Fix CI

docker-compose.yml

@@ -28,7 +28,7 @@ x-proxy-common: &proxy-common
   no_proxy: *no-proxy
 
 x-build-args-common: &build-args-common
-  <<: *proxy-common
+  <<: [*proxy-common]
 
 x-pixl-common-env: &pixl-common-env
   ENV: ${ENV}
@@ -80,8 +80,7 @@ services:
       args:
         <<: *build-args-common
     environment:
-      <<: *proxy-common
-      <<: *pixl-common-env
+      <<: [*proxy-common, *pixl-common-env]
       AZURE_CLIENT_ID: ${HASHER_API_AZ_CLIENT_ID}
       AZURE_CLIENT_SECRET: ${HASHER_API_AZ_CLIENT_PASSWORD}
       AZURE_TENANT_ID: ${HASHER_API_AZ_TENANT_ID}
@@ -110,6 +109,7 @@ services:
         <<: *build-args-common
     command: /run/secrets
     environment:
+      <<: [*proxy-common, *pixl-common-env]
       ORTHANC_NAME: "PIXL: Anon"
       ORTHANC_USERNAME: ${ORTHANC_ANON_USERNAME}
       ORTHANC_PASSWORD: ${ORTHANC_ANON_PASSWORD}
@@ -131,8 +131,6 @@ services:
       AZ_DICOM_TOKEN_REFRESH_SECS: "600"
       TIME_OFFSET: "${STUDY_TIME_OFFSET}"
       SALT_VALUE: ${SALT_VALUE}"
-      <<: *proxy-common
-      <<: *pixl-common-env
     ports:
       - "${ORTHANC_ANON_DICOM_PORT}:4242"
       - "${ORTHANC_ANON_WEB_PORT}:8042"
@@ -161,6 +159,7 @@ services:
         <<: *build-args-common
     command: /run/secrets
     environment:
+      <<: [*pixl-db, *proxy-common, *pixl-common-env]
       ORTHANC_NAME: "PIXL: Raw"
       ORTHANC_USERNAME: ${ORTHANC_RAW_USERNAME}
       ORTHANC_PASSWORD: ${ORTHANC_RAW_PASSWORD}
@@ -175,9 +174,6 @@ services:
       ORTHANC_ANON_AE_TITLE: ${ORTHANC_ANON_AE_TITLE}
       ORTHANC_ANON_DICOM_PORT: "4242"
       ORTHANC_ANON_HOSTNAME: "orthanc-anon"
-      <<: *pixl-db
-      <<: *proxy-common
-      <<: *pixl-common-env
     ports:
       - "${ORTHANC_RAW_DICOM_PORT}:4242"
       - "${ORTHANC_RAW_WEB_PORT}:8042"
@@ -227,11 +223,7 @@ services:
       args:
         <<: *build-args-common
     environment:
-      <<: *pixl-db
-      <<: *emap-db
-      <<: *proxy-common
-      <<: *pixl-common-env
-      <<: *pixl-rabbit-mq
+      <<: [*pixl-db, *emap-db, *proxy-common, *pixl-common-env, *pixl-rabbit-mq]
       AZURE_CLIENT_ID: ${PIXL_EHR_API_AZ_CLIENT_ID}
       AZURE_CLIENT_SECRET: ${PIXL_EHR_API_AZ_CLIENT_SECRET}
       AZURE_TENANT_ID: ${PIXL_EHR_API_AZ_TENANT_ID}
@@ -273,8 +265,7 @@ services:
     networks:
       - pixl-net
     environment:
-      <<: *pixl-rabbit-mq
-      <<: *proxy-common
+      <<: [*pixl-rabbit-mq, *proxy-common]
       ORTHANC_RAW_USERNAME: ${ORTHANC_RAW_USERNAME}
       ORTHANC_RAW_PASSWORD: ${ORTHANC_RAW_PASSWORD}
       ORTHANC_RAW_AE_TITLE: ${ORTHANC_RAW_AE_TITLE}

hasher/src/requirements.txt

@@ -1,15 +1,15 @@
 azure-identity==1.12.0
 azure-keyvault==4.2.0
 black==22.8.0
-fastapi==0.85.2
+fastapi==0.103.2
 flake8==5.0.4
 flake8-return==1.1.3
 hypothesis==6.56.0
 isort==5.10.1
 environs==9.5.0
-ipython==8.5.0
-mypy==0.991
-pytest==7.1.3
+mypy==1.6.0
+httpx==0.25.0
+pytest==7.4.2
 pytest-mock==3.8.2
-requests==2.28.1
-uvicorn==0.19.0
+requests==2.31.0
+uvicorn==0.23.2

patient_queue/src/requirements.txt

@@ -5,7 +5,7 @@ flake8==5.0.4
 flake8-return==1.1.3
 isort==5.10.1
 environs==9.5.0
-mypy==0.991
+mypy==1.6.0
 pytest==7.1.3
 pytest-asyncio==0.20.2
 python-decouple==3.6

pixl_ehr/src/pixl_ehr/main.py

@@ -80,7 +80,9 @@ async def update_tb_refresh_rate(item: TokenRefreshUpdate) -> str:
 
 
 @app.get(
-    "/token-bucket-refresh-rate", summary="Get the refresh rate in items per second"
+    "/token-bucket-refresh-rate",
+    summary="Get the refresh rate in items per second",
+    response_model=TokenRefreshUpdate,
 )
 async def get_tb_refresh_rate() -> BaseModel:
     return TokenRefreshUpdate(rate=state.token_bucket.rate)

pixl_ehr/src/pixl_ehr/tests/test_app.py

@@ -16,15 +16,10 @@
 """
 from fastapi.testclient import TestClient
 from pixl_ehr.main import AppState, app, state
-from requests import Response
 
 client = TestClient(app)
 
 
-def _is_error(response: Response) -> bool:
-    return bool(400 <= int(response.status_code) < 450)
-
-
 def test_heartbeat_response_is_200() -> None:
     response = client.get("/heart-beat")
     assert response.status_code == 200
@@ -37,13 +32,13 @@ def test_initial_state_has_no_token() -> None:
 def test_updating_the_token_refresh_rate_to_negative_fails() -> None:
 
     response = client.post("/token-bucket-refresh-rate", json={"rate": -1})
-    assert _is_error(response)
+    assert response.is_error
 
 
 def test_updating_the_token_refresh_rate_to_string_fails() -> None:
 
     response = client.post("/token-bucket-refresh-rate", json={"rate": "a string"})
-    assert _is_error(response)
+    assert response.is_error
 
 
 def test_updating_the_token_refresh_rate_updates_state() -> None:

pixl_ehr/src/requirements.txt

@@ -1,17 +1,17 @@
 black==22.8.0
+fastapi==0.103.2
 flake8==5.0.4
 flake8-return==1.1.3
+hypothesis==6.56.0
 isort==5.10.1
 environs==9.5.0
-mypy==0.991
-pytest==7.1.3
-click==8.1.3
-coloredlogs==15.0.1
-fastapi==0.85.2
-pydantic==1.9.2
-uvicorn==0.19.0
-requests==2.28.1
-types-requests==2.28.*
+mypy==1.6.0
+httpx==0.25.0
+pytest==7.4.2
+requests==2.31.0
+uvicorn==0.23.2
+pydantic==1.10.13
+types-requests==2.31.0
 psycopg2-binary==2.9.5
 azure-identity==1.12.0
 azure-storage-blob==12.14.1

pixl_pacs/src/pixl_pacs/main.py

@@ -76,7 +76,8 @@ async def update_tb_refresh_rate(item: TokenRefreshUpdate) -> str:
 
 
 @app.get(
-    "/token-bucket-refresh-rate", summary="Get the refresh rate in items per second"
+    "/token-bucket-refresh-rate", summary="Get the refresh rate in items per second",
+    response_model=TokenRefreshUpdate,
 )
 async def get_tb_refresh_rate() -> BaseModel:
     return TokenRefreshUpdate(rate=state.token_bucket.rate)

pixl_rd/src/requirements.txt

@@ -3,8 +3,8 @@ flake8==5.0.4
 flake8-return==1.1.3
 isort==5.10.1
 environs==9.5.0
-mypy==0.991
-pytest==7.1.3
+mypy==1.6.0
+pytest==7.4.2
 presidio-analyzer==2.2.29
 presidio-anonymizer==2.2.29
 python-decouple==3.6

test/docker-compose.yml

@@ -64,7 +64,8 @@ services:
       context: ..
       dockerfile: test/Dockerfile.fake_emap_star
       args:
-        N_TABLE_ROWS: 1
+        N_TABLE_ROWS: 2
+        INFORMDB_PAT: ${INFORMDB_PAT}
     environment:
       POSTGRES_USER: ${EMAP_UDS_USER}
       POSTGRES_PASSWORD: ${EMAP_UDS_PASSWORD}

token_buffer/src/requirements.txt

@@ -2,7 +2,7 @@ black==22.8.0
 flake8==5.0.4
 flake8-return==1.1.3
 isort==5.10.1
-mypy==0.991
-pytest==7.1.3
+mypy==1.6.0
+pytest==7.4.2
 token-bucket==0.3.0
 python-decouple==3.6