Example 1 with SelectorExtensionFilter
use of org.vcell.util.gui.exporter.SelectorExtensionFilter in project vcell by virtualcell.
the class ChooseFile method showBioModelXMLFileChooser.
/**
* Insert the method's description here.
* Creation date: (5/31/2004 6:04:14 PM)
*/
private File showBioModelXMLFileChooser(Hashtable<String, Object> hashTable) throws java.lang.Exception {
BioModel bioModel = (BioModel) hashTable.get("documentToExport");
JFrame currentWindow = (JFrame) hashTable.get("currentWindow");
UserPreferences userPreferences = (UserPreferences) hashTable.get("userPreferences");
TopLevelWindowManager topLevelWindowManager = (TopLevelWindowManager) hashTable.get("topLevelWindowManager");
SelectorExtensionFilter forceFileFilter = null;
{
Object obj = hashTable.get(FORCE_FILE_FILTER);
if (obj != null) {
VCAssert.ofType(obj, SelectorExtensionFilter.class);
forceFileFilter = (SelectorExtensionFilter) obj;
VCAssert.assertTrue(forceFileFilter.supports(Selector.FULL_MODEL), "only " + Selector.FULL_MODEL + " filters supported for force file filter");
}
}
if (topLevelWindowManager == null) {
throw new RuntimeException("toplLevelWindowManager required");
}
File defaultPath = userPreferences.getCurrentDialogPath();
// JFileChooser fileChooser = new JFileChooser(defaultPath);
VCFileChooser fileChooser = new VCFileChooser(defaultPath);
fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
fileChooser.setMultiSelectionEnabled(false);
final SimulationContext[] simContexts = bioModel.getSimulationContexts();
boolean spatialDeterministicSim = false;
boolean nonspatialDeterministicSim = false;
boolean stochasticSim = false;
@SuppressWarnings("unused") boolean // add logic to set this
bnglSim = false;
for (SimulationContext sc : simContexts) {
if (sc.getApplicationType() == Application.NETWORK_STOCHASTIC) {
stochasticSim = true;
} else {
if (sc.getGeometry().getDimension() > 0) {
spatialDeterministicSim = true;
} else {
nonspatialDeterministicSim = true;
}
}
}
FileFilter defaultFileFilter;
if (forceFileFilter == null) {
List<FileFilter> dlist = FileFilters.supports(SelectorExtensionFilter.Selector.DEFAULT);
VCAssert.assertTrue(dlist.size() == 1, "Exactly one filter must be designated default");
defaultFileFilter = dlist.get(0);
// use a set to avoid duplicated entries; TreeSet show listing is alphabetical
Set<FileFilter> filters = new TreeSet<>();
filters.addAll(FileFilters.supports(SelectorExtensionFilter.Selector.FULL_MODEL));
if (spatialDeterministicSim) {
filters.addAll(FileFilters.supports(SelectorExtensionFilter.Selector.DETERMINISTIC, SelectorExtensionFilter.Selector.SPATIAL));
}
if (nonspatialDeterministicSim) {
filters.addAll(FileFilters.supports(SelectorExtensionFilter.Selector.DETERMINISTIC, SelectorExtensionFilter.Selector.NONSPATIAL));
}
if (stochasticSim) {
filters.addAll(FileFilters.supports(SelectorExtensionFilter.Selector.STOCHASTIC));
}
/*add BNGL selector here
if (bnglSim) {
filters.addAll(FileFilters.supports(SelectorExtensionFilter.Selector.BNGL));
}
*/
fileChooser.addChoosableFileFilter(defaultFileFilter);
for (FileFilter f : filters) {
if (f == defaultFileFilter) {
continue;
}
fileChooser.addChoosableFileFilter(f);
}
/*
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_12);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_21);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_22);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_23);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_24);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_31_CORE);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SBML_31_SPATIAL);
// fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_CELLML);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SEDML);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_VCML);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_MATLABV6);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_PDF);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SMOLDYN_INPUT);
*/
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_SEDML);
fileChooser.addChoosableFileFilter(FileFilters.FILE_FILTER_OMEX);
} else {
defaultFileFilter = forceFileFilter;
}
// remove all selectors
fileChooser.removeChoosableFileFilter(fileChooser.getAcceptAllFileFilter());
// Set the default file filter...
fileChooser.setFileFilter(defaultFileFilter);
fileChooser.setSelectedFile(new java.io.File(TokenMangler.fixTokenStrict(bioModel.getName())));
fileChooser.setDialogTitle("Export Virtual Cell BioModel As...");
if (fileChooser.showSaveDialog(currentWindow) != JFileChooser.APPROVE_OPTION) {
// user didn't choose save
throw UserCancelException.CANCEL_FILE_SELECTION;
}
File selectedFile = fileChooser.getSelectedFile();
FileFilter gfileFilter = fileChooser.getFileFilter();
VCAssert.ofType(gfileFilter, SelectorExtensionFilter.class);
// only ExtensionFilters should have been added;
SelectorExtensionFilter fileFilter = (SelectorExtensionFilter) gfileFilter;
if (selectedFile == null) {
// no file selected (no name given)
throw UserCancelException.CANCEL_FILE_SELECTION;
}
final File fileUserSpecified = selectedFile.getCanonicalFile();
// /
String selectedFileName = recordAndRemoveExtension(selectedFile.getPath());
if (extensionUserProvided != null && !extensionUserProvided.isEmpty() && !extensionUserProvided.startsWith(".")) {
extensionUserProvided = "." + extensionUserProvided;
}
if (fileFilter.isValidExtension(extensionUserProvided)) {
selectedFileName += extensionUserProvided;
} else {
selectedFileName += fileFilter.getPrimaryExtension();
}
selectedFile = new File(selectedFileName);
checkForOverwrites(selectedFile, topLevelWindowManager.getComponent(), userPreferences);
// put the filter in the hash so the export task knows what to do...
hashTable.put(FILE_FILTER, fileFilter);
if (fileFilter.supports(SelectorExtensionFilter.Selector.FULL_MODEL)) {
// nothing more to do in this case
resetPreferredFilePath(selectedFile, userPreferences);
return selectedFile;
}
// ArrayList<String> applicableAppNameList = new ArrayList<String>();
ArrayList<SimulationContext> applicableSimContexts = new ArrayList<>();
for (SimulationContext sc : simContexts) {
if (sc.getGeometry().getDimension() == 0) {
if (!fileFilter.supports(SelectorExtensionFilter.Selector.NONSPATIAL)) {
continue;
}
} else if (!fileFilter.supports(SelectorExtensionFilter.Selector.SPATIAL)) {
continue;
}
if (sc.getApplicationType() == Application.NETWORK_STOCHASTIC) {
if (!fileFilter.supports(SelectorExtensionFilter.Selector.STOCHASTIC)) {
continue;
}
} else if (!fileFilter.supports(SelectorExtensionFilter.Selector.DETERMINISTIC)) {
continue;
}
applicableSimContexts.add(sc);
}
/*
{} else {
// all apps
for (int i=0;i<simContexts.length;i++){
applicableAppNameList.add(simContexts[i].getName());
}
}
*/
final String exportDesc = fileFilter.getShortDescription();
List<SimulationContext> all = new ArrayList<>(Arrays.asList(simContexts));
all.removeAll(applicableSimContexts);
if (!all.isEmpty()) {
SimContextAdapter[] removed = adapt(all);
StringBuilder sb = new StringBuilder();
sb.append("The following applications are not supported by ");
sb.append(exportDesc);
sb.append(" and are not available for exporting: \n\n");
// sb.append(StringUtils.join(removed,", "));
for (SimulationContext sc : all) {
// sb.append(" " + sc.getName() + " ( " + sc.getApplicationType() + " ).\n");
int dim = sc.getGeometry().getDimension();
sb.append(" " + sc.getName() + " ( " + sc.getMathType() + ", " + (dim == 0 ? "Non-Spatial" : "Spatial") + " ).\n");
}
sb.append("\n");
sb.append("Press Ok to continue or Cancel to abort.\n");
String reply = DialogUtils.showOKCancelWarningDialog(currentWindow, "Verify Export", sb.toString());
if (!SimpleUserMessage.OPTION_OK.equals(reply)) {
throw UserCancelException.CANCEL_GENERIC;
}
}
SimulationContext chosenSimContext = null;
if (applicableSimContexts.size() == 1) {
chosenSimContext = applicableSimContexts.get(0);
} else /*
else if (!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_PDF.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_12.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_21.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_22.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_23.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_24.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_31_CORE.getDescription()) &&
!fileFilter.getDescription().equals(FileFilters.FILE_FILTER_SBML_31_SPATIAL.getDescription())) {
if(fileFilter.getDescription().equals(FileFilters.FILE_FILTER_BNGL.getDescription())) {
boolean hasReactions = bioModel.getModel().getReactionSteps().length > 0 ? true : false;
System.out.println(hasReactions);
if(hasReactions) { // mixed
String errMsg = "Simple Reactions cannot be exported to .bngl format.";
errMsg += "<br>Some information will be lost.";
errMsg += "<br><br>Continue anyway?";
errMsg = "<html>" + errMsg + "</html>";
int dialogButton = JOptionPane.YES_NO_OPTION;
int returnCode = JOptionPane.showConfirmDialog(topLevelWindowManager.getComponent(), errMsg, "Exporting to .bngl", dialogButton);
if (returnCode != JOptionPane.YES_OPTION) {
throw UserCancelException.CANCEL_FILE_SELECTION;
}
}
}
//String[] applicationNames = (String[])org.vcell.util.BeanUtils.getArray(applicableAppNameList,String.class);
} */
{
// String[] applicationNames = applicableAppNameList.toArray(new String[applicableAppNameList.size()]);
SimContextAdapter[] scarray = adapt(applicableSimContexts);
String message = "Multiple Applications are compatible with " + exportDesc + "\nPlease select one.\n";
Object choice = DialogUtils.showListDialog(topLevelWindowManager.getComponent(), scarray, "Application selection", null, message);
if (choice == null) {
throw UserCancelException.CANCEL_FILE_SELECTION;
}
VCAssert.ofType(choice, SimContextAdapter.class);
SimContextAdapter sca = (SimContextAdapter) choice;
chosenSimContext = sca.simCtx;
}
hashTable.put(SIM_CONTEXT, chosenSimContext);
// boolean isSbml = fileFilter.supports(SelectorExtensionFilter.Selector.SBML);
if (fileFilter.requiresMoreChoices()) {
ExtensionFilter.ChooseContext ctx = new ExtensionFilter.ChooseContext(hashTable, topLevelWindowManager, currentWindow, chosenSimContext, selectedFile, selectedFileName);
fileFilter.askUser(ctx);
}
{
boolean showConfirm = false;
if (fileFilter instanceof SbmlExtensionFilter) {
SbmlExtensionFilter sbmlef = (SbmlExtensionFilter) fileFilter;
if (sbmlef.isExportingOverrides()) {
showConfirm = true;
}
}
if (applicableSimContexts.size() > 1) {
showConfirm = true;
}
// showConfirm = someContextsFiltered;
if (!showConfirm) {
final File fileAfterProcessing = selectedFile.getCanonicalFile();
if (!fileAfterProcessing.equals(fileUserSpecified)) {
final String nameUserSpecified = fileUserSpecified.getCanonicalPath();
final String nameAfterProcessing = fileAfterProcessing.getCanonicalPath();
if (FilenameUtils.indexOfExtension(nameUserSpecified) > 0) {
// have extension on user path
showConfirm = true;
} else {
// don't prompt if user left extension off
String nameAfterNoExtension = FilenameUtils.getFullPath(nameAfterProcessing) + FilenameUtils.getBaseName(nameAfterProcessing);
if (!nameAfterNoExtension.equals(nameUserSpecified)) {
showConfirm = true;
}
}
}
}
if (showConfirm) {
// final String exportDesc = fileFilter.getShortDescription();
StringBuilder sb = new StringBuilder();
SimContextAdapter[] included = adapt(applicableSimContexts);
if (fileFilter instanceof SbmlExtensionFilter) {
SbmlExtensionFilter sbmlef = (SbmlExtensionFilter) fileFilter;
if (sbmlef.isExportingOverrides()) {
String overrideSimName = sbmlef.getSimulationOverrideName();
sb.append("Export model from application '" + chosenSimContext.getName() + "', simulation '" + overrideSimName + "' (with overrides) ");
} else {
sb.append("Export model from application '" + chosenSimContext.getName() + "' (default values) ");
}
} else {
sb.append("Export model with simulations ");
sb.append(StringUtils.join(included, ", "));
}
sb.append(" to file of type ");
sb.append(exportDesc);
sb.append(' ');
sb.append(selectedFile.getCanonicalPath());
sb.append('?');
String reply = DialogUtils.showOKCancelWarningDialog(currentWindow, "Verify Export", sb.toString());
if (!SimpleUserMessage.OPTION_OK.equals(reply)) {
throw UserCancelException.CANCEL_GENERIC;
}
}
}
resetPreferredFilePath(selectedFile, userPreferences);
return selectedFile;
}
Also used :
UserPreferences(cbit.vcell.client.server.UserPreferences)
TopLevelWindowManager(cbit.vcell.client.TopLevelWindowManager)
ArrayList(java.util.ArrayList)
JFrame(javax.swing.JFrame)
TreeSet(java.util.TreeSet)
ExtensionFilter(org.vcell.util.gui.exporter.ExtensionFilter)
SelectorExtensionFilter(org.vcell.util.gui.exporter.SelectorExtensionFilter)
SbmlExtensionFilter(org.vcell.util.gui.exporter.SbmlExtensionFilter)
VCFileChooser(org.vcell.util.gui.VCFileChooser)
FileFilter(javax.swing.filechooser.FileFilter)
SelectorExtensionFilter(org.vcell.util.gui.exporter.SelectorExtensionFilter)
SimulationContext(cbit.vcell.mapping.SimulationContext)
File(java.io.File)
BioModel(cbit.vcell.biomodel.BioModel)
File(java.io.File)
SbmlExtensionFilter(org.vcell.util.gui.exporter.SbmlExtensionFilter)
Example 2 with SelectorExtensionFilter
use of org.vcell.util.gui.exporter.SelectorExtensionFilter 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_OMEX)) {
// 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, mathModel.getOutputFunctionContext());
} 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();
}
}
}
Also used :
MathModel(cbit.vcell.mathmodel.MathModel)
SimulationTask(cbit.vcell.messaging.server.SimulationTask)
VCDocument(org.vcell.util.document.VCDocument)
SmoldynFileWriter(org.vcell.solver.smoldyn.SmoldynFileWriter)
MathDescription(cbit.vcell.math.MathDescription)
DocumentManager(cbit.vcell.clientdb.DocumentManager)
SelectorExtensionFilter(org.vcell.util.gui.exporter.SelectorExtensionFilter)
SimulationContext(cbit.vcell.mapping.SimulationContext)
IOException(java.io.IOException)
ExpressionException(cbit.vcell.parser.ExpressionException)
MathException(cbit.vcell.math.MathException)
Geometry(cbit.vcell.geometry.Geometry)
Simulation(cbit.vcell.solver.Simulation)
ExtensionFilter(org.vcell.util.gui.exporter.ExtensionFilter)
SelectorExtensionFilter(org.vcell.util.gui.exporter.SelectorExtensionFilter)
BioModel(cbit.vcell.biomodel.BioModel)
FileOutputStream(java.io.FileOutputStream)
RandomAccessFile(java.io.RandomAccessFile)
File(java.io.File)
SimulationJob(cbit.vcell.solver.SimulationJob)
Aggregations
BioModel (cbit.vcell.biomodel.BioModel)2
SimulationContext (cbit.vcell.mapping.SimulationContext)2
File (java.io.File)2
ExtensionFilter (org.vcell.util.gui.exporter.ExtensionFilter)2
SelectorExtensionFilter (org.vcell.util.gui.exporter.SelectorExtensionFilter)2
TopLevelWindowManager (cbit.vcell.client.TopLevelWindowManager)1
UserPreferences (cbit.vcell.client.server.UserPreferences)1
DocumentManager (cbit.vcell.clientdb.DocumentManager)1
Geometry (cbit.vcell.geometry.Geometry)1
MathDescription (cbit.vcell.math.MathDescription)1
MathException (cbit.vcell.math.MathException)1
MathModel (cbit.vcell.mathmodel.MathModel)1
SimulationTask (cbit.vcell.messaging.server.SimulationTask)1
ExpressionException (cbit.vcell.parser.ExpressionException)1
Simulation (cbit.vcell.solver.Simulation)1
SimulationJob (cbit.vcell.solver.SimulationJob)1
FileOutputStream (java.io.FileOutputStream)1
IOException (java.io.IOException)1
RandomAccessFile (java.io.RandomAccessFile)1
ArrayList (java.util.ArrayList)1
