Use Exsiting VCell Connection for Parmater Estimation Request

vcell-admin/src/main/java/org/vcell/standalone/VCellStandaloneModule.java

@@ -1,17 +1,13 @@
 package org.vcell.standalone;
 
 import cbit.vcell.field.db.LocalExternalDataIdentifierServiceImpl;
-import cbit.vcell.message.VCMessagingService;
-import cbit.vcell.message.jms.activeMQ.VCMessagingServiceActiveMQ;
 import cbit.vcell.message.server.bootstrap.LocalVCellConnectionFactory;
 import cbit.vcell.message.server.bootstrap.LocalVCellConnectionServiceImpl;
 import cbit.vcell.server.LocalVCellConnectionService;
 import cbit.vcell.server.VCellConnectionFactory;
 import cbit.vcell.simdata.ExternalDataIdentifierService;
 import com.google.inject.AbstractModule;
 import org.vcell.api.utils.Auth0ConnectionUtils;
-import org.vcell.service.registration.RegistrationService;
-import org.vcell.service.registration.localdb.LocaldbRegistrationService;
 
 public class VCellStandaloneModule extends AbstractModule {
     @Override
@@ -22,6 +18,5 @@ protected void configure() {
         bind(Auth0ConnectionUtils.class).toInstance(new Auth0ConnectionUtils());
         bind(VCellConnectionFactory.class).to(LocalVCellConnectionFactory.class).asEagerSingleton();
 
-        bind(RegistrationService.class).toInstance(new LocaldbRegistrationService());
     }
 }

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 {
@@ -363,22 +359,6 @@ public String handleResponse(final HttpResponse response) throws ClientProtocolE
 						message = reader.lines().collect(Collectors.joining());
 					}
 					return message;
-//					HttpEntity entity = response.getEntity();
-//					if (lg.isInfoEnabled()) {
-//						try (BufferedReader reader = new BufferedReader(new InputStreamReader(entity.getContent()));){
-//							lg.info("optimizationId = "+reader.readLine());
-//						}
-//					}
-//			        final Header locationHeader = response.getFirstHeader("location");
-//			        if (locationHeader == null) {
-//			            // got a redirect response, but no location header
-//			            throw new ClientProtocolException(
-//			                    "Received redirect response " + response.getStatusLine()
-//			                    + " but no location header");
-//			        }
-//			        final String location = locationHeader.getValue();
-//			        URI uri = createLocationURI(location);
-//					return uri.toString();
 				} else {
 					HttpEntity entity = response.getEntity();
 					String message = null;
@@ -398,8 +378,6 @@ public String handleResponse(final HttpResponse response) throws ClientProtocolE
 		}
 
 		return responseUri;
-//		String optimizationId = responseUri.substring(responseUri.lastIndexOf('/') + 1);
-//		return optimizationId;
 	}
 
 	/**

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

@@ -23,9 +23,9 @@
 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.service.registration.RegistrationService;
 import org.vcell.util.Compare;
 import org.vcell.util.DataAccessException;
 import org.vcell.util.VCellThreadChecker;
@@ -823,7 +823,11 @@ void setDisconnected() {
 	setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), getClientServerInfo().getApihost(), getClientServerInfo().getApiport(), ConnectionStatus.DISCONNECTED));
 }
 
-public RegistrationService getRegistrationProvider() {
-	return new VCellConnectionRegistrationProvider(this.vcellConnection);
-}
+	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

@@ -21,6 +21,7 @@
 import cbit.vcell.server.VCellConnectionFactory;
 import com.google.inject.Inject;
 import com.install4j.api.launcher.ApplicationLauncher;
+import org.vcell.api.client.VCellApiClient;
 import org.vcell.api.messaging.RemoteProxyVCellConnectionFactory;
 import org.vcell.api.server.ClientServerManager;
 import org.vcell.api.server.ClientServerManager.InteractiveContextDefaultProvider;
@@ -47,7 +48,7 @@ public class VCellClient {
 
 	private static VCellClient instance = null;
 
-	public static void setInstance(VCellClient instance) {
+	private static void setInstance(VCellClient instance) {
 		VCellClient.instance = instance;
 	}
 	public static VCellClient getInstance() {

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

@@ -1,5 +1,8 @@
 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;
 import cbit.vcell.opt.OptimizationException;
@@ -25,20 +28,13 @@ public static OptimizationResultSet solveRemoteApi(
             ParameterEstimationTask parameterEstimationTask,
             CopasiOptSolverCallbacks optSolverCallbacks,
             ClientTaskStatusSupport clientTaskStatusSupport,
-            ClientServerInfo clientServerInfo) {
+            ClientRequestManager requestManager) {
 
         // return solveLocalPython(parameterEstimationTask);
 
         try {
-            boolean bIgnoreCertProblems = PropertyLoader.getBooleanProperty(PropertyLoader.sslIgnoreCertProblems, false);
-            boolean bIgnoreHostMismatch = PropertyLoader.getBooleanProperty(PropertyLoader.sslIgnoreHostMismatch, false);
-
-            String host = clientServerInfo.getApihost();
-            int port = clientServerInfo.getApiport();
-            String pathPrefixV0 = clientServerInfo.getPathPrefix_v0();
             // e.g. vcell.serverhost=vcellapi.cam.uchc.edu:443
-            VCellApiClient apiClient = new VCellApiClient(host, port, pathPrefixV0, bIgnoreCertProblems, bIgnoreHostMismatch);
-            apiClient.authenticate(bIgnoreCertProblems);
+            VCellApiClient apiClient = requestManager.getClientServerManager().getVCellApiClient();
 
             OptProblem optProblem = CopasiUtils.paramTaskToOptProblem(parameterEstimationTask);
 

vcell-client/src/main/java/org/vcell/dependency/client/VCellClientModule.java

@@ -1,13 +1,11 @@
 package org.vcell.dependency.client;
 
-import org.vcell.api.messaging.RemoteProxyVCellConnectionFactory;
 import cbit.vcell.server.VCellConnectionFactory;
 import cbit.vcell.simdata.ExternalDataIdentifierService;
 import com.google.inject.AbstractModule;
 import com.google.inject.name.Names;
 import org.vcell.DependencyConstants;
-import org.vcell.service.registration.RegistrationService;
-import org.vcell.util.network.RemoteRegistrationService;
+import org.vcell.api.messaging.RemoteProxyVCellConnectionFactory;
 import org.vcell.util.document.ExternalDataIdentifier;
 import org.vcell.util.document.User;
 
@@ -49,8 +47,6 @@ protected void configure() {
 
         bind(VCellConnectionFactory.class).to(RemoteProxyVCellConnectionFactory.class).asEagerSingleton();
 
-        // RegistrationService interface is not clean - mixes new registration with updates - is there another way?
-        bind(RegistrationService.class).toInstance(new RemoteRegistrationService()); // used on remote client.
 
         bind(String.class).annotatedWith(Names.named(DependencyConstants.VCELL_API_HOST)).toInstance(apiHost);
         bind(Integer.class).annotatedWith(Names.named(DependencyConstants.VCELL_API_PORT)).toInstance(apiPort);

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.");
+                }
             }
 
         };

vcell-core/src/main/java/cbit/vcell/client/server/ClientServerInterface.java

@@ -8,7 +8,6 @@
 import cbit.vcell.server.SessionManager;
 import cbit.vcell.server.VCellConnection;
 import cbit.vcell.simdata.VCDataManager;
-import org.vcell.service.registration.RegistrationService;
 
 import java.io.IOException;
 
@@ -39,5 +38,4 @@ public interface ClientServerInterface extends SessionManager, DataSetController
     public void removePropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener);
     public void sendErrorReport(Throwable exception );
     public void sendErrorReport(Throwable exception, VCellConnection.ExtraContext extraContext);
-    public RegistrationService getRegistrationProvider();
 }

vcell-server/src/main/java/org/vcell/dependency/server/VCellServerModule.java

@@ -8,8 +8,6 @@
 import cbit.vcell.server.LocalVCellConnectionService;
 import cbit.vcell.server.VCellConnectionFactory;
 import cbit.vcell.simdata.ExternalDataIdentifierService;
-import org.vcell.service.registration.RegistrationService;
-import org.vcell.service.registration.localdb.LocaldbRegistrationService;
 
 public class VCellServerModule extends com.google.inject.AbstractModule {
     @Override
@@ -21,11 +19,6 @@ protected void configure() {
         bind(LocalVCellConnectionService.class).toInstance(new LocalVCellConnectionServiceImpl());
         bind(VCellConnectionFactory.class).to(LocalVCellConnectionFactory.class).asEagerSingleton();
 
-        // server-side implementation (talk directly to database)
-        // RegistrationService interface is not clean - mixes new registration with updates - is there another way?
-        bind(RegistrationService.class).toInstance(new LocaldbRegistrationService());
-        //bind(RegistrationService.class).toInstance(new RemoteRegistrationService()); // used on remote client.
-
         bind(VCMessagingService.class).toInstance(new VCMessagingServiceActiveMQ());
         //bind(VCMessagingService.class).toInstance(new VCMessagingServiceEmbedded()); // used for testing.