update main

applications/virtual-fly-brain/Dockerfile

@@ -3,12 +3,20 @@ ARG CLOUDHARNESS_FLASK
 FROM ${CLOUDHARNESS_FLASK}
 
 ARG DOMAIN
+ARG BE_DOMAIN
 
 ENV MODULE_NAME=virtual_fly_brain
 ENV WORKERS=2
 ENV PORT=8080
 ENV BUILDDIR=/app
 
+# Update ImageMagick to fix critical security vulnerabilities
+# CVE-2025-57807, CVE-2025-55298, CVE-2025-55154, CVE-2025-55212, CVE-2025-57803
+RUN apt-get update && apt-get upgrade -y imagemagick
+
+# Remove bluez if present (CVE-2023-44431 - no fix available, not needed for this app)
+RUN apt-get remove -y bluez bluez-obexd libbluetooth3 || true
+
 RUN apt-get update && apt-get install -y \
     git \
     build-essential \
@@ -43,14 +51,20 @@ ENV MESA_GL_VERSION_OVERRIDE=3.3
 
 COPY frontend ${BUILDDIR}
 WORKDIR ${BUILDDIR}
-ENV VFB_DOMAIN=https://${DOMAIN}
 RUN yarn install
-RUN yarn run build
+# Debug: Print all environment variables and the VFB_DOMAIN value
+RUN echo "=== Environment Check ===" && \
+    echo "BE_DOMAIN ARG: ${BE_DOMAIN}" && \
+    echo "Full VFB_DOMAIN value: https://${BE_DOMAIN}" && \
+    export VFB_DOMAIN="https://${BE_DOMAIN}" && \
+    echo "Exported VFB_DOMAIN: $VFB_DOMAIN" && \
+    echo "========================"
+# Pass VFB_DOMAIN to Vite build process explicitly
+RUN export VFB_DOMAIN="https://${BE_DOMAIN}" && yarn run build
 
 WORKDIR /usr/src/app
 COPY backend/requirements.txt /usr/src/app/
 RUN pip3 install --no-cache-dir -r requirements.txt
-RUN echo 'test s'
 COPY backend/ /usr/src/app
 RUN pip3 install -e .
 

applications/virtual-fly-brain/backend/requirements.txt

@@ -4,16 +4,16 @@ connexion[swagger-ui] <= 2.3.0; python_version=="3.5" or python_version=="3.4"
 # connexion requires werkzeug but connexion < 2.4.0 does not install werkzeug
 # we must peg werkzeug versions below to fix connexion
 # https://github.com/zalando/connexion/pull/1044
-Werkzeug == 2.3.7;
+Werkzeug >= 3.0.3;
 swagger-ui-bundle >= 0.0.2
 python_dateutil >= 2.6.0
 setuptools >= 21.0.0
-Flask == 2.2.2
+Flask >= 2.3.2
 psycopg2-binary
-gunicorn==20.1.0
-flask_cors==3.0.10
+gunicorn >= 22.0.0
+flask_cors >= 4.0.1
 dataclasses_json >= 0.5.7
 dacite >= 1.6.0
 pandas >= 1.0.0
 numpy >= 1.19.0
-vfbquery==0.3.4
+vfbquery==0.5.1

applications/virtual-fly-brain/backend/setup.py

@@ -4,7 +4,7 @@
 from setuptools import setup, find_packages
 
 NAME = "virtual_fly_brain"
-VERSION = "1.0.0"
+VERSION = "1.1.0"
 
 # To install the library, run the following
 #
@@ -37,4 +37,3 @@
     virtual_fly_brain
     """
 )
-

applications/virtual-fly-brain/backend/tests/test_main.py

@@ -21,7 +21,11 @@ def test_get_instances(self):
         self.assertEqual(response.status_code, 200)
         # # Parse the JSON response
         data = json.loads(response.data)
-        self.assertIsInstance(data, list)
+        self.assertIsInstance(data, dict)
+        self.assertIn('count', data)
+        self.assertIn('headers', data)
+        self.assertIn('rows', data)
+        self.assertIsInstance(data['rows'], list)
 
     def test_get_term_info(self):
         """Test the /get_term_info route."""

applications/virtual-fly-brain/frontend/package.json

@@ -1,7 +1,7 @@
 {
   "name": "frontend",
   "private": true,
-  "version": "0.0.0",
+  "version": "1.1.0",
   "type": "module",
   "scripts": {
     "dev": "vite",
@@ -41,7 +41,7 @@
     "@types/react": "^18.2.0",
     "@types/react-dom": "^18.2.1",
     "@types/react-redux": "^7.1.24",
-    "axios": "^0.27.2",
+    "axios": "^1.7.0",
     "bloodhound-js": "1.2.3",
     "create-react-class": "^15.7.0",
     "file-saver": "^2.0.5",
@@ -85,5 +85,9 @@
     "less": "^3.10.3",
     "less-vars-to-js": "^1.3.0",
     "vite": "^7.0.4"
+  },
+  "resolutions": {
+    "node-fetch": "^2.6.7",
+    "cross-spawn": "^7.0.6"
   }
 }

applications/virtual-fly-brain/frontend/src/components/StackViewer.jsx

@@ -152,36 +152,69 @@ const VFBStackViewer = (props) => {
   const config = useMemo(() => {
     let result = {
       serverUrl: 'http://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi',
-      templateId: 'NOTSET'
+      templateId: 'NOTSET',
+      templateDomainIds: [],
+      templateDomainNames: [],
+      templateDomainTypeIds: [],
+      subDomains: []
     };
-    
-    data?.forEach( stackViewerData => {
+
+    data?.forEach(stackViewerData => {
       if (stackViewerData?.metadata?.IsTemplate) {
-        let keys = Object.keys(stackViewerData.metadata?.Images);
-        result = stackViewerData.metadata?.Images[keys[0]]?.[0];
-        result.serverUrl = 'http://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi';
-        if ( stackViewerData?.metadata?.Domains ){
-          keys = Object.keys(stackViewerData?.metadata?.Domains);
+        const imageKeys = Object.keys(stackViewerData.metadata?.Images || {});
+        if (!imageKeys.length) {
+          return;
+        }
+
+        const imageMeta =
+          stackViewerData.metadata?.Images[imageKeys[0]]?.[0];
+        if (!imageMeta) {
+          return;
         }
-        let ids = [parseInt(keys[keys?.length - 1]) + 1], labels = [parseInt(keys[keys?.length - 1]) + 1], classID = [parseInt(keys[keys?.length - 1]) + 1]; 
-        keys?.forEach( key => {
-          ids[parseInt(key)] = (stackViewerData?.metadata?.Domains?.[key]?.id);
-          labels[parseInt(key)] = (stackViewerData?.metadata?.Domains?.[key]?.type_label);
-          classID[parseInt(key)] = (stackViewerData?.metadata?.Domains?.[key]?.type_id);
-        })
-        let voxels = [];
-        if (result?.voxel != undefined) {
-          voxelSizeRef.current.x = Number(result.voxel.X || 0.622088);
-          voxelSizeRef.current.y = Number(result.voxel.Y || 0.622088);
-          voxelSizeRef.current.z = Number(result.voxel.Z || 0.622088);
-          voxels = [voxelSizeRef.current.x, voxelSizeRef.current.y, voxelSizeRef.current.z];
+
+        const domains = stackViewerData.metadata?.Domains || {};
+        const domainKeys = Object.keys(domains);
+        const maxIndex = domainKeys.reduce(
+          (acc, k) => Math.max(acc, Number(k) || 0),
+          0
+        );
+
+        const ids = new Array(maxIndex + 1);
+        const labels = new Array(maxIndex + 1);
+        const classIDs = new Array(maxIndex + 1);
+
+        domainKeys.forEach(key => {
+          const idx = Number(key);
+          const d = domains[key];
+          ids[idx] = d?.id;
+          labels[idx] = d?.type_label;
+          classIDs[idx] = d?.type_id;
+        });
+
+        const voxels = [];
+        if (imageMeta?.voxel) {
+          voxelSizeRef.current.x = Number(imageMeta.voxel.X || 0.622088);
+          voxelSizeRef.current.y = Number(imageMeta.voxel.Y || 0.622088);
+          voxelSizeRef.current.z = Number(imageMeta.voxel.Z || 0.622088);
+          voxels.push(
+            voxelSizeRef.current.x,
+            voxelSizeRef.current.y,
+            voxelSizeRef.current.z
+          );
         }
 
-        let subDomains = [voxels, ids, labels, classID]
-        result.subDomains = subDomains;
+        result = {
+          ...imageMeta,
+          serverUrl: 'http://www.virtualflybrain.org/fcgi/wlziipsrv.fcgi',
+          templateId: stackViewerData.metadata?.Id,
+          templateDomainIds: ids,
+          templateDomainNames: labels,
+          templateDomainTypeIds: classIDs,
+          subDomains: [voxels, ids, labels, classIDs]
+        };
       }
     });
-    
+
     return result;
   }, [data]);
 

applications/virtual-fly-brain/frontend/src/components/StackViewerComponent.jsx

@@ -981,16 +981,14 @@ const rgbToHex = (color) => {
     createImages: async function () {
       if (this.state.stack.length > 0) {
         var i, x, y, w, h, d, offX, offY, t, image, Xpos, Ypos, XboundMax, YboundMax, XboundMin, YboundMin;
-        /*
-         * move through tiles
-         * console.log('Creating slice view...');
-         */
+
         this.state.visibleTiles = [];
-        w = Math.ceil(((this.state.imageX / 10.0) * this.state.scl) / this.state.tileX);
-        h = Math.ceil(((this.state.imageY / 10.0) * this.state.scl) / this.state.tileY);
-        // console.log('Tile grid is ' + w.toString() + ' wide by ' + h.toString() + ' high');
+
+        w = Math.ceil(this.state.imageX / this.state.tileX);
+        h = Math.ceil(this.state.imageY / this.state.tileY);
         this.state.numTiles = w * h;
-
+        // console.log('Tile grid is ' + w.toString() + ' wide by ' + h.toString() + ' high');
+
         for (t = 0; t < w * h; t++) {
           x = 0;
           y = 0;
@@ -1683,12 +1681,23 @@ const StackViewerComponent = () => createClass({
       }
 
       // detect available wheel event
-      support = "onwheel" in document.createElement("div") ? "wheel" // Modern browsers support "wheel"
-        : document.onmousewheel !== undefined ? "mousewheel" // Webkit and IE support at least "mousewheel"
-          : "DOMMouseScroll"; // let's assume that remaining browsers are older Firefox
-      this?.addWheelListener(document.getElementById(this.props.data.id + 'displayArea'), (e) => {
+      support = "onwheel" in document.createElement("div")
+      ? "wheel"                            // Modern browsers
+      : document.onmousewheel !== undefined
+        ? "mousewheel"                     // Webkit / IE
+        : "DOMMouseScroll";                // Older Firefox
+
+      const displayElem =
+      document.getElementById((this.props.data && this.props.data.id) + 'displayArea') ||
+      document.getElementById('slice-viewer');
+
+      if (displayElem) {
+      this.addWheelListener(displayElem, (e) => {
         this.onWheelEvent(e);
       });
+      } else {
+      console.warn('StackViewer: wheel listener target not found for slice viewer');
+      }
 
       if (this.props.data && this.props.data != null && this.props.data.instances && this.props.data.instances != null) {
         this.setState(this.handleInstances(this.props.data.instances));
@@ -1732,24 +1741,30 @@ const StackViewerComponent = () => createClass({
           newState.voxelY = Number(this.props.config.subDomains[0][1] || 0.622088);
           newState.voxelZ = Number(this.props.config.subDomains[0][2] || 0.622088);
         }
-        if (this.props.config && this.props.config != null) {
-          if (this.props.config.subDomains && this.props.config.subDomains != null && this.props.config.subDomains.length) {
-            if (this.props.config.subDomains.length > 0 && this.props.config.subDomains[0] && this.props.config.subDomains[0].length && this.props.config.subDomains[0].length > 2) {
-              newState.voxelX = Number(this.props.config.subDomains[0][0] || 0.622088);
-              newState.voxelY = Number(this.props.config.subDomains[0][1] || 0.622088);
-              newState.voxelZ = Number(this.props.config.subDomains[0][2] || 0.622088);
-            }
-            if (this.props.config.subDomains.length > 3 && this.props.config.subDomains[1] != null) {
-              newState.tempName = this.props.config.subDomains[2];
-              newState.tempId = this.props.config.subDomains[1];
-              newState.tempType = this.props.config.subDomains[3];
-              // FIXME : Add extra subdomain to match previous configuration
-              // if (this.props.config.subDomains[4] && this.props.config.subDomains[4].length && this.props.config.subDomains[4].length > 0) {
-              //   newState.fxp = JSON.parse(this.props.config.subDomains[4][0]);
-              // }
-            }
+        if (this.props.config) {
+          const {
+            subDomains = [],
+            templateDomainIds,
+            templateDomainNames,
+            templateDomainTypeIds
+          } = this.props.config;
+
+          if (subDomains.length > 0 && subDomains[0] && subDomains[0].length > 2) {
+            newState.voxelX = Number(subDomains[0][0] || 0.622088);
+            newState.voxelY = Number(subDomains[0][1] || 0.622088);
+            newState.voxelZ = Number(subDomains[0][2] || 0.622088);
           }
-        }
+
+          const templateIds = templateDomainIds || subDomains[1];
+          const templateNames = templateDomainNames || subDomains[2];
+          const templateTypes = templateDomainTypeIds || subDomains[3];
+
+          if (templateIds && templateNames && templateTypes) {
+            newState.tempId = templateIds;
+            newState.tempName = templateNames;
+            newState.tempType = templateTypes;
+          }
+        }                
         for (instance in instances) {
           try {
             if ((instances[instance].wrappedObj.id != undefined) && (instances[instance].parent != null) ){
@@ -1792,7 +1807,7 @@ const StackViewerComponent = () => createClass({
 
     componentWillUnmount: function () {
       this._isMounted = false;
-      return true;
+      return true;      
     },
     /**
      * Event handler for clicking zoom in. Increments the zoom level