Fix the DICOMweb uploader and its tests

pixl_core/src/core/uploader/_dicomweb.py

@@ -36,13 +36,15 @@ def __init__(self, project_slug: str, keyvault_alias: Optional[str]) -> None:
     def _set_config(self) -> None:
         # Use the Azure KV alias as prefix if it exists, otherwise use the project name
         az_prefix = self.keyvault_alias
-        az_prefix = az_prefix if az_prefix else self.project_slug
+        self.az_prefix = az_prefix if az_prefix else self.project_slug
 
-        self.user = self.keyvault.fetch_secret(f"{az_prefix}--dicomweb--username")
-        self.password = self.keyvault.fetch_secret(f"{az_prefix}--dicomweb--password")
+        self.orthanc_user = config("ORTHANC_USERNAME")
+        self.orthanc_password = config("ORTHANC_PASSWORD")
         self.orthanc_url = config("ORTHANC_URL")
-        self.endpoint_name = self.keyvault.fetch_secret(f"{az_prefix}--dicomweb--url")
-        self.url = self.orthanc_url + "/dicom-web/servers/" + self.endpoint_name
+        self.endpoint_user = self.keyvault.fetch_secret(f"{self.az_prefix}--dicomweb--username")
+        self.endpoint_password = self.keyvault.fetch_secret(f"{self.az_prefix}--dicomweb--password")
+        self.endpoint_url = self.keyvault.fetch_secret(f"{self.az_prefix}--dicomweb--url")
+        self.orthanc_dicomweb_url = self.orthanc_url + "/dicom-web/servers/" + self.az_prefix
 
     def upload_dicom_image(self) -> None:
         msg = "Currently not implemented. Use `send_via_stow()` instead."
@@ -59,8 +61,8 @@ def send_via_stow(self, resource_id: str) -> requests.Response:
 
         try:
             response = requests.post(
-                self.url + "/stow",
-                auth=(self.user, self.password),
+                self.orthanc_dicomweb_url + "/stow",
+                auth=(self.orthanc_user, self.orthanc_password),
                 headers=headers,
                 data=json.dumps(payload),
                 timeout=30,
@@ -75,7 +77,9 @@ def send_via_stow(self, resource_id: str) -> requests.Response:
 
     def _check_dicomweb_server(self) -> bool:
         """Checks if the dicomweb server exists."""
-        response = requests.get(self.url, auth=(self.user, self.password), timeout=30)
+        response = requests.get(
+            self.orthanc_dicomweb_url, auth=(self.orthanc_user, self.orthanc_password), timeout=30
+        )
         success_code = 200
         if response.status_code != success_code:
             return False
@@ -87,31 +91,30 @@ def _setup_dicomweb_credentials(self) -> None:
         This dyniamically creates a new endpoint in Orthanc with the necessary credentials, so we
         can avoid hardcoding the credentials in the Orthanc configuration at build time.
         """
-        DICOM_ENDPOINT_URL = config("DICOM_ENDPOINT_URL")
         HTTP_TIMEOUT = int(config("HTTP_TIMEOUT", default=30))
 
         dicomweb_config = {
-            "Url": DICOM_ENDPOINT_URL,
-            "Username": self.user,
-            "Password": self.password,
+            "Url": self.endpoint_url,
+            "Username": self.endpoint_user,
+            "Password": self.endpoint_password,
             "HasDelete": True,
             "Timeout": HTTP_TIMEOUT,
         }
 
         headers = {"content-type": "application/json"}
         try:
             requests.put(
-                self.url,
-                auth=(self.user, self.password),
+                self.orthanc_dicomweb_url,
+                auth=(self.orthanc_user, self.orthanc_password),
                 headers=headers,
                 data=json.dumps(dicomweb_config),
                 timeout=10,
             )
         except requests.exceptions.RequestException:
-            logger.error("Failed to update DICOMweb token")
+            logger.error("Failed to update DICOMweb config for {}", self.orthanc_dicomweb_url)
             raise
         else:
-            logger.info("DICOMweb token updated")
+            logger.info("Set up DICOMweb config for {}", self.orthanc_dicomweb_url)
 
     def upload_parquet_files(self) -> None:
         msg = "DICOMWeb uploader does not support parquet files"

pixl_core/tests/conftest.py

@@ -53,9 +53,10 @@
 os.environ["ORTHANC_URL"] = "http://localhost:8043"
 os.environ["ORTHANC_USERNAME"] = "orthanc"
 os.environ["ORTHANC_PASSWORD"] = "orthanc"  # noqa: S105, hardcoded password
-os.environ["DICOM_ENDPOINT_NAME"] = "test"
 # Endpoint for DICOMWeb server as seen from within Orthanc
-os.environ["DICOM_ENDPOINT_URL"] = "http://localhost:8042/dicom-web/"
+os.environ["DICOMWEB_URL"] = "http://dicomweb-server:8042/dicom-web"
+os.environ["DICOMWEB_USERNAME"] = "orthanc_dicomweb"
+os.environ["DICOMWEB_PASSWORD"] = "orthanc_dicomweb"  # noqa: S105, hardcoded password
 
 
 @pytest.fixture(scope="package")
@@ -67,7 +68,7 @@ def run_containers() -> Generator[subprocess.CompletedProcess[bytes], None, None
         timeout=60,
     )
     yield run_subprocess(
-        shlex.split("docker compose up --build --wait"),
+        shlex.split("docker compose up --build --wait --remove-orphans"),
         TEST_DIR,
         timeout=60,
     )
@@ -79,30 +80,7 @@ def run_containers() -> Generator[subprocess.CompletedProcess[bytes], None, None
 
 
 @pytest.fixture(scope="package")
-def run_dicomweb_containers() -> Generator[subprocess.CompletedProcess[bytes], None, None]:
-    """
-    Spins up 2 Orthanc containers, one that acts as the base storage, mimicking our orthanc-anon
-    or orthanc-raw servers, and the other one as a DICOMweb server to upload DICOM files to.
-    """
-    run_subprocess(
-        shlex.split("docker compose down --volumes"),
-        TEST_DIR,
-        timeout=60,
-    )
-    yield run_subprocess(
-        shlex.split("docker compose -f docker-compose.dicomweb.yml up --build --wait"),
-        TEST_DIR,
-        timeout=60,
-    )
-    run_subprocess(
-        shlex.split("docker compose down --volumes"),
-        TEST_DIR,
-        timeout=60,
-    )
-
-
-@pytest.fixture(scope="package")
-def study_id(run_dicomweb_containers) -> str:
+def study_id(run_containers) -> str:
     """Uploads a DICOM file to the Orthanc server and returns the study ID."""
     DCM_FILE = Path(__file__).parents[2] / "test" / "resources" / "Dicom1.dcm"
     ORTHANC_URL = os.environ["ORTHANC_URL"]

pixl_core/tests/docker-compose.yml

@@ -11,22 +11,75 @@
 #  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
-version: "3.8"
-
+networks:
+    pixl-test:
 
 services:
+    queue:
+        container_name: pixl-test-queue
+        image: rabbitmq:3.12.9-management
+        environment:
+            RABBITMQ_DEFAULT_USER: guest
+            RABBITMQ_DEFAULT_PASS: guest
+        ports:
+            - "25672:5672"
+            - "35672:15672"
+        healthcheck:
+            test: rabbitmq-diagnostics -q check_running
+            interval: 10s
+            timeout: 5s
+            retries: 5
+
+    orthanc:
+        image: orthancteam/orthanc:24.4.0
+        platform: linux/amd64
+        environment:
+            ORTHANC_NAME: "orthanc"
+            ORTHANC_USERNAME: "orthanc"
+            ORTHANC_PASSWORD: "orthanc"
+            ORTHANC_AE_TITLE: "orthanc"
+            RAW_AE_TITLE: ORHTANCRAW
+            RAW_DICOM_PORT: "4242"
+            RAW_IP_ADDR: "orthanc-raw" # aka. hostname
+            DICOM_WEB_PLUGIN_ENABLED: true
+        ports:
+            - "4243:4242"
+            - "8043:8042"
+        networks:
+            - pixl-test
+        healthcheck:
+            test: ["CMD-SHELL", "/probes/test-aliveness.py --user=orthanc --pwd=orthanc"]
+            start_period: 10s
+            retries: 2
+            interval: 3s
+            timeout: 2s
 
-  queue:
-    container_name: pixl-test-queue
-    image: rabbitmq:3.12.9-management
-    environment:
-      RABBITMQ_DEFAULT_USER: guest
-      RABBITMQ_DEFAULT_PASS: guest
-    ports:
-      - "25672:5672"
-      - "35672:15672"
-    healthcheck:
-      test: rabbitmq-diagnostics -q check_running
-      interval: 10s
-      timeout: 5s
-      retries: 5
+    dicomweb-server:
+        image: orthancteam/orthanc:24.4.0
+        platform: linux/amd64
+        environment:
+            ORTHANC_NAME: "dicomweb"
+            ORTHANC_USERNAME: "orthanc_dicomweb"
+            ORTHANC_PASSWORD: "orthanc_dicomweb"
+            ORTHANC_AE_TITLE: "DICOMWEB"
+            RAW_AE_TITLE: ORHTANCRAW
+            RAW_DICOM_PORT: "4242"
+            RAW_IP_ADDR: "dicom-web" # aka. hostname
+            DICOM_WEB_PLUGIN_ENABLED: true
+        ports:
+            - "4244:4242"
+            - "8044:8042"
+        volumes:
+            - ../../test/dicomweb_config/:/run/secrets:ro
+        networks:
+            - pixl-test
+        healthcheck:
+            test:
+                [
+                    "CMD-SHELL",
+                    "/probes/test-aliveness.py --user=orthanc_dicomweb --pwd=orthanc_dicomweb",
+                ]
+            start_period: 10s
+            retries: 2
+            interval: 3s
+            timeout: 2s