No Globals

Removed the global getter for VCellApiConnection, forcing proper communication methods instead of bypassing layers.

Author: Ezequiel-Valencia

vcell-apiclient/src/main/java/org/vcell/api/client/VCellApiClient.java

@@ -121,11 +121,7 @@ public String handleResponse(HttpResponse response) throws HttpResponseException
 	}
 
 	public VCellApiClient(String host, int port, String pathPrefix_v0) throws KeyManagementException, NoSuchAlgorithmException, KeyStoreException {
-		this(host, port, pathPrefix_v0, false, false);
-	}
-
-	public VCellApiClient(String host, int port, String pathPrefix_v0, boolean bIgnoreCertProblems, boolean bIgnoreHostMismatch) throws KeyManagementException, NoSuchAlgorithmException, KeyStoreException{
-		this(host, port, pathPrefix_v0, false, bIgnoreCertProblems, bIgnoreHostMismatch);
+		this(host, port, pathPrefix_v0, false, false, false);
 	}
 
 	public VCellApiClient(String host, int port, String pathPrefix_v0, boolean bSkipSSL, boolean bIgnoreCertProblems, boolean bIgnoreHostMismatch) throws NoSuchAlgorithmException, KeyStoreException, KeyManagementException {

vcell-apiclient/src/main/java/org/vcell/api/server/ClientServerManager.java

@@ -23,6 +23,7 @@
 import cbit.vcell.simdata.VCDataManager;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.vcell.api.client.VCellApiClient;
 import org.vcell.api.messaging.RemoteProxyVCellConnectionFactory;
 import org.vcell.api.utils.Auth0ConnectionUtils;
 import org.vcell.util.Compare;
@@ -822,4 +823,11 @@ void setDisconnected() {
 	setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), getClientServerInfo().getApihost(), getClientServerInfo().getApiport(), ConnectionStatus.DISCONNECTED));
 }
 
+	public VCellApiClient getVCellApiClient(){
+		if (vcellConnectionFactory instanceof RemoteProxyVCellConnectionFactory remoteProxyVCellConnectionFactory){
+			return remoteProxyVCellConnectionFactory.getVCellApiClient();
+		}
+		throw new UnsupportedOperationException("This function should only be called with RemoteProxyVCellConnectionFactory");
+	}
+
 }

vcell-client/src/main/java/cbit/vcell/client/ClientRequestManager.java

@@ -2833,7 +2833,7 @@ public AsynchMessageManager getAsynchMessageManager() {
 		return getClientServerManager().getAsynchMessageManager();
 	}
 
-	private ClientServerManager getClientServerManager() {
+	public ClientServerManager getClientServerManager() {
 		// shorthand
 		return getVcellClient().getClientServerManager();
 	}

vcell-client/src/main/java/cbit/vcell/client/VCellClient.java

@@ -144,13 +144,6 @@ public RequestManager getRequestManager() {
 	return requestManager;
 }
 
-public VCellApiClient getVCellApiClient(){
-	if (vcellConnectionFactory instanceof RemoteProxyVCellConnectionFactory){
-		return ((RemoteProxyVCellConnectionFactory) vcellConnectionFactory).getVCellApiClient();
-	}
-	throw new RuntimeException("Can not get VCell Api Client unless Remote Connection Factory is being used.");
-}
-
 
 StatusUpdater getStatusUpdater() {
 	return statusUpdater;

vcell-client/src/main/java/copasi/CopasiOptimizationSolverRemote.java

@@ -1,5 +1,7 @@
 package copasi;
 
+import cbit.vcell.client.ClientRequestManager;
+import cbit.vcell.client.RequestManager;
 import cbit.vcell.client.VCellClient;
 import cbit.vcell.client.server.ClientServerInfo;
 import cbit.vcell.modelopt.ParameterEstimationTask;
@@ -26,13 +28,13 @@ public static OptimizationResultSet solveRemoteApi(
             ParameterEstimationTask parameterEstimationTask,
             CopasiOptSolverCallbacks optSolverCallbacks,
             ClientTaskStatusSupport clientTaskStatusSupport,
-            ClientServerInfo clientServerInfo) {
+            ClientRequestManager requestManager) {
 
         // return solveLocalPython(parameterEstimationTask);
 
         try {
             // e.g. vcell.serverhost=vcellapi.cam.uchc.edu:443
-            VCellApiClient apiClient = VCellClient.getInstance().getVCellApiClient();
+            VCellApiClient apiClient = requestManager.getClientServerManager().getVCellApiClient();
 
             OptProblem optProblem = CopasiUtils.paramTaskToOptProblem(parameterEstimationTask);
 

vcell-client/src/main/java/org/vcell/optimization/gui/ParameterEstimationRunTaskPanel.java

@@ -14,6 +14,7 @@
 import cbit.plot.PlotData;
 import cbit.plot.gui.Plot2DPanel;
 import cbit.vcell.client.ClientRequestManager;
+import cbit.vcell.client.RequestManager;
 import cbit.vcell.client.TopLevelWindowManager;
 import cbit.vcell.client.VCellLookAndFeel;
 import cbit.vcell.client.constants.GuiConstants;
@@ -1162,14 +1163,18 @@ public void run(Hashtable<String, Object> hashTable) throws Exception {
         };
         taskList.add(task1);
 
-        AsynchClientTask task2 = new AsynchClientTask("Starting param esitmation job...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
+        AsynchClientTask task2 = new AsynchClientTask("Starting param estimation job...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
             @Override
             public void run(Hashtable<String, Object> hashTable) throws Exception {
                 // OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(parameterEstimationTask);
-                ClientServerInfo clientServerInfo = TopLevelWindowManager.activeManager().getRequestManager().getClientServerInfo();
                 optSolverCallbacks.setProgressReport(new OptProgressReport());
-                OptimizationResultSet optResultSet = CopasiOptimizationSolverRemote.solveRemoteApi(parameterEstimationTask, optSolverCallbacks, getClientTaskStatusSupport(), clientServerInfo);
-                hashTable.put(ORS_KEY, optResultSet);
+                RequestManager requestManager = TopLevelWindowManager.activeManager().getRequestManager();
+                if (requestManager instanceof ClientRequestManager clientRequestManager){
+                    OptimizationResultSet optResultSet = CopasiOptimizationSolverRemote.solveRemoteApi(parameterEstimationTask, optSolverCallbacks, getClientTaskStatusSupport(), clientRequestManager);
+                    hashTable.put(ORS_KEY, optResultSet);
+                } else {
+                    throw new UnsupportedOperationException("Requires remote connection to do parameter estimation.");
+                }
             }
 
         };