Examples with VCDocumentInfo org.vcell.util.document.VCDocumentInfo used on opensource projects

Example 6 with VCDocumentInfo

use of org.vcell.util.document.VCDocumentInfo in project vcell by virtualcell.

the class ClientDocumentManager method curate.

/**
 * Insert the method's description here.
 * Creation date: (5/23/2006 9:23:34 AM)
 */
public void curate(CurateSpec curateSpec) throws DataAccessException {
    try {
        VCDocumentInfo newVCDocumentInfo = getSessionManager().getUserMetaDbServer().curate(curateSpec);
        xmlHash.remove(curateSpec.getVCDocumentInfo().getVersion().getVersionKey());
        if (curateSpec.getVCDocumentInfo() instanceof MathModelInfo) {
            mathModelInfoHash.remove(curateSpec.getVCDocumentInfo().getVersion().getVersionKey());
            mathModelInfoHash.put(newVCDocumentInfo.getVersion().getVersionKey(), (MathModelInfo) newVCDocumentInfo);
        } else if (curateSpec.getVCDocumentInfo() instanceof BioModelInfo) {
            bioModelInfoHash.remove(curateSpec.getVCDocumentInfo().getVersion().getVersionKey());
            bioModelInfoHash.put(newVCDocumentInfo.getVersion().getVersionKey(), (BioModelInfo) newVCDocumentInfo);
        }
        fireDatabaseUpdate(new DatabaseEvent(this, DatabaseEvent.UPDATE, curateSpec.getVCDocumentInfo(), newVCDocumentInfo));
    } catch (Exception e) {
        e.printStackTrace();
        throw new DataAccessException(e.getClass().getName() + " " + e.getMessage());
    }
}

Example 7 with VCDocumentInfo

use of org.vcell.util.document.VCDocumentInfo 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 8 with VCDocumentInfo

use of org.vcell.util.document.VCDocumentInfo 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 9 with VCDocumentInfo

use of org.vcell.util.document.VCDocumentInfo in project vcell by virtualcell.

the class VCDocumentDbTreeModel method initOwners.

protected static synchronized TreeMap<String, BioModelNode> initOwners(VCDocumentInfo[] vcDocumentInfos, User loginUser, VCDocumentDbTreeModel subTreeParent, Method subTreeMethod) {
    // 
    // get list of users (owners)
    // 
    Vector<User> userList = new Vector<User>();
    userList.addElement(loginUser);
    for (int i = 0; i < vcDocumentInfos.length; i++) {
        VCDocumentInfo vcDocumentInfo = vcDocumentInfos[i];
        if (!userList.contains(vcDocumentInfo.getVersion().getOwner())) {
            userList.addElement(vcDocumentInfo.getVersion().getOwner());
        }
    }
    // 
    // for each user
    // 
    TreeMap<String, BioModelNode> treeMap = new TreeMap<String, BioModelNode>(new Comparator<String>() {

        public int compare(String o1, String o2) {
            return o1.compareToIgnoreCase(o2);
        }
    });
    for (int ownerIndex = 0; ownerIndex < userList.size(); ownerIndex++) {
        User owner = (User) userList.elementAt(ownerIndex);
        BioModelNode ownerNode = null;
        try {
            if (vcDocumentInfos instanceof BioModelInfo[]) {
                ownerNode = (BioModelNode) subTreeMethod.invoke(subTreeParent, new Object[] { owner, (BioModelInfo[]) vcDocumentInfos });
            } else if (vcDocumentInfos instanceof MathModelInfo[]) {
                ownerNode = (BioModelNode) subTreeMethod.invoke(subTreeParent, new Object[] { owner, (MathModelInfo[]) vcDocumentInfos });
            } else if (vcDocumentInfos instanceof GeometryInfo[]) {
                ownerNode = (BioModelNode) subTreeMethod.invoke(subTreeParent, new Object[] { owner, (GeometryInfo[]) vcDocumentInfos });
            } else {
                throw new Exception("Unimplemented VCDocumentInfo type=" + vcDocumentInfos.getClass().getName());
            }
        } catch (Exception e) {
            ownerNode = new BioModelNode("Error" + e.getMessage());
        }
        if (owner.equals(loginUser) || ownerNode.getChildCount() > 0) {
            treeMap.put(owner.getName(), ownerNode);
        }
    }
    return treeMap;
}

Example 10 with VCDocumentInfo

use of org.vcell.util.document.VCDocumentInfo in project vcell by virtualcell.

the class DatabaseWindowPanel method currentDocumentInfo.

/**
 * Comment
 */
private void currentDocumentInfo() {
    VCDocumentInfo selectedDocInfo = null;
    switch(getJTabbedPane1().getSelectedIndex()) {
        case 0:
            {
                // VCDocumentType.BIOMODEL_DOC
                selectedDocInfo = (BioModelInfo) getBioModelDbTreePanel1().getSelectedVersionInfo();
                break;
            }
        case 1:
            {
                // VCDocumentType.MATHMODEL_DOC
                selectedDocInfo = (MathModelInfo) getMathModelDbTreePanel1().getSelectedVersionInfo();
                break;
            }
        case 2:
            {
                // VCDocumentType.GEOMETRY_DOC
                selectedDocInfo = (GeometryInfo) getGeometryTreePanel1().getSelectedVersionInfo();
                break;
            }
    }
    setSelectedDocumentInfo(selectedDocInfo);
}