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

Example 11 with XMLSource

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

the class RestDatabaseService method saveSimulation.

public SimulationSaveResponse saveSimulation(BiomodelSimulationSaveServerResource resource, User vcellUser, List<OverrideRepresentation> overrideRepresentations) throws PermissionException, ObjectNotFoundException, DataAccessException, SQLException, XmlParseException, PropertyVetoException, MappingException, ExpressionException {
    String simId = resource.getAttribute(VCellApiApplication.SIMULATIONID);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    boolean myModel = simRep.getOwner().compareEqual(vcellUser);
    // get the bioModel
    String biomodelId = resource.getAttribute(VCellApiApplication.BIOMODELID);
    KeyValue biomodelKey = new KeyValue(biomodelId);
    BigString bioModelXML = this.databaseServerImpl.getBioModelXML(vcellUser, biomodelKey);
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    // copy the simulation as new
    Simulation origSimulation = null;
    for (Simulation sim : bioModel.getSimulations()) {
        if (sim.getKey().equals(simKey)) {
            origSimulation = sim;
        }
    }
    if (origSimulation == null) {
        throw new RuntimeException("cannot find original Simulation");
    }
    SimulationContext simContext = bioModel.getSimulationContext(origSimulation);
    Simulation newUnsavedSimulation = simContext.copySimulation(origSimulation);
    // make appropriate changes
    // MATH OVERRIDES
    MathOverrides mathOverrides = new MathOverrides(newUnsavedSimulation);
    for (OverrideRepresentation overrideRep : overrideRepresentations) {
        overrideRep.applyMathOverrides(mathOverrides);
    }
    newUnsavedSimulation.setMathOverrides(mathOverrides);
    // save bioModel
    String editedBioModelXML = XmlHelper.bioModelToXML(bioModel);
    ServerDocumentManager serverDocumentManager = new ServerDocumentManager(this.databaseServerImpl);
    String modelName = bioModel.getName();
    if (!myModel) {
        modelName = modelName + "_" + Math.abs(new Random().nextInt());
    }
    String newBioModelXML = serverDocumentManager.saveBioModel(new QueryHashtable(), vcellUser, editedBioModelXML, modelName, null);
    BioModel savedBioModel = XmlHelper.XMLToBioModel(new XMLSource(newBioModelXML));
    Simulation savedSimulation = null;
    for (Simulation sim : savedBioModel.getSimulations()) {
        if (sim.getName().equals(newUnsavedSimulation.getName())) {
            savedSimulation = sim;
        }
    }
    if (savedSimulation == null) {
        throw new RuntimeException("cannot find new Simulation");
    }
    return new SimulationSaveResponse(savedBioModel, savedSimulation);
}

Example 12 with XMLSource

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

the class BioModelEditor method createNewBiomodelFromApp.

private void createNewBiomodelFromApp() {
    SimulationContext simulationContext = getSelectedSimulationContext();
    if (simulationContext == null) {
        PopupGenerator.showErrorDialog(this, "Please select an application.");
        return;
    }
    // bioModel.getVCMetaData().cleanupMetadata();
    try {
        String newBMXML = XmlHelper.bioModelToXML(bioModel);
        BioModel newBioModel = XmlHelper.XMLToBioModel(new XMLSource(newBMXML));
        newBioModel.clearVersion();
        SimulationContext[] newBMSimcontexts = newBioModel.getSimulationContexts();
        for (int i = 0; i < newBMSimcontexts.length; i++) {
            if (!newBMSimcontexts[i].getName().equals(simulationContext.getName())) {
                // Remove sims before removing simcontext
                Simulation[] newBMSims = newBMSimcontexts[i].getSimulations();
                for (int j = 0; j < newBMSims.length; j++) {
                    newBMSimcontexts[i].removeSimulation(newBMSims[j]);
                }
                newBioModel.removeSimulationContext(newBMSimcontexts[i]);
            }
        }
        VCDocument.DocumentCreationInfo newBMDocCreateInfo = new VCDocument.DocumentCreationInfo(VCDocumentType.BIOMODEL_DOC, VCDocument.BIO_OPTION_DEFAULT);
        newBMDocCreateInfo.setPreCreatedDocument(newBioModel);
        AsynchClientTask[] newBMTasks = getBioModelWindowManager().newDocument(newBMDocCreateInfo);
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), newBMTasks);
    } catch (Exception e) {
        e.printStackTrace();
        PopupGenerator.showErrorDialog(this, "Error creating new BioModel from Application '" + simulationContext.getName() + "'\n" + e.getMessage());
    }
}

Example 13 with XMLSource

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

the class RestDatabaseService method query.

public SimulationRepresentation query(BiomodelSimulationServerResource resource, User vcellUser) throws SQLException, DataAccessException, ExpressionException, XmlParseException, MappingException, MathException, MatrixException, ModelException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    ArrayList<String> conditions = new ArrayList<String>();
    String bioModelID = (String) resource.getRequestAttributes().get(VCellApiApplication.BIOMODELID);
    if (bioModelID != null) {
        conditions.add("(" + BioModelTable.table.id.getQualifiedColName() + " = " + bioModelID + ")");
    } else {
        throw new RuntimeException(VCellApiApplication.BIOMODELID + " not specified");
    }
    StringBuffer conditionsBuffer = new StringBuffer();
    for (String condition : conditions) {
        if (conditionsBuffer.length() > 0) {
            conditionsBuffer.append(" AND ");
        }
        conditionsBuffer.append(condition);
    }
    int startRow = 1;
    int maxRows = 1;
    BioModelRep[] bioModelReps = databaseServerImpl.getBioModelReps(vcellUser, conditionsBuffer.toString(), null, startRow, maxRows);
    for (BioModelRep bioModelRep : bioModelReps) {
        KeyValue[] simContextKeys = bioModelRep.getSimContextKeyList();
        for (KeyValue scKey : simContextKeys) {
            SimContextRep scRep = getSimContextRep(scKey);
            if (scRep != null) {
                bioModelRep.addSimContextRep(scRep);
            }
        }
        KeyValue[] simulationKeys = bioModelRep.getSimKeyList();
        for (KeyValue simKey : simulationKeys) {
            SimulationRep simulationRep = getSimulationRep(simKey);
            if (simulationRep != null) {
                bioModelRep.addSimulationRep(simulationRep);
            }
        }
    }
    if (bioModelReps == null || bioModelReps.length != 1) {
        // 
        // try to determine if the current credentials are insufficient, try to fetch BioModel again with administrator privilege.
        // 
        User adminUser = new User(PropertyLoader.ADMINISTRATOR_ACCOUNT, new KeyValue(PropertyLoader.ADMINISTRATOR_ID));
        BioModelRep[] allBioModelReps = databaseServerImpl.getBioModelReps(adminUser, conditionsBuffer.toString(), null, startRow, 1);
        if (allBioModelReps != null && allBioModelReps.length >= 0) {
            throw new PermissionException("insufficient privilege to retrive BioModel " + bioModelID);
        } else {
            throw new RuntimeException("failed to get biomodel");
        }
    }
    String simulationId = (String) resource.getRequestAttributes().get(VCellApiApplication.SIMULATIONID);
    if (simulationId == null) {
        throw new RuntimeException(VCellApiApplication.SIMULATIONID + " not specified");
    }
    SimulationRep simRep = getSimulationRep(new KeyValue(simulationId));
    BigString bioModelXML = databaseServerImpl.getBioModelXML(vcellUser, bioModelReps[0].getBmKey());
    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
    return new SimulationRepresentation(simRep, bioModel);
}

Example 14 with XMLSource

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

the class MathVerifier method testDocumentLoad.

private void testDocumentLoad(boolean bUpdateDatabase, User user, VCDocumentInfo documentInfo, VCDocument vcDocumentFromDBCache) {
    KeyValue versionKey = documentInfo.getVersion().getVersionKey();
    // try{
    // String vcDocumentXMLFromDBCacheRoundtrip = null;
    // Compare self same
    Exception bSameCachedAndNotCachedXMLExc = null;
    Exception bSameCachedAndNotCachedObjExc = null;
    Exception bSameSelfXMLCachedRoundtripExc = null;
    Boolean bSameCachedAndNotCachedXML = null;
    Boolean bSameCachedAndNotCachedObj = null;
    Boolean bSameSelfCachedRoundtrip = null;
    // Boolean bSameSelfObjCachedRoundTrip = null;
    long startTime = 0;
    // Long compareXMLTime = null;
    // Long compareObjTime = null;
    // Long loadOriginalXMLTime = null;
    Long loadUnresolvedTime = null;
    if (documentInfo instanceof BioModelInfo) {
        Level existingLogLevel = VCMLComparator.getLogLevel();
        try {
            String xmlRndTrip0 = XmlHelper.bioModelToXML((BioModel) vcDocumentFromDBCache);
            BioModel bioModelRndTrip0 = XmlHelper.XMLToBioModel(new XMLSource(xmlRndTrip0));
            String xmlRndTrip1 = XmlHelper.bioModelToXML((BioModel) bioModelRndTrip0);
            BioModel bioModelRndTrip1 = XmlHelper.XMLToBioModel(new XMLSource(xmlRndTrip1));
            if (Compare.logger != null) {
                Compare.loggingEnabled = true;
                VCMLComparator.setLogLevel(Level.DEBUG);
            }
            bSameSelfCachedRoundtrip = VCMLComparator.compareEquals(xmlRndTrip0, xmlRndTrip1, true);
            System.out.println("----------XML same=" + bSameSelfCachedRoundtrip);
            boolean objectSame = bioModelRndTrip0.compareEqual(bioModelRndTrip1);
            System.out.println("----------Objects same=" + objectSame);
            bSameSelfCachedRoundtrip = bSameSelfCachedRoundtrip && objectSame;
        } catch (Exception e) {
            bSameSelfCachedRoundtrip = null;
            lg.error(e.getMessage(), e);
            bSameSelfXMLCachedRoundtripExc = e;
        } finally {
            Compare.loggingEnabled = false;
            VCMLComparator.setLogLevel(existingLogLevel);
        }
        String fromDBBioModelUnresolvedXML = null;
        try {
            startTime = System.currentTimeMillis();
            fromDBBioModelUnresolvedXML = dbServerImpl.getServerDocumentManager().getBioModelUnresolved(new QueryHashtable(), user, versionKey);
            BioModel vcDocumentFromDBNotCached = XmlHelper.XMLToBioModel(new XMLSource(fromDBBioModelUnresolvedXML));
            loadUnresolvedTime = System.currentTimeMillis() - startTime;
            bSameCachedAndNotCachedObj = vcDocumentFromDBCache.compareEqual(vcDocumentFromDBNotCached);
        } catch (Exception e) {
            lg.error(e.getMessage(), e);
            bSameCachedAndNotCachedObjExc = e;
        }
        if (fromDBBioModelUnresolvedXML != null) {
            try {
                String vcDocumentXMLFromDBCacheRegenerate = XmlHelper.bioModelToXML((BioModel) vcDocumentFromDBCache);
                bSameCachedAndNotCachedXML = VCMLComparator.compareEquals(vcDocumentXMLFromDBCacheRegenerate, fromDBBioModelUnresolvedXML, true);
            } catch (Exception e) {
                lg.error(e.getMessage(), e);
                bSameCachedAndNotCachedXMLExc = e;
            }
        }
    } else {
        Level existingLogLevel = VCMLComparator.getLogLevel();
        try {
            String xmlRndTrip0 = XmlHelper.mathModelToXML((MathModel) vcDocumentFromDBCache);
            MathModel mathModelRndTrip0 = XmlHelper.XMLToMathModel(new XMLSource(xmlRndTrip0));
            String xmlRndTrip1 = XmlHelper.mathModelToXML((MathModel) mathModelRndTrip0);
            MathModel mathModelRndTrip1 = XmlHelper.XMLToMathModel(new XMLSource(xmlRndTrip1));
            if (Compare.logger != null) {
                Compare.loggingEnabled = true;
                VCMLComparator.setLogLevel(Level.DEBUG);
            }
            bSameSelfCachedRoundtrip = VCMLComparator.compareEquals(xmlRndTrip0, xmlRndTrip1, true);
            bSameSelfCachedRoundtrip = bSameSelfCachedRoundtrip && mathModelRndTrip0.compareEqual(mathModelRndTrip1);
        } catch (Exception e) {
            bSameSelfCachedRoundtrip = null;
            lg.error(e.getMessage(), e);
            bSameSelfXMLCachedRoundtripExc = e;
        } finally {
            Compare.loggingEnabled = false;
            VCMLComparator.setLogLevel(existingLogLevel);
        }
        String fromDBMathModelUnresolvedXML = null;
        try {
            startTime = System.currentTimeMillis();
            MathModel vcDocumentFromDBNotCached = dbServerImpl.getServerDocumentManager().getMathModelUnresolved(new QueryHashtable(), user, versionKey);
            loadUnresolvedTime = System.currentTimeMillis() - startTime;
            fromDBMathModelUnresolvedXML = XmlHelper.mathModelToXML(vcDocumentFromDBNotCached);
            bSameCachedAndNotCachedObj = vcDocumentFromDBCache.compareEqual(vcDocumentFromDBNotCached);
        } catch (Exception e) {
            lg.error(e.getMessage(), e);
            bSameCachedAndNotCachedObjExc = e;
        }
        if (fromDBMathModelUnresolvedXML != null) {
            try {
                String vcDocumentXMLFromDBCacheRegenerate = XmlHelper.mathModelToXML((MathModel) vcDocumentFromDBCache);
                bSameCachedAndNotCachedXML = VCMLComparator.compareEquals(vcDocumentXMLFromDBCacheRegenerate, fromDBMathModelUnresolvedXML, true);
            } catch (Exception e) {
                lg.error(e.getMessage(), e);
                bSameCachedAndNotCachedXMLExc = e;
            }
        }
    }
    if (bUpdateDatabase) {
        updateLoadModelsStatTable_CompareTest(versionKey, null, /*loadOriginalXMLTime*/
        loadUnresolvedTime, bSameCachedAndNotCachedXML, bSameCachedAndNotCachedObj, bSameSelfCachedRoundtrip, bSameCachedAndNotCachedXMLExc, bSameCachedAndNotCachedObjExc, bSameSelfXMLCachedRoundtripExc);
    } else {
        System.out.println("loadOriginalXMLTime=" + null + /*loadOriginalXMLTime*/
        " loadUnresolvedTime=" + loadUnresolvedTime);
        System.out.println("bSameCachedAndNotCachedXML=" + bSameCachedAndNotCachedXML + " bSameCachedAndNotCachedObj=" + bSameCachedAndNotCachedObj + " bSameSelfXMLCachedRoundtrip=" + bSameSelfCachedRoundtrip);
        System.out.println("bSameCachedAndNotCachedXMLExc=" + bSameCachedAndNotCachedXMLExc + "\nbSameCachedAndNotCachedObjExc=" + bSameCachedAndNotCachedObjExc + "\nbSameSelfXMLCachedRoundtripExc=" + bSameSelfXMLCachedRoundtripExc);
        System.out.println();
    }
}

Example 15 with XMLSource

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

the class MathVerifier method scan.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 */
public void scan(User[] users, boolean bUpdateDatabase, KeyValue[] bioAndMathModelKeys) throws MathException, MappingException, SQLException, DataAccessException, ModelException, ExpressionException {
    // java.util.Calendar calendar = java.util.GregorianCalendar.getInstance();
    // //	calendar.set(2002,java.util.Calendar.MAY,7+1);
    // calendar.set(2002,java.util.Calendar.JULY,1);
    // final java.util.Date fluxCorrectionOrDisablingBugFixDate = calendar.getTime();
    // //	calendar.set(2001,java.util.Calendar.JUNE,13+1);
    // calendar.set(2002,java.util.Calendar.JANUARY,1);
    // final java.util.Date totalVolumeCorrectionFixDate = calendar.getTime();
    KeyValue[] sortedBioAndMathModelKeys = null;
    if (bioAndMathModelKeys != null) {
        sortedBioAndMathModelKeys = bioAndMathModelKeys.clone();
        Arrays.sort(sortedBioAndMathModelKeys, keyValueCpmparator);
    }
    for (int i = 0; i < users.length; i++) {
        User user = users[i];
        BioModelInfo[] bioModelInfos0 = dbServerImpl.getBioModelInfos(user, false);
        MathModelInfo[] mathModelInfos0 = dbServerImpl.getMathModelInfos(user, false);
        if (lg.isTraceEnabled())
            lg.trace("Testing user '" + user + "'");
        Vector<VCDocumentInfo> userBioAndMathModelInfoV = new Vector<VCDocumentInfo>();
        userBioAndMathModelInfoV.addAll(Arrays.asList(bioModelInfos0));
        userBioAndMathModelInfoV.addAll(Arrays.asList(mathModelInfos0));
        // 
        for (int j = 0; j < userBioAndMathModelInfoV.size(); j++) {
            // 
            // if certain Bio or Math models are requested, then filter all else out
            // 
            VCDocumentInfo documentInfo = userBioAndMathModelInfoV.elementAt(j);
            KeyValue versionKey = documentInfo.getVersion().getVersionKey();
            if (sortedBioAndMathModelKeys != null) {
                int srch = Arrays.binarySearch(sortedBioAndMathModelKeys, versionKey, keyValueCpmparator);
                if (srch < 0) {
                    continue;
                }
            }
            if (!(documentInfo instanceof BioModelInfo)) {
                continue;
            }
            // 
            if (skipHash.contains(versionKey)) {
                System.out.println("skipping " + (documentInfo instanceof BioModelInfo ? "BioModel" : "MathModel") + " with key '" + versionKey + "'");
                continue;
            }
            try {
                // 
                // read in the BioModel and MathModel from the database
                // 
                VCDocument vcDocumentFromDBCache = null;
                BigString vcDocumentXMLFromDBCache = null;
                try {
                    long startTime = System.currentTimeMillis();
                    if (documentInfo instanceof BioModelInfo) {
                        vcDocumentXMLFromDBCache = new BigString(dbServerImpl.getServerDocumentManager().getBioModelXML(new QueryHashtable(), user, versionKey, false));
                        vcDocumentFromDBCache = XmlHelper.XMLToBioModel(new XMLSource(vcDocumentXMLFromDBCache.toString()));
                    } else {
                        vcDocumentXMLFromDBCache = new BigString(dbServerImpl.getServerDocumentManager().getMathModelXML(new QueryHashtable(), user, versionKey, false));
                        vcDocumentFromDBCache = XmlHelper.XMLToMathModel(new XMLSource(vcDocumentXMLFromDBCache.toString()));
                    }
                    if (bUpdateDatabase && testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                        updateLoadModelsStatTable_LoadTest(System.currentTimeMillis() - startTime, versionKey, null);
                    }
                } catch (Exception e) {
                    lg.error(e.getMessage(), e);
                    if (bUpdateDatabase && testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                        updateLoadModelsStatTable_LoadTest(0, versionKey, e);
                    }
                }
                if (testFlag.equals(MathVerifier.MV_LOAD_XML)) {
                    // 
                    if (vcDocumentXMLFromDBCache != null) {
                        testDocumentLoad(bUpdateDatabase, user, documentInfo, vcDocumentFromDBCache);
                    }
                } else if (testFlag.equals(MathVerifier.MV_DEFAULT)) {
                    // 
                    if (vcDocumentFromDBCache instanceof BioModel) {
                        BioModel bioModel = (BioModel) vcDocumentFromDBCache;
                        checkMathForBioModel(vcDocumentXMLFromDBCache, bioModel, user, bUpdateDatabase);
                    }
                }
            } catch (Throwable e) {
                // exception in whole BioModel
                lg.error(e.getMessage(), e);
            // can't update anything in database, since we don't know what simcontexts are involved
            }
        }
    }
}