use of cbit.vcell.server.VCellConnection in project vcell by virtualcell.
the class ClientServerManager method connect.
/**
* Insert the method's description here.
* Creation date: (5/17/2004 6:26:14 PM)
*/
public void connect(InteractiveContext requester) {
asynchMessageManager.stopPolling();
reconnectStat = ReconnectStatus.NOT;
checkClientServerSoftwareVersion(requester, clientServerInfo);
// get new server connection
VCellConnection newVCellConnection = connectToServer(requester);
// update managers, status, etc.
changeConnection(requester, newVCellConnection);
if (fieldConnectionStatus.getStatus() == ConnectionStatus.CONNECTED) {
// start polling if haven't already
asynchMessageManager.startPolling();
}
}
use of cbit.vcell.server.VCellConnection in project vcell by virtualcell.
the class ClientServerManager method connectToServer.
/**
* Insert the method's description here.
* Creation date: (5/12/2004 4:48:13 PM)
*/
private VCellConnection connectToServer(InteractiveContext requester) {
VCellThreadChecker.checkRemoteInvocation();
VCellConnection newVCellConnection = null;
VCellConnectionFactory vcConnFactory = null;
String badConnStr = "";
try {
switch(getClientServerInfo().getServerType()) {
case SERVER_REMOTE:
{
String apihost = getClientServerInfo().getApihost();
Integer apiport = getClientServerInfo().getApiport();
try {
badConnStr += apihost + ":" + apiport;
vcConnFactory = new RemoteProxyVCellConnectionFactory(apihost, apiport, getClientServerInfo().getUserLoginInfo());
setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), apihost, apiport, ConnectionStatus.INITIALIZING));
newVCellConnection = vcConnFactory.createVCellConnection();
} catch (AuthenticationException ex) {
throw ex;
}
break;
}
case SERVER_LOCAL:
{
new PropertyLoader();
LocalVCellConnectionService localVCellConnectionService = VCellServiceHelper.getInstance().loadService(LocalVCellConnectionService.class);
vcConnFactory = localVCellConnectionService.getLocalVCellConnectionFactory(getClientServerInfo().getUserLoginInfo());
setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), null, null, ConnectionStatus.INITIALIZING));
newVCellConnection = vcConnFactory.createVCellConnection();
break;
}
}
requester.clearConnectWarning();
reconnectStat = ReconnectStatus.NOT;
} catch (AuthenticationException aexc) {
aexc.printStackTrace(System.out);
requester.showErrorDialog(aexc.getMessage());
} catch (ConnectionException cexc) {
String msg = badConnectMessage(badConnStr) + "\n" + cexc.getMessage();
cexc.printStackTrace(System.out);
ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
if (reconnectStat != ReconnectStatus.SUBSEQUENT) {
requester.showConnectWarning(msg);
}
} catch (Exception exc) {
exc.printStackTrace(System.out);
String msg = badConnectMessage(badConnStr) + "\nException:\n" + exc.getMessage();
ErrorUtils.sendRemoteLogMessage(getClientServerInfo().getUserLoginInfo(), msg);
requester.showErrorDialog(msg);
}
return newVCellConnection;
}
use of cbit.vcell.server.VCellConnection in project vcell by virtualcell.
the class ClientServerManager method reconnect.
/**
* attempt reconnect now
*/
void reconnect() {
Reconnector rc = getReconnector();
rc.notificationPause(true);
try {
switch(reconnectStat) {
case NOT:
reconnectStat = ReconnectStatus.FIRST;
break;
case FIRST:
reconnectStat = ReconnectStatus.SUBSEQUENT;
break;
default:
}
InteractiveContext requester = defaultInteractiveContextProvider.getInteractiveContext();
VCellConnection connection = connectToServer(requester);
if (connection != null) {
// success
changeConnection(requester, connection);
rc.stop();
asynchMessageManager.startPolling();
return;
}
setConnectionStatus(new ClientConnectionStatus(getClientServerInfo().getUsername(), getClientServerInfo().getApihost(), getClientServerInfo().getApiport(), ConnectionStatus.DISCONNECTED));
} finally {
rc.notificationPause(false);
}
}
use of cbit.vcell.server.VCellConnection in project vcell by virtualcell.
the class NagiosVCellMonitor method checkVCell.
private CheckResults checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int criticalTimeout, int monitorPort) throws Exception {
SimulationStatusPersistent lastSimStatus = null;
String vcellVersion = null;
TreeMap<VCELL_CHECK_LEVEL, Long> levelTimesMillisec = new TreeMap<NagiosVCellMonitor.VCELL_CHECK_LEVEL, Long>();
long startTime = System.currentTimeMillis();
VCellConnection vcellConnection = null;
try {
if (rmiHostName == null || rmiPort == -1) {
throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
}
String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
VCellBootstrap vcellBootstrap = null;
try {
vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
} catch (Exception e) {
throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
}
vcellVersion = vcellBootstrap.getVCellSoftwareVersion();
levelTimesMillisec.put(VCELL_CHECK_LEVEL.RMI_ONLY_0, System.currentTimeMillis() - startTime);
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
if (vcellNagiosPassword == null) {
throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
}
UserLoginInfo userLoginInfo = new UserLoginInfo(VCELL_NAGIOS_USER, new DigestedPassword(vcellNagiosPassword));
vcellConnection = vcellBootstrap.getVCellConnection(userLoginInfo);
levelTimesMillisec.put(VCELL_CHECK_LEVEL.CONNECT_1, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.RMI_ONLY_0));
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
levelTimesMillisec.put(VCELL_CHECK_LEVEL.INFOS_2, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.CONNECT_1));
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
KeyValue bioModelKey = null;
final String testModelName = "Solver Suite 5.1 (BETA only ode)";
for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(testModelName)) {
bioModelKey = bioModelInfo.getVersion().getVersionKey();
break;
}
}
BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
bioModel.refreshDependencies();
levelTimesMillisec.put(VCELL_CHECK_LEVEL.LOAD_3, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.INFOS_2));
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
final String testSimContextName = "non-spatial ODE";
SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
final String testSimName = "Copy of combined ida/cvode";
Simulation simulation = simulationContext.getSimulation(testSimName);
if (simulation == null) {
throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
}
VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
levelTimesMillisec.put(VCELL_CHECK_LEVEL.DATA_4, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.LOAD_3));
if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
KeyValue copy1Key = null;
KeyValue copy2Key = null;
VCSimulationIdentifier testRunSimID = null;
try {
if (simulationContext.getSimulations().length != 1) {
throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
}
SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
if (!simulationStatus.isCompleted()) {
throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
}
String copyModelName = testModelName + "_" + rmiHostName + "_rmi" + rmiPort + "_siteprt" + monitorPort;
boolean bForceCleanup = true;
while (true) {
boolean bMessy = false;
for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
if (userLoginInfo.getUserName().equals(bioModelInfo.getVersion().getOwner().getName()) && bioModelInfo.getVersion().getName().equals(copyModelName)) {
bMessy = true;
if (bForceCleanup) {
try {
vcellConnection.getUserMetaDbServer().deleteBioModel(bioModelInfo.getVersion().getVersionKey());
} catch (Exception e) {
e.printStackTrace();
}
} else {
throw new MessyTestEnvironmentException("Messy test environment, not expecting " + copyModelName + " and couldn't cleanup");
}
}
}
if (!bMessy) {
break;
}
// get new vcInfoContainer without cleaned-up model
vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
bForceCleanup = false;
}
BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
copy1Key = copyBioModel.getVersion().getVersionKey();
copyBioModel.refreshDependencies();
Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
final String copyTestSimName = "test";
copySim.setName(copyTestSimName);
copyBioModel.refreshDependencies();
copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
copy2Key = copyBioModel.getVersion().getVersionKey();
copyBioModel.refreshDependencies();
Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
if (simulationStatus != null && !simulationStatus.isNeverRan()) {
throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
}
testRunSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
vcellConnection.getSimulationController().startSimulation(testRunSimID, 1);
lastSimStatus = simulationStatus;
MessageEvent[] messageEvents = null;
while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
Thread.sleep(200);
if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
vcellConnection.getSimulationController().stopSimulation(testRunSimID);
vcellConnection.getMessageEvents();
break;
}
simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
lastSimStatus = simulationStatus;
}
if (simulationStatus != null && simulationStatus.isFailed()) {
throw new Exception("time " + ((System.currentTimeMillis() - startTime) / 1000) + ", Sim execution failed key:" + testRunSimID.getSimulationKey() + " sim " + newSimulation.getName() + " model " + copyBioModel.getVersion().getName() + " messg " + simulationStatus.getFailedMessage());
}
messageEvents = vcellConnection.getMessageEvents();
}
} finally {
try {
if (copy1Key != null) {
vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
}
} catch (Exception e) {
e.printStackTrace();
}
try {
if (copy2Key != null) {
vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
}
} catch (Exception e) {
e.printStackTrace();
}
if (testRunSimID != null) {
deleteSimData(testRunSimID);
}
}
levelTimesMillisec.put(VCELL_CHECK_LEVEL.RUN_5, System.currentTimeMillis() - startTime - levelTimesMillisec.get(VCELL_CHECK_LEVEL.DATA_4));
}
}
}
}
}
return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, null);
} catch (Exception e) {
return new CheckResults(vcellVersion, levelTimesMillisec, lastSimStatus, System.currentTimeMillis() - startTime, e);
} finally {
vcellConnection = null;
}
}
use of cbit.vcell.server.VCellConnection in project vcell by virtualcell.
the class LoginChecker method attemptLogin.
private static boolean attemptLogin(SiteInfo si, String user, String password) {
long start = 0;
try {
if (VERBOSE) {
start = System.currentTimeMillis();
}
String url = si.bootStrapUrl();
VCellBootstrap vcellBootstrap = (VCellBootstrap) java.rmi.Naming.lookup(url);
DigestedPassword dp = new UserLoginInfo.DigestedPassword(password);
UserLoginInfo uli = new UserLoginInfo(user, dp);
VCellConnection vcellConnection = vcellBootstrap.getVCellConnection(uli);
if (vcellConnection == null) {
if (VERBOSE) {
System.out.println("no connection on " + si + " in " + elapsed(start) + " seconds");
}
return false;
}
UserMetaDbServer dataServer = vcellConnection.getUserMetaDbServer();
@SuppressWarnings("unused") BioModelInfo[] bmi = dataServer.getBioModelInfos(true);
if (VERBOSE) {
System.out.println("success on " + si + " in " + elapsed(start) + " seconds");
}
return true;
} catch (MalformedURLException e) {
e.printStackTrace();
throw new Error("bad code");
} catch (Exception e) {
if (VERBOSE) {
System.out.println("failed in " + elapsed(start) + " seconds");
}
e.printStackTrace();
return false;
}
}
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