Example 1 with SbmlExtensionFilter
use of org.vcell.util.gui.exporter.SbmlExtensionFilter 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)
Aggregations
BioModel (cbit.vcell.biomodel.BioModel)1
TopLevelWindowManager (cbit.vcell.client.TopLevelWindowManager)1
UserPreferences (cbit.vcell.client.server.UserPreferences)1
SimulationContext (cbit.vcell.mapping.SimulationContext)1
File (java.io.File)1
ArrayList (java.util.ArrayList)1
TreeSet (java.util.TreeSet)1
JFrame (javax.swing.JFrame)1
FileFilter (javax.swing.filechooser.FileFilter)1
VCFileChooser (org.vcell.util.gui.VCFileChooser)1
ExtensionFilter (org.vcell.util.gui.exporter.ExtensionFilter)1
SbmlExtensionFilter (org.vcell.util.gui.exporter.SbmlExtensionFilter)1
SelectorExtensionFilter (org.vcell.util.gui.exporter.SelectorExtensionFilter)1
