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

Example 16 with VCDocument

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

the class ExportDocument 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 {
    VCDocument documentToExport = (VCDocument) hashTable.get("documentToExport");
    File exportFile = fetch(hashTable, EXPORT_FILE, File.class, true);
    ExtensionFilter fileFilter = fetch(hashTable, FILE_FILTER, ExtensionFilter.class, true);
    DocumentManager documentManager = fetch(hashTable, DocumentManager.IDENT, DocumentManager.class, true);
    String resultString = null;
    FileCloseHelper closeThis = null;
    try {
        if (documentToExport instanceof BioModel) {
            if (!(fileFilter instanceof SelectorExtensionFilter)) {
                throw new Exception("Expecting fileFilter type " + SelectorExtensionFilter.class.getName() + " but got " + fileFilter.getClass().getName());
            }
            BioModel bioModel = (BioModel) documentToExport;
            SimulationContext chosenSimContext = fetch(hashTable, SIM_CONTEXT, SimulationContext.class, false);
            ((SelectorExtensionFilter) fileFilter).writeBioModel(documentManager, bioModel, exportFile, chosenSimContext);
        /*		DELETE this after finishing validation testing
			
			// check format requested
			if (fileFilter.getDescription().equals(FileFilters.FILE_FILTER_MATLABV6.getDescription())){
				// matlab from application; get application
		
				SimulationContext chosenSimContext = fetch(hashTable,SIM_CONTEXT,SimulationContext.class, true);
				// regenerate a fresh MathDescription
				MathMapping mathMapping = chosenSimContext.createNewMathMapping();
				MathDescription mathDesc = mathMapping.getMathDescription();
				if(mathDesc != null && !mathDesc.isSpatial() && !mathDesc.isNonSpatialStoch()){
					// do export
					resultString = exportMatlab(exportFile, fileFilter, mathDesc);
				}else{
					throw new Exception("Matlab export failed: NOT an non-spatial deterministic application!");
				}
			} else if (fileFilter.equals(FileFilters.FILE_FILTER_PDF)) {   
				FileOutputStream fos = null;
				try {
					fos = new FileOutputStream(exportFile);
					documentManager.generatePDF(bioModel, fos);				
				} finally {
					if(fos != null) {
						fos.close();					
					}
				}
				return; 									//will take care of writing to the file as well.
			}
			//Export a simulation to Smoldyn input file, if there are parameter scans
			//in simulation, we'll export multiple Smoldyn input files.
			else if (fileFilter.equals(FileFilters.FILE_FILTER_SMOLDYN_INPUT)) 
			{ 
				Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
				if (selectedSim != null) {
					int scanCount = selectedSim.getScanCount();
					if(scanCount > 1) // has parameter scan
					{
						String baseExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf("."));
						for(int i=0; i<scanCount; i++)
						{
							SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, i, null),0);
							// Need to export each parameter scan into a separate file
							String newExportFileName = baseExportFileName + "_" + i + SMOLDYN_INPUT_FILE_EXTENSION;
							exportFile = new File(newExportFileName);
							
							PrintWriter pw = new PrintWriter(exportFile);
							SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
							smf.write();
							pw.close();	
						}
					}
					else if(scanCount == 1)// regular simulation, no parameter scan
					{
						SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null),0);
						// export the simulation to the selected file
						PrintWriter pw = new PrintWriter(exportFile);
						SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
						smf.write();
						pw.close();
					}
					else
					{
						throw new Exception("Simulation scan count is smaller than 1.");
					}
				}
				return;
													
			} else {
				// convert it if other format
				if (!fileFilter.equals(FileFilters.FILE_FILTER_VCML)) {
					// SBML or CellML; get application name
					if ((fileFilter.equals(FileFilters.FILE_FILTER_SBML_12)) || (fileFilter.equals(FileFilters.FILE_FILTER_SBML_21)) || 
						(fileFilter.equals(FileFilters.FILE_FILTER_SBML_22)) || (fileFilter.equals(FileFilters.FILE_FILTER_SBML_23)) || 
						(fileFilter.equals(FileFilters.FILE_FILTER_SBML_24)) || (fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_CORE)) || 
						(fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL)) ) {
						SimulationContext selectedSimContext = (SimulationContext)hashTable.get("selectedSimContext");
						Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
						int sbmlLevel = 0;
						int sbmlVersion = 0;
						int sbmlPkgVersion = 0;
						boolean bIsSpatial = false;
						if ((fileFilter.equals(FileFilters.FILE_FILTER_SBML_12))) {
							sbmlLevel = 1;
							sbmlVersion = 2;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_21)) {
							sbmlLevel = 2;
							sbmlVersion = 1;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_22)) {
							sbmlLevel = 2;
							sbmlVersion = 2;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_23)) {
							sbmlLevel = 2;
							sbmlVersion = 3;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_24)) {
							sbmlLevel = 2;
							sbmlVersion = 4;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_CORE)) {
							sbmlLevel = 3;
							sbmlVersion = 1;
						} else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL)) {
							sbmlLevel = 3;
							sbmlVersion = 1;
							sbmlPkgVersion = 1;
							bIsSpatial = true;
						}
						if (selectedSim == null) {
							resultString = XmlHelper.exportSBML(bioModel, sbmlLevel, sbmlVersion, sbmlPkgVersion, bIsSpatial, selectedSimContext, null);
							XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
							return;
						} else {
							for (int sc = 0; sc < selectedSim.getScanCount(); sc++) {
								SimulationJob simJob = new SimulationJob(selectedSim, sc, null);
								resultString = XmlHelper.exportSBML(bioModel, sbmlLevel, sbmlVersion, sbmlPkgVersion, bIsSpatial, selectedSimContext, simJob);
								// Need to export each parameter scan into a separate file 
								String newExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf(".xml")) + "_" + sc + ".xml";
								exportFile.renameTo(new File(newExportFileName));
								XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
							}
							return;
						}
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_BNGL)) {
						RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
						StringWriter bnglStringWriter = new StringWriter();
						PrintWriter pw = new PrintWriter(bnglStringWriter);
						RbmNetworkGenerator.writeBngl(bioModel, pw);
						resultString = bnglStringWriter.toString();
						pw.close();
						
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_NFSIM)) {
						// TODO: get the first thing we find for now, in the future we'll need to modify ChooseFile 
						//       to only offer the applications / simulations with bngl content
						SimulationContext simContexts[] = bioModel.getSimulationContexts();
						SimulationContext aSimulationContext = simContexts[0];
						Simulation selectedSim = aSimulationContext.getSimulations(0);
						//Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
						SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null),0);
						long randomSeed = 0;	// a fixed seed will allow us to run reproducible simulations
						//long randomSeed = System.currentTimeMillis();
						NFsimSimulationOptions nfsimSimulationOptions = new NFsimSimulationOptions();
						// we get the data we need from the math description
						Element root = NFsimXMLWriter.writeNFsimXML(simTask, randomSeed, nfsimSimulationOptions);
						Document doc = new Document();
						doc.setRootElement(root);
						XMLOutputter xmlOut = new XMLOutputter();
						resultString = xmlOut.outputString(doc);
	
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_CELLML)) {
						Integer chosenSimContextIndex = (Integer)hashTable.get("chosenSimContextIndex");
						String applicationName = bioModel.getSimulationContext(chosenSimContextIndex.intValue()).getName();
						resultString = XmlHelper.exportCellML(bioModel, applicationName);
						// cellml still uses default character encoding for now ... maybe UTF-8 in the future
					} else if (fileFilter.equals(FileFilters.FILE_FILTER_SEDML)) {
						// export the entire biomodel to a SEDML file (for now, only non-spatial,non-stochastic applns)
						int sedmlLevel = 1;
						int sedmlVersion = 1;
						String sPath = FileUtils.getFullPathNoEndSeparator(exportFile.getAbsolutePath());
						String sFile = FileUtils.getBaseName(exportFile.getAbsolutePath());
						String sExt = FileUtils.getExtension(exportFile.getAbsolutePath());
						
						SEDMLExporter sedmlExporter = null;
						if (bioModel instanceof BioModel) {
							sedmlExporter = new SEDMLExporter(bioModel, sedmlLevel, sedmlVersion);
							resultString = sedmlExporter.getSEDMLFile(sPath);
						} else {
							throw new RuntimeException("unsupported Document Type " + bioModel.getClass().getName() + " for SedML export");
						}
						if(sExt.equals("sedx")) {
							sedmlExporter.createManifest(sPath, sFile);
							String sedmlFileName = sPath + FileUtils.WINDOWS_SEPARATOR + sFile + ".sedml";
							XmlUtil.writeXMLStringToFile(resultString, sedmlFileName, true);
							sedmlExporter.addSedmlFileToList(sFile + ".sedml");
							sedmlExporter.addSedmlFileToList("manifest.xml");
							sedmlExporter.createZipArchive(sPath, sFile);
							return;
						} else {
							XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
						}
					}
				} else {
					// if format is VCML, get it from biomodel.
					bioModel.getVCMetaData().cleanupMetadata();
					resultString = XmlHelper.bioModelToXML(bioModel);
					XmlUtil.writeXMLStringToFile(resultString, exportFile.getAbsolutePath(), true);
					return;
				}
			}*/
        } else if (documentToExport instanceof MathModel) {
            MathModel mathModel = (MathModel) documentToExport;
            // check format requested
            if (fileFilter.equals(FileFilters.FILE_FILTER_MATLABV6)) {
                // check if it's ODE
                if (mathModel.getMathDescription() != null && (!mathModel.getMathDescription().isSpatial() && !mathModel.getMathDescription().isNonSpatialStoch())) {
                    MathDescription mathDesc = mathModel.getMathDescription();
                    resultString = exportMatlab(exportFile, fileFilter, mathDesc);
                } else {
                    throw new Exception("Matlab export failed: NOT an non-spatial deterministic model.");
                }
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_PDF)) {
                FileOutputStream fos = new FileOutputStream(exportFile);
                documentManager.generatePDF(mathModel, fos);
                fos.close();
                // will take care of writing to the file as well.
                return;
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_VCML)) {
                resultString = XmlHelper.mathModelToXML(mathModel);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_CELLML)) {
                resultString = XmlHelper.exportCellML(mathModel, null);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_23)) {
                resultString = XmlHelper.exportSBML(mathModel, 2, 3, 0, false, null, null);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_SBML_24)) {
                resultString = XmlHelper.exportSBML(mathModel, 2, 4, 0, false, null, null);
            } else // in simulation, we'll export multiple Smoldyn input files.
            if (fileFilter.equals(FileFilters.FILE_FILTER_SMOLDYN_INPUT)) {
                Simulation selectedSim = (Simulation) hashTable.get("selectedSimulation");
                if (selectedSim != null) {
                    int scanCount = selectedSim.getScanCount();
                    // -----
                    String baseExportFileName = (scanCount == 1 ? null : exportFile.getPath().substring(0, exportFile.getPath().indexOf(".")));
                    for (int i = 0; i < scanCount; i++) {
                        SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, i, null), 0);
                        // Need to export each parameter scan into a separate file
                        File localExportFile = (scanCount == 1 ? exportFile : new File(baseExportFileName + "_" + i + SMOLDYN_INPUT_FILE_EXTENSION));
                        FileCloseHelper localCloseThis = new FileCloseHelper(localExportFile);
                        try {
                            SmoldynFileWriter smf = new SmoldynFileWriter(localCloseThis.getPrintWriter(), true, null, simTask, false);
                            smf.write();
                        } finally {
                            if (localCloseThis != null) {
                                localCloseThis.close();
                            }
                        }
                    }
                }
                return;
            }
        } else if (documentToExport instanceof Geometry) {
            Geometry geom = (Geometry) documentToExport;
            if (fileFilter.equals(FileFilters.FILE_FILTER_PDF)) {
                documentManager.generatePDF(geom, (closeThis = new FileCloseHelper(exportFile)).getFileOutputStream());
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_VCML)) {
                resultString = XmlHelper.geometryToXML(geom);
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_AVS)) {
                cbit.vcell.export.AVS_UCD_Exporter.writeUCDGeometryOnly(geom.getGeometrySurfaceDescription(), (closeThis = new FileCloseHelper(exportFile)).getFileWriter());
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_STL)) {
                // make sure filename end with .stl
                File stlFile = exportFile;
                if (!exportFile.getName().toLowerCase().endsWith(".stl")) {
                    stlFile = new File(exportFile.getParentFile(), exportFile.getName() + ".stl");
                }
                cbit.vcell.geometry.surface.StlExporter.writeBinaryStl(geom.getGeometrySurfaceDescription(), (closeThis = new FileCloseHelper(stlFile)).getRandomAccessFile("rw"));
            } else if (fileFilter.equals(FileFilters.FILE_FILTER_PLY)) {
                writeStanfordPolygon(geom.getGeometrySurfaceDescription(), (closeThis = new FileCloseHelper(exportFile)).getFileWriter());
            }
        }
        if (resultString != null) {
            (closeThis = new FileCloseHelper(exportFile)).getFileWriter().write(resultString);
        }
    } finally {
        if (closeThis != null) {
            closeThis.close();
        }
    }
}

Example 17 with VCDocument

use of org.vcell.util.document.VCDocument 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 18 with VCDocument

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

the class VCellClientTest method startupWithOpen.

private static VCDocument startupWithOpen(String fileName) {
    VCDocument initialDocument = null;
    try {
        Document xmlDoc = XmlUtil.readXML(new File(fileName));
        String vcmlString = XmlUtil.xmlToString(xmlDoc, false);
        java.awt.Component parent = null;
        VCLogger vcLogger = new TranslationLogger(parent);
        initialDocument = XmlHelper.XMLToDocument(vcLogger, vcmlString);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        JOptionPane.showMessageDialog(null, e.getMessage(), "vcell startup error", JOptionPane.ERROR_MESSAGE);
    }
    return initialDocument;
}

Example 19 with VCDocument

use of org.vcell.util.document.VCDocument 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 20 with VCDocument

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

the class VCellClient method startClient.

/**
 * Insert the method's description here.
 * Creation date: (5/5/2004 3:51:06 PM)
 * @param bioModel cbit.vcell.biomodel.BioModel
 */
public static VCellClient startClient(final VCDocument startupDoc, final ClientServerInfo clientServerInfo) {
    /* Set Look and Feel */
    VCellLookAndFeel.setVCellLookAndFeel();
    // instantiate app
    final VCellClient vcellClient = new VCellClient();
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    AsynchClientTask task1 = new AsynchClientTask("Starting Virtual Cell", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // start management layer
            InteractiveContextDefaultProvider defaultRequester = new VCellGuiInteractiveContextDefaultProvider();
            vcellClient.setClientServerManager(new ClientServerManager(clientServerInfo, defaultRequester));
            vcellClient.setRequestManager(new ClientRequestManager(vcellClient));
            vcellClient.setMdiManager(new ClientMDIManager(vcellClient.getRequestManager()));
            // start auxilliary stuff
            vcellClient.startStatusThreads();
            // make sure we have at least a blank document to start with
            if (startupDoc != null) {
                hashTable.put("startupDoc", startupDoc);
            } else {
                VCDocument newStartupDoc = ((ClientRequestManager) vcellClient.getRequestManager()).createDefaultDocument(VCDocumentType.BIOMODEL_DOC);
                hashTable.put("startupDoc", newStartupDoc);
            }
            DocumentWindowAboutBox.parseVCellVersion();
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Creating GUI", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // fire up the GUI
            VCDocument startupDoc = (VCDocument) hashTable.get("startupDoc");
            // needs to be set first, else throw away dirty/needs paint information stored in previous instance.
            RepaintManager.setCurrentManager(new VCellClient.CheckThreadViolationRepaintManager());
            DocumentWindowManager currWindowManager = vcellClient.createAndShowGUI(startupDoc);
            if (currWindowManager != null) {
                hashTable.put("currWindowManager", currWindowManager);
            }
            if (clientServerInfo.getUsername() == null) {
                // we were not supplied login credentials; pop-up dialog
                VCellClient.login(vcellClient.getRequestManager(), clientServerInfo, currWindowManager);
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("Connecting to Server", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // try server connection
            if (clientServerInfo.getUsername() != null) {
                DocumentWindowManager currWindowManager = (DocumentWindowManager) hashTable.get("currWindowManager");
                // we were not supplied login credentials; pop-up dialog
                vcellClient.getRequestManager().connectToServer(currWindowManager, clientServerInfo);
            }
        }
    };
    AsynchClientTask[] taskArray = new AsynchClientTask[] { task1, task2, task3 };
    ClientTaskDispatcher.dispatch(null, hash, taskArray);
    return vcellClient;
}