feat: added support for mongodb

backend/tests/Dockerfile.run_pytest

@@ -0,0 +1,32 @@
+# set base image (host OS)
+ARG PY_VERSION=3.10 CI_DEPENDENCY_PROXY_GROUP_IMAGE_PREFIX
+
+FROM python:${PY_VERSION}
+
+ARG BEC_ATLAS_BRANCH=main BEC_CORE_BRANCH=main
+
+RUN echo "Building BEC Atlas environment for branch ${BEC_ATLAS_BRANCH} with BEC branch ${BEC_CORE_BRANCH}"
+
+RUN apt update
+RUN apt install git -y
+RUN apt install netcat-openbsd -y
+
+# set the working directory in the container
+WORKDIR /code
+
+# clone the bec repo
+RUN git clone --branch ${BEC_CORE_BRANCH} https://gitlab.psi.ch/bec/bec.git
+
+WORKDIR /code/bec/
+RUN pip install -e bec_lib[dev]
+
+WORKDIR /code
+RUN git clone --branch ${BEC_ATLAS_BRANCH} https://gitlab.psi.ch/bec/bec_atlas.git
+
+WORKDIR /code/bec_atlas
+RUN pip install -e ./backend[dev]
+
+RUN mkdir -p /code/bec_atlas/test_files
+
+# command to run on container start
+ENTRYPOINT [ "./backend/tests/coverage_run.sh" ]

backend/tests/conftest.py

@@ -3,11 +3,11 @@ import os
 from typing import Iterator
 
 import pytest
-from bec_atlas.main import AtlasApp
-from bec_atlas.utils.setup_database import setup_database
 from fastapi.testclient import TestClient
 from pytest_docker.plugin import DockerComposeExecutor, Services
 
+from bec_atlas.main import AtlasApp
+
 
 def pytest_addoption(parser):
     parser.addoption(
@@ -101,42 +101,39 @@ def docker_services(
         yield docker_service
 
 
-@pytest.fixture(scope="session")
-def scylla_container(docker_ip, docker_services):
-    host = docker_ip
-    if os.path.exists("/.dockerenv"):
-        # if we are running in the CI, scylla was started as 'scylla' service
-        host = "scylla"
-    if docker_services is None:
-        port = 9042
-    else:
-        port = docker_services.port_for("scylla", 9042)
-
-    setup_database(host=host, port=port)
-    return host, port
-
-
 @pytest.fixture(scope="session")
 def redis_container(docker_ip, docker_services):
     host = docker_ip
     if os.path.exists("/.dockerenv"):
-        # if we are running in the CI, scylla was started as 'scylla' service
         host = "redis"
     if docker_services is None:
         port = 6380
     else:
         port = docker_services.port_for("redis", 6379)
 
-    return host, port
+    return "localhost", port
 
 
 @pytest.fixture(scope="session")
-def backend(scylla_container, redis_container):
-    scylla_host, scylla_port = scylla_container
+def mongo_container(docker_ip, docker_services):
+    host = docker_ip
+    if os.path.exists("/.dockerenv"):
+        host = "mongo"
+    if docker_services is None:
+        port = 27017
+    else:
+        port = docker_services.port_for("mongodb", 27017)
+
+    return "localhost", port
+
+
+@pytest.fixture(scope="session")
+def backend(redis_container, mongo_container):
     redis_host, redis_port = redis_container
+    mongo_host, mongo_port = mongo_container
     config = {
-        "scylla": {"hosts": [(scylla_host, scylla_port)]},
         "redis": {"host": redis_host, "port": redis_port},
+        "mongodb": {"host": mongo_host, "port": mongo_port},
     }
 
     app = AtlasApp(config)

backend/tests/coverage_run.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# check if redis is running on port 6380 and mongodb on port 27017 and scylladb on port 9070
+if [ "$(nc -z localhost 6380; echo $?)" -ne 0 ]; then
+    echo "Redis is not running on port 6380"
+    exit 1
+fi
+
+if [ "$(nc -z localhost 27017; echo $?)" -ne 0 ]; then
+    echo "MongoDB is not running on port 27017"
+    exit 1
+fi
+
+coverage run --concurrency=thread --source=./backend --omit=*/backend/tests/* -m pytest -v --junitxml=./test_files/report.xml --skip-docker --random-order --full-trace ./backend/tests
+
+EXIT_STATUS=$?
+
+if [ $EXIT_STATUS -ne 0 ]; then
+    exit $EXIT_STATUS
+fi
+
+coverage report
+coverage xml -o ./test_files/coverage.xml

backend/tests/docker-compose.yml

@@ -1,10 +1,10 @@
 version: '2'
 services:
-  scylla:
-    image: scylladb/scylla:latest
-    ports:
-      - "9070:9042"
   redis:
     image: redis:latest
     ports:
-      - "6380:6379"
+      - "6380:6379"
+  mongodb:
+    image: mongo:latest
+    ports:
+      - "27017:27017"

backend/tests/test_redis_websocket.py

@@ -72,7 +72,7 @@ async def test_redis_websocket_multiple_disconnect_same_sid(backend_client):
 async def test_redis_websocket_register_wrong_endpoint_raises(backend_client):
     client, app = backend_client
     with mock.patch.object(app.redis_websocket.socket, "emit") as emit:
-        app.redis_websocket.socket.handlers["/"]["connect"]("sid")
+        await app.redis_websocket.socket.handlers["/"]["connect"]("sid")
         await app.redis_websocket.socket.handlers["/"]["register"](
             "sid", json.dumps({"endpoint": "wrong_endpoint"})
         )

backend/tests/test_scan_ingestor.py

@@ -0,0 +1,107 @@
+import pytest
+from bec_lib import messages
+
+from bec_atlas.ingestor.data_ingestor import DataIngestor
+
+
+@pytest.fixture
+def scan_ingestor(backend):
+    client, app = backend
+    app.redis_websocket.users = {}
+    ingestor = DataIngestor(config=app.config)
+    yield ingestor
+    ingestor.shutdown()
+
+
+@pytest.mark.timeout(60)
+def test_scan_ingestor_create_scan(scan_ingestor, backend):
+    """
+    Test that the login endpoint returns a token.
+    """
+    client, app = backend
+    msg = messages.ScanStatusMessage(
+        metadata={},
+        scan_id="92429a81-4bd4-41c2-82df-eccfaddf3d96",
+        status="open",
+        # session_id="5cc67967-744d-4115-a46b-13246580cb3f",
+        info={
+            "readout_priority": {
+                "monitored": ["bpm3i", "diode", "ftp", "bpm5c", "bpm3x", "bpm3z", "bpm4x"],
+                "baseline": ["ddg1a", "bs1y", "mobdco"],
+                "async": ["eiger", "monitor_async", "waveform"],
+                "continuous": [],
+                "on_request": ["flyer_sim"],
+            },
+            "file_suffix": None,
+            "file_directory": None,
+            "user_metadata": {"sample_name": "testA"},
+            "RID": "5cc67967-744d-4115-a46b-13246580cb3f",
+            "scan_id": "92429a81-4bd4-41c2-82df-eccfaddf3d96",
+            "queue_id": "7d77d976-bee0-4bb8-aabb-2b862b4506ec",
+            "session_id": "5cc67967-744d-4115-a46b-13246580cb3f",
+            "scan_motors": ["samx"],
+            "num_points": 10,
+            "positions": [
+                [-5.0024118137239455],
+                [-3.8913007026128343],
+                [-2.780189591501723],
+                [-1.6690784803906122],
+                [-0.557967369279501],
+                [0.5531437418316097],
+                [1.6642548529427212],
+                [2.775365964053833],
+                [3.886477075164944],
+                [4.9975881862760545],
+            ],
+            "scan_name": "line_scan",
+            "scan_type": "step",
+            "scan_number": 2,
+            "dataset_number": 2,
+            "exp_time": 0,
+            "frames_per_trigger": 1,
+            "settling_time": 0,
+            "readout_time": 0,
+            "acquisition_config": {"default": {"exp_time": 0, "readout_time": 0}},
+            "scan_report_devices": ["samx"],
+            "monitor_sync": "bec",
+            "scan_msgs": [
+                "metadata={'file_suffix': None, 'file_directory': None, 'user_metadata': {'sample_name': 'testA'}, 'RID': '5cc67967-744d-4115-a46b-13246580cb3f'} scan_type='line_scan' parameter={'args': {'samx': [-5, 5]}, 'kwargs': {'steps': 10, 'exp_time': 0, 'relative': True, 'system_config': {'file_suffix': None, 'file_directory': None}}} queue='primary'"
+            ],
+            "args": {"samx": [-5, 5]},
+            "kwargs": {
+                "steps": 10,
+                "exp_time": 0,
+                "relative": True,
+                "system_config": {"file_suffix": None, "file_directory": None},
+            },
+        },
+        timestamp=1732610545.15924,
+    )
+    scan_ingestor.update_scan_status(msg)
+
+    response = client.post(
+        "/api/v1/user/login", json={"username": "admin@bec_atlas.ch", "password": "admin"}
+    )
+    client.headers.update({"Authorization": f"Bearer {response.json()}"})
+
+    session_id = msg.info.get("session_id")
+    scan_id = msg.scan_id
+    response = client.get(f"/api/v1/scans/session/{session_id}")
+    assert response.status_code == 200
+    out = response.json()[0]
+    # assert out["session_id"] == session_id
+    assert out["scan_id"] == scan_id
+    assert out["status"] == "open"
+
+    msg.status = "closed"
+    scan_ingestor.update_scan_status(msg)
+    response = client.get(f"/api/v1/scans/id/{scan_id}")
+    assert response.status_code == 200
+    out = response.json()
+    assert out["status"] == "closed"
+    assert out["scan_id"] == scan_id
+
+    response = client.get(f"/api/v1/scans/session/{session_id}")
+    assert response.status_code == 200
+    out = response.json()
+    assert len(out) == 1