wip

osm/schemas/schemas.py

@@ -3,7 +3,6 @@
 from typing import Annotated, Optional, Union
 
 import pandas as pd
-from bson import ObjectId
 from pydantic import (
     BaseModel,
     BeforeValidator,
@@ -107,7 +106,7 @@ class Invocation(BaseModel):
     model_config = ConfigDict(
         populate_by_name=True,
         arbitrary_types_allowed=True,
-        json_encoders={datetime.datetime: lambda dt: dt.isoformat(), ObjectId: str},
+        json_encoders={datetime.datetime: lambda dt: dt.isoformat()},
     )
     # class Settings:
     #     keep_nulls = False

tests/test_api.py

@@ -3,91 +3,101 @@
 
 import nest_asyncio
 import pytest
+from bson import ObjectId
 
-from osm.schemas import Client, Component, Invocation, RtransparentMetrics, Work
+from osm.schemas import Invocation
 
 nest_asyncio.apply()
-SIMPLE_INV = Invocation(
-    work=Work(),
-    client=Client(compute_context_id=1),
-)
-SAMPLE_INV = Invocation(
-    work=Work(filename="test_file"),
-    client=Client(compute_context_id="1"),
-    osm_version="1.0.0",
-    user_comment="Test comment",
-    components=[Component(name="TestComponent", version="1.0", sample=b"long text")],
-    funder=["Test Funder"],
-    rtransparent_metrics=RtransparentMetrics(
-        is_open_code=True, is_open_data=False, funding_text="long text"
-    ),
-    data_tags=["test_tag"],
-    created_at=datetime.datetime.now(datetime.UTC).replace(microsecond=0),
-)
+SIMPLE_DOC = {"work": {}, "client": {"compute_context_id": 1}}
 
-
-@pytest.mark.asyncio
-async def test_swagger_ui(client):
-    response = await client.get("/docs")
-    assert response.status_code == 200
-    assert response.headers["content-type"] == "text/html; charset=utf-8"
-    assert "swagger-ui-dist" in response.text
-    assert (
-        "oauth2RedirectUrl: window.location.origin + '/docs/oauth2-redirect'"
-        in response.text
-    )
-
-
-@pytest.mark.parametrize("_", [x for x in range(3)])
-@pytest.mark.asyncio
-async def test_db_upload(db, _):
-    asyncio.run(db.invocations.insert_one(SIMPLE_INV.model_dump(mode="json")))
-    saved_inv = asyncio.run(db.invocations.find_one())
-    assert saved_inv is not None
-    assert saved_inv["client"]["compute_context_id"] == 1
+SAMPLE_DOC = {
+    "work": {"filename": "test_file"},
+    "client": {"compute_context_id": 1},
+    "osm_version": "1.0.0",
+    "user_comment": "Test comment",
+    "components": [
+        {"name": "TestComponent", "version": "1.0", "sample": "bG9uZyB0ZXh0"}
+    ],
+    "funder": ["Test Funder"],
+    "rtransparent_metrics": {
+        "is_open_code": True,
+        "is_open_data": False,
+        "funding_text": "long text",
+    },
+    "data_tags": ["test_tag"],
+    "created_at": datetime.datetime.now(datetime.UTC)
+    .replace(microsecond=0)
+    .isoformat(),
+}
 
 
 @pytest.mark.asyncio
 async def test_upload_path(client, db):
+    # from requests import post
+    # response = post("/upload/", json=SAMPLE_DOC.model_dump(mode="json", exclude_none=True))
+    # breakpoint()
     response = asyncio.run(
-        client.put(
+        client.post(
             "/upload/",
-            json=SAMPLE_INV.model_dump(mode="json", exclude_none=True),
+            json=SAMPLE_DOC,
         )
     )
-
-    assert response.status_code == 200, response.text
+    assert response.status_code == 201, response.text
 
     # Retrieve the saved invocation to verify it was saved correctly
-    record = asyncio.run(db.invocations.find_one())
+    record = asyncio.run(
+        db.invocations.find_one({"_id": ObjectId(response.json()["id"])})
+    )
+    breakpoint()
     assert record is not None, "Saved invocation not found"
     saved_invocation = Invocation(**record)
-    assert saved_invocation["id"] == SAMPLE_INV.id, "IDs do not match"
+    assert saved_invocation.id is not None, "IDs should be created automatically"
+    breakpoint()
+    assert isinstance(saved_invocation.id, str), "ID should be a string"
     assert (
-        saved_invocation["work"]["filename"] == SAMPLE_INV.work.filename
+        saved_invocation.work.filename == SAMPLE_DOC.work.filename
     ), "Work data does not match"
     assert (
-        saved_invocation["client"]["compute_context_id"]
-        == SAMPLE_INV.client.compute_context_id
+        saved_invocation.client.compute_context_id
+        == SAMPLE_DOC.client.compute_context_id
     ), "Client data does not match"
     assert (
-        saved_invocation["osm_version"] == SAMPLE_INV.osm_version
+        saved_invocation.osm_version == SAMPLE_DOC.osm_version
     ), "OSM version does not match"
     assert (
-        saved_invocation["user_comment"] == SAMPLE_INV.user_comment
+        saved_invocation.user_comment == SAMPLE_DOC.user_comment
     ), "User comment does not match"
     assert (
-        saved_invocation["components"][0]["name"] == SAMPLE_INV.components[0].name
+        saved_invocation.components[0].name == SAMPLE_DOC.components[0].name
     ), "Component name does not match"
     assert (
-        saved_invocation["components"][0]["version"] == SAMPLE_INV.components[0].version
+        saved_invocation.components[0].version == SAMPLE_DOC.components[0].version
     ), "Component version does not match"
-    assert saved_invocation["funder"] == SAMPLE_INV.funder, "Funder does not match"
-    assert (
-        saved_invocation["data_tags"] == SAMPLE_INV.data_tags
-    ), "Data tags do not match"
+    assert saved_invocation.funder == SAMPLE_DOC.funder, "Funder does not match"
+    assert saved_invocation.data_tags == SAMPLE_DOC.data_tags, "Data tags do not match"
     # TODO: fix tzinfo issue
-    breakpoint()
+
     assert (
-        saved_invocation["created_at"] == SAMPLE_INV.created_at
+        saved_invocation.created_at == SAMPLE_DOC.created_at
     ), "Created at does not match"
+
+
+@pytest.mark.parametrize("doc", [SIMPLE_DOC, SAMPLE_DOC])
+@pytest.mark.asyncio
+async def test_db_upload(db, doc):
+    res = asyncio.run(db.invocations.insert_one(doc))
+    saved_inv = asyncio.run(db.invocations.find_one({"_id": res.inserted_id}))
+    assert saved_inv is not None
+    assert saved_inv["client"]["compute_context_id"] == 1
+
+
+@pytest.mark.asyncio
+async def test_swagger_ui(client):
+    response = await client.get("/docs")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/html; charset=utf-8"
+    assert "swagger-ui-dist" in response.text
+    assert (
+        "oauth2RedirectUrl: window.location.origin + '/docs/oauth2-redirect'"
+        in response.text
+    )

web/api/main.py

@@ -6,7 +6,8 @@
 from contextlib import asynccontextmanager
 
 import uvicorn
-from fastapi import FastAPI, File, Form, HTTPException, UploadFile
+from bson import ObjectId
+from fastapi import Body, FastAPI, File, Form, HTTPException, UploadFile, status
 from fastapi.responses import JSONResponse
 
 from osm import db as osm_db
@@ -22,17 +23,26 @@ async def lifespan(app: FastAPI):
 app = FastAPI(lifespan=lifespan)
 
 
-@app.put("/upload/", response_model=Invocation)
+@app.post(
+    "/upload/",
+    response_description="Upload the OSM client output",
+    response_model=Invocation,
+    status_code=status.HTTP_201_CREATED,
+    response_model_by_alias=False,
+)
 async def upload_invocation(
-    invocation: Invocation,
+    invocation: Invocation = Body(...),
 ):
     db = osm_db.get_mongo_db()
-    result = await db.invocations.insert_one(invocation.model_dump(mode="json"))
+    result = await db.invocations.insert_one(
+        invocation.model_dump(by_alias=True, exclude=["id"])
+    )
     inserted_invocation = await db.invocations.find_one({"_id": result.inserted_id})
-    return Invocation(**{k: v for k, v in inserted_invocation.items() if k != "id"})
+    return inserted_invocation
+    # return Invocation(**{k: v for k, v in inserted_invocation.items() if k != "id"})
 
 
-@app.put("/payload_error/", response_model=PayloadError)
+@app.post("/payload_error/", response_model=PayloadError)
 async def upload_failed_payload_construction(payload_error: PayloadError):
     db = osm_db.get_mongo_db()
     result = await db.payload_errors.insert_one(payload_error.model_dump(mode="json"))
@@ -44,15 +54,15 @@ async def upload_failed_payload_construction(payload_error: PayloadError):
     )
 
 
-@app.put("/quarantine/", response_model=Quarantine)
+@app.post("/quarantine/", response_model=Quarantine)
 async def upload_failed_invocation(quarantine: Quarantine):
     db = osm_db.get_mongo_db()
     result = await db.quarantines.insert_one(quarantine.model_dump(mode="json"))
     inserted_quarantine = await db.quarantines.find_one({"_id": result.inserted_id})
     return Quarantine(**{k: v for k, v in inserted_quarantine.items() if k != "id"})
 
 
-@app.put("/quarantine2/")
+@app.post("/quarantine2/")
 async def upload_failed_quarantine(
     file: UploadFile = File(...), error_message: str = Form(...)
 ):
@@ -65,9 +75,14 @@ async def upload_failed_quarantine(
     )
 
 
-@app.get("/invocations/{id}", response_model=Invocation)
+@app.get(
+    "/invocations/{id}",
+    response_description="Get a single record by its ID",
+    response_model=Invocation,
+    response_model_by_alias=False,
+)
 async def get_invocation_by_id(id: str):
-    invocation = await Invocation.find_one(id)
+    invocation = await Invocation.find_one({"_id": ObjectId(id)})
     if invocation is None:
         raise HTTPException(404)
     return invocation