Examples with XMLSource cbit.vcell.xml.XMLSource used on opensource projects

Example 1 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientRobot method run.

/**
 * Insert the method's description here.
 * Creation date: (3/8/01 3:04:15 PM)
 */
public void run() {
    try {
        String[] args = { host, userid, password };
        setManagerManager(cbit.vcell.client.test.ClientTester.mainInit(args, "ClientRobot", null));
        for (int i = 0; i < 10; i++) {
            log.print("Robot " + getName() + "starting loop : " + i);
            BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelFile));
            String newName = "bioModel_" + getName() + "_" + Math.random();
            log.print("Saving bioModel \"" + newName + "\"");
            getManagerManager().getDocumentManager().saveAsNew(bioModel, newName, null);
            BioModelInfo[] bioModelInfos = getManagerManager().getDocumentManager().getBioModelInfos();
            if (bioModelInfos != null && bioModelInfos.length > 0) {
                for (int j = 0; j < bioModelInfos.length; j++) {
                    log.print("bioModelInfo[" + j + "] = " + bioModelInfos[j]);
                }
            }
        }
    } catch (Throwable e) {
        log.exception(e);
    } finally {
        log.alert("Robot " + getName() + " exiting");
    }
}

Example 2 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class SBMLExportTest method getBiomodelByName.

static BioModel getBiomodelByName(VCellConnection vcn, String name) throws RemoteProxyException, DataAccessException, XmlParseException {
    EscapedName eName = new EscapedName(name);
    UserMetaDbServer dataServer = vcn.getUserMetaDbServer();
    for (BioModelInfo bmi : dataServer.getBioModelInfos(false)) {
        String mName = bmi.getVersion().getName();
        if (eName.matches(mName)) {
            KeyValue bioModelKey = bmi.getVersion().getVersionKey();
            BigString bioModelXML = dataServer.getBioModelXML(bioModelKey);
            BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
            return bioModel;
        }
    }
    // if not found, list what's available
    for (BioModelInfo bmi : dataServer.getBioModelInfos(false)) {
        String mName = bmi.getVersion().getName();
        System.out.println(mName);
    }
    return null;
}

Example 3 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientRequestManager method openAfterChecking.

private void openAfterChecking(VCDocumentInfo documentInfo, final TopLevelWindowManager requester, final boolean inNewWindow) {
    final String DOCUMENT_INFO = "documentInfo";
    final String SEDML_TASK = "SedMLTask";
    final String SEDML_MODELS = "SedMLModels";
    final String BNG_UNIT_SYSTEM = "bngUnitSystem";
    final String BMDB_DEFAULT_APPLICATION = "Deterministic";
    /* asynchronous and not blocking any window */
    bOpening = true;
    Hashtable<String, Object> hashTable = new Hashtable<String, Object>();
    // may want to insert corrected VCDocumentInfo later if our import debugger
    // corrects it (BNGL Debugger).
    hashTable.put(DOCUMENT_INFO, documentInfo);
    hashTable.put("isBMDB", false);
    hashTable.put("isSEDML", false);
    // start a thread that gets it and updates the GUI by creating a new document
    // desktop
    String taskName = null;
    if (documentInfo instanceof ExternalDocInfo) {
        taskName = "Importing document";
        ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
        File file = externalDocInfo.getFile();
        if (file != null && !file.getName().isEmpty() && file.getName().endsWith("bngl")) {
            BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
            String fileText;
            String originalFileText;
            try {
                fileText = BeanUtils.readBytesFromFile(file, null);
                originalFileText = new String(fileText);
            } catch (IOException e1) {
                e1.printStackTrace();
                DialogUtils.showErrorDialog(requester.getComponent(), "<html>Error reading file " + file.getPath() + "</html>");
                return;
            }
            Reader reader = externalDocInfo.getReader();
            boolean bException = true;
            while (bException) {
                try {
                    BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
                    boolean bStochastic = true;
                    boolean bRuleBased = true;
                    SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("temp NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
                    List<SimulationContext> appList = new ArrayList<SimulationContext>();
                    appList.add(ruleBasedSimContext);
                    RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                    RbmUtils.reactionRuleLabelIndex = 0;
                    RbmUtils.reactionRuleNames.clear();
                    ASTModel astModel = RbmUtils.importBnglFile(reader);
                    // for now, hasUnitSystem() always returns false
                    if (astModel.hasUnitSystem()) {
                        bngUnitSystem = astModel.getUnitSystem();
                    }
                    if (astModel.hasCompartments()) {
                        Structure struct = bioModel.getModel().getStructure(0);
                        if (struct != null) {
                            bioModel.getModel().removeStructure(struct);
                        }
                    }
                    BnglObjectConstructionVisitor constructionVisitor = null;
                    if (!astModel.hasMolecularDefinitions()) {
                        System.out.println("Molecular Definition Block missing.");
                        constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
                    } else {
                        constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
                    }
                    astModel.jjtAccept(constructionVisitor, rbmModelContainer);
                    bException = false;
                } catch (final Exception e) {
                    e.printStackTrace(System.out);
                    BNGLDebuggerPanel panel = new BNGLDebuggerPanel(fileText, e);
                    int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, "Bngl Debugger: " + file.getName());
                    if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
                        throw new UserCancelException("Canceling Import");
                    }
                    // inserting <potentially> corrected DocumentInfo
                    fileText = panel.getText();
                    externalDocInfo = new ExternalDocInfo(panel.getText());
                    reader = externalDocInfo.getReader();
                    hashTable.put(DOCUMENT_INFO, externalDocInfo);
                }
            }
            if (!originalFileText.equals(fileText)) {
                // file has been modified
                String message = "Importing <b>" + file.getName() + "</b> into vCell. <br>Overwrite the file on the disk?<br>";
                message = "<html>" + message + "</html>";
                Object[] options = { "Overwrite and Import", "Import Only", "Cancel" };
                int returnCode = JOptionPane.showOptionDialog(requester.getComponent(), message, "Bngl Debugger", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, options, options[2]);
                if (returnCode == JOptionPane.YES_OPTION) {
                    try {
                        FileWriter fw = new FileWriter(file);
                        fw.write(fileText);
                        fw.close();
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                } else if (returnCode == JOptionPane.CANCEL_OPTION || returnCode == JOptionPane.CLOSED_OPTION) {
                    return;
                }
            }
            if (!(bngUnitSystem.getOrigin() == BngUnitOrigin.PARSER)) {
                BNGLUnitsPanel panel = new BNGLUnitsPanel(bngUnitSystem);
                int oKCancel = DialogUtils.showComponentOKCancelDialog(requester.getComponent(), panel, " Bngl Units Selector", null, false);
                if (oKCancel == JOptionPane.CANCEL_OPTION || oKCancel == JOptionPane.DEFAULT_OPTION) {
                    // TODO: or do nothing and continue with default values?
                    return;
                } else {
                    bngUnitSystem = panel.getUnits();
                }
            }
            hashTable.put(BNG_UNIT_SYSTEM, bngUnitSystem);
        } else if (file != null && !file.getName().isEmpty() && file.getName().toLowerCase().endsWith(".sedml")) {
            try {
                XMLSource xmlSource = externalDocInfo.createXMLSource();
                File sedmlFile = xmlSource.getXmlFile();
                SedML sedml = Libsedml.readDocument(sedmlFile).getSedMLModel();
                if (sedml == null || sedml.getModels().isEmpty()) {
                    return;
                }
                // AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(),
                // file.getName());
                List<SedML> sedmls = new ArrayList<>();
                sedmls.add(sedml);
                hashTable.put(SEDML_MODELS, sedmls);
            // hashTable.put(SEDML_TASK, chosenTask);
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read document: " + e.getMessage(), e);
            }
        } else if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
            try {
                ArchiveComponents ac = null;
                ac = Libsedml.readSEDMLArchive(new FileInputStream(file));
                List<SEDMLDocument> docs = ac.getSedmlDocuments();
                List<SedML> sedmls = new ArrayList<>();
                for (SEDMLDocument doc : docs) {
                    SedML sedml = doc.getSedMLModel();
                    if (sedml == null) {
                        throw new RuntimeException("Failed importing " + file.getName());
                    }
                    if (sedml.getModels().isEmpty()) {
                        throw new RuntimeException("Unable to find any model in " + file.getName());
                    }
                    sedmls.add(sedml);
                }
                // AbstractTask chosenTask = SEDMLChooserPanel.chooseTask(sedml, requester.getComponent(),
                // file.getName());
                hashTable.put(SEDML_MODELS, sedmls);
            // hashTable.put(SEDML_TASK, chosenTask);
            } catch (Exception e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read archive: " + e.getMessage(), e);
            }
        }
    } else {
        taskName = "Loading document '" + documentInfo.getVersion().getName() + "' from database";
    }
    AsynchClientTask task0 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (!inNewWindow) {
                // request was to replace the document in an existing window
                getMdiManager().blockWindow(requester.getManagerID());
            }
        }
    };
    AsynchClientTask task1 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = null;
            List<VCDocument> docs = new ArrayList<>();
            boolean isBMDB = false;
            boolean isSEDML = false;
            VCDocumentInfo documentInfo = (VCDocumentInfo) hashTable.get(DOCUMENT_INFO);
            if (documentInfo instanceof BioModelInfo) {
                BioModelInfo bmi = (BioModelInfo) documentInfo;
                doc = getDocumentManager().getBioModel(bmi);
            } else if (documentInfo instanceof MathModelInfo) {
                MathModelInfo mmi = (MathModelInfo) documentInfo;
                doc = getDocumentManager().getMathModel(mmi);
            } else if (documentInfo instanceof GeometryInfo) {
                GeometryInfo gmi = (GeometryInfo) documentInfo;
                doc = getDocumentManager().getGeometry(gmi);
            } else if (documentInfo instanceof ExternalDocInfo) {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
                File file = externalDocInfo.getFile();
                if (file != null && !file.getName().isEmpty() && (file.getName().toLowerCase().endsWith(".sedx") || file.getName().toLowerCase().endsWith(".omex"))) {
                    TranslationLogger transLogger = new TranslationLogger(requester);
                    // iterate through one or more SEDML objects
                    List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
                    for (SedML sedml : sedmls) {
                        // default to import all tasks
                        List<VCDocument> vcdocs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, null, false);
                        for (VCDocument vcdoc : vcdocs) {
                            docs.add(vcdoc);
                        }
                    }
                    // treat the same since OMEX is just and archive with SED-ML file(s)
                    isSEDML = true;
                } else if (!externalDocInfo.isXML()) {
                    if (hashTable.containsKey(BNG_UNIT_SYSTEM)) {
                        // not XML, look for BNGL etc.
                        // we use the BngUnitSystem already created during the 1st pass
                        BngUnitSystem bngUnitSystem = (BngUnitSystem) hashTable.get(BNG_UNIT_SYSTEM);
                        BioModel bioModel = createDefaultBioModelDocument(bngUnitSystem);
                        SimulationContext ruleBasedSimContext = bioModel.addNewSimulationContext("NFSim app", SimulationContext.Application.RULE_BASED_STOCHASTIC);
                        SimulationContext odeSimContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
                        List<SimulationContext> appList = new ArrayList<SimulationContext>();
                        appList.add(ruleBasedSimContext);
                        appList.add(odeSimContext);
                        // set convention for initial conditions in generated application for seed
                        // species (concentration or count)
                        ruleBasedSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
                        odeSimContext.setUsingConcentration(bngUnitSystem.isConcentration());
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        RbmUtils.reactionRuleLabelIndex = 0;
                        RbmUtils.reactionRuleNames.clear();
                        Reader reader = externalDocInfo.getReader();
                        ASTModel astModel = RbmUtils.importBnglFile(reader);
                        if (bioModel.getModel() != null && bioModel.getModel().getVcMetaData() != null) {
                            VCMetaData vcMetaData = bioModel.getModel().getVcMetaData();
                            vcMetaData.setFreeTextAnnotation(bioModel, astModel.getProlog());
                        }
                        if (astModel.hasCompartments()) {
                            Structure struct = bioModel.getModel().getStructure(0);
                            if (struct != null) {
                                bioModel.getModel().removeStructure(struct);
                            }
                        }
                        BnglObjectConstructionVisitor constructionVisitor = null;
                        if (!astModel.hasMolecularDefinitions()) {
                            System.out.println("Molecular Definition Block missing. Extracting it from Species, Reactions, Obserbables.");
                            constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, false);
                        } else {
                            constructionVisitor = new BnglObjectConstructionVisitor(bioModel.getModel(), appList, bngUnitSystem, true);
                        }
                        // we'll convert the kinetic parameters to BngUnitSystem inside the
                        // visit(ASTKineticsParameter...)
                        astModel.jjtAccept(constructionVisitor, rbmModelContainer);
                        // set the volume in the newly created application to
                        // BngUnitSystem.bnglModelVolume
                        // TODO: set the right values if we import compartments from the bngl file!
                        // if(!bngUnitSystem.isConcentration()) {
                        Expression sizeExpression = new Expression(bngUnitSystem.getVolume());
                        ruleBasedSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
                        odeSimContext.getGeometryContext().getStructureMapping(0).getSizeParameter().setExpression(sizeExpression);
                        // }
                        // we remove the NFSim application if any seed species is clamped because NFSim
                        // doesn't know what to do with it
                        boolean bClamped = false;
                        for (SpeciesContextSpec scs : ruleBasedSimContext.getReactionContext().getSpeciesContextSpecs()) {
                            if (scs.isConstant()) {
                                bClamped = true;
                                break;
                            }
                        }
                        if (bClamped) {
                            bioModel.removeSimulationContext(ruleBasedSimContext);
                        }
                        // // TODO: DON'T delete this code
                        // // the code below is needed if we also want to create simulations, example for 1 rule based simulation
                        // // it is rule-based so it wont have to flatten, should be fast.
                        // MathMappingCallback callback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
                        // NetworkGenerationRequirements networkGenerationRequirements = null; // network generation should not be executed.
                        // ruleBasedSimContext.refreshMathDescription(callback,networkGenerationRequirements);
                        // Simulation sim = ruleBasedSimContext.addNewSimulation(SimulationOwner.DEFAULT_SIM_NAME_PREFIX,callback,networkGenerationRequirements);
                        doc = bioModel;
                    }
                } else {
                    // is XML
                    try (TranslationLogger transLogger = new TranslationLogger(requester)) {
                        XMLSource xmlSource = externalDocInfo.createXMLSource();
                        org.jdom.Element rootElement = xmlSource.getXmlDoc().getRootElement();
                        String xmlType = rootElement.getName();
                        String modelXmlType = null;
                        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.
                            @SuppressWarnings("unchecked") List<Element> childElementList = rootElement.getChildren();
                            // assuming first child is the biomodel,
                            Element modelElement = childElementList.get(0);
                            // mathmodel or geometry.
                            modelXmlType = modelElement.getName();
                        }
                        if (xmlType.equals(XMLTags.BioModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.BioModelTag))) {
                            doc = XmlHelper.XMLToBioModel(xmlSource);
                        } else if (xmlType.equals(XMLTags.MathModelTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.MathModelTag))) {
                            doc = XmlHelper.XMLToMathModel(xmlSource);
                        } else if (xmlType.equals(XMLTags.GeometryTag) || (xmlType.equals(XMLTags.VcmlRootNodeTag) && modelXmlType.equals(XMLTags.GeometryTag))) {
                            doc = XmlHelper.XMLToGeometry(xmlSource);
                        } else if (xmlType.equals(XMLTags.SbmlRootNodeTag)) {
                            Namespace namespace = rootElement.getNamespace(XMLTags.SBML_SPATIAL_NS_PREFIX);
                            isBMDB = externalDocInfo.isBioModelsNet();
                            boolean bIsSpatial = (namespace == null) ? false : true;
                            doc = XmlHelper.importSBML(transLogger, xmlSource, bIsSpatial);
                        } else if (xmlType.equals(XMLTags.CellmlRootNodeTag)) {
                            if (requester instanceof BioModelWindowManager) {
                                doc = XmlHelper.importBioCellML(transLogger, xmlSource);
                            } else {
                                doc = XmlHelper.importMathCellML(transLogger, xmlSource);
                            }
                        } else if (xmlType.equals(MicroscopyXMLTags.FRAPStudyTag)) {
                            doc = VFrapXmlHelper.VFRAPToBioModel(hashTable, xmlSource, getDocumentManager(), requester);
                        } else if (xmlType.equals(XMLTags.SedMLTypeTag)) {
                            // we know it is a single SedML since it is an actual XML source
                            List<SedML> sedmls = (List<SedML>) hashTable.get(SEDML_MODELS);
                            SedML sedml = sedmls.get(0);
                            // default to import all tasks
                            docs = XmlHelper.sedmlToBioModel(transLogger, externalDocInfo, sedml, null, externalDocInfo.getFile().getAbsolutePath(), false);
                            isSEDML = true;
                        } else {
                            // unknown XML format
                            throw new RuntimeException("unsupported XML format, first element tag is <" + rootElement.getName() + ">");
                        }
                        if (externalDocInfo.getDefaultName() != null) {
                            doc.setName(externalDocInfo.getDefaultName());
                        }
                    }
                }
                if (doc == null && docs == null) {
                    File f = externalDocInfo.getFile();
                    if (f != null) {
                        throw new RuntimeException("Unable to determine type of file " + f.getCanonicalPath());
                    }
                    throw new ProgrammingException();
                }
            }
            // create biopax objects using annotation
            if (doc instanceof BioModel) {
                BioModel bioModel = (BioModel) doc;
                try {
                    bioModel.getVCMetaData().createBioPaxObjects(bioModel);
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
            requester.prepareDocumentToLoad(doc, inNewWindow);
            hashTable.put("isBMDB", isBMDB);
            hashTable.put("isSEDML", isSEDML);
            if (!isSEDML) {
                hashTable.put("doc", doc);
            } else {
                hashTable.put("docs", docs);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("Showing document", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            try {
                Throwable exc = (Throwable) hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR);
                if (exc == null) {
                    boolean isSEDML = (boolean) hashTable.get("isSEDML");
                    if (isSEDML) {
                        List<VCDocument> docs = (List<VCDocument>) hashTable.get("docs");
                        List<DocumentWindowManager> windowManagers = new ArrayList<DocumentWindowManager>();
                        for (VCDocument doc : docs) {
                            DocumentWindowManager windowManager = createDocumentWindowManager(doc);
                            getMdiManager().createNewDocumentWindow(windowManager);
                            windowManagers.add(windowManager);
                        }
                        hashTable.put("managers", windowManagers);
                        hashTable.put("docs", docs);
                    } else {
                        VCDocument doc = (VCDocument) hashTable.get("doc");
                        DocumentWindowManager windowManager = null;
                        if (inNewWindow) {
                            windowManager = createDocumentWindowManager(doc);
                            // request was to create a new top-level window with this doc
                            getMdiManager().createNewDocumentWindow(windowManager);
                        } else {
                            // request was to replace the document in an existing window
                            windowManager = (DocumentWindowManager) requester;
                            getMdiManager().setCanonicalTitle(requester.getManagerID());
                            windowManager.resetDocument(doc);
                        }
                        hashTable.put(WIN_MGR_KEY, windowManager);
                        hashTable.put("doc", doc);
                    }
                }
            } catch (Exception ex) {
                ex.printStackTrace();
            // TODO: check why getMdiManager().createNewDocumentWindow(windowManager) fails sometimes
            } finally {
                if (!inNewWindow) {
                    getMdiManager().unBlockWindow(requester.getManagerID());
                }
                bOpening = false;
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("Special Layout", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (documentInfo instanceof ExternalDocInfo) {
                ExternalDocInfo externalDocInfo = (ExternalDocInfo) documentInfo;
                boolean isSEDML = (boolean) hashTable.get("isSEDML");
                if (externalDocInfo.isBioModelsNet() || externalDocInfo.isFromXmlFile() || !isSEDML) {
                    DocumentWindowManager windowManager = (DocumentWindowManager) hashTable.get(WIN_MGR_KEY);
                    if (windowManager instanceof BioModelWindowManager) {
                        ((BioModelWindowManager) windowManager).specialLayout();
                    }
                }
                if (isSEDML) {
                    List<DocumentWindowManager> windowManagers = (List<DocumentWindowManager>) hashTable.get("managers");
                    if (windowManagers != null) {
                        for (DocumentWindowManager manager : windowManagers) {
                            ((BioModelWindowManager) manager).specialLayout();
                        }
                    }
                }
            }
        }
    };
    AsynchClientTask task4 = new AsynchClientTaskFunction(ClientRequestManager::setWindowFocus, "Set window focus", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false);
    AsynchClientTask task6 = new AsynchClientTask("Renaming, please wait...", // TASKTYPE_NONSWING_BLOCKING
    AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, // TASKTYPE_NONSWING_BLOCKING
    false, // TASKTYPE_NONSWING_BLOCKING
    false) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            VCDocument doc = (VCDocument) hashTable.get("doc");
            if (!(doc instanceof BioModel)) {
                return;
            }
            boolean isBMDB = (boolean) hashTable.get("isBMDB");
            if (documentInfo instanceof ExternalDocInfo) {
                if (isBMDB) {
                    idToNameConversion(doc);
                }
            }
            if (isBMDB) {
                BioModel bioModel = (BioModel) doc;
                SimulationContext simulationContext = bioModel.getSimulationContext(0);
                simulationContext.setName(BMDB_DEFAULT_APPLICATION);
                MathMappingCallback callback = new MathMappingCallback() {

                    @Override
                    public void setProgressFraction(float fractionDone) {
                    }

                    @Override
                    public void setMessage(String message) {
                    }

                    @Override
                    public boolean isInterrupted() {
                        return false;
                    }
                };
                MathMapping mathMapping = simulationContext.createNewMathMapping(callback, NetworkGenerationRequirements.ComputeFullNoTimeout);
                MathDescription mathDesc = null;
                try {
                    mathDesc = mathMapping.getMathDescription(callback);
                    simulationContext.setMathDescription(mathDesc);
                    Simulation sim = new Simulation(mathDesc);
                    sim.setName(simulationContext.getBioModel().getFreeSimulationName());
                    simulationContext.addSimulation(sim);
                    bioModel.refreshDependencies();
                } catch (MappingException | MathException | MatrixException | ExpressionException | ModelException e1) {
                    e1.printStackTrace();
                }
                hashTable.put("doc", doc);
            }
        }
    };
    ClientTaskDispatcher.dispatch(requester.getComponent(), hashTable, new AsynchClientTask[] { task0, task1, task6, task2, task3, task4 }, false);
}

Example 4 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class BiomodelBNGLServerResource method getBiomodelBNGL.

private String getBiomodelBNGL(User vcellUser) {
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        // Make temporary resource compatible with restDatabaseService so we can re-use
        BiomodelVCMLServerResource bmsr = new BiomodelVCMLServerResource() {

            @Override
            public Map<String, Object> getRequestAttributes() {
                HashMap<String, Object> hashMap = new HashMap<String, Object>();
                hashMap.put(VCellApiApplication.BIOMODELID, BiomodelBNGLServerResource.this.biomodelid);
                return hashMap;
            }

            @Override
            public Request getRequest() {
                // TODO Auto-generated method stub
                return BiomodelBNGLServerResource.this.getRequest();
            }
        };
        StringWriter bnglStringWriter = new StringWriter();
        PrintWriter pw = new PrintWriter(bnglStringWriter);
        String biomodelVCML = restDatabaseService.query(bmsr, vcellUser);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(biomodelVCML));
        SimulationContext chosenSimContext = bioModel.getSimulationContext(0);
        RbmNetworkGenerator.writeBngl(chosenSimContext, pw, false, true);
        String resultString = bnglStringWriter.toString();
        return resultString;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

Example 5 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class VCComprehensiveStatistics method waitForModel.

private Object waitForModel(final BigString modelXML, final boolean bMath) {
    final Object[] modelArr = new Object[] { null };
    final Exception[] excArr = new Exception[] { null };
    final Boolean[] flagArr = new Boolean[] { false };
    long startTime = System.currentTimeMillis();
    Thread processThread = new Thread(new Runnable() {

        @Override
        public void run() {
            try {
                if (bMath) {
                    modelArr[0] = XmlHelper.XMLToMathModel(new XMLSource(modelXML.toString()));
                    ((MathModel) modelArr[0]).refreshDependencies();
                } else {
                    modelArr[0] = XmlHelper.XMLToBioModel(new XMLSource(modelXML.toString()));
                    ((BioModel) modelArr[0]).refreshDependencies();
                }
                flagArr[0] = true;
            } catch (Exception e) {
                e.printStackTrace();
                excArr[0] = e;
            }
        }
    });
    processThread.start();
    boolean bOK = false;
    while (true) {
        if ((System.currentTimeMillis() - startTime) > 60 * 1000) {
            break;
        }
        if (excArr[0] != null) {
            break;
        }
        if (flagArr[0]) {
            bOK = true;
            break;
        }
        try {
            Thread.sleep(500);
        } catch (InterruptedException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    if (!bOK) {
        return null;
    }
    if (bMath) {
        return (MathModel) modelArr[0];
    } else {
        return (BioModel) modelArr[0];
    }
}