Examples with DocumentWindowManager cbit.vcell.client.DocumentWindowManager used on opensource projects

Example 1 with DocumentWindowManager

use of cbit.vcell.client.DocumentWindowManager in project vcell by virtualcell.

the class PDEExportDataPanel method createSimulationSelector.

private ExportSpecs.SimulationSelector createSimulationSelector() {
    ExportSpecs.SimulationSelector simulationSelector = new ExportSpecs.SimulationSelector() {

        private ExportSpecs.SimNameSimDataID[] multiSimNameSimDataIDs;

        // private ExportSpecs.ExportParamScanInfo exportParamScanInfo;
        private int[] selectedParamScanIndexes;

        private Simulation[] simulations;

        public SimNameSimDataID[] getSelectedSimDataInfo() {
            // }
            if (multiSimNameSimDataIDs == null) {
                return new ExportSpecs.SimNameSimDataID[] { currentSimNameSimDataID };
            }
            return multiSimNameSimDataIDs;
        }

        public void selectSimulations() {
            getNumAvailableSimulations();
            String[][] rowData = new String[simulations.length][5];
            for (int i = 0; i < rowData.length; i++) {
                rowData[i][0] = simulations[i].getName();
                rowData[i][1] = simulations[i].getMeshSpecification().getSamplingSize().toString();
                rowData[i][2] = simulations[i].getSolverTaskDescription().getExpectedNumTimePoints() + "";
                rowData[i][3] = simulations[i].getSolverTaskDescription().getTimeBounds().getEndingTime() + "";
                rowData[i][4] = simulations[i].getSolverTaskDescription().getOutputTimeSpec().getShortDescription();
            }
            try {
                int[] choices = DialogUtils.showComponentOKCancelTableList(PDEExportDataPanel.this, "Choose Sims to export together", new String[] { "Simulation", "Mesh x,y,z", "NumTimePoints", "EndTime", "Output Descr." }, rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
                if (choices != null) {
                    multiSimNameSimDataIDs = new ExportSpecs.SimNameSimDataID[choices.length];
                    for (int i = 0; i < choices.length; i++) {
                        multiSimNameSimDataIDs[i] = new ExportSpecs.SimNameSimDataID(simulations[choices[i]].getName(), simulations[choices[i]].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(simulations[choices[i]], (currentSimNameSimDataID == null ? 0 : currentSimNameSimDataID.getDefaultJobIndex())));
                    }
                }
            } catch (UserCancelException uce) {
            // ignore
            }
        }

        public void selectParamScanInfo() {
            String[][] rowData = new String[currentSimNameSimDataID.getExportParamScanInfo().getParamScanJobIndexes().length][currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames().length];
            for (int i = 0; i < rowData.length; i++) {
                for (int j = 0; j < rowData[i].length; j++) {
                    rowData[i][j] = currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantValues()[i][j];
                }
            }
            try {
                int[] choices = DialogUtils.showComponentOKCancelTableList(PDEExportDataPanel.this, "Choose ParameterScans to export together", currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames(), rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
                if (choices != null && choices.length > 0) {
                    selectedParamScanIndexes = new int[choices.length];
                    // String[][] selectedParamScanValues = new String[choices.length][currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames().length];
                    for (int i = 0; i < choices.length; i++) {
                        selectedParamScanIndexes[i] = choices[i];
                    // for (int j = 0; j < currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames().length; j++) {
                    // selectedParamScanValues[i][j] = currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantValues()[choices[i]][j];
                    // }
                    }
                // exportParamScanInfo =
                // new ExportSpecs.ExportParamScanInfo(selectedParamScanIndexes, selectedParamScanIndexes[0], currentSimNameSimDataID.getExportParamScanInfo().getParamScanConstantNames(), selectedParamScanValues);
                } else {
                    selectedParamScanIndexes = null;
                }
            } catch (UserCancelException uce) {
            // ignore
            }
        }

        public int[] getselectedParamScanIndexes() {
            return selectedParamScanIndexes;
        }

        public int getNumAvailableParamScans() {
            if (currentSimNameSimDataID == null || currentSimNameSimDataID.getExportParamScanInfo() == null) {
                return 0;
            }
            return currentSimNameSimDataID.getExportParamScanInfo().getParamScanJobIndexes().length;
        }

        public int getNumAvailableSimulations() {
            if (simulations == null) {
                VCDocument thisDocument = (getDataViewerManager() instanceof DocumentWindowManager ? ((DocumentWindowManager) getDataViewerManager()).getVCDocument() : null);
                if (thisDocument instanceof BioModel) {
                    String thisSimContextName = dataInfoProvider.getSimulationModelInfo().getContextName();
                    SimulationContext[] simContexts = ((BioModel) thisDocument).getSimulationContexts();
                    SimulationContext thisSimulationContext = null;
                    for (int i = 0; i < simContexts.length; i++) {
                        if (thisSimContextName.equals(thisDocument.getName() + "::" + simContexts[i].getName())) {
                            thisSimulationContext = simContexts[i];
                            break;
                        }
                    }
                    simulations = thisSimulationContext.getSimulations();
                } else if (thisDocument instanceof MathModel) {
                    simulations = ((MathModel) thisDocument).getSimulations();
                } else {
                    simulations = new Simulation[0];
                }
            }
            return simulations.length;
        }
    };
    return simulationSelector;
}

Example 2 with DocumentWindowManager

use of cbit.vcell.client.DocumentWindowManager in project vcell by virtualcell.

the class DocumentValidTask method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    if (documentWindowManager.getVCDocument() instanceof BioModel) {
        // try to successfully generate math and geometry region info
        BioModel bioModel = (BioModel) documentWindowManager.getVCDocument();
        SimulationContext[] scArray = bioModel.getSimulationContexts();
        if (scArray != null) {
            MathDescription[] mathDescArray = new MathDescription[scArray.length];
            for (int i = 0; i < scArray.length; i++) {
                // check if all structure sizes are specified
                scArray[i].checkValidity();
                // 
                // compute Geometric Regions if necessary
                // 
                cbit.vcell.geometry.surface.GeometrySurfaceDescription geoSurfaceDescription = scArray[i].getGeometry().getGeometrySurfaceDescription();
                if (geoSurfaceDescription != null && geoSurfaceDescription.getGeometricRegions() == null) {
                    cbit.vcell.geometry.surface.GeometrySurfaceUtils.updateGeometricRegions(geoSurfaceDescription);
                }
                if (scArray[i].getModel() != bioModel.getModel()) {
                    throw new Exception("The BioModel's physiology doesn't match that for Application '" + scArray[i].getName() + "'");
                }
                // 
                // create new MathDescription
                // 
                MathDescription math = scArray[i].createNewMathMapping().getMathDescription();
                // 
                // load MathDescription into SimulationContext
                // (BioModel is responsible for propagating this to all applicable Simulations).
                // 
                mathDescArray[i] = math;
            }
            hashTable.put("mathDescArray", mathDescArray);
        }
        // check issues for errors
        DocumentValidUtil.checkIssuesForErrors(bioModel);
    // Vector<Issue> issueList = new Vector<Issue>();
    // IssueContext issueContext = new IssueContext();
    // bioModel.gatherIssues(issueContext,issueList);
    // for (int i = 0; i < issueList.size(); i++){
    // Issue issue = issueList.elementAt(i);
    // if (issue.getSeverity() == Issue.SEVERITY_ERROR){
    // String errMsg = "Error: ";
    // Object issueSource = issue.getSource();
    // if (issueSource instanceof OutputFunctionIssueSource) {
    // SimulationOwner simulationOwner = ((OutputFunctionIssueSource)issueSource).getOutputFunctionContext().getSimulationOwner();
    // String funcName = ((OutputFunctionIssueSource)issueSource).getAnnotatedFunction().getDisplayName();
    // if (simulationOwner instanceof SimulationContext) {
    // String opErrMsg = "Output Function '" + funcName + "' in application '" + simulationOwner.getName() + "' ";
    // if (issue.getCategory().equals(IssueCategory.OUTPUTFUNCTIONCONTEXT_FUNCTION_EXPBINDING)) {
    // opErrMsg += "refers to an unknown variable. Either the model changed or this version of VCell generates variable names differently.\n\n";
    // }
    // errMsg += opErrMsg;
    // }
    // }
    // throw new Exception(errMsg + issue.getMessage());
    // }
    // }
    }
    if (documentWindowManager.getVCDocument() instanceof cbit.vcell.geometry.Geometry) {
        // try to successfully generate GeometricRegions if spatial and not present.
        cbit.vcell.geometry.Geometry geometry = (cbit.vcell.geometry.Geometry) documentWindowManager.getVCDocument();
        if (geometry.getGeometrySurfaceDescription() != null && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
            try {
                cbit.vcell.geometry.surface.GeometrySurfaceUtils.updateGeometricRegions(geometry.getGeometrySurfaceDescription());
            } catch (Exception e) {
                throw new Exception("Error determining regions in spatial geometry '" + geometry.getName() + "': \n" + e.getMessage());
            }
        }
    }
    if (documentWindowManager.getVCDocument() instanceof cbit.vcell.mathmodel.MathModel) {
        // try to successfully generate GeometricRegions if spatial and not present.
        cbit.vcell.mathmodel.MathModel mathModel = (cbit.vcell.mathmodel.MathModel) documentWindowManager.getVCDocument();
        cbit.vcell.geometry.Geometry geometry = mathModel.getMathDescription().getGeometry();
        if (geometry.getGeometrySurfaceDescription() != null && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
            try {
                cbit.vcell.geometry.surface.GeometrySurfaceUtils.updateGeometricRegions(geometry.getGeometrySurfaceDescription());
            } catch (Exception e) {
                throw new Exception("Error determining regions in spatial geometry '" + geometry.getName() + "': \n" + e.getMessage());
            }
        }
    }
}

Example 3 with DocumentWindowManager

use of cbit.vcell.client.DocumentWindowManager in project vcell by virtualcell.

the class NewName method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    VCDocument document = documentWindowManager.getVCDocument();
    if (document.getDocumentType() == VCDocumentType.MATHMODEL_DOC) {
        if (((MathModelWindowManager) documentWindowManager).hasUnappliedChanges()) {
            String msg = "Changes have been made in VCML Editor, please click \"Apply Changes\" or \"Cancel\" to proceed.";
            PopupGenerator.showErrorDialog(documentWindowManager, msg);
            throw UserCancelException.CANCEL_UNAPPLIED_CHANGES;
        }
    }
    MDIManager mdiManager = (MDIManager) hashTable.get("mdiManager");
    String oldName = document.getName();
    User user = mdiManager.getFocusedWindowManager().getRequestManager().getDocumentManager().getUser();
    DocumentManager documentManager = mdiManager.getFocusedWindowManager().getRequestManager().getDocumentManager();
    VCDocumentInfo[] vcDocumentInfos = new VCDocumentInfo[0];
    String documentTypeDescription = "unknown";
    if (document.getDocumentType() == VCDocumentType.MATHMODEL_DOC) {
        documentTypeDescription = "MathModel";
        vcDocumentInfos = documentManager.getMathModelInfos();
    } else if (document.getDocumentType() == VCDocumentType.BIOMODEL_DOC) {
        documentTypeDescription = "BioModel";
        vcDocumentInfos = documentManager.getBioModelInfos();
    } else if (document.getDocumentType() == VCDocumentType.GEOMETRY_DOC) {
        documentTypeDescription = "Geometry";
        vcDocumentInfos = documentManager.getGeometryInfos();
    }
    String newDocumentName = (oldName == null ? "New" + documentTypeDescription : oldName);
    while (true) {
        newDocumentName = mdiManager.getDatabaseWindowManager().showSaveDialog(document.getDocumentType(), (Component) hashTable.get("currentDocumentWindow"), newDocumentName);
        if (newDocumentName == null || newDocumentName.trim().length() == 0) {
            newDocumentName = null;
            DialogUtils.showWarningDialog((Component) hashTable.get("currentDocumentWindow"), "New " + documentTypeDescription + " name cannot be empty.");
            continue;
        }
        // Check name conflict
        boolean bNameConflict = false;
        for (int i = 0; i < vcDocumentInfos.length; i++) {
            if (vcDocumentInfos[i].getVersion().getOwner().compareEqual(user)) {
                if (vcDocumentInfos[i].getVersion().getName().equals(newDocumentName)) {
                    bNameConflict = true;
                    break;
                }
            }
        }
        if (bNameConflict) {
            DialogUtils.showWarningDialog((Component) hashTable.get("currentDocumentWindow"), "A " + documentTypeDescription + " with name '" + newDocumentName + "' already exists.  Choose a different name.");
            continue;
        } else {
            break;
        }
    }
    hashTable.put("newName", newDocumentName);
}

Example 4 with DocumentWindowManager

use of cbit.vcell.client.DocumentWindowManager in project vcell by virtualcell.

the class VCellClientTest method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    class ParseVCellUserEvents implements Runnable {

        AWTEvent event;

        public ParseVCellUserEvents(AWTEvent event) {
            this.event = event;
        }

        @Override
        public void run() {
            if (event instanceof MouseEvent) {
                MouseEvent mouseEvent = (MouseEvent) event;
                Object details = null;
                if (mouseEvent.getID() == MouseEvent.MOUSE_RELEASED) {
                    if (mouseEvent.getComponent() instanceof JTable) {
                        JTable comp = (JTable) mouseEvent.getComponent();
                        int[] selRows = comp.getSelectedRows();
                        if (selRows != null && selRows.length > 0) {
                            StringBuffer sb = new StringBuffer();
                            for (int i = 0; i < selRows.length; i++) {
                                for (int j = 0; j < comp.getColumnCount(); j++) {
                                    try {
                                        sb.append((j == 0 ? "" : ",") + comp.getColumnName(j) + "='" + comp.getModel().getValueAt(selRows[i], j) + "'");
                                    } catch (Exception e) {
                                        e.printStackTrace();
                                    }
                                }
                            }
                            details = sb.toString();
                        }
                    } else if (mouseEvent.getComponent() instanceof JTree) {
                        JTree comp = (JTree) mouseEvent.getComponent();
                        TreePath treePath = comp.getSelectionPath();
                        if (treePath != null) {
                            details = treePath.getLastPathComponent();
                            // BioModel, MathModel, Geometry document tree selections
                            if (details instanceof BioModelNode) {
                                // VCellBasicCellRenderer.VCDocumentInfoNode
                                BioModelNode bioModelNode = (BioModelNode) details;
                                boolean isVCDocumentInfo = bioModelNode.getUserObject() instanceof VCDocumentInfo;
                                boolean isBioModelsNetModelInfo = bioModelNode.getUserObject() instanceof BioModelsNetModelInfo;
                                if (!isVCDocumentInfo && bioModelNode.getChildCount() > 0 && bioModelNode.getUserObject() instanceof VCellBasicCellRenderer.VCDocumentInfoNode) {
                                    TreeNode treeNode = bioModelNode.getFirstChild();
                                    if (treeNode instanceof BioModelNode && ((BioModelNode) treeNode).getUserObject() instanceof VCDocumentInfo) {
                                        details = ((BioModelNode) treeNode).getUserObject();
                                    }
                                } else if (isBioModelsNetModelInfo) {
                                    details = BioModelsNetModelInfo.class.getSimpleName() + " '" + ((BioModelsNetModelInfo) bioModelNode.getUserObject()).getName() + "'";
                                }
                            }
                        }
                    } else if (mouseEvent.getComponent() instanceof JTabbedPane) {
                        JTabbedPane comp = (JTabbedPane) mouseEvent.getComponent();
                        details = "'" + comp.getTitleAt(comp.getSelectedIndex()) + "'";
                    } else if (mouseEvent.getComponent() instanceof JMenuItem) {
                        JMenuItem comp = (JMenuItem) mouseEvent.getComponent();
                        details = "'" + comp.getText() + "'";
                    } else if (mouseEvent.getComponent() instanceof AbstractButton) {
                        AbstractButton comp = (AbstractButton) mouseEvent.getComponent();
                        Boolean bSelected = (comp instanceof JToggleButton ? ((JToggleButton) comp).isSelected() : null);
                        details = (bSelected != null ? "(" + (bSelected ? "selected" : "unselected") + ")" : "") + "'" + comp.getText() + "'";
                    } else if (mouseEvent.getComponent() instanceof JComboBox<?>) {
                        JComboBox<?> comp = (JComboBox<?>) mouseEvent.getComponent();
                        details = "'" + comp.getSelectedItem().toString() + "'";
                    } else if (mouseEvent.getComponent() instanceof JList<?>) {
                        JList<?> comp = (JList<?>) mouseEvent.getComponent();
                        details = "'" + comp.getSelectedValue() + "'";
                    } else {
                        details = "TBD " + mouseEvent.getComponent();
                    }
                    Component parentComponent = mouseEvent.getComponent();
                    StringBuffer parentInfo = new StringBuffer();
                    SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US);
                    do {
                        String title = "";
                        if (parentComponent instanceof Dialog) {
                            title = ((Dialog) parentComponent).getTitle();
                        } else if (parentComponent instanceof Frame) {
                            title = ((Frame) parentComponent).getTitle();
                        }
                        parentInfo.append(parentComponent.getClass().getTypeName() + "(" + parentComponent.getName() + (title != null && title.length() > 0 ? ",title='" + title + "'" : "") + ")");
                        if (parentComponent instanceof DocumentWindow && ((DocumentWindow) parentComponent).getTopLevelWindowManager() instanceof DocumentWindowManager) {
                            VCDocument vcDocument = ((DocumentWindowManager) ((DocumentWindow) parentComponent).getTopLevelWindowManager()).getVCDocument();
                            if (vcDocument != null) {
                                String date = (vcDocument.getVersion() != null && vcDocument.getVersion().getDate() != null ? simpleDateFormat.format(vcDocument.getVersion().getDate()) : "nodate");
                                parentInfo.append("doc=" + vcDocument.getDocumentType() + " '" + vcDocument.getName() + "' " + date);
                            }
                        }
                        parentInfo.append(" -> ");
                    } while ((parentComponent = parentComponent.getParent()) != null);
                    // try to add event, if full remove an event from the top
                    while (!recordedUserEvents.offer(mouseEvent.getClickCount() + " " + (details == null ? "null" : details.toString()) + BeanUtils.PLAINTEXT_EMAIL_NEWLINE + parentInfo.toString())) {
                        recordedUserEvents.poll();
                    }
                }
            }
        }
    }
    ;
    AWTEventListener awtEventListener = new AWTEventListener() {

        @Override
        public void eventDispatched(final AWTEvent event) {
            if (event instanceof MouseEvent) {
                if (((MouseEvent) event).getID() == MouseEvent.MOUSE_RELEASED) {
                    new Thread(new ParseVCellUserEvents(event)).start();
                }
            }
        }
    };
    Toolkit.getDefaultToolkit().addAWTEventListener(awtEventListener, AWTEvent.MOUSE_EVENT_MASK);
    // check synchronize Proxy prefs, Proxy Properties
    Preferences prefs = Preferences.userNodeForPackage(RemoteProxyVCellConnectionFactory.class);
    Boolean bHttp = (System.getProperty(NetworkProxyUtils.PROXY_HTTP_HOST) == null && System.getProperty(NetworkProxyUtils.PROXY_SOCKS_HOST) == null ? null : System.getProperty(NetworkProxyUtils.PROXY_HTTP_HOST) != null);
    String currentProxyHost = (bHttp == null ? null : (bHttp ? System.getProperty(NetworkProxyUtils.PROXY_HTTP_HOST) : System.getProperty(NetworkProxyUtils.PROXY_SOCKS_HOST)));
    String currentProxyPort = (bHttp == null ? null : (bHttp ? System.getProperty(NetworkProxyUtils.PROXY_HTTP_PORT) : System.getProperty(NetworkProxyUtils.PROXY_SOCKS_PORT)));
    NetworkProxyUtils.setProxyProperties(false, null, prefs.get(NetworkProxyPreferences.prefProxyType, NetworkProxyPreferences.prefProxyType), currentProxyHost, currentProxyPort, prefs.get(NetworkProxyPreferences.prefProxyType, NetworkProxyPreferences.prefProxyType), prefs.get(NetworkProxyPreferences.prefProxyHost, NetworkProxyPreferences.prefProxyHost), prefs.get(NetworkProxyPreferences.prefProxyPort, NetworkProxyPreferences.prefProxyPort));
    final boolean IS_DEBUG = ManagementFactory.getRuntimeMXBean().getInputArguments().toString().indexOf("-agentlib:jdwp") > 0;
    if (!IS_DEBUG) {
        String siteName = VCellSoftwareVersion.fromSystemProperty().getSite().name().toLowerCase();
        ConsoleCapture.getInstance().captureStandardOutAndError(new File(ResourceUtil.getLogDir(), "vcellrun_" + siteName + ".log"));
    }
    Logging.init();
    ErrorUtils.setDebug(IS_DEBUG);
    if (args != null && args.length >= 1 && args[0].equals("-console")) {
        // remove install4j parameter
        List<String> newArgs = new ArrayList<String>();
        newArgs.addAll(Arrays.asList(args));
        newArgs.remove(0);
        args = newArgs.toArray(new String[0]);
    }
    StringBuffer stringBuffer = new StringBuffer();
    for (int i = 0; i < args.length; i++) {
        stringBuffer.append("arg" + i + "=\"" + args[i] + "\" ");
    }
    System.out.println("starting with arguments [" + stringBuffer + "]");
    System.out.println("Running under Java major version: ONE point " + ResourceUtil.getJavaVersion().toString() + ".  Specifically: Java " + (System.getProperty("java.version")) + ", published by " + (System.getProperty("java.vendor")) + ", on the " + (System.getProperty("os.arch")) + " architecture running version " + (System.getProperty("os.version")) + " of the " + (System.getProperty("os.name")) + " operating system");
    ClientServerInfo csInfo = null;
    String hoststr = System.getProperty(PropertyLoader.vcellServerHost);
    String[] hosts = null;
    if (hoststr != null) {
        StringTokenizer st = new StringTokenizer(hoststr, " ,;");
        if (st.countTokens() >= 1) {
            hosts = new String[st.countTokens()];
            int count = 0;
            while (st.hasMoreTokens()) {
                hosts[count++] = st.nextToken();
            }
        }
    }
    if (hosts == null) {
        hosts = new String[1];
    }
    String user = null;
    String password = null;
    VCDocument initialDocument = null;
    if (args.length == 3) {
        hosts[0] = args[0];
        user = args[1];
        password = args[2];
    } else if (args.length == 0) {
    // this is ok
    } else if (args.length == 1) {
        // Check if arg is drag-n-drop file or a 'hostname'
        try {
            // drag and drop file on install4j VCell launcher will pass filepath as single arg to VCell
            File openThisVCellFile = new File(args[0]);
            if (openThisVCellFile.exists() && openThisVCellFile.isFile()) {
                initialDocument = startupWithOpen(args[0]);
            }
        } catch (Exception e) {
            e.printStackTrace();
        // continue to hostname check
        }
        // If startup file not exist assume arg is a hostname
        if (initialDocument == null) {
            hosts[0] = args[0];
        }
    // If install4j drag-n-drop, hosts[0] stays null and host is assumed to be loaded from a client property
    } else if (args.length == 2 && args[0].equals("-open")) {
        // hosts[0] = "-local";
        initialDocument = startupWithOpen(args[1]);
    } else {
        System.out.println("usage: VCellClientTest ( ((-local|host[:port]) [userid password]) | ([-open] filename) )");
        System.exit(1);
    }
    if (hosts[0] != null && hosts[0].equalsIgnoreCase("-local")) {
        csInfo = ClientServerInfo.createLocalServerInfo(user, (password == null || password.length() == 0 ? null : new UserLoginInfo.DigestedPassword(password)));
    } else {
        String[] hostParts = hosts[0].split(":");
        String apihost = hostParts[0];
        int apiport = Integer.parseInt(hostParts[1]);
        csInfo = ClientServerInfo.createRemoteServerInfo(apihost, apiport, user, (password == null || password.length() == 0 ? null : new UserLoginInfo.DigestedPassword(password)));
    }
    try {
        String propertyFile = PropertyLoader.getProperty(PropertyLoader.propertyFileProperty, "");
        if (propertyFile.length() > 0) {
            PropertyLoader.loadProperties(ArrayUtils.addAll(REQUIRED_CLIENT_PROPERTIES, REQUIRED_LOCAL_PROPERTIES));
            try {
                VCMongoMessage.enabled = true;
                VCMongoMessage.serviceStartup(ServiceName.client, null, null);
                PropertyLoader.sendErrorsToMongo();
            } catch (Exception e) {
                System.out.println("failed to start Mongo logging");
            }
        } else {
            PropertyLoader.loadProperties(REQUIRED_CLIENT_PROPERTIES);
            VCMongoMessage.enabled = false;
        }
        // call in main thread, since it's quick and not necessarily thread safe
        ResourceUtil.setNativeLibraryDirectory();
        vcellClient = VCellClient.startClient(initialDocument, csInfo);
        VCellClientDataService vcellClientDataService = new VCellClientDataServiceImpl(vcellClient);
        VCellProxyServer.startVCellVisitDataServerThread(vcellClientDataService);
        // starting loading libraries
        new LibraryLoaderThread(true).start();
        try {
            PythonSupport.verifyInstallation(PythonPackage.values());
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    // SimulationService.Iface simService = new SimulationServiceImpl();
    // VCellIJServer.startVCellVisitDataServerThread(simService, false);
    } catch (Throwable exception) {
        ErrorUtils.sendRemoteLogMessage(csInfo.getUserLoginInfo(), csInfo.toString() + "\nvcell startup failed\n\n" + exception.getMessage());
        JOptionPane.showMessageDialog(null, exception.getMessage(), "Fatal Error", JOptionPane.OK_OPTION);
        System.err.println("Exception occurred in main() of VCellApplication");
        exception.printStackTrace(System.out);
    }
}

Example 5 with DocumentWindowManager

use of cbit.vcell.client.DocumentWindowManager in project vcell by virtualcell.

the class DocumentWindow method showViewJobsDialog.

public void showViewJobsDialog() {
    System.out.println("ViewJobs menu item pressed.");
    // https://vcellapi.cam.uchc.edu:8080/simtask?submitLow=&submitHigh=&startRow=1&maxRows=100&serverId=&computeHost+value%3D=&simId=&jobId=&taskId=&hasData=all&queued=on&dispatched=on&running=on
    DocumentWindowManager dwm = getWindowManager();
    ViewJobsPanel panel = new ViewJobsPanel(dwm);
    panel.setPreferredSize(new Dimension(1000, 600));
    if (viewSpeciesDialog != null) {
        // uncomment these 3 lines to allow only one instance of the dialog
        viewSpeciesDialog.dispose();
    }
    JOptionPane pane = new JOptionPane(panel, JOptionPane.PLAIN_MESSAGE, 0, null, new Object[] { "Close" });
    viewSpeciesDialog = pane.createDialog(this, "View Simulation Jobs Status");
    viewSpeciesDialog.setModal(false);
    viewSpeciesDialog.setResizable(true);
    viewSpeciesDialog.setVisible(true);
}