git
+**/.venv
+.venv

api/.vscode/settings.json

@@ -4,7 +4,7 @@
     ],
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
-    "python.testing.cwd": "${workspaceFolder}",
+    "python.testing.cwd": "${workspaceFolder}/api",
     "[python]": {
         "editor.defaultFormatter": "ms-python.black-formatter",
         "editor.formatOnSave": true

api/Dockerfile

@@ -3,27 +3,23 @@ FROM python:3.10.0
 
 EXPOSE 8080
 
-
-# Override default shell and use bash and bia env
-#RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
-#    /bin/bash ~/miniconda.sh -b -p /opt/conda
-#ENV PATH=/opt/conda/bin:$PATH
-#RUN conda env create -f conda_env.yml
-
 RUN curl -sSL https://install.python-poetry.org | python3 -
 ENV PATH=/root/.local/bin:$PATH
 
 # add files that poetry needs first so layers up to (including) pulling dependencies get reused
+WORKDIR /bia-integrator
+
 #   only add poetry.lock if it exists (building on local)
-ADD ./poetry.lock* /integrator-api/poetry.lock
-ADD ./pyproject.toml /integrator-api/pyproject.toml
-WORKDIR /integrator-api
+ADD ./api/poetry.lock* api/poetry.lock
+ADD ./api/pyproject.toml api/pyproject.toml
+ADD ./bia-shared-datamodels bia-shared-datamodels
 
+WORKDIR /bia-integrator/api
 RUN poetry install
 
 # Everything up to here should be reused most times
 
 # add the actual project, which is what is often changed in between two different container builds
-ADD ./ /integrator-api
+ADD ./api ./
 
-CMD ["poetry", "run", "uvicorn", "--workers", "4", "--port", "8080", "--log-config", "./src/log_config.yml", "--host", "0.0.0.0", "src.app:app"]
+CMD ["poetry", "run", "uvicorn", "--workers", "4", "--port", "8080", "--log-config", "./src/log_config.yml", "--host", "0.0.0.0", "api.app:app"]

api/api/app.py

@@ -1,14 +1,26 @@
 from . import public
 from . import private
+from .models.repository import repository_create, Repository
+
 
-import uvicorn
 from fastapi import FastAPI
+from typing import AsyncGenerator
+
+
+async def repository_dependency() -> AsyncGenerator[Repository, None]:
+    db = await repository_create(init=False)
+    try:
+        yield db
+    finally:
+        db.close()
+
 
 app = FastAPI(
     generate_unique_id_function=lambda route: route.name,
     # Setting this to true results in duplicated client classes (into *Input and *Output) where the api model has default values
     # See https://fastapi.tiangolo.com/how-to/separate-openapi-schemas/#do-not-separate-schemas
     separate_input_output_schemas=False,
+    debug=True,
 )
 
 app.openapi_version = "3.0.2"

api/api/private.py

@@ -3,8 +3,15 @@
 
 # ?
 import bia_shared_datamodels.bia_data_model as shared_data_models
+from .models.repository import Repository
+from . import constants
+from fastapi import APIRouter, Depends
 
-router = APIRouter()
+router = APIRouter(
+    prefix="/private",
+    # dependencies=[Depends(get_current_user)], TODO
+    tags=[constants.OPENAPI_TAG_PRIVATE],
+)
 models_private = [
     shared_data_models.Study,
     shared_data_models.ImageAnnotationDataset,
@@ -15,8 +22,8 @@
 
 
 def make_post_item(t):
-    def post_item(doc: t) -> None:
-        print(t)
+    async def post_item(doc: t, db: Repository = Depends()) -> None:
+        await db.persist_doc(doc)
 
     return post_item
 

api/api/public.py

@@ -1,8 +1,10 @@
-from fastapi import APIRouter
+from fastapi import APIRouter, Depends
 from pydantic.alias_generators import to_snake
 
 # ?
 import bia_shared_datamodels.bia_data_model as shared_data_models
+from .models.repository import Repository
+
 
 router = APIRouter()
 models_public = [
@@ -19,10 +21,10 @@ def make_get_item(t):
     # https://eev.ee/blog/2011/04/24/gotcha-python-scoping-closures/
 
     # @TODO: nicer wrapper?
-    def get_item(uuid: shared_data_models.UUID) -> dict:
-        print(t)
-
-        return {}
+    async def get_item(
+        uuid: shared_data_models.UUID, db: Repository = Depends()
+    ) -> dict:
+        return db.get_doc(uuid, t)
 
     return get_item
 
@@ -43,6 +45,6 @@ def not_overwritten(n: int) -> int:
     return n
 
 
-@router.get("/Study")
+@router.get("/study")
 def yes_overwritten(n: int) -> int:
     return n

api/api/tests/test_dummy.py

@@ -0,0 +1,64 @@
+from fastapi.testclient import TestClient
+import pytest
+import uuid as uuid_lib
+
+
+TEST_SERVER_BASE_URL = "http://localhost.com/v2"
+
+
+def get_uuid() -> str:
+    # @TODO: make this constant and require mongo to always be clean?
+    generated = uuid_lib.uuid4()
+
+    return str(generated)
+
+
+def get_client(**kwargs) -> TestClient:
+    from fastapi.responses import JSONResponse
+    from fastapi import Request
+    import traceback
+
+    from ..app import app
+
+    @app.exception_handler(Exception)
+    def generic_exception_handler(request: Request, exc: Exception):
+        return JSONResponse(
+            status_code=500,
+            content=traceback.format_exception(exc, value=exc, tb=exc.__traceback__),
+        )
+
+    return TestClient(app, base_url=TEST_SERVER_BASE_URL, **kwargs)
+
+
+@pytest.fixture(scope="module")
+def api_client() -> TestClient:
+    client = get_client(raise_server_exceptions=False)
+    # authenticate_client(client)  # @TODO: DELETEME
+
+    return client
+
+
+def test_create_thing(api_client: TestClient):
+    study_uuid = get_uuid()
+    study = {
+        "uuid": study_uuid,
+        "version": 0,
+        "release_date": "2023-01-31",
+        "accession_id": study_uuid,
+        "title": "Test BIA study",
+        "description": "description",
+        "licence": "CC_BY_4.0",
+        "see_also": [],
+        "model": {"type_name": "Study", "version": 1},
+        "author": [
+            {
+                "display_name": "Georg Brenneis",
+                "contact_email": "[email protected]",
+                "affiliation": [{"display_name": "University of Vienna"}],
+            }
+        ],
+        "attribute": {},
+    }
+
+    rsp = api_client.post("private/study", json=study)
+    assert rsp.status_code == 201, rsp.json()

api/docker-compose.yml

@@ -20,20 +20,19 @@ services:
       #     #- "./.share/keyfile.secret:/home/share/keyfile/keyfile.secret"
   bia-integrator-api:
     build:
-      context: .
+      context: ..
+      dockerfile: ./api/Dockerfile
+    env_file: ./.env_compose
     container_name: api
     hostname: api
     ports:
       - 8080:8080
     expose:
       - 8080
-    volumes:
-      - "./.env_compose:/integrator-api/.env"
     depends_on:
       - biaint-mongo
 
-
 volumes:
   api_data:
     #? do we always want a 'seed db'?
-    #external: true
+    #external: true

api/pyproject.toml

@@ -23,7 +23,8 @@ ome-types = "^0.4.2"
 xsdata = "23.8"
 lxml = "^4.9.3"
 json-log-formatter = "^1.0"
-bia-shared-datamodels = { path = "../bia-shared-datamodels", develop = true }
+#@TODO: CHANGEME
+bia-shared-datamodels = { path = "../../prs/bia-integrator/bia-shared-datamodels", develop = true }
 
 [tool.poetry.group.dev.dependencies]
 locust = "^2.16.1"