Examples with BioModel cbit.vcell.biomodel.BioModel used on opensource projects

Search in sources :

Example 31 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class ClientDocumentManager method getBioModelFromDatabaseXML.

private BioModel getBioModelFromDatabaseXML(XMLHolder<BioModel> bioModelXMLHolder) throws DataAccessException {
    try {
        BioModel bm = bioModelXMLHolder.getDocument();
        if (bm == null) {
            bm = XmlHelper.XMLToBioModel(new XMLSource(bioModelXMLHolder.getXmlString()));
        }
        cacheSimulations(bm.getSimulations());
        // bm.refreshDependencies();
        return bm;
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new DataAccessException(e.getMessage());
    }
}
Also used : BioModel(cbit.vcell.biomodel.BioModel) XmlParseException(cbit.vcell.xml.XmlParseException) XMLSource(cbit.vcell.xml.XMLSource) DataAccessException(org.vcell.util.DataAccessException)

Example 32 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class BnglExtensionFilter method askUser.

@Override
public void askUser(ChooseContext ctx) throws UserCancelException {
    BioModel bioModel = ctx.chosenContext.getBioModel();
    boolean hasReactions = bioModel.getModel().getReactionSteps().length > 0 ? true : false;
    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(ctx.topLevelWindowManager.getComponent(), errMsg, "Exporting to .bngl", dialogButton);
        if (returnCode != JOptionPane.YES_OPTION) {
            throw UserCancelException.CANCEL_FILE_SELECTION;
        }
    }
}
Also used : BioModel(cbit.vcell.biomodel.BioModel)

Example 33 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class SbmlExtensionFilter method askUser.

@Override
public void askUser(ChooseContext c) throws UserCancelException {
    BioModel bioModel = c.chosenContext.getBioModel();
    JFrame currentWindow = c.currentWindow;
    selectedSimWOSBE = null;
    selectedSimContext = c.chosenContext;
    // get user choice of structure and its size and computes absolute sizes of compartments using the StructureSizeSolver.
    Structure[] structures = bioModel.getModel().getStructures();
    // get the nonspatial simulationContexts corresponding to names in applicableAppNameList
    // This is needed in ApplnSelectionAndStructureSizeInputPanel
    String strucName = null;
    double structSize = 1.0;
    int structSelection = -1;
    int option = JOptionPane.CANCEL_OPTION;
    ApplnSelectionAndStructureSizeInputPanel applnStructInputPanel = null;
    while (structSelection < 0) {
        applnStructInputPanel = new ApplnSelectionAndStructureSizeInputPanel();
        applnStructInputPanel.setSimContext(c.chosenContext);
        applnStructInputPanel.setStructures(structures);
        if (applnStructInputPanel.isNeedStructureSizes()) {
            applnStructInputPanel.setPreferredSize(new java.awt.Dimension(350, 400));
            applnStructInputPanel.setMaximumSize(new java.awt.Dimension(350, 400));
            option = DialogUtils.showComponentOKCancelDialog(currentWindow, applnStructInputPanel, "Specify Structure Size to Export:");
            structSelection = applnStructInputPanel.getStructSelectionIndex();
            if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
                break;
            } else if (option == JOptionPane.OK_OPTION && structSelection < 0) {
                DialogUtils.showErrorDialog(currentWindow, "Please select a structure and set its size");
            }
        } else {
            // adapt to legacy logic ...
            structSelection = 0;
            option = JOptionPane.OK_OPTION;
        }
    }
    if (option == JOptionPane.OK_OPTION) {
        applnStructInputPanel.applyStructureNameAndSizeValues();
        strucName = applnStructInputPanel.getSelectedStructureName();
        selectedSimContext = applnStructInputPanel.getSelectedSimContext();
        GeometryContext geoContext = selectedSimContext.getGeometryContext();
        if (!isSpatial) {
            // calculate structure Sizes only if appln is not spatial
            structSize = applnStructInputPanel.getStructureSize();
            // Invoke StructureSizeEvaluator to compute absolute sizes of compartments if all sizes are not set
            if ((geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || ((strucName == null || structSize <= 0.0) && (geoContext.isAllSizeSpecifiedNull() && geoContext.isAllVolFracAndSurfVolSpecified())) || (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecifiedNull()) || (!geoContext.isAllSizeSpecifiedPositive() && !geoContext.isAllVolFracAndSurfVolSpecified()) || (geoContext.isAllSizeSpecifiedNull() && !geoContext.isAllVolFracAndSurfVolSpecified())) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment sizes being set. This can be automatically " + " computed if the absolute size of at least one compartment and the relative sizes (Surface-to-volume-ratio/Volume-fraction) " + " of all compartments are known. Sufficient information is not available to perform this computation." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure sizes in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
            if (!geoContext.isAllSizeSpecifiedPositive() && geoContext.isAllVolFracAndSurfVolSpecified()) {
                Structure chosenStructure = selectedSimContext.getModel().getStructure(strucName);
                StructureMapping chosenStructMapping = selectedSimContext.getGeometryContext().getStructureMapping(chosenStructure);
                try {
                    StructureSizeSolver.updateAbsoluteStructureSizes(selectedSimContext, chosenStructure, structSize, chosenStructMapping.getSizeParameter().getUnitDefinition());
                } catch (Exception e) {
                    throw new ProgrammingException("exception updating sizes", e);
                }
            }
        } else {
            if (!geoContext.isAllUnitSizeParameterSetForSpatial()) {
                DialogUtils.showErrorDialog(currentWindow, "Cannot export to SBML without compartment size ratios being set." + "\n\nThis can be fixed by going back to the application '" + selectedSimContext.getName() + "' and setting structure" + " size ratios in the 'StructureMapping' tab.");
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
        // Select simulation whose overrides need to be exported
        // If simContext doesn't have simulations, don't pop up simulationSelectionPanel
        Simulation[] sims = bioModel.getSimulations(selectedSimContext);
        // display only those simulations that have overrides in the simulationSelectionPanel.
        Vector<Simulation> orSims = new Vector<Simulation>();
        for (int s = 0; (sims != null) && (s < sims.length); s++) {
            if (sims[s].getMathOverrides().hasOverrides()) {
                orSims.addElement(sims[s]);
            }
        }
        Simulation[] overriddenSims = orSims.toArray(new Simulation[orSims.size()]);
        if (overriddenSims.length > 0) {
            SimulationSelectionPanel simSelectionPanel = new SimulationSelectionPanel();
            simSelectionPanel.setPreferredSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setMaximumSize(new java.awt.Dimension(600, 400));
            simSelectionPanel.setSimulations(overriddenSims);
            int simOption = DialogUtils.showComponentOKCancelDialog(currentWindow, simSelectionPanel, "Select Simulation whose overrides should be exported:");
            if (simOption == JOptionPane.OK_OPTION) {
                selectedSimWOSBE = simSelectionPanel.getSelectedSimulation();
            // if (chosenSimulation != null) {
            // CARRY						hashTable.put("selectedSimulation", chosenSimulation);
            // }
            } else if (simOption == JOptionPane.CANCEL_OPTION || simOption == JOptionPane.CLOSED_OPTION) {
                // Hence canceling the entire export to SBML operation.
                throw UserCancelException.CANCEL_XML_TRANSLATION;
            }
        }
    } else if (option == JOptionPane.CANCEL_OPTION || option == JOptionPane.CLOSED_OPTION) {
        // Hence canceling the entire export to SBML operation.
        throw UserCancelException.CANCEL_XML_TRANSLATION;
    }
    if (selectedSimWOSBE != null) {
        String selectedFileName = c.filename;
        // rename file to contain exported simulation.
        String ext = FilenameUtils.getExtension(selectedFileName);
        String base = FilenameUtils.getBaseName(selectedFileName);
        String path = FilenameUtils.getPath(selectedFileName);
        base += "_" + TokenMangler.mangleToSName(selectedSimWOSBE.getName());
        selectedFileName = path + base + ext;
        c.selectedFile.renameTo(new File(selectedFileName));
    }
}
Also used : SimulationSelectionPanel(org.vcell.sbml.gui.SimulationSelectionPanel) StructureMapping(cbit.vcell.mapping.StructureMapping) ProgrammingException(org.vcell.util.ProgrammingException) UserCancelException(org.vcell.util.UserCancelException) Simulation(cbit.vcell.solver.Simulation) JFrame(javax.swing.JFrame) ApplnSelectionAndStructureSizeInputPanel(org.vcell.sbml.gui.ApplnSelectionAndStructureSizeInputPanel) BioModel(cbit.vcell.biomodel.BioModel) GeometryContext(cbit.vcell.mapping.GeometryContext) ProgrammingException(org.vcell.util.ProgrammingException) Structure(cbit.vcell.model.Structure) Vector(java.util.Vector) File(java.io.File)

Example 34 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class SedmlExtensionFilter method writeBioModel.

@Override
public void writeBioModel(DocumentManager documentManager, BioModel bioModel, File exportFile, SimulationContext ignored) throws Exception {
    String resultString;
    // 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);
    }
}
Also used : SEDMLExporter(org.vcell.sedml.SEDMLExporter) BioModel(cbit.vcell.biomodel.BioModel)

Example 35 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class ClientDocumentManager method substituteFieldFuncNames.

public void substituteFieldFuncNames(VCDocument vcDocument, VersionableTypeVersion originalOwner) throws DataAccessException, MathException, ExpressionException {
    Vector<ExternalDataIdentifier> errorCleanupExtDataIDV = new Vector<ExternalDataIdentifier>();
    try {
        if (originalOwner == null || originalOwner.getVersion().getOwner().compareEqual(getUser())) {
            // Substitution for FieldFunc not needed for new doc or if we own doc
            return;
        }
        // Get Objects from Document that might need to have FieldFuncs replaced
        Vector<Object> fieldFunctionContainer_mathDesc_or_simContextV = new Vector<Object>();
        if (vcDocument instanceof MathModel) {
            fieldFunctionContainer_mathDesc_or_simContextV.add(((MathModel) vcDocument).getMathDescription());
        } else if (vcDocument instanceof BioModel) {
            SimulationContext[] simContextArr = ((BioModel) vcDocument).getSimulationContexts();
            for (int i = 0; i < simContextArr.length; i += 1) {
                fieldFunctionContainer_mathDesc_or_simContextV.add(simContextArr[i]);
            }
        }
        // Get original Field names
        Vector<String> origFieldFuncNamesV = new Vector<String>();
        for (int i = 0; i < fieldFunctionContainer_mathDesc_or_simContextV.size(); i += 1) {
            Object fieldFunctionContainer = fieldFunctionContainer_mathDesc_or_simContextV.elementAt(i);
            FieldFunctionArguments[] fieldFuncArgsArr = null;
            if (fieldFunctionContainer instanceof MathDescription) {
                fieldFuncArgsArr = FieldUtilities.getFieldFunctionArguments((MathDescription) fieldFunctionContainer);
            } else if (fieldFunctionContainer instanceof SimulationContext) {
                fieldFuncArgsArr = ((SimulationContext) fieldFunctionContainer).getFieldFunctionArguments();
            }
            for (int j = 0; j < fieldFuncArgsArr.length; j += 1) {
                if (!origFieldFuncNamesV.contains(fieldFuncArgsArr[j].getFieldName())) {
                    origFieldFuncNamesV.add(fieldFuncArgsArr[j].getFieldName());
                }
            }
        }
        if (origFieldFuncNamesV.size() == 0) {
            // No FieldFunctions to substitute
            return;
        }
        FieldDataDBOperationResults copyNamesFieldDataOpResults = fieldDataDBOperation(FieldDataDBOperationSpec.createCopyNoConflictExtDataIDsSpec(getUser(), origFieldFuncNamesV.toArray(new String[0]), originalOwner));
        errorCleanupExtDataIDV.addAll(copyNamesFieldDataOpResults.oldNameNewIDHash.values());
        // Copy Field Data on Data Server FileSystem
        for (String fieldname : origFieldFuncNamesV) {
            KeyValue sourceSimDataKey = copyNamesFieldDataOpResults.oldNameOldExtDataIDKeyHash.get(fieldname);
            if (sourceSimDataKey == null) {
                throw new DataAccessException("Couldn't find original data key for FieldFunc " + fieldname);
            }
            ExternalDataIdentifier newExtDataID = copyNamesFieldDataOpResults.oldNameNewIDHash.get(fieldname);
            getSessionManager().fieldDataFileOperation(FieldDataFileOperationSpec.createCopySimFieldDataFileOperationSpec(newExtDataID, sourceSimDataKey, originalOwner.getVersion().getOwner(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT, getUser()));
        }
        // Finally substitute new Field names
        for (int i = 0; i < fieldFunctionContainer_mathDesc_or_simContextV.size(); i += 1) {
            Object fieldFunctionContainer = fieldFunctionContainer_mathDesc_or_simContextV.elementAt(i);
            if (fieldFunctionContainer instanceof MathDescription) {
                MathDescription mathDesc = (MathDescription) fieldFunctionContainer;
                FieldUtilities.substituteFieldFuncNames(mathDesc, copyNamesFieldDataOpResults.oldNameNewIDHash);
            } else if (fieldFunctionContainer instanceof SimulationContext) {
                SimulationContext simContext = (SimulationContext) fieldFunctionContainer;
                simContext.substituteFieldFuncNames(copyNamesFieldDataOpResults.oldNameNewIDHash);
            }
        }
        fireFieldDataDB(new FieldDataDBEvent(this));
    } catch (Exception e) {
        e.printStackTrace();
        // Cleanup
        for (int i = 0; i < errorCleanupExtDataIDV.size(); i += 1) {
            try {
                fieldDataDBOperation(FieldDataDBOperationSpec.createDeleteExtDataIDSpec(errorCleanupExtDataIDV.elementAt(i)));
            } catch (Exception e2) {
            // ignore, we tried to cleanup
            }
            try {
                fieldDataFileOperation(FieldDataFileOperationSpec.createDeleteFieldDataFileOperationSpec(errorCleanupExtDataIDV.elementAt(i)));
            } catch (Exception e1) {
            // ignore, we tried to cleanup
            }
        }
        throw new RuntimeException("Error copying Field Data \n" + e.getMessage());
    }
}
Also used : MathModel(cbit.vcell.mathmodel.MathModel) KeyValue(org.vcell.util.document.KeyValue) FieldFunctionArguments(cbit.vcell.field.FieldFunctionArguments) MathDescription(cbit.vcell.math.MathDescription) BigString(org.vcell.util.BigString) SimulationContext(cbit.vcell.mapping.SimulationContext) PermissionException(org.vcell.util.PermissionException) ObjectNotFoundException(org.vcell.util.ObjectNotFoundException) XmlParseException(cbit.vcell.xml.XmlParseException) RemoteProxyException(cbit.vcell.message.server.bootstrap.client.RemoteProxyVCellConnectionFactory.RemoteProxyException) DataAccessException(org.vcell.util.DataAccessException) ExpressionException(cbit.vcell.parser.ExpressionException) MathException(cbit.vcell.math.MathException) BioModel(cbit.vcell.biomodel.BioModel) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) FieldDataDBOperationResults(cbit.vcell.field.FieldDataDBOperationResults) Vector(java.util.Vector) DataAccessException(org.vcell.util.DataAccessException)

Aggregations

BioModel (cbit.vcell.biomodel.BioModel)158 SimulationContext (cbit.vcell.mapping.SimulationContext)72 Simulation (cbit.vcell.solver.Simulation)53 XMLSource (cbit.vcell.xml.XMLSource)37 KeyValue (org.vcell.util.document.KeyValue)36 MathModel (cbit.vcell.mathmodel.MathModel)33 DataAccessException (org.vcell.util.DataAccessException)29 XmlParseException (cbit.vcell.xml.XmlParseException)28 File (java.io.File)28 Model (cbit.vcell.model.Model)27 BioModelInfo (org.vcell.util.document.BioModelInfo)25 MathDescription (cbit.vcell.math.MathDescription)24 IOException (java.io.IOException)24 BigString (org.vcell.util.BigString)22 Geometry (cbit.vcell.geometry.Geometry)21 UserCancelException (org.vcell.util.UserCancelException)20 User (org.vcell.util.document.User)20 ObjectNotFoundException (org.vcell.util.ObjectNotFoundException)19 SpeciesContext (cbit.vcell.model.SpeciesContext)17 VCDocument (org.vcell.util.document.VCDocument)16
About Me
UseOf

Java Tutorials :

Simple Java RabbitMQ Example with Spring
Simple Springboot JPA Eclipeslink Example
Simple SpringBoot JPA Hibernate Example
Jackson JSON @JsonIgnore and @JsonIgnoreProperties Examples
Java Infinite recursion (StackOverflowError) Jackson solutions
Simple Java Jackson Serialize Objects to JSON and convert them back To Object
ElasticSearch 5 - Upload files using Java API in binary field Example
Java JAXB marshall unmarshall Examples from String and Stream
Java 8 forEach List and Map examples
ElasticSearch 5 Java API SearchRequestBuilder examples
Java ElasticSearch 5 examples with node index and mapping - running local
Convert String to int or Integer Java 8
Java 9 in action - JShell - Ubuntu
Java - removing invalid characters from a file name
Hello world!? or Hello Tutorial