Examples with VCDocument org.vcell.util.document.VCDocument used on opensource projects

Example 11 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class XmlHelper method importMathCellML.

public static VCDocument importMathCellML(VCLogger vcLogger, XMLSource xmlSource) throws Exception {
    // checks that the string is not empty
    if (xmlSource == null) {
        throw new XmlParseException("Invalid params for importing cellml model to Mathmodel.");
    }
    Document xmlDoc = xmlSource.getXmlDoc();
    String xmlString = XmlUtil.xmlToString(xmlDoc, false);
    CellQuanVCTranslator cellmlTranslator = new CellQuanVCTranslator();
    VCDocument vcDoc = cellmlTranslator.translate(new StringReader(xmlString), false);
    vcDoc.refreshDependencies();
    return vcDoc;
}

Example 12 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class XmlHelper method XMLToDocument.

/**
 * Insert the method's description here.
 * Creation date: (2/7/2006 4:45:26 PM)
 * @return cbit.vcell.document.VCDocument
 * @param xmlString java.lang.String
 */
public static VCDocument XMLToDocument(VCLogger vcLogger, String xmlString) throws Exception {
    VCDocument doc = null;
    XMLSource xmlSource = new XMLSource(xmlString);
    // some overhead.
    org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
    String xmlType = rootElement.getName();
    if (xmlType.equals(XMLTags.VcmlRootNodeTag)) {
        // For now, assuming that <vcml> element has only one child (biomodel, mathmodel or geometry).
        // Will deal with multiple children of <vcml> Element when we get to model composition.
        java.util.List<?> childElementList = rootElement.getChildren();
        // assuming first child is the biomodel, mathmodel or geometry.
        Element modelElement = (Element) childElementList.get(0);
        xmlType = modelElement.getName();
    }
    if (xmlType.equals(XMLTags.BioModelTag)) {
        doc = XmlHelper.XMLToBioModel(xmlSource);
    } else if (xmlType.equals(XMLTags.MathModelTag)) {
        doc = XmlHelper.XMLToMathModel(xmlSource);
    } else if (xmlType.equals(XMLTags.GeometryTag)) {
        doc = XmlHelper.XMLToGeometry(xmlSource);
    } else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
        Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
        boolean bIsSpatial = (namespace == null) ? false : true;
        doc = XmlHelper.importSBML(vcLogger, xmlSource, bIsSpatial);
    } else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
        doc = XmlHelper.importMathCellML(vcLogger, xmlSource);
    } else {
        // unknown XML format
        throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
    }
    return doc;
}

Example 13 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class XmlHelper method importSBML.

/**
 *Allows the translation process to interact with the user via TranslationMessager
 */
public static VCDocument importSBML(VCLogger vcLogger, XMLSource xmlSource, boolean bSpatial) throws Exception {
    // checks that the source is not empty
    if (xmlSource == null) {
        throw new XmlParseException("Invalid params for importing sbml model.");
    }
    // First try getting xmlfile from xmlSource. If not file, get xmlStr and save it in file
    // (since we send only file name to SBMLImporter). If xmlString is also not present in xmlSource, throw exception.
    File sbmlFile = xmlSource.getXmlFile();
    if (sbmlFile == null) {
        String sbmlStr = xmlSource.getXmlString();
        if (sbmlStr != null) {
            sbmlFile = File.createTempFile("temp", ".xml");
            sbmlFile.deleteOnExit();
            XmlUtil.writeXMLStringToFile(sbmlStr, sbmlFile.getAbsolutePath(), true);
        } else {
            throw new RuntimeException("Error importing from SBML : no SBML source.");
        }
    }
    VCDocument vcDoc = null;
    // if (!bSpatial) {
    SBMLImporter sbmlImporter = new SBMLImporter(sbmlFile.getAbsolutePath(), vcLogger, bSpatial);
    vcDoc = sbmlImporter.getBioModel();
    // } else {
    // SBMLSpatialImporter sbmlSpatialImporter = new SBMLSpatialImporter(sbmlFile.getAbsolutePath(), vcLogger);
    // vcDoc = sbmlSpatialImporter.getBioModel();
    // }
    vcDoc.refreshDependencies();
    return vcDoc;
}

Example 14 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class XmlHelper method sedmlToBioModel.

public static VCDocument sedmlToBioModel(VCLogger transLogger, ExternalDocInfo externalDocInfo, SedML sedml, AbstractTask selectedTask) throws Exception {
    if (sedml.getModels().isEmpty()) {
        return null;
    }
    VCDocument doc = null;
    try {
        // extract the path only from the sedml file
        String fullPath = FileUtils.getFullPath(externalDocInfo.getFile().getAbsolutePath());
        // Namespace namespace = sedml.getNamespace();
        // iterate through all the elements and show them at the console
        List<org.jlibsedml.Model> mmm = sedml.getModels();
        for (Model mm : mmm) {
            System.out.println(mm.toString());
        }
        List<org.jlibsedml.Simulation> sss = sedml.getSimulations();
        for (org.jlibsedml.Simulation ss : sss) {
            System.out.println(ss.toString());
        }
        List<AbstractTask> ttt = sedml.getTasks();
        for (AbstractTask tt : ttt) {
            System.out.println(tt.toString());
        }
        List<DataGenerator> ddd = sedml.getDataGenerators();
        for (DataGenerator dd : ddd) {
            System.out.println(dd.toString());
        }
        List<Output> ooo = sedml.getOutputs();
        for (Output oo : ooo) {
            System.out.println(oo.toString());
        }
        KisaoTerm sedmlKisao = null;
        // this will become the vCell simulation
        org.jlibsedml.Simulation sedmlSimulation = null;
        // the "original" model referred to by the task
        org.jlibsedml.Model sedmlOriginalModel = null;
        String sedmlOriginalModelName = null;
        if (selectedTask == null) {
            // no task, just pick the Model and find its sbml file
            sedmlOriginalModelName = SEDMLUtil.getName(mmm.get(0));
        } else {
            if (selectedTask instanceof Task) {
                sedmlOriginalModel = sedml.getModelWithId(selectedTask.getModelReference());
                sedmlSimulation = sedml.getSimulation(selectedTask.getSimulationReference());
            } else if (selectedTask instanceof RepeatedTask) {
                RepeatedTask rt = (RepeatedTask) selectedTask;
                assert (rt.getSubTasks().size() == 1);
                // first (and only) subtask
                SubTask st = rt.getSubTasks().entrySet().iterator().next().getValue();
                String taskId = st.getTaskId();
                AbstractTask t = sedml.getTaskWithId(taskId);
                // get model and simulation from subtask
                sedmlOriginalModel = sedml.getModelWithId(t.getModelReference());
                sedmlSimulation = sedml.getSimulation(t.getSimulationReference());
            } else {
                throw new RuntimeException("Unexpected task " + selectedTask);
            }
            sedmlOriginalModelName = sedmlOriginalModel.getId();
            sedmlKisao = KisaoOntology.getInstance().getTermById(sedmlSimulation.getAlgorithm().getKisaoID());
        }
        // UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=1.0, outputStartTime=0.0,
        // Algorithm [kisaoID=KISAO:0000019], getId()=SimSlow]
        // identify the vCell solvers that would match best the sedml solver kisao id
        List<SolverDescription> solverDescriptions = new ArrayList<>();
        for (SolverDescription sd : SolverDescription.values()) {
            KisaoTerm solverKisaoTerm = KisaoOntology.getInstance().getTermById(sd.getKisao());
            if (solverKisaoTerm == null) {
                break;
            }
            boolean isExactlySame = solverKisaoTerm.equals(sedmlKisao);
            if (isExactlySame && !solverKisaoTerm.isObsolete()) {
                // we make a list with all the solvers that match the kisao
                solverDescriptions.add(sd);
            }
        }
        // from the list of vcell solvers that match the sedml kisao we select the ones that have a matching time step
        SolverDescription solverDescription = null;
        for (SolverDescription sd : solverDescriptions) {
            if (true) {
                solverDescription = sd;
                break;
            }
        }
        // find out everything else we need about the application we're going to use,
        // some of the info will be needed when we parse the sbml file
        boolean bSpatial = false;
        Application appType = Application.NETWORK_DETERMINISTIC;
        Set<SolverDescription.SolverFeature> sfList = solverDescription.getSupportedFeatures();
        for (SolverDescription.SolverFeature sf : sfList) {
            switch(sf) {
                case Feature_Rulebased:
                    appType = Application.RULE_BASED_STOCHASTIC;
                    break;
                case Feature_Stochastic:
                    appType = Application.NETWORK_STOCHASTIC;
                    break;
                case Feature_Deterministic:
                    appType = Application.NETWORK_DETERMINISTIC;
                    break;
                case Feature_Spatial:
                    bSpatial = true;
                    break;
                default:
                    break;
            }
        }
        // -------------------------------------------------------------------------------------------
        // extract bioModel name from sedx (or sedml) file
        String bioModelName = FileUtils.getBaseName(externalDocInfo.getFile().getAbsolutePath());
        // if we have repeated task, we ignore them, we just use the normal resolvers for archive and changes
        // once the application and simulation are built, we iterate through the repeated tasks and
        // add math overrides to the simulation for each repeated task
        ArchiveComponents ac = null;
        if (externalDocInfo.getFile().getPath().toLowerCase().endsWith("sedx") || externalDocInfo.getFile().getPath().toLowerCase().endsWith("omex")) {
            ac = Libsedml.readSEDMLArchive(new FileInputStream(externalDocInfo.getFile().getPath()));
        }
        ModelResolver resolver = new ModelResolver(sedml);
        if (ac != null) {
            resolver.add(new ArchiveModelResolver(ac));
        }
        resolver.add(new FileModelResolver());
        resolver.add(new RelativeFileModelResolver(fullPath));
        String newMdl = resolver.getModelString(sedmlOriginalModel);
        // sbmlSource with all the changes applied
        XMLSource sbmlSource = new XMLSource(newMdl);
        doc = XmlHelper.importSBML(transLogger, sbmlSource, bSpatial);
        BioModel bioModel = (BioModel) doc;
        bioModel.setName(bioModelName);
        // we already have an application loaded from the sbml file, with initial conditions and stuff
        // which may be not be suitable because the sedml kisao may need a different app type
        // so we do a "copy as" to the right type and then delete the original we loaded from the sbml file
        // the new application we're making from the old one
        SimulationContext newSimulationContext = null;
        if (bioModel.getSimulationContexts().length == 1) {
            SimulationContext oldSimulationContext = bioModel.getSimulationContext(0);
            newSimulationContext = SimulationContext.copySimulationContext(oldSimulationContext, sedmlOriginalModelName, bSpatial, appType);
            bioModel.removeSimulationContext(oldSimulationContext);
            bioModel.addSimulationContext(newSimulationContext);
        } else {
            // length == 0
            newSimulationContext = bioModel.addNewSimulationContext(sedmlOriginalModelName, appType);
        }
        // making the new vCell simulation based on the sedml simulation
        newSimulationContext.refreshDependencies();
        MathMappingCallback callback = new MathMappingCallbackTaskAdapter(null);
        newSimulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        Simulation newSimulation = new Simulation(newSimulationContext.getMathDescription());
        newSimulation.setName(SEDMLUtil.getName(sedmlSimulation));
        // TODO: make sure that everything has proper names
        // we check the repeated tasks, if any, and add to the list of math overrides
        // if(selectedTask instanceof RepeatedTask) {
        // for(Change change : ((RepeatedTask) selectedTask).getChanges()) {
        // if(!(change instanceof SetValue)) {
        // throw new RuntimeException("Only 'SetValue' changes are supported for repeated tasks.");
        // }
        // SetValue setValue = (SetValue)change;
        // // TODO: extract target from XPath
        // // ......
        // //
        // String target = "s0";	// for now we just use a hardcoded thing
        // ConstantArraySpec cas;
        // Range range = ((RepeatedTask) selectedTask).getRange(setValue.getRangeReference());
        // if(range instanceof UniformRange) {
        // cas = ConstantArraySpec.createIntervalSpec(target, ((UniformRange) range).getStart(), ((UniformRange) range).getEnd(),
        // range.getNumElements(), ((UniformRange) range).getType() == UniformRange.UniformType.LOG ? true : false);
        // } else if(range instanceof VectorRange) {
        // //    				List<String> constants = new ArrayList<> ();
        // //    				for(int i=0; i<range.getNumElements(); i++) {
        // //    					constants.add(new Constant(i+"", new Expression(range.getElementAt(i))));
        // //    				}
        // //    				cas = ConstantArraySpec.createListSpec(target, constants);
        // 
        // } else {
        // throw new RuntimeException("Only 'Uniform Range' and 'Vector Range' are supported at this time.");
        // }
        // 
        // }
        // }
        // we identify the type of sedml simulation (uniform time course, etc)
        // and set the vCell simulation parameters accordingly
        SolverTaskDescription simTaskDesc = newSimulation.getSolverTaskDescription();
        TimeBounds timeBounds = new TimeBounds();
        TimeStep timeStep = new TimeStep();
        double outputTimeStep = 0.1;
        if (sedmlSimulation instanceof UniformTimeCourse) {
            // we translate initial time to zero, we provide output for the duration of the simulation
            // because we can't select just an interval the way the SEDML simulation can
            double initialTime = ((UniformTimeCourse) sedmlSimulation).getInitialTime();
            double outputStartTime = ((UniformTimeCourse) sedmlSimulation).getOutputStartTime();
            double outputEndTime = ((UniformTimeCourse) sedmlSimulation).getOutputEndTime();
            double outputNumberOfPoints = ((UniformTimeCourse) sedmlSimulation).getNumberOfPoints();
            outputTimeStep = (outputEndTime - outputStartTime) / outputNumberOfPoints;
            timeBounds = new TimeBounds(0, outputEndTime - initialTime);
        } else if (sedmlSimulation instanceof OneStep) {
        // for anything other than UniformTimeCourse we just ignore
        } else if (sedmlSimulation instanceof SteadyState) {
        } else {
        }
        OutputTimeSpec outputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
        simTaskDesc.setTimeBounds(timeBounds);
        simTaskDesc.setTimeStep(timeStep);
        simTaskDesc.setOutputTimeSpec(outputTimeSpec);
        newSimulation.setSolverTaskDescription(simTaskDesc);
        bioModel.addSimulation(newSimulation);
        newSimulation.refreshDependencies();
    } catch (Exception e) {
        e.printStackTrace();
        throw new RuntimeException("Unable to initialize bioModel for the given selection.");
    }
    return doc;
}

Example 15 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class ChooseFile 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 = fetch(hashTable, DocumentToExport.EXPORT_DOCUMENT, VCDocument.class, true);
    File exportFile = null;
    if (documentToExport instanceof BioModel) {
        exportFile = showBioModelXMLFileChooser(hashTable);
    } else if (documentToExport instanceof MathModel) {
        exportFile = showMathModelXMLFileChooser(hashTable);
    } else if (documentToExport instanceof Geometry) {
        exportFile = showGeometryModelXMLFileChooser(hashTable);
    } else {
        throw new Exception("Unsupported document type for XML export: " + documentToExport.getClass());
    }
    // check to see if we've changed extension from what user entered
    if (extensionUserProvided != null && !extensionUserProvided.isEmpty()) {
        String fp = exportFile.getAbsolutePath();
        String currentExt = FilenameUtils.getExtension(fp);
        if (!extensionUserProvided.equals(currentExt)) {
            hashTable.put(RENAME_KEY, fp);
        }
    }
    hashTable.put(EXPORT_FILE, exportFile);
}