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

Example 1 with GroupAccessNone

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

the class DbDriver method insertVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.KeyValue
 * @param versionable cbit.sql.Versionable
 * @param pRef cbit.sql.KeyValue
 * @param bCommit boolean
 */
protected Version insertVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, String name, String annot, boolean bVersion) throws SQLException, DataAccessException {
    if (hash.getDatabaseKey(versionable) != null) {
        throw new DataAccessException(versionable + " already inserted in this transaction");
    }
    VersionableType vType = VersionTable.versionableTypeFromVersionable(versionable);
    if (vType.getIsTopLevel() && isNameUsed(con, vType, user, name)) {
        throw new DataAccessException("'" + user.getName() + "' already has a " + vType.getTypeName() + " with name '" + name + "'");
    }
    User owner = user;
    // AccessInfo accessInfo = new AccessInfo(AccessInfo.PRIVATE_CODE);
    GroupAccess accessInfo = new GroupAccessNone();
    KeyValue versionKey = keyFactory.getNewKey(con);
    java.util.Date date = getNewDate(con);
    // if(versionable.getVersion().getVersionKey() != null){
    // throw new DataAccessException("GeomDbDriver:insertVersionable, VersionKey must be null to insert");
    // }
    String versionName = name;
    // Check for Archive and Publish not needed in insert because versionflag is always forced to Current
    VersionFlag versionFlag = null;
    // if(bVersion){
    // versionFlag = VersionFlag.Archived;
    // }else{
    versionFlag = VersionFlag.Current;
    // }
    KeyValue PRefKey = null;
    java.math.BigDecimal branchID = getNewBranchID(con);
    // 
    // Insert Software Version
    // 
    insertSoftwareVersion(con, versionKey);
    // 
    return new Version(versionKey, versionName, owner, accessInfo, PRefKey, branchID, date, versionFlag, annot);
}

Example 2 with GroupAccessNone

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

the class DbDriver method groupAddUser.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param user cbit.vcell.server.User
 * @param versionable cbit.sql.Versionable
 */
public static void groupAddUser(Connection con, KeyFactory keyFactory, User owner, VersionableType vType, KeyValue vKey, String userAddToGroupString, boolean isHiddenFromOwner, DatabaseSyntax dbSyntax) throws SQLException, ObjectNotFoundException, DataAccessException {
    User userAddToGroup = getUserFromUserid(con, userAddToGroupString);
    if (userAddToGroup == null) {
        throw new IllegalArgumentException("User name " + userAddToGroupString + " not found");
    }
    // 
    if ((con == null) || (vType == null) || (owner == null) || (vKey == null) || (userAddToGroup == null)) {
        throw new IllegalArgumentException("Improper parameters for groupAddUser userAddToGroupString=" + (userAddToGroupString == null ? "NULL" : userAddToGroupString));
    }
    // 
    Version currentVersion = permissionInit(con, vType, vKey, owner);
    // If userAddToGroup is already in group it is an error
    // ----- Also can't add members to GroupAccessAll(Public) (CHANGED!!!) -----
    boolean bExists = false;
    if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
        bExists = (((GroupAccessSome) currentVersion.getGroupAccess()).isNormalMember(userAddToGroup) && !isHiddenFromOwner) || (((GroupAccessSome) currentVersion.getGroupAccess()).isHiddenMember(userAddToGroup) && isHiddenFromOwner);
    }
    // }
    if (currentVersion.getOwner().compareEqual(userAddToGroup) || bExists) {
        throw new DataAccessException(userAddToGroup + " Already a member of group");
    }
    if (lg.isTraceEnabled())
        lg.trace("DbDriver.groupAddUser(user=" + owner + ", type =" + vType + ", key=" + vKey + ")");
    VersionTable vTable = VersionTable.getVersionTable(vType);
    // 
    // 
    BigDecimal newHash = null;
    // 
    if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
        // Calculate the hash of the currentVersion's group plus a new user
        GroupAccessSome currentGroup = (GroupAccessSome) currentVersion.getGroupAccess();
        newHash = currentGroup.calculateHashWithNewMember(userAddToGroup, isHiddenFromOwner);
    } else if (currentVersion.getGroupAccess() instanceof GroupAccessNone || currentVersion.getGroupAccess() instanceof GroupAccessAll) {
        // Calculate hash for a new group with only userAddToGroup in it
        KeyValue[] kvArr = new KeyValue[1];
        boolean[] hiddenArr = new boolean[1];
        kvArr[0] = userAddToGroup.getID();
        hiddenArr[0] = isHiddenFromOwner;
        newHash = GroupAccess.calculateHash(kvArr, hiddenArr);
    }
    // 
    BigDecimal updatedGroupID = null;
    // 
    // See if the newly calculated hash is present in the database GroupTable
    // indicating a group we can reuse by reference
    // 
    String sql = "SELECT groupid FROM " + GroupTable.table.getTableName() + " WHERE groupMemberHash = " + newHash.toString();
    java.sql.Statement stmt = con.createStatement();
    try {
        java.sql.ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            // There may be more than one, just get the first, all have the same groupid and hash
            // Group already exists,Re-Use the groupid, we don't have to make a new group
            updatedGroupID = rset.getBigDecimal(GroupTable.table.groupid.toString());
        }
    } finally {
        stmt.close();
    }
    // 
    if (updatedGroupID == null) {
        // Create new Group id
        updatedGroupID = getNewGroupID(con, keyFactory);
        int groupMemberCount = 1;
        // Get all the members of the currentVersion Group or skip if currentVersion group is GroupAccessNone
        // Don't worry about GroupAccessAll, we couldn't have gotten this far
        // 
        // Add new User
        // 
        sql = "INSERT INTO " + GroupTable.table.getTableName() + " VALUES ( " + keyFactory.getNewKey(con).toString() + "," + updatedGroupID + "," + userAddToGroup.getID().toString() + "," + (isHiddenFromOwner ? "1" : "0") + "," + newHash + " )";
        updateCleanSQL(con, sql);
        if (currentVersion.getGroupAccess() instanceof GroupAccessSome) {
            // Add all the old Normal Users
            User[] normalUsers = ((GroupAccessSome) currentVersion.getGroupAccess()).getNormalGroupMembers();
            for (int i = 0; normalUsers != null && i < normalUsers.length; i += 1) {
                String userRef = normalUsers[i].getID().toString();
                sql = "INSERT INTO " + GroupTable.table.getTableName() + " VALUES ( " + keyFactory.getNewKey(con).toString() + "," + updatedGroupID + "," + userRef + "," + (false ? "1" : "0") + "," + newHash + " )";
                updateCleanSQL(con, sql);
            }
            // Add all the old Hidden Users
            User[] hiddenUsers = ((GroupAccessSome) currentVersion.getGroupAccess()).getHiddenGroupMembers();
            for (int i = 0; hiddenUsers != null && i < hiddenUsers.length; i += 1) {
                String userRef = hiddenUsers[i].getID().toString();
                sql = "INSERT INTO " + GroupTable.table.getTableName() + " VALUES ( " + keyFactory.getNewKey(con).toString() + "," + updatedGroupID + "," + userRef + "," + (true ? "1" : "0") + "," + newHash + " )";
                updateCleanSQL(con, sql);
            }
        }
    }
    // Update the vTable to point to the new Group
    String set = vTable.privacy.getQualifiedColName() + " = " + updatedGroupID;
    String cond = vTable.id.getQualifiedColName() + " = " + vKey;
    // " AND " + vTable.ownerRef.getQualifiedColName() + " = " + owner.getID();
    sql = DatabasePolicySQL.enforceOwnershipUpdate(owner, vTable, set, cond);
    // System.out.println(sql);
    int numRowsProcessed = updateCleanSQL(con, sql);
    if (numRowsProcessed != 1) {
        // 
        // check if update failed
        // 
        Vector<VersionInfo> versionInfoList = getVersionableInfos(con, owner, vType, false, vKey, true, dbSyntax);
        if (versionInfoList.size() == 0) {
            throw new DataAccessException("Add User " + userAddToGroup + " Permission to access failed, " + vType.getTypeName() + "(" + vKey + ") record not found");
        } else {
            throw new DataAccessException("Add User " + userAddToGroup + " Permission to access failed " + vType.getTypeName() + "(" + vKey + ")");
        }
    }
}

Example 3 with GroupAccessNone

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

the class Generate2DExpModelOpAbstract method generateModel.

public final GeneratedModelResults generateModel(double deltaX, double bleachRadius, double cellRadius, double bleachDuration, double bleachRate, double postbleachDelay, double postbleachDuration, double psfSigma, double outputTimeStep, double primaryDiffusionRate, double primaryFraction, double bleachMonitorRate, double secondaryDiffusionRate, double secondaryFraction, String extracellularName, String cytosolName, Context context) throws PropertyVetoException, ExpressionException, GeometryException, ImageException, ModelException, MappingException, MathException, MatrixException {
    double domainSize = 2.2 * cellRadius;
    Extent extent = new Extent(domainSize, domainSize, 1.0);
    Origin origin = new Origin(-extent.getX() / 2.0, -extent.getY() / 2.0, -extent.getZ() / 2.0);
    String EXTRACELLULAR_NAME = extracellularName;
    String CYTOSOL_NAME = cytosolName;
    AnalyticSubVolume cytosolSubVolume = new AnalyticSubVolume(CYTOSOL_NAME, new Expression("pow(x,2)+pow(y,2)<pow(" + cellRadius + ",2)"));
    AnalyticSubVolume extracellularSubVolume = new AnalyticSubVolume(EXTRACELLULAR_NAME, new Expression(1.0));
    Geometry geometry = new Geometry("geometry", 2);
    geometry.getGeometrySpec().setExtent(extent);
    geometry.getGeometrySpec().setOrigin(origin);
    geometry.getGeometrySpec().addSubVolume(extracellularSubVolume);
    geometry.getGeometrySpec().addSubVolume(cytosolSubVolume, true);
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    model.addFeature(EXTRACELLULAR_NAME);
    Feature extracellular = (Feature) model.getStructure(EXTRACELLULAR_NAME);
    model.addFeature(CYTOSOL_NAME);
    Feature cytosol = (Feature) model.getStructure(CYTOSOL_NAME);
    SpeciesContext immobileSC = model.createSpeciesContext(cytosol);
    SpeciesContext primarySC = model.createSpeciesContext(cytosol);
    SpeciesContext secondarySC = model.createSpeciesContext(cytosol);
    // 
    // common bleaching rate for all species
    // 
    double bleachStart = 10 * outputTimeStep - bleachDuration - postbleachDelay;
    double bleachEnd = bleachStart + bleachDuration;
    Expression bleachRateExp = createBleachExpression(bleachRadius, bleachRate, bleachMonitorRate, bleachStart, bleachEnd);
    {
        SimpleReaction immobileBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics immobileBWMKinetics = new GeneralKinetics(immobileBWM);
        immobileBWM.setKinetics(immobileBWMKinetics);
        immobileBWM.addReactant(immobileSC, 1);
        immobileBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(immobileSC.getName())));
    }
    {
        SimpleReaction primaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics primaryBWMKinetics = new GeneralKinetics(primaryBWM);
        primaryBWM.setKinetics(primaryBWMKinetics);
        primaryBWM.addReactant(primarySC, 1);
        primaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(primarySC.getName())));
    }
    {
        SimpleReaction secondaryBWM = model.createSimpleReaction(cytosol);
        GeneralKinetics secondaryBWMKinetics = new GeneralKinetics(secondaryBWM);
        secondaryBWM.setKinetics(secondaryBWMKinetics);
        secondaryBWM.addReactant(secondarySC, 1);
        secondaryBWMKinetics.getReactionRateParameter().setExpression(Expression.mult(bleachRateExp, new Expression(secondarySC.getName())));
    }
    // create simulation context
    SimulationContext simContext = bioModel.addNewSimulationContext("simContext", SimulationContext.Application.NETWORK_DETERMINISTIC);
    simContext.setGeometry(geometry);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    // unused? SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    double fixedFraction = 1.0 - primaryFraction - secondaryFraction;
    SpeciesContextSpec immobileSCS = simContext.getReactionContext().getSpeciesContextSpec(immobileSC);
    immobileSCS.getInitialConditionParameter().setExpression(new Expression(fixedFraction));
    immobileSCS.getDiffusionParameter().setExpression(new Expression(0.0));
    SpeciesContextSpec primarySCS = simContext.getReactionContext().getSpeciesContextSpec(primarySC);
    primarySCS.getInitialConditionParameter().setExpression(new Expression(primaryFraction));
    primarySCS.getDiffusionParameter().setExpression(new Expression(primaryDiffusionRate));
    SpeciesContextSpec secondarySCS = simContext.getReactionContext().getSpeciesContextSpec(secondarySC);
    secondarySCS.getInitialConditionParameter().setExpression(new Expression(secondaryFraction));
    secondarySCS.getDiffusionParameter().setExpression(new Expression(secondaryDiffusionRate));
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(immobileSC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(primarySC);
    simContext.getMicroscopeMeasurement().addFluorescentSpecies(secondarySC);
    simContext.getMicroscopeMeasurement().setConvolutionKernel(new GaussianConvolutionKernel(new Expression(psfSigma), new Expression(psfSigma)));
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    simContext.setMathDescription(mathDesc);
    User owner = context.getDefaultOwner();
    int meshSize = (int) (domainSize / deltaX);
    if (meshSize % 2 == 0) {
        // want an odd-sized mesh in x and y ... so centered at the origin.
        meshSize = meshSize + 1;
    }
    TimeBounds timeBounds = new TimeBounds(0.0, postbleachDuration);
    // 
    // simulation to use for data generation (output time steps as recorded by the microscope)
    // 
    double bleachBlackoutBegin = bleachStart - postbleachDelay;
    double bleachBlackoutEnd = bleachEnd + postbleachDelay;
    // ArrayList<Double> times = new ArrayList<Double>();
    // double time = 0;
    // while (time<=timeBounds.getEndingTime()){
    // if (time<=bleachBlackoutBegin || time>bleachBlackoutEnd){
    // // postbleachDelay is the time it takes to switch the filters.
    // times.add(time);
    // }
    // time += outputTimeStep.getData();
    // }
    // double[] timeArray = new double[times.size()];
    // for (int i=0;i<timeArray.length;i++){
    // timeArray[i] = times.get(i);
    // }
    // OutputTimeSpec fakeDataSimOutputTimeSpec = new ExplicitOutputTimeSpec(timeArray);
    OutputTimeSpec fakeDataSimOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep);
    KeyValue fakeDataSimKey = context.createNewKeyValue();
    SimulationVersion fakeDataSimVersion = new SimulationVersion(fakeDataSimKey, "fakeDataSim", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fakeDataSim = new Simulation(fakeDataSimVersion, mathDesc);
    simContext.addSimulation(fakeDataSim);
    fakeDataSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fakeDataSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fakeDataSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fakeDataSim.getSolverTaskDescription().setOutputTimeSpec(fakeDataSimOutputTimeSpec);
    // 
    // simulation to use for viewing the protocol (output time steps to understand the physics)
    // 
    KeyValue fullExperimentSimKey = context.createNewKeyValue();
    SimulationVersion fullExperimentSimVersion = new SimulationVersion(fullExperimentSimKey, "fullExperiment", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation fullExperimentSim = new Simulation(fullExperimentSimVersion, mathDesc);
    simContext.addSimulation(fullExperimentSim);
    OutputTimeSpec fullExperimentOutputTimeSpec = new UniformOutputTimeSpec(outputTimeStep / 10.0);
    fullExperimentSim.getSolverTaskDescription().setTimeBounds(timeBounds);
    fullExperimentSim.getMeshSpecification().setSamplingSize(new ISize(meshSize, meshSize, 1));
    fullExperimentSim.getSolverTaskDescription().setSolverDescription(SolverDescription.SundialsPDE);
    fullExperimentSim.getSolverTaskDescription().setOutputTimeSpec(fullExperimentOutputTimeSpec);
    GeneratedModelResults results = new GeneratedModelResults();
    results.bioModel_2D = bioModel;
    results.simulation_2D = fakeDataSim;
    results.bleachBlackoutBeginTime = bleachBlackoutBegin;
    results.bleachBlackoutEndTime = bleachBlackoutEnd;
    return results;
}

Example 4 with GroupAccessNone

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

the class FRAPStudy method createNewRefBioModel.

public static BioModel createNewRefBioModel(FRAPStudy sourceFrapStudy, String baseDiffusionRate, TimeStep tStep, KeyValue simKey, User owner, FieldDataIdentifierSpec psfFDIS, int startingIndexForRecovery) throws Exception {
    if (owner == null) {
        throw new Exception("Owner is not defined");
    }
    ROI cellROI_2D = sourceFrapStudy.getFrapData().getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    Extent extent = sourceFrapStudy.getFrapData().getImageDataset().getExtent();
    TimeBounds timeBounds = FRAPOptData.getEstimatedRefTimeBound(sourceFrapStudy);
    double timeStepVal = FRAPOptData.REFERENCE_DIFF_DELTAT;
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    int subVolume0PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(0).setName((subVolume0PixVal == EXTRACELLULAR_PIXVAL ? EXTRACELLULAR_NAME : CYTOSOL_NAME));
    int subVolume1PixVal = ((ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1)).getPixelValue();
    geometry.getGeometrySpec().getSubVolume(1).setName((subVolume1PixVal == CYTOSOL_PIXVAL ? CYTOSOL_NAME : EXTRACELLULAR_NAME));
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    String roiDataName = FRAPStudy.ROI_EXTDATA_NAME;
    final int ONE_DIFFUSION_SPECIES_COUNT = 1;
    final int MOBILE_SPECIES_INDEX = 0;
    Expression[] diffusionConstants = new Expression[ONE_DIFFUSION_SPECIES_COUNT];
    Species[] species = new Species[ONE_DIFFUSION_SPECIES_COUNT];
    SpeciesContext[] speciesContexts = new SpeciesContext[ONE_DIFFUSION_SPECIES_COUNT];
    Expression[] initialConditions = new Expression[ONE_DIFFUSION_SPECIES_COUNT];
    // Mobile Species
    diffusionConstants[MOBILE_SPECIES_INDEX] = new Expression(baseDiffusionRate);
    species[MOBILE_SPECIES_INDEX] = new Species(SPECIES_NAME_PREFIX_MOBILE, "Mobile bleachable species");
    speciesContexts[MOBILE_SPECIES_INDEX] = new SpeciesContext(null, species[MOBILE_SPECIES_INDEX].getCommonName(), species[MOBILE_SPECIES_INDEX], cytosol);
    FieldFunctionArguments postBleach_first = new FieldFunctionArguments(roiDataName, "postbleach_first", new Expression(0), VariableType.VOLUME);
    FieldFunctionArguments prebleach_avg = new FieldFunctionArguments(roiDataName, "prebleach_avg", new Expression(0), VariableType.VOLUME);
    Expression expPostBleach_first = new Expression(postBleach_first.infix());
    Expression expPreBleach_avg = new Expression(prebleach_avg.infix());
    initialConditions[MOBILE_SPECIES_INDEX] = Expression.div(expPostBleach_first, expPreBleach_avg);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    for (int i = 0; i < initialConditions.length; i++) {
        model.addSpecies(species[i]);
        model.addSpeciesContext(speciesContexts[i]);
    }
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(speciesContexts[i]);
        scs.getInitialConditionParameter().setExpression(initialConditions[i]);
        scs.getDiffusionParameter().setExpression(diffusionConstants[i]);
    }
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription mathDesc = mathMapping.getMathDescription();
    // Add PSF function
    mathDesc.addVariable(new Function(Simulation.PSF_FUNCTION_NAME, new Expression(psfFDIS.getFieldFuncArgs().infix()), null));
    simContext.setMathDescription(mathDesc);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}

Example 5 with GroupAccessNone

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

the class XmlReader method getGroupAccess.

/**
 * This method returns a GroupAccess object from an XML format.
 * Creation date: (5/23/2003 7:27:10 PM)
 * @return cbit.vcell.server.GroupAccess
 * @param xmlGroup org.jdom.Element
 */
private GroupAccess getGroupAccess(Element xmlGroup) {
    // guess the type of group
    String temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag);
    java.math.BigDecimal type = new java.math.BigDecimal(temp);
    if (type.equals(GroupAccess.GROUPACCESS_ALL)) {
        // Type ALL
        return new GroupAccessAll();
    } else if (type.equals(GroupAccess.GROUPACCESS_NONE)) {
        // Type NONE
        return new GroupAccessNone();
    } else {
        // Type SOME
        // Read attributes
        // *groupid
        temp = xmlGroup.getAttributeValue(XMLTags.TypeAttrTag);
        java.math.BigDecimal groupid = new java.math.BigDecimal(temp);
        // *hash
        temp = xmlGroup.getAttributeValue(XMLTags.HashAttrTag);
        java.math.BigDecimal hashcode = new java.math.BigDecimal(temp);
        // *users
        List<Element> userlist = xmlGroup.getChildren(XMLTags.UserTag, vcNamespace);
        User[] userArray = new User[userlist.size()];
        boolean[] booleanArray = new boolean[userlist.size()];
        int counter = 0;
        for (Element userElement : userlist) {
            String userid = unMangle(userElement.getAttributeValue(XMLTags.NameAttrTag));
            KeyValue key = new KeyValue(userElement.getAttributeValue(XMLTags.KeyValueAttrTag));
            boolean hidden = Boolean.valueOf(userElement.getAttributeValue(XMLTags.HiddenTag)).booleanValue();
            userArray[counter] = new User(userid, key);
            booleanArray[counter] = hidden;
            counter++;
        }
        // create and return the GroupAccess
        return new GroupAccessSome(groupid, hashcode, userArray, booleanArray);
    }
}