Examples with DocumentManager cbit.vcell.clientdb.DocumentManager used on opensource projects

Example 1 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class DatabaseWindowManager method accessPermissions.

/**
 * Insert the method's description here.
 * Creation date: (5/14/2004 5:35:55 PM)
 */
public void accessPermissions(final Component requester, final VersionInfo selectedVersionInfo) {
    final GroupAccess groupAccess = selectedVersionInfo.getVersion().getGroupAccess();
    final DocumentManager docManager = getRequestManager().getDocumentManager();
    AsynchClientTask task1 = new AsynchClientTask("show dialog", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            getAclEditor().clearACLList();
            getAclEditor().setACLState(new ACLEditor.ACLState(groupAccess));
            Object choice = showAccessPermissionDialog(getAclEditor(), requester);
            if (choice != null) {
                hashTable.put("choice", choice);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("access permission", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Object choice = hashTable.get("choice");
            if (choice != null && choice.equals("OK")) {
                ACLEditor.ACLState aclState = getAclEditor().getACLState();
                if (aclState != null) {
                    if (aclState.isAccessPrivate() || (aclState.getAccessList() != null && aclState.getAccessList().length == 0)) {
                        VersionInfo vInfo = null;
                        if (selectedVersionInfo instanceof BioModelInfo) {
                            vInfo = docManager.setGroupPrivate((BioModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof MathModelInfo) {
                            vInfo = docManager.setGroupPrivate((MathModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof GeometryInfo) {
                            vInfo = docManager.setGroupPrivate((GeometryInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof VCImageInfo) {
                            vInfo = docManager.setGroupPrivate((VCImageInfo) selectedVersionInfo);
                        }
                    } else if (aclState.isAccessPublic()) {
                        VersionInfo vInfo = null;
                        if (selectedVersionInfo instanceof BioModelInfo) {
                            vInfo = docManager.setGroupPublic((BioModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof MathModelInfo) {
                            vInfo = docManager.setGroupPublic((MathModelInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof GeometryInfo) {
                            vInfo = docManager.setGroupPublic((GeometryInfo) selectedVersionInfo);
                        } else if (selectedVersionInfo instanceof VCImageInfo) {
                            vInfo = docManager.setGroupPublic((VCImageInfo) selectedVersionInfo);
                        }
                    } else {
                        String[] aclUserNames = aclState.getAccessList();
                        String[] originalGroupAccesNames = new String[0];
                        // Turn User[] into String[]
                        if (groupAccess instanceof GroupAccessSome) {
                            GroupAccessSome gas = (GroupAccessSome) groupAccess;
                            User[] originalUsers = gas.getNormalGroupMembers();
                            for (int i = 0; i < originalUsers.length; i += 1) {
                                originalGroupAccesNames = (String[]) BeanUtils.addElement(originalGroupAccesNames, originalUsers[i].getName());
                            }
                        }
                        // Determine users needing adding
                        String[] needToAddUsers = new String[0];
                        for (int i = 0; i < aclUserNames.length; i += 1) {
                            if (!BeanUtils.arrayContains(originalGroupAccesNames, aclUserNames[i])) {
                                System.out.println("Added user=" + aclUserNames[i]);
                                needToAddUsers = (String[]) BeanUtils.addElement(needToAddUsers, aclUserNames[i]);
                            }
                        }
                        // Determine users needing removing
                        String[] needToRemoveUsers = new String[0];
                        for (int i = 0; i < originalGroupAccesNames.length; i += 1) {
                            if (!BeanUtils.arrayContains(aclUserNames, originalGroupAccesNames[i])) {
                                System.out.println("Removed user=" + originalGroupAccesNames[i]);
                                needToRemoveUsers = (String[]) BeanUtils.addElement(needToRemoveUsers, originalGroupAccesNames[i]);
                            }
                        }
                        VersionInfo vInfo = null;
                        String errorNames = "";
                        // Add Users to Group Access List
                        for (int i = 0; i < needToAddUsers.length; i++) {
                            try {
                                if (selectedVersionInfo instanceof BioModelInfo) {
                                    vInfo = docManager.addUserToGroup((BioModelInfo) selectedVersionInfo, needToAddUsers[i]);
                                } else if (selectedVersionInfo instanceof MathModelInfo) {
                                    vInfo = docManager.addUserToGroup((MathModelInfo) selectedVersionInfo, needToAddUsers[i]);
                                } else if (selectedVersionInfo instanceof GeometryInfo) {
                                    vInfo = docManager.addUserToGroup((GeometryInfo) selectedVersionInfo, needToAddUsers[i]);
                                } else if (selectedVersionInfo instanceof VCImageInfo) {
                                    vInfo = docManager.addUserToGroup((VCImageInfo) selectedVersionInfo, needToAddUsers[i]);
                                }
                            } catch (ObjectNotFoundException e) {
                                errorNames += "Error changing permissions.\n" + selectedVersionInfo.getVersionType().getTypeName() + " \"" + selectedVersionInfo.getVersion().getName() + "\" edition (" + selectedVersionInfo.getVersion().getDate() + ")\nnot found, " + "your model list may be out of date, please go to menu Server->Reconnect to refresh the model list" + "\n";
                                break;
                            } catch (DataAccessException e) {
                                errorNames += "Error adding user '" + needToAddUsers[i] + "' : " + e.getMessage() + "\n";
                            }
                        }
                        // Remove users from Group Access List
                        for (int i = 0; i < needToRemoveUsers.length; i++) {
                            try {
                                if (selectedVersionInfo instanceof BioModelInfo) {
                                    vInfo = docManager.removeUserFromGroup((BioModelInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                } else if (selectedVersionInfo instanceof MathModelInfo) {
                                    vInfo = docManager.removeUserFromGroup((MathModelInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                } else if (selectedVersionInfo instanceof GeometryInfo) {
                                    vInfo = docManager.removeUserFromGroup((GeometryInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                } else if (selectedVersionInfo instanceof VCImageInfo) {
                                    vInfo = docManager.removeUserFromGroup((VCImageInfo) selectedVersionInfo, needToRemoveUsers[i]);
                                }
                            } catch (DataAccessException e) {
                                errorNames += "Error Removing user '" + needToRemoveUsers[i] + "'\n  -----" + e.getMessage() + "\n";
                            }
                        }
                        if (errorNames.length() > 0) {
                            if (DatabaseWindowManager.this.getComponent() != null) {
                                PopupGenerator.showErrorDialog(DatabaseWindowManager.this, errorNames);
                            } else {
                                DialogUtils.showErrorDialog(requester, errorNames);
                            }
                            accessPermissions(requester, selectedVersionInfo);
                        }
                    }
                }
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 2 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class DBReactionWizardPanel method searchUserReactions.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:45:44 PM)
 */
private void searchUserReactions(final ReactionQuerySpec reactionQuerySpec) {
    if (getDocumentManager() != null) {
        final DocumentManager docManager = getDocumentManager();
        final JList jlist = getReactionsJList();
        // 
        final String RXSTRING_VALUE_KEY = "rxString";
        // 
        AsynchClientTask searchReactions = new AsynchClientTask("searching reactions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                try {
                    mapRXStringtoRXIDs.clear();
                    // 
                    ReactionDescription[] dbrd = docManager.getUserReactionDescriptions(reactionQuerySpec);
                    // 
                    if (dbrd != null && !(getStructure() instanceof Membrane)) {
                        Vector<ReactionDescription> noflux = new Vector<ReactionDescription>();
                        for (int i = 0; i < dbrd.length; i += 1) {
                            if (!dbrd[i].isFluxReaction()) {
                                noflux.add(dbrd[i]);
                            }
                        }
                        if (noflux.size() > 0) {
                            dbrd = new ReactionDescription[noflux.size()];
                            noflux.copyInto(dbrd);
                        }
                    }
                    // 
                    String[] dbrdS = null;
                    if (dbrd != null) {
                        // if(mapRXStringtoRXIDs == null){mapRXStringtoRXIDs = new java.util.Hashtable();}
                        for (int i = 0; i < dbrd.length; i += 1) {
                            String rxString = dbrd[i].toString();
                            if (!mapRXStringtoRXIDs.containsKey(rxString)) {
                                mapRXStringtoRXIDs.put(rxString, new Vector<String>());
                            }
                            mapRXStringtoRXIDs.get(rxString).add(dbrd[i].getVCellRXID().toString());
                            mapRXIDtoBMIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellBioModelID());
                            mapRXIDtoStructRefIDs.put(dbrd[i].getVCellRXID(), dbrd[i].getVCellStructRef());
                        }
                        dbrdS = (String[]) mapRXStringtoRXIDs.keySet().toArray(new String[0]);
                    }
                    // 
                    if (dbrd != null && dbrd.length > 0) {
                        hash.put(RXSTRING_VALUE_KEY, dbrdS);
                    }
                } catch (DataAccessException e) {
                    PopupGenerator.showErrorDialog(DBReactionWizardPanel.this, e.getMessage());
                }
            }
        };
        // 
        AsynchClientTask updateRXList = new AsynchClientTask("updateRXList", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                String[] dbrdS = (String[]) hash.get(RXSTRING_VALUE_KEY);
                if (dbrdS != null) {
                    jlist.setListData(dbrdS);
                } else {
                    jlist.setListData(new String[0]);
                }
                afterSearchConfigure();
            }
        };
        // 
        Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
        ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXList }, false);
    }
}

Example 3 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class DBReactionWizardPanel method search.

/**
 * Comment
 */
private void search() {
    if (getDocumentManager() != null) {
        String textSearchS = getFindTextJTextField().getText();
        if (textSearchS != null && textSearchS.length() == 0) {
            textSearchS = null;
        }
        final ReactionQuerySpec reactionQuerySpec = new ReactionQuerySpec((getFindRXTextRadioButton().isSelected() ? formatLikeString(textSearchS) : null), (getKeggMoleculeJRadioButton().isSelected() ? getCurrentDBFormalSpecies() : null));
        if (getSearchUserJRadioButton().isSelected()) {
            searchUserReactions(reactionQuerySpec);
            return;
        }
        final DocumentManager docManager = getDocumentManager();
        final javax.swing.JList jlist = getReactionsJList();
        // 
        final String RXDESC_VALUE_KEY = "rxDesc";
        AsynchClientTask searchReactions = new AsynchClientTask("searching reactions", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) throws DataAccessException {
                ReactionDescription[] dbfr = docManager.getDictionaryReactions(reactionQuerySpec);
                if (dbfr != null && dbfr.length > 0) {
                    hash.put(RXDESC_VALUE_KEY, dbfr);
                }
            }
        };
        // 
        AsynchClientTask updateRXList = new AsynchClientTask("updateRXList", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hash) {
                ReactionDescription[] dbfr = (ReactionDescription[]) hash.get(RXDESC_VALUE_KEY);
                if (dbfr != null) {
                    jlist.setListData(dbfr);
                } else {
                    jlist.setListData(new ReactionDescription[0]);
                }
                afterSearchConfigure();
            }
        };
        // 
        Hashtable<String, Object> hashTemp = new Hashtable<String, Object>();
        ClientTaskDispatcher.dispatch(this, hashTemp, new AsynchClientTask[] { searchReactions, updateRXList }, false);
    }
}

Example 4 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager in project vcell by virtualcell.

the class TestingFrameworkPanel method setdocumentManager1.

/**
 * Set the documentManager1 to a new value.
 * @param newValue cbit.vcell.clientdb.DocumentManager
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setdocumentManager1(DocumentManager newValue) {
    if (ivjdocumentManager1 != newValue) {
        try {
            DocumentManager oldValue = getdocumentManager1();
            ivjdocumentManager1 = newValue;
            if (oldValue != null) {
                oldValue.removeDatabaseListener(ivjEventHandler);
            }
            if (ivjdocumentManager1 != null) {
                ivjdocumentManager1.addDatabaseListener(ivjEventHandler);
            }
            connPtoP2SetSource();
            connEtoM1(ivjdocumentManager1);
            firePropertyChange(CommonTask.DOCUMENT_MANAGER.name, oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}

Example 5 with DocumentManager

use of cbit.vcell.clientdb.DocumentManager 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();
        }
    }
}