Task status update and execution handling

.env

@@ -1,4 +1,13 @@
-# Container Images
-## change the value from "ghcr.io/brain-link/scanhub/scanhub-base:latest" to "scanhub-base" if the local scanhub-base image shall be used
-#SCANHUB_BASE_IMAGE=scanhub-base
+# BASE IMAGE CONFIGURATION
+
+# Change the value from "ghcr.io/brain-link/scanhub/scanhub-base:latest" to "scanhub-base" 
+# if the local scanhub-base image shall be used for the service containers
+
+# SCANHUB_BASE_IMAGE=scanhub-base
 SCANHUB_BASE_IMAGE=ghcr.io/brain-link/scanhub/scanhub-base:latest
+
+
+# Configuration of data lake directory
+# The data lake contains all the acquisition, reconstruction and processing data
+
+DATA_LAKE_DIR="./data_lake"

docker-compose.yml

@@ -1,8 +1,8 @@
 x-dagster-common: &dagster_common
-  image: scanhub-dagster:latest
+  image: scanhub-orchestration-engine:latest
   pull_policy: never  # Don't pull the image, use the local build
   build:
-    context: ./services/dagster
+    context: ./services/orchestration-engine
     args:
       BASE_IMG: ${SCANHUB_BASE_IMAGE}
   environment:
@@ -11,12 +11,16 @@ x-dagster-common: &dagster_common
   volumes:
     # Persistent storage for Dagster instance data (run logs, schedules, sensors, etc.)
     - dagster_storage:/opt/dagster/dagster_home
-    # Mount dagster.yaml config file into the container
-    - ./services/dagster/dagster.yaml:/opt/dagster/dagster_home/dagster.yaml
-    # Mount the Dagster application source code (repository, jobs, ops, etc.)
-    - ./services/dagster:/opt/dagster/app
+
+    # For development
+    # Mount dagster.yaml and workspace.yaml configuration files into the dagster home directory
+    - ./services/orchestration-engine/dagster.yaml:/opt/dagster/dagster_home/dagster.yaml
+    - ./services/orchestration-engine/workspace.yaml:/opt/dagster/dagster_home/workspace.yaml
+    # Mount the Dagster application source code (repository, jobs, ops, etc.) - only for development!
+    - ./services/orchestration-engine:/opt/dagster/app
+
     # Shared data lake between services
-    - ./data_lake:/data
+    - ${DATA_LAKE_DIR}:/data
 
 services:
   # SERVICES
@@ -29,8 +33,7 @@ services:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/workflow-manager/app/:/app/
-      # - data_lake:/data
-      - ./data_lake:/data
+      - ${DATA_LAKE_DIR}:/data
     environment:
       DATA_LAKE_DIRECTORY: /data
     healthcheck:
@@ -42,7 +45,7 @@ services:
     depends_on:
       scanhub-database:
         condition: service_healthy
-      dagster-dagit:
+      dagster-webserver:
         condition: service_healthy
       dagster-daemon:
         condition: service_healthy
@@ -55,7 +58,7 @@ services:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/device-manager/app/:/app/
-      - ./data_lake:/data
+      - ${DATA_LAKE_DIR}:/data
     environment:
       DATA_LAKE_DIRECTORY: /data
     healthcheck:
@@ -80,7 +83,7 @@ services:
         - BASE_IMG=${SCANHUB_BASE_IMAGE}
     volumes:
       - ./services/exam-manager/app/:/app/
-      - ./data_lake:/data
+      - ${DATA_LAKE_DIR}:/data
     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"]
@@ -168,6 +171,8 @@ services:
     container_name: db-scanhub
     image: postgres:15.2-bullseye
     restart: always # unless-stopped
+    ports:
+      - 5432:5432 # For development only
     volumes:
       - postgres_data_scanhub:/var/lib/postgresql/data/
     environment:
@@ -260,10 +265,10 @@ services:
         condition: service_healthy
       user-login-manager:
         condition: service_healthy
-      dagster-dagit:
-        condition: service_healthy
-      scanhub-ui:
+      dagster-webserver:
         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
     secrets:
@@ -289,12 +294,12 @@ services:
       start_period: 30s
 
   # DAGSTER
-  dagster-dagit:
+  dagster-webserver:
     <<: *dagster_common
-    container_name: dagster-dagit
-    command: ["dagster-webserver", "-h", "0.0.0.0", "-p", "3000", "--path-prefix", "/dagit"]
+    container_name: dagster-webserver
+    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/dagit/server-status"]
+      test: ["CMD", "curl", "-f", "http://localhost:3000/dagster/server-status"]
       interval: 10s
       timeout: 5s
       retries: 5
@@ -306,7 +311,7 @@ services:
     <<: *dagster_common
     container_name: dagster-daemon
     user: "0:0"
-    entrypoint: ["dagster-daemon", "run"]
+    entrypoint: ["dagster-daemon", "run", "-w", "/opt/dagster/app/workspace.yaml"]
     healthcheck:
       test: ["CMD", "pgrep", "-f", "dagster-daemon"]
       interval: 10s

infrastructure/nginx_config.conf

@@ -106,8 +106,8 @@ server {
   # --------------------------------------
   # Dagster Dagit UI (already WS-ready)
   # --------------------------------------
-  location /dagit/ {
-      proxy_pass http://dagster-dagit:3000/dagit/;
+  location /dagster/ {
+      proxy_pass http://dagster-webserver:3000/dagster/;
       proxy_http_version 1.1;
 
       # WebSocket support
@@ -119,10 +119,10 @@ server {
       proxy_set_header X-Real-IP $remote_addr;
       proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
       proxy_set_header X-Forwarded-Proto $scheme;
-      proxy_set_header X-Forwarded-Prefix /dagit;
+      proxy_set_header X-Forwarded-Prefix /dagster;
 
       # Optional: rewrite trailing slash
-      rewrite ^/dagit$ /dagit/ permanent;
+      rewrite ^/dagster$ /dagster/ permanent;
   }
 
   # --------------------------------------

scanhub-ui/.eslintrc.json

@@ -24,7 +24,8 @@
         "camelcase": "warn",
         "spaced-comment": "error",
         "quotes": ["error", "single"],
-        "no-duplicate-imports": "off"
+        "no-duplicate-imports": "off",
+        "@typescript-eslint/no-explicit-any": "off"
     },
     "settings": {
         "import/resolver": {

scanhub-ui/package.json

@@ -76,8 +76,8 @@
     "dev": "vite",
     "build": "vite build",
     "preview": "vite preview",
-    "lint": "eslint ./src/**/*.tsx",
-    "lint+fix": "eslint --fix './src/**/*.tsx'",
+    "lint": "eslint ./src --ext .ts,.tsx,.js,.jsx",
+    "lint+fix": "eslint ./src --ext .ts,.tsx,.js,.jsx --fix",
     "format": "prettier --write './src/**/*.tsx' --config ./.prettierrc",
     "generate-all-clients": "./src/openapi/generate-all-clients.sh",
     "ts-unused-exports": "ts-unused-exports tsconfig.json --excludePathsFromReport=rc/generated-client"

scanhub-ui/src/Routes.tsx

@@ -16,10 +16,8 @@ import {
   Experimental_CssVarsProvider as MaterialCssVarsProvider,
   extendTheme as materialExtendTheme,
 } from '@mui/material/styles'
-const materialTheme = materialExtendTheme()
 
 import LoginContext from './LoginContext'
-
 import App from './pages/App'
 import Login from './pages/LoginView'
 import PatientListView from './pages/PatientListView'
@@ -28,8 +26,8 @@ import TemplatesView from './pages/TemplatesView'
 import UserManagementView from './pages/UserManagementView'
 import SequenceView from './pages/SequenceView'
 import DeviceView from './pages/DeviceView'
-import ConnectionStatus from './components/ConnectionStatus'
 
+const materialTheme = materialExtendTheme()
 
 export function RouteConfiguration() {
   const navigate = useNavigate()
@@ -49,10 +47,7 @@ export function RouteConfiguration() {
               '--Transition-duration': '0.4s', // set to `none` to disable transition
               '--Sidebar-width': '360px',
               '--Navigation-height': '60px',
-              // '--Navigation-height': '64px',  // set height of navigation bar
-              // '--PatientView-toolbarHeight': '54px',
-              // '--PatientView-drawerWidth': '300px',
-              // '--PatientView-recordWidth': '300px',
+              '--Status-height': '22px',
             },
           }}
         />
@@ -65,7 +60,6 @@ export function RouteConfiguration() {
             <Route path='/devices' element={<DeviceView />} />
             <Route path='/sequences' element={<SequenceView />} />
             <Route path='/users' element={<UserManagementView />} />
-            <Route path='/connections' element={<ConnectionStatus buttonOrPage='page' />} />
           </Route>
 
           <Route

scanhub-ui/src/components/AccordionWithMenu.tsx

@@ -9,34 +9,47 @@ import React from 'react';
 import Stack from '@mui/joy/Stack';
 import IconButton from '@mui/joy/IconButton';
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
-import KeyboardArrowLeftIcon from '@mui/icons-material/KeyboardArrowLeft';
+import KeyboardArrowRightIcon from '@mui/icons-material/KeyboardArrowRight';
+import Tooltip from '@mui/joy/Tooltip'
 
 import { AccordionWithMenuInterface } from '../interfaces/components.interface';
 
 
 export default function AccordionWithMenu(props: AccordionWithMenuInterface) {
 
-    const [expanded, setExpanded] = React.useState(false);
+  const [expanded, setExpanded] = React.useState(false);
 
-    return (
-        <Stack direction='column' width='100%'>
-            <Stack direction='row' alignItems='center' justifyContent='space-between'>
-                {props.accordionSummary}
-                <Stack direction='row' alignItems='center'>
-                    {props.accordionMenu}
-                    <IconButton
-                        onClick={() => setExpanded(!expanded)}
-                    >
-                        {expanded ? <ExpandMoreIcon /> : <KeyboardArrowLeftIcon />}
-                    </IconButton>
-                </Stack>
-            </Stack>
-            <Stack
-                direction='column'
-                sx={{ paddingLeft: 3 }}
+  return (
+    <Stack direction='column' width='100%'>
+      <Stack direction='row' alignItems='center'>
+        <Tooltip
+          placement='right'
+          variant='outlined'
+          describeChild={false}
+          arrow
+          title={ props.toolTipContent }
+          modifiers={[
+            { name: 'offset', options: { offset: [0, 64] } }, // skidding=8 (down), distance=20 (further right)
+          ]}
+        >
+          <Stack direction='row' alignItems='center' flexGrow={1}>
+            <IconButton
+              onClick={() => setExpanded(!expanded)}
             >
-                {expanded ? props.children : undefined}
-            </Stack>
-        </Stack>
-    )
+              {expanded ? <ExpandMoreIcon /> : <KeyboardArrowRightIcon />}
+            </IconButton>
+            { props.accordionSummary }
+          </Stack>
+        </Tooltip>
+        { props.accordionMenu }
+      </Stack>
+      <Stack
+        direction='column'
+        sx={{ paddingLeft: 2 }}
+      >
+        {expanded ? props.children : undefined}
+      </Stack>
+
+    </Stack>
+  )
 }

scanhub-ui/src/components/AcquisitionControl.tsx

@@ -6,7 +6,6 @@
  */
 import PlayCircleIcon from '@mui/icons-material/PlayCircle'
 import StopCircleIcon from '@mui/icons-material/StopCircle';
-import CheckCircleIcon from '@mui/icons-material/CheckCircle';
 import Box from '@mui/joy/Box'
 import IconButton from '@mui/joy/IconButton'
 import LinearProgress from '@mui/joy/LinearProgress'
@@ -45,17 +44,13 @@ function AcquisitionControl({ itemSelection, openConfirmModal }: {
     },
   })
 
-  let actionIcon = <PlayCircleIcon />
-  if (itemSelection.status == ItemStatus.Started) actionIcon = <StopCircleIcon />
-  if (itemSelection.status == ItemStatus.Finished) actionIcon = <CheckCircleIcon />
-
   return (
     <Box sx={{ display: 'flex', gap: 1, alignItems: 'center' }}>
       <IconButton 
         size='sm' 
         variant='plain' 
         color={'neutral'}
-        disabled={processTaskMutation.isPending}
+        disabled={processTaskMutation.isPending || !(itemSelection.type == 'DAG' || itemSelection.type == 'ACQUISITION')}
         onClick={() => {
           openConfirmModal(() => {
             // By now, only tasks can be executed
@@ -72,7 +67,7 @@ function AcquisitionControl({ itemSelection, openConfirmModal }: {
           })
         }}
       >
-        {actionIcon}
+        { itemSelection.status == ItemStatus.Started ? <StopCircleIcon /> : <PlayCircleIcon /> }
       </IconButton>
 
       <Stack direction='column' sx={{ flex: 1 }}>
@@ -84,9 +79,12 @@ function AcquisitionControl({ itemSelection, openConfirmModal }: {
         </Typography>
         <Typography level='body-xs'>{'ID: ' + itemSelection.itemId}</Typography>
         <LinearProgress 
-          determinate value={itemSelection.progress}
+          determinate={itemSelection.progress !== undefined && itemSelection.progress > 0}
+          value={itemSelection.progress !== undefined && itemSelection.progress > 0 ? itemSelection.progress : (
+              itemSelection.status === ItemStatus.Inprogress ? 25 : 0
+            )
+          }
           sx={{marginTop: 1}}
-          color={itemSelection.status == ItemStatus.Finished ? 'success' : 'primary'}
         />
       </Stack>
     </Box>