Merge pull request #6 from the-virtual-brain/dev_LM

VT-23. Finalize POC of extension

.gitignore

@@ -124,3 +124,5 @@ dmypy.json
 
 # Yarn cache
 .yarn/
+workspace_export.py
+test_output

src/App.tsx

@@ -10,13 +10,15 @@ import TreeViewComponent from './components/TreeView';
 const App: React.FC = () => {
   const [selectedNode, setSelectedNode] = useState<ISelectedNodeType | null>(null);
 
-  const [workspace, setWorkspace] = useState<IWorkspaceState>({
+  const initialWorkspaceState: IWorkspaceState = {
     model: null,
-    connectivity: null,
+    parcellation: null,
+    tractogram: null,
     coupling: null,
     noise: null,
     integrationMethod: null
-  });
+  };
+  const [workspace, setWorkspace] = useState<IWorkspaceState>(initialWorkspaceState);
 
   const addToWorkspace = (node: ISelectedNodeType) => {
     setWorkspace(prevWorkspace => {
@@ -35,10 +37,24 @@ const App: React.FC = () => {
     });
   };
 
+  const updateConnectivityOptions = (optionType: 'parcellation' | 'tractogram', value: string) => {
+    setWorkspace(prev => {
+      return {
+        ...prev,
+        parcellation: optionType === 'parcellation' ? value : prev.parcellation,
+        tractogram: optionType === 'tractogram' ? value : prev.tractogram,
+      };
+    });
+  };
+
+  const resetWorkspace = () => {
+    setWorkspace(initialWorkspaceState);
+  };
+
   return (
     <div className="layout">
       <InfoBoxComponent selectedNode={selectedNode} addToWorkspace={addToWorkspace} />
-      <WorkspaceComponent workspace={workspace} />
+      <WorkspaceComponent workspace={workspace} updateConnectivityOptions={updateConnectivityOptions} resetWorkspace={resetWorkspace}/>
       <TreeViewComponent selectedNode={selectedNode} />
       <GraphViewComponent setSelectedNode={setSelectedNode} />
     </div>

src/components/GaphView.tsx

@@ -40,6 +40,7 @@ export const GraphViewComponent: React.FC<IGraphViewProps> = ({
       type: node.type,
       definition: node.definition,
       iri: node.iri,
+      requires: node.requires,
       childNodes: node.childNodes,
       childLinks: node.childLinks,
       collapsed: false
@@ -111,7 +112,7 @@ export const GraphViewComponent: React.FC<IGraphViewProps> = ({
     }
   };
 
-  // for graph centering when it is first rendered
+  // center graph when it is first rendered
   useEffect(() => {
     if (fgRef.current && data.nodes.length > 0 && isInitialRender) {
       fgRef.current.centerAt(75, 75);

src/components/InfoBox.tsx

@@ -1,5 +1,6 @@
 import React from 'react';
 import { ISelectedNodeType } from './interfaces/InfoBoxInterfaces';
+import { fetchNodeByLabel } from '../handler';
 
 interface IInfoBoxProps {
   selectedNode: {
@@ -8,23 +9,46 @@ interface IInfoBoxProps {
     type: string;
     definition: string;
     iri: string;
+    requires: string[];
   } | null;
   addToWorkspace: (node: ISelectedNodeType) => void;
 }
 
-const InfoBoxComponent: React.FC<IInfoBoxProps> = ({
-  selectedNode,
-  addToWorkspace
-}) => {
+const InfoBoxComponent: React.FC<IInfoBoxProps> = ({ selectedNode, addToWorkspace }) => {
   // Valid types for adding objects to workspace
   // TODO: add valid type for connectivity
   const validTypes = ['Neural Mass Model', 'Noise', 'Coupling', 'Integrator'];
 
   const isAddable = selectedNode && validTypes.includes(selectedNode.type);
 
+  const handleAddToWorkspace = async () => {
+    if (!selectedNode) return;
+
+    if (isAddable) {
+      addToWorkspace(selectedNode);
+
+      // check requirements of selected node
+      if (selectedNode.requires && selectedNode.requires.length > 0) {
+        const requiredNodePromises = selectedNode.requires.map(label => fetchNodeByLabel(label));
+        const requiredNodesResponses = await Promise.all(requiredNodePromises);
+
+        requiredNodesResponses.forEach(response => {
+          const { nodes } = response; // Extract nodes from the response
+          nodes.forEach(node => {
+            if (validTypes.includes(node.type) && (node.type !== selectedNode.type)) {  // check for same type as selected node to not overwrite it
+              addToWorkspace(node);
+            }
+          });
+        });
+      }
+    } else {
+      console.warn(`Node type "${selectedNode.type}" is not allowed in the workspace.`);
+    }
+  };
+
   return (
     <div className="info-box">
-      <h3>Concept Details</h3>
+      <h3>Node Details</h3>
       {selectedNode ? (
         <div>
           <div className="node-info-container">
@@ -48,7 +72,7 @@ const InfoBoxComponent: React.FC<IInfoBoxProps> = ({
             </div>
             <button
               className="add-button"
-              onClick={() => addToWorkspace(selectedNode)}
+              onClick={handleAddToWorkspace}
               disabled={!isAddable}
             >
               Add to Workspace

src/components/TreeView.tsx

@@ -14,6 +14,7 @@ interface INodeRelation {
 const TreeViewComponent: React.FC<ITreeViewProps> = ({ selectedNode }) => {
   const [parents, setParents] = useState<INodeRelation[]>([]);
   const [children, setChildren] = useState<INodeRelation[]>([]);
+  const [requirements, setRequirements] = useState<string[]>([]);
 
   useEffect(() => {
     if (!selectedNode) {
@@ -45,6 +46,12 @@ const TreeViewComponent: React.FC<ITreeViewProps> = ({ selectedNode }) => {
 
     fetchAndSetParents();
     fetchAndSetChildren();
+
+    if (selectedNode.requires && selectedNode.requires.length > 0) {
+      setRequirements(selectedNode.requires);
+    } else {
+      setRequirements([]);
+    }
   }, [selectedNode]);
 
   const processNodeRelations = (
@@ -68,10 +75,12 @@ const TreeViewComponent: React.FC<ITreeViewProps> = ({ selectedNode }) => {
 
   return (
     <div className="tree-view">
+      <h3>Node Connections</h3>
       {selectedNode ? (
         <>
           <h2 style={{ textAlign: 'center' }}>{selectedNode.label}</h2>
           <div style={{ display: 'flex', justifyContent: 'space-between' }}>
+            {/* Parents Column */}
             <div>
               <h3>Parents</h3>
               {parents.length > 0 ? (
@@ -87,7 +96,8 @@ const TreeViewComponent: React.FC<ITreeViewProps> = ({ selectedNode }) => {
               )}
             </div>
 
-            <div>
+            {/* Children Column */}
+            <div style={{ marginLeft: '20px' }}>
               <h3>Children</h3>
               {children.length > 0 ? (
                 <ul>
@@ -101,10 +111,21 @@ const TreeViewComponent: React.FC<ITreeViewProps> = ({ selectedNode }) => {
                 <p>No children found.</p>
               )}
             </div>
+            {/* Requires Column */}
+            {requirements.length > 0 && (
+              <div style={{ marginLeft: '20px' }}>
+                <h3>Requires</h3>
+                <ul>
+                  {requirements.map((requirement, index) => (
+                    <li key={index}>{requirement}</li>
+                  ))}
+                </ul>
+              </div>
+            )}
           </div>
         </>
       ) : (
-        <p>Please select a node first</p>
+        <p>Please select a node to see its connections</p>
       )}
     </div>
   );

src/components/Workspace.tsx

@@ -1,26 +1,36 @@
-import React, { useState } from 'react';
+import React, { useEffect, useState } from 'react';
 import { IWorkspaceProps } from './interfaces/WorkspaceInterfaces';
-import { exportWorkspace } from '../handler';
+import { exportWorkspace, runSimulation } from '../handler';
 
-const WorkspaceComponent: React.FC<IWorkspaceProps> = ({ workspace }) => {
-  const [exportType, setExportType] = useState('python file');
+const WorkspaceComponent: React.FC<IWorkspaceProps> = ({ workspace, updateConnectivityOptions, resetWorkspace }) => {
+  const [exportType, setExportType] = useState('py');
   const [message, setMessage] = useState<string | null>(null);
-  const [filename, setFilename] = useState('workspace_export'); // Default filename
+  const [directory, setDirectory] = useState('');
 
-  const handleExport = async () => {
+  const parcellationOptions = ['DesikanKilliany', 'Destrieux', 'Schaefer1000', 'hcpmmp1', 'virtualdbs'];
+  const tractogramOptions = ['MghUscHcp32', 'PPMI85', 'dTOR'];
+
+  const constructNodeData = () => {
     const nodeData = {
       model: workspace.model ? workspace.model.label : 'None',
-      connectivity: workspace.connectivity ? workspace.connectivity.label : 'None',
+      parcellation: workspace.parcellation ? workspace.parcellation : 'None',
+      tractogram: workspace.tractogram ? workspace.tractogram : 'None',
       coupling: workspace.coupling ? workspace.coupling.label : 'None',
       noise: workspace.noise ? workspace.noise.label : 'None',
       integrationMethod: workspace.integrationMethod ? workspace.integrationMethod.label : 'None',
     };
 
+    return nodeData;
+  };
+
+  const handleExport = async () => {
+    const nodeData = constructNodeData();
+
     try {
-      const response = await exportWorkspace(exportType, nodeData, filename);
+      const response = await exportWorkspace(exportType, nodeData, directory);
 
       if (response.status === 'success') {
-        setMessage(`File saved successfully: ${response.message}`);
+        setMessage(`${response.message}`);
       } else {
         setMessage(`Failed to save file: ${response.error}`);
       }
@@ -33,16 +43,83 @@ const WorkspaceComponent: React.FC<IWorkspaceProps> = ({ workspace }) => {
     }
   };
 
+  const handleRunSimulation = async () => {
+    const nodeData = constructNodeData();
+
+    try {
+      const response = await runSimulation(exportType, nodeData, directory);
+
+      if (response.status === 'success') {
+        setMessage(`${response.message}`);
+      } else {
+        setMessage(`${response.error}`);
+      }
+    } catch (error) {
+      if (error instanceof Error) {
+        setMessage(`Error during simulation run: ${error.message}`);
+      } else {
+        setMessage('An unknown error occurred during simulation run.');
+      }
+    }
+  };
+
+  // set timer for success/error message
+  useEffect(() => {
+    if (message) {
+      const timer = setTimeout(() => {
+        setMessage(null);
+      }, 30000);
+
+      return () => clearTimeout(timer);
+    }
+  }, [message]);
+
   return (
     <div className="workspace">
-      <h3>Workspace</h3>
+      <div className="workspace-header">
+        <h3>Workspace</h3>
+        <button className="reset-button" onClick={resetWorkspace}>Reset Workspace</button>
+      </div>
       <div>
         <h4>Model</h4>
         <p>{workspace.model ? workspace.model.label : 'None'}</p>
       </div>
       <div>
-        <h4>Connectivity</h4>
-        <p>{workspace.connectivity ? workspace.connectivity.label : 'None'}</p>
+        <div className="dropdown-container">
+          {/* Parcellation Dropdown */}
+          <div className="dropdown-section">
+            <label htmlFor="parcellation">Parcellation:</label>
+            <select
+              id="parcellation"
+              value={workspace.parcellation || ''}
+              onChange={(e) => updateConnectivityOptions('parcellation', e.target.value)} // Update state on change
+            >
+              <option value="" disabled>Select a parcellation</option>
+              {parcellationOptions.map((option, index) => (
+                <option key={index} value={option}>
+                  {option}
+                </option>
+              ))}
+            </select>
+          </div>
+
+          {/* Tractogram Dropdown */}
+          <div className="dropdown-section">
+            <label htmlFor="tractogram">Tractogram:</label>
+            <select
+              id="tractogram"
+              value={workspace.tractogram || ''}
+              onChange={(e) => updateConnectivityOptions('tractogram', e.target.value)} // Update state on change
+            >
+              <option value="" disabled>Select a tractogram</option>
+              {tractogramOptions.map((option, index) => (
+                <option key={index} value={option}>
+                  {option}
+                </option>
+              ))}
+            </select>
+          </div>
+        </div>
       </div>
       <div>
         <h4>Coupling</h4>
@@ -60,28 +137,35 @@ const WorkspaceComponent: React.FC<IWorkspaceProps> = ({ workspace }) => {
       {/* Export controls */}
       <div className="export-controls">
         <div className="export-control">
-          <label htmlFor="export-type">Select export type: </label>
-          <select
-            id="export-type"
-            value={exportType}
-            onChange={(e) => setExportType(e.target.value)}
-          >
-            <option value="python file">Python File</option>
-            <option value="xml file">XML File</option>
-          </select>
+          <div className="dropdown-section">
+            <label htmlFor="export-type">Select export type: </label>
+            <select
+              id="export-type"
+              value={exportType}
+              onChange={(e) => setExportType(e.target.value)}
+            >
+              <option value="py">Simulation code (.py)</option>
+              <option value="xml">Model specification (.xml)</option>
+              <option value="yaml">Metadata (.yaml)</option>
+            </select>
+          </div>
         </div>
 
         <div className="export-control">
-          <label htmlFor="filename">Filename: </label>
+          <label htmlFor="directory">Save Directory Path: </label>
           <input
-            id="filename"
+            id="directory"
             type="text"
-            value={filename}
-            onChange={(e) => setFilename(e.target.value)}
+            value={directory}
+            onChange={(e) => setDirectory(e.target.value)}
+            placeholder="/home/user/downloads"
           />
         </div>
 
-        <button className="export-button" onClick={handleExport}>Export</button>
+        <div className="button-container">
+          <button className="export-button" onClick={handleExport}>Export</button>
+          <button className="export-button" onClick={handleRunSimulation}>Run Simulation</button>
+        </div>
         {message && <p>{message}</p>} {/* Display success/error message */}
       </div>
     </div>

src/components/interfaces/GraphViewInterfaces.tsx

@@ -4,6 +4,7 @@ export interface INodeType {
   type: string;
   definition: string;
   iri: string;
+  requires: string[];
   x?: number;
   y?: number;
   collapsed?: boolean;