Biosimulators Prototype

examples/src/Viewer.tsx

@@ -128,6 +128,7 @@ class Viewer extends React.Component<InputParams, ViewerState> {
     private panMode = false;
     private focusMode = true;
     private orthoMode = false;
+    private smoldynInput = "100";
     private netConnectionSettings: NetConnectionParams;
 
     public constructor(props: InputParams) {
@@ -353,6 +354,28 @@ class Viewer extends React.Component<InputParams, ViewerState> {
             });
     }
 
+    public loadSmoldynSim() {
+        simulariumController.checkServerHealth(
+            this.onHealthCheckResponse,
+            this.netConnectionSettings
+        );
+        const fileName = "smoldyn_sim" + uuidv4() + ".simularium"
+        simulariumController
+            .startSmoldynSim(this.netConnectionSettings, fileName, this.smoldynInput)
+            .then(() => {
+                this.clearPendingFile();
+            })
+            .then(() => {
+                simulariumController.initNewFile(
+                    { netConnectionSettings: this.netConnectionSettings, },
+                    true,
+                )
+            })
+            .catch((err) => {
+                console.error(err);
+            });
+    }
+
     public clearPendingFile() {
         this.setState({ filePending: null });
     }
@@ -430,11 +453,10 @@ class Viewer extends React.Component<InputParams, ViewerState> {
 
     public receiveConvertedFile(): void {
         simulariumController
-            .changeFile(
+            .initNewFile(
                 {
                     netConnectionSettings: this.netConnectionSettings,
                 },
-                this.state.conversionFileName
             )
             .then(() => {
                 simulariumController.gotoTime(0);
@@ -773,6 +795,17 @@ class Viewer extends React.Component<InputParams, ViewerState> {
                     Load a smoldyn trajectory
                 </button>
                 <br />
+                <label>
+                    Initial Rabbit Count:
+                    <input
+                        defaultValue="100"
+                        onChange={(event) => {this.smoldynInput = event.target.value}}
+                    />
+                </label>
+                <button onClick={() => this.loadSmoldynSim()}>
+                    Run Smoldyn
+                </button>
+                <br />
                 <button onClick={() => simulariumController.resume()}>
                     Play
                 </button>

src/controller/index.ts

@@ -118,6 +118,9 @@ export default class SimulariumController {
         this.setFocusMode = this.setFocusMode.bind(this);
         this.convertTrajectory = this.convertTrajectory.bind(this);
         this.setCameraType = this.setCameraType.bind(this);
+        this.startSmoldynSim = this.startSmoldynSim.bind(this);
+        this.cancelCurrentFile = this.cancelCurrentFile.bind(this);
+        this.initNewFile = this.initNewFile.bind(this);
     }
 
     private createSimulatorConnection(
@@ -240,6 +243,8 @@ export default class SimulariumController {
         fileType: TrajectoryType,
         providedFileName?: string
     ): Promise<void> {
+        const fileName = providedFileName ?? `${uuidv4()}.simularium`;
+        this.cancelCurrentFile(fileName);
         try {
             if (!this.isRemoteOctopusClientConfigured()) {
                 this.configureNetwork(netConnectionConfig);
@@ -250,7 +255,6 @@ export default class SimulariumController {
             if (!this.simulator) {
                 throw new Error("Simulator not initialized");
             }
-            const fileName = providedFileName ?? `${uuidv4()}.simularium`;
             return this.octopusClient.convertTrajectory(
                 dataToConvert,
                 fileType,
@@ -278,6 +282,28 @@ export default class SimulariumController {
         }
     }
 
+    public startSmoldynSim(
+        netConnectionConfig: NetConnectionParams,
+        fileName: string,
+        smoldynInput: string
+    ): Promise<void> {
+        this.cancelCurrentFile(fileName);
+        try {
+            if (!this.isRemoteOctopusClientConfigured()) {
+                this.configureNetwork(netConnectionConfig);
+            }
+            if (!this.octopusClient) {
+                throw new Error("Octopus client not configured");
+            }
+            if (!this.simulator) {
+                throw new Error("Simulator not initialized");
+            }
+            return this.octopusClient.sendSmoldynData(fileName, smoldynInput);
+        } catch (e) {
+            return Promise.reject(e);
+        }
+    }
+
     public gotoTime(time: number): void {
         // If in the middle of changing files, ignore any gotoTime requests
         if (this.isFileChanging || !this.simulator) return;
@@ -331,12 +357,7 @@ export default class SimulariumController {
         }
     }
 
-    public changeFile(
-        connectionParams: SimulatorConnectionParams,
-        // TODO: push newFileName into connectionParams
-        newFileName: string,
-        keepRemoteConnection = false
-    ): Promise<FileReturn> {
+    public cancelCurrentFile(newFileName: string): void {
         this.isFileChanging = true;
         this.playBackFile = newFileName;
 
@@ -345,7 +366,12 @@ export default class SimulariumController {
 
         this.visData.WaitForFrame(0);
         this.visData.clearForNewTrajectory();
+    }
 
+    public initNewFile(
+        connectionParams: SimulatorConnectionParams,
+        keepRemoteConnection = false
+    ): Promise<FileReturn> {
         const shouldConfigureNewSimulator = !(
             keepRemoteConnection && this.isRemoteOctopusClientConfigured()
         );
@@ -391,6 +417,16 @@ export default class SimulariumController {
         });
     }
 
+    public changeFile(
+        connectionParams: SimulatorConnectionParams,
+        // TODO: push newFileName into connectionParams
+        newFileName: string,
+        keepRemoteConnection = false
+    ): Promise<FileReturn> {
+        this.cancelCurrentFile(newFileName);
+        return this.initNewFile(connectionParams, keepRemoteConnection);
+    }
+
     public markFileChangeAsHandled(): void {
         this.isFileChanging = false;
     }

src/simularium/OctopusClient.ts

@@ -62,4 +62,20 @@ export class OctopusServicesClient {
             "Request server health check"
         );
     }
+
+    public async sendSmoldynData(
+        outFileName: string,
+        smoldynInput: string
+    ): Promise<void> {
+        await this.webSocketClient.connectToRemoteServer();
+        this.lastRequestedFile = outFileName;
+        this.webSocketClient.sendWebSocketRequest(
+            {
+                msgType: NetMessageEnum.ID_START_SMOLDYN,
+                fileName: outFileName,
+                smoldynInputVal: smoldynInput ?? undefined,
+            },
+            "Start smoldyn simulation"
+        );
+    }
 }

src/simularium/WebsocketClient.ts

@@ -57,6 +57,7 @@ export const enum NetMessageEnum {
     ID_CHECK_HEALTH_REQUEST = 22,
     ID_SERVER_HEALTHY_RESPONSE = 23,
     ID_CANCEL_CONVERSION = 24,
+    ID_START_SMOLDYN = 25,
     // insert new values here before LENGTH
     LENGTH,
 }
@@ -70,6 +71,7 @@ export const enum ServerErrorCodes {
     FRAME_NOT_FOUND = 5,
     FILENAME_MISMATCH = 6,
     NO_RUNNING_SIMULATION = 7,
+    SMOLDYN_ERROR = 8,
     LENGTH,
 }