Example 1 with ExtensionFilter
use of org.vcell.util.gui.exporter.ExtensionFilter 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();
}
}
}
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)1
DocumentManager (cbit.vcell.clientdb.DocumentManager)1
Geometry (cbit.vcell.geometry.Geometry)1
SimulationContext (cbit.vcell.mapping.SimulationContext)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
File (java.io.File)1
FileOutputStream (java.io.FileOutputStream)1
IOException (java.io.IOException)1
RandomAccessFile (java.io.RandomAccessFile)1
SmoldynFileWriter (org.vcell.solver.smoldyn.SmoldynFileWriter)1
VCDocument (org.vcell.util.document.VCDocument)1
ExtensionFilter (org.vcell.util.gui.exporter.ExtensionFilter)1
SelectorExtensionFilter (org.vcell.util.gui.exporter.SelectorExtensionFilter)1
