Workflow and device communication: Robustness and performance update

.gitignore

@@ -139,6 +139,8 @@ orthanc-db
 *.pyc
 *settings.json
 *.seq
+*.dcm
+*.mrd
 */build
 /infrastructure/monai/.md/*
 .examples

README.md

@@ -1,5 +1,6 @@
 <p align="center">
-  <a href="https://brain-link.de/wp-content/uploads/2022/03/ScanHub.svg"><img src="https://brain-link.de/wp-content/uploads/2022/03/ScanHub.svg" width="300" height="150" alt="ScanHub"></a>
+    <img src="scanhub-ui/src/media/logo.png" width="100" alt="ScanHub">
+    <h1 align="center">ScanHub</h3>
 </p>
 
 <p align="center">
@@ -15,9 +16,9 @@
 </a>
 </p>
 
----
 
-# Scanhub
+
+# About
 
 ScanHub is intended to be a multi modal acquisition software, which allows individualizable, modular and cloud-based processing of functional and anatomical medical images. 
 It seamlessly merges the acquisition with the processing of complex data on a single platform.

docker-compose.yml

@@ -1,6 +1,6 @@
 x-dagster-common: &dagster_common
   image: scanhub-orchestration-engine:latest
-  pull_policy: never  # Don't pull the image, use the local build
+  pull_policy: never # Don't pull the image, use the local build
   build:
     context: ./services/orchestration-engine
     args:
@@ -27,18 +27,19 @@ services:
   # Workflow manager, device manager and exam manager create data tables in postgres DB
   workflow-manager:
     container_name: workflow-manager
-    build: 
+    build:
       context: ./services/workflow-manager
-      args: 
+      args:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/workflow-manager/app/:/app/
       - ${DATA_LAKE_DIR}:/data
     environment:
       DATA_LAKE_DIRECTORY: /data
+      SCANHUB_ALLOWED_ORIGINS: ${SCANHUB_ALLOWED_ORIGINS}
     healthcheck:
       # TODO: host.docker.internal is only working with docker desktop, must be replaced in product
-      test: ["CMD", "curl", "http://workflow-manager:8000/api/v1/workflowmanager/health/readiness"]
+      test: [ "CMD", "curl", "http://workflow-manager:8000/api/v1/workflowmanager/health/readiness" ]
       interval: 5s
       timeout: 5s
       retries: 10
@@ -54,16 +55,17 @@ services:
     container_name: device-manager
     build:
       context: ./services/device-manager
-      args: 
+      args:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/device-manager/app/:/app/
       - ${DATA_LAKE_DIR}:/data
     environment:
       DATA_LAKE_DIRECTORY: /data
+      SCANHUB_ALLOWED_ORIGINS: ${SCANHUB_ALLOWED_ORIGINS}
     healthcheck:
       # TODO: host.docker.internal is only working with docker desktop, must be replaced in product
-      test: ["CMD", "curl", "http://device-manager:8000/api/v1/device/health/readiness"]
+      test: [ "CMD", "curl", "http://device-manager:8000/api/v1/device/health/readiness" ]
       interval: 5s
       timeout: 5s
       retries: 10
@@ -77,16 +79,24 @@ services:
 
   exam-manager:
     container_name: exam-manager
-    build: 
+    build:
       context: ./services/exam-manager
-      args: 
+      args:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/exam-manager/app/:/app/
       - ${DATA_LAKE_DIR}:/data
+    environment:
+      SCANHUB_ALLOWED_ORIGINS: ${SCANHUB_ALLOWED_ORIGINS}
+      XNAT_HOST: ${XNAT_HOST:-http://host.docker.internal:8081}
+      XNAT_USER: ${XNAT_USER:-admin}
+      XNAT_PASSWORD: ${XNAT_PASSWORD:-admin}
+      XNAT_PROJECT_ID: ${XNAT_PROJECT_ID:-A4IM}
+    extra_hosts:
+      - 'host.docker.internal:host-gateway'
     healthcheck:
       # TODO: host.docker.internal is only working with docker desktop, must be replaced in product
-      test: ["CMD", "curl", "http://exam-manager:8000/api/v1/exam/health/readiness"]
+      test: [ "CMD", "curl", "http://exam-manager:8000/api/v1/exam/health/readiness" ]
       interval: 5s
       timeout: 5s
       retries: 10
@@ -108,15 +118,17 @@ services:
 
   patient-manager:
     container_name: patient-manager
-    build: 
+    build:
       context: ./services/patient-manager
-      args: 
-          - BASE_IMG=${SCANHUB_BASE_IMAGE}
+      args:
+        - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/patient-manager/app:/app/
+    environment:
+      SCANHUB_ALLOWED_ORIGINS: ${SCANHUB_ALLOWED_ORIGINS}
     healthcheck:
       # TODO: host.docker.internal is only working with docker desktop, must be replaced in product
-      test: ["CMD", "curl", "http://patient-manager:8100/api/v1/patient/health/readiness"]
+      test: [ "CMD", "curl", "http://patient-manager:8100/api/v1/patient/health/readiness" ]
       interval: 5s
       timeout: 5s
       retries: 10
@@ -130,15 +142,17 @@ services:
 
   user-login-manager:
     container_name: user-login-manager
-    build: 
+    build:
       context: ./services/user-login-manager
-      args: 
+      args:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/user-login-manager/app/:/app/
+    environment:
+      SCANHUB_ALLOWED_ORIGINS: ${SCANHUB_ALLOWED_ORIGINS}
     healthcheck:
       # TODO: host.docker.internal is only working with docker desktop, must be replaced in product
-      test: ["CMD", "curl", "http://user-login-manager:8000/api/v1/userlogin/health/readiness"]
+      test: [ "CMD", "curl", "http://user-login-manager:8000/api/v1/userlogin/health/readiness" ]
       interval: 5s
       timeout: 5s
       retries: 10
@@ -179,13 +193,13 @@ services:
       POSTGRES_USER_FILE: /run/secrets/scanhub_database_postgres_user
       POSTGRES_PASSWORD_FILE: /run/secrets/scanhub_database_postgres_password
       POSTGRES_DB_FILE: /run/secrets/scanhub_database_postgres_db_name
-    healthcheck:  
+    healthcheck:
       # Workflow, device and exam microservices depend on healthy postgres database
-      test: ["CMD-SHELL", "pg_isready"]
+      test: [ "CMD-SHELL", "pg_isready" ]
       interval: 5s
       timeout: 5s
       retries: 10
-      start_period: 5s 
+      start_period: 5s
     secrets:
       - scanhub_database_postgres_user
       - scanhub_database_postgres_password
@@ -202,9 +216,9 @@ services:
       POSTGRES_USER_FILE: /run/secrets/patient_database_postgres_user
       POSTGRES_PASSWORD_FILE: /run/secrets/patient_database_postgres_password
       POSTGRES_DB_FILE: /run/secrets/patient_database_postgres_db_name
-    healthcheck:  
+    healthcheck:
       # init-db container is started, after health check passed
-      test: ["CMD-SHELL", "pg_isready", "-d", "db_prod"]
+      test: [ "CMD-SHELL", "pg_isready", "-d", "db_prod" ]
       interval: 10s
       timeout: 5s
       retries: 5
@@ -214,7 +228,6 @@ services:
       - patient_database_postgres_password
       - patient_database_postgres_db_name
 
-
   # MRI Sequence mongo database: Contains (pulseq) mri sequence files
   sequence-database:
     container_name: db-sequence
@@ -235,7 +248,6 @@ services:
       - sequence_database_root_username
       - sequence_database_root_password
 
-
   # API Gateway
   nginx:
     container_name: api-gateway
@@ -250,7 +262,7 @@ services:
     volumes:
       - ./infrastructure/nginx_config.conf:/etc/nginx/conf.d/default.conf
     healthcheck:
-      test: ["CMD", "curl", "http://api-gateway/health"]
+      test: [ "CMD", "curl", "http://api-gateway/health" ]
       interval: 5s
       timeout: 5s
       retries: 10
@@ -259,7 +271,7 @@ services:
         condition: service_healthy
       workflow-manager:
         condition: service_healthy
-      exam-manager: 
+      exam-manager:
         condition: service_healthy
       patient-manager:
         condition: service_healthy
@@ -269,37 +281,37 @@ services:
         condition: service_healthy
       # scanhub-ui:
       #   condition: service_healthy
-    extra_hosts:                                # somehow needed to find host.docker.internal under linux
-      - 'host.docker.internal:host-gateway'     # for the access to host.docker.internal to work the firewall of the host needs to allow incoming connections
+    extra_hosts:
+      # somehow needed to find host.docker.internal under linux
+      - 'host.docker.internal:host-gateway' # for the access to host.docker.internal to work the firewall of the host needs to allow incoming connections
     secrets:
       - certificate
       - privatekey
-
 
   # FRONTEND/SCANHUB-UI
-  scanhub-ui:
-    container_name: scanhub-ui
-    build:
-      context: ./scanhub-ui
-      dockerfile: ./Dockerfile
-      args:
-        NODE_ENV: "production" # or "development"
-    volumes:
-      - ./scanhub-ui/src:/app/src
-    healthcheck:
-      test: ["CMD", "curl", "-f", "http://localhost:3000/"]
-      interval: 10s
-      timeout: 5s
-      retries: 10
-      start_period: 30s
+  # scanhub-ui:
+  #   container_name: scanhub-ui
+  #   build:
+  #     context: ./scanhub-ui
+  #     dockerfile: ./Dockerfile
+  #     args:
+  #       NODE_ENV: "production" # or "development"
+  #   volumes:
+  #     - ./scanhub-ui/src:/app/src
+  #   healthcheck:
+  #     test: ["CMD", "curl", "-f", "http://localhost:3000/"]
+  #     interval: 10s
+  #     timeout: 5s
+  #     retries: 10
+  #     start_period: 30s
 
   # DAGSTER
   dagster-webserver:
     <<: *dagster_common
     container_name: dagster-webserver
-    command: ["dagster-webserver", "-h", "0.0.0.0", "-p", "3000", "--path-prefix", "/dagster", "-w", "/opt/dagster/app/workspace.yaml"]
+    command: [ "dagster-webserver", "-h", "0.0.0.0", "-p", "3000", "--path-prefix", "/dagster", "-w", "/opt/dagster/app/workspace.yaml" ]
     healthcheck:
-      test: ["CMD", "curl", "-f", "http://localhost:3000/dagster/server-status"]
+      test: [ "CMD", "curl", "-f", "http://localhost:3000/dagster/server-status" ]
       interval: 10s
       timeout: 5s
       retries: 5
@@ -311,14 +323,13 @@ services:
     <<: *dagster_common
     container_name: dagster-daemon
     user: "0:0"
-    entrypoint: ["dagster-daemon", "run", "-w", "/opt/dagster/app/workspace.yaml"]
+    entrypoint: [ "dagster-daemon", "run", "-w", "/opt/dagster/app/workspace.yaml" ]
     healthcheck:
-      test: ["CMD", "pgrep", "-f", "dagster-daemon"]
+      test: [ "CMD", "pgrep", "-f", "dagster-daemon" ]
       interval: 10s
       timeout: 5s
       retries: 5
 
-
 volumes:
   # data_lake:  # Use bind-mount to inspect files, make sure data_lake/ exists at project root
   mongodb_data_sequence:
@@ -347,4 +358,4 @@ secrets:
   certificate:
     file: secrets/certificate.pem
   privatekey:
-    file: secrets/privatekey.pem
+    file: secrets/privatekey.pem

scanhub-ui/package.json

@@ -7,16 +7,17 @@
   "source": "index.html",
   "dependencies": {
     "@cornerstonejs/codec-charls": "^1.2.3",
-    "@cornerstonejs/codec-libjpeg-turbo-8bit": "1.2.2",
+    "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
     "@cornerstonejs/codec-openjpeg": "^1.2.4",
     "@cornerstonejs/codec-openjph": "^2.4.7",
-    "@cornerstonejs/core": "^3.32.10",
-    "@cornerstonejs/dicom-image-loader": "^3.32.10",
-    "@cornerstonejs/tools": "^3.32.10",
+    "@cornerstonejs/core": "^4",
+    "@cornerstonejs/dicom-image-loader": "^4",
+    "@cornerstonejs/tools": "^4",
     "@emotion/react": "^11.11.1",
     "@emotion/styled": "^11.11.0",
     "@fontsource/roboto": "^5.0.5",
     "@kitware/vtk.js": "32.12.1",
+    "@monaco-editor/react": "^4.7.0",
     "@mui/icons-material": "^7.1.1",
     "@mui/joy": "^5.0.0-beta.52",
     "@mui/material": "^7.1.1",

scanhub-ui/src/Routes.tsx

@@ -26,6 +26,7 @@ import TemplatesView from './pages/TemplatesView'
 import UserManagementView from './pages/UserManagementView'
 import SequenceView from './pages/SequenceView'
 import DeviceView from './pages/DeviceView'
+import LibraryView from './pages/Library';
 
 const materialTheme = materialExtendTheme()
 
@@ -46,16 +47,18 @@ export function RouteConfiguration() {
               '--Form-maxWidth': '700px',
               '--Transition-duration': '0.4s', // set to `none` to disable transition
               '--Sidebar-width': '360px',
-              '--Navigation-height': '60px',
+              '--Navigation-height': '50px',
               '--Status-height': '22px',
+              '--IconFontSize': '22px',
             },
           }}
         />
 
         <Routes>
-          <Route path='/' element={user ? <App /> : <Navigate to='/login' state={{from: location}} />}>
+          <Route path='/' element={user ? <App /> : <Navigate to='/login' state={{ from: location }} />}>
             <Route index element={<PatientListView />} />
             <Route path=':patientId' element={<AcquisitionView />} />
+            <Route path='/library' element={<LibraryView />} />
             <Route path='/templates' element={<TemplatesView />} />
             <Route path='/devices' element={<DeviceView />} />
             <Route path='/sequences' element={<SequenceView />} />

scanhub-ui/src/api.tsx

@@ -5,7 +5,7 @@
  * api.tsx contains instances of the different apis.
  */
 import { PatientsApi, HealthApi as PatientManagerHealthApi } from './openapi/generated-client/patient'
-import { ExamsApi, WorkflowsApi, TasksApi, ResultsApi, MriSequencesApi, HealthApi as ExamManagerHealthApi } from './openapi/generated-client/exam'
+import { ExamsApi, WorkflowsApi, TasksApi, ResultsApi, MriSequencesApi, DataApi, HealthApi as ExamManagerHealthApi } from './openapi/generated-client/exam'
 import { WorkflowManagerApi, HealthApi as WorkflowManagerHealthApi } from './openapi/generated-client/workflowmanager'
 import { UserApi, LoginApi, HealthApi as UserLoginManagerHealthApi } from './openapi/generated-client/userlogin'
 import { DevicesApi, HealthApi as DeviceManagerHealthApi } from './openapi/generated-client/device'
@@ -20,6 +20,7 @@ export const workflowsApi = new WorkflowsApi(undefined, baseUrls.examService)
 export const taskApi = new TasksApi(undefined, baseUrls.examService)
 export const resultApi = new ResultsApi(undefined, baseUrls.examService)
 export const sequenceApi = new MriSequencesApi(undefined, baseUrls.examService)
+export const dataApi = new DataApi(undefined, baseUrls.examService)
 export const examManagerHealthApi = new ExamManagerHealthApi(undefined, baseUrls.examService)
 
 export const workflowManagerApi = new WorkflowManagerApi(undefined, baseUrls.workflowManagerService)