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

Example 41 with KeyValue

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

the class RunSimulation2DOp method runRefSimulation.

public ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, String varName, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, varName, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}

Example 42 with KeyValue

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

the class RunRefSimulationOp method runRefSimulation.

private static ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, ROI cellROI, double timeStepVal, TimeBounds timeBounds, FloatImage initRefConc, double baseDiffusionRate, ClientTaskStatusSupport progressListener) throws Exception {
    String INITCONC_EXTDATA_NAME = "initConc";
    String INITCONC_EXTDATA_VARNAME = "conc";
    String VAR_NAME = "species";
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), baseDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), initialConcentrationExtData.getExternalDataIdentifier(), progressListener, true);
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simKey, owner), 0);
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, VAR_NAME, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}

Example 43 with KeyValue

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

the class RunRefSimulationOp method createNewExternalDataInfo.

private static ExternalDataInfo createNewExternalDataInfo(LocalWorkspace localWorkspace, String extDataIDName) {
    File targetDir = new File(localWorkspace.getDefaultSimDataDirectory());
    KeyValue key = LocalWorkspace.createNewKeyValue();
    User owner = LocalWorkspace.getDefaultOwner();
    ExternalDataIdentifier newImageDataExtDataID = new ExternalDataIdentifier(key, owner, extDataIDName);
    String filename = new File(targetDir, newImageDataExtDataID.getID() + SimDataConstants.LOGFILE_EXTENSION).getAbsolutePath();
    ExternalDataInfo newImageDataExtDataInfo = new ExternalDataInfo(newImageDataExtDataID, filename);
    return newImageDataExtDataInfo;
}

Example 44 with KeyValue

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

the class DisplayTimeSeriesOp method displayImageTimeSeries.

public void displayImageTimeSeries(final ImageTimeSeries<? extends Image> imageTimeSeries, final String title, final WindowListener windowListener) throws ImageException, IOException {
    try {
        System.out.println("starting to prepare data for time series viewing");
        final PDEDataViewer pdeDataViewer = new PDEDataViewer();
        DataSetControllerProvider dataSetControllerProvider;
        try {
            dataSetControllerProvider = getDataSetControllerProvider(imageTimeSeries, pdeDataViewer);
        } catch (ImageException | IOException e1) {
            e1.printStackTrace();
            throw new RuntimeException(e1.getMessage(), e1);
        }
        VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

            public User getOwner() {
                return new User("nouser", null);
            }

            public KeyValue getDataKey() {
                return null;
            }

            public String getID() {
                return "mydata";
            }
        };
        PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
        final ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
        final RequestManager requestManager = new RequestManagerAdapter() {
        };
        final DataViewerManager dataViewerManager = new DataViewerManager() {

            public void dataJobMessage(DataJobEvent event) {
            }

            public void exportMessage(ExportEvent event) {
            }

            public void addDataListener(DataListener newListener) {
            }

            public UserPreferences getUserPreferences() {
                // getRequestManager().getUserPreferences();
                return null;
            }

            public void removeDataListener(DataListener newListener) {
            }

            public void startExport(Component requester, OutputContext outputContext, ExportSpecs exportSpecs) {
            // getLocalRequestManager().startExport(outputContext, FieldDataWindowManager.this, exportSpecs);
            }

            public void simStatusChanged(SimStatusEvent simStatusEvent) {
            }

            public User getUser() {
                return new User("dummy", new KeyValue("123"));
            // return getRequestManager().getDocumentManager().getUser();
            }

            public RequestManager getRequestManager() {
                return requestManager;
            }
        };
        System.out.println("ready to display time series");
        SwingUtilities.invokeAndWait(new Runnable() {

            @Override
            public void run() {
                JFrame jframe = new TopLevelFrame();
                jframe.setTitle(title);
                jframe.getContentPane().add(pdeDataViewer);
                jframe.setSize(1000, 600);
                jframe.setVisible(true);
                if (windowListener != null) {
                    jframe.addWindowListener(windowListener);
                }
                try {
                    pdeDataViewer.setDataViewerManager(dataViewerManager);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
                pdeDataViewer.setPdeDataContext(myPdeDataContext);
            }
        });
    } catch (InvocationTargetException | InterruptedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 45 with KeyValue

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

the class MigrateDbManager method migrate.

public static void migrate(Table table, ConnectionFactory conFactory_from, ConnectionFactory conFactory_to) throws SQLException {
    System.out.println("starting migration of table " + table.getTableName());
    assert (conFactory_from.getDatabaseSyntax() == DatabaseSyntax.ORACLE);
    assert (conFactory_to.getDatabaseSyntax() == DatabaseSyntax.POSTGRES);
    Connection con_from = null;
    Connection con_to = null;
    try {
        con_from = conFactory_from.getConnection(new Object());
        con_to = conFactory_to.getConnection(new Object());
        con_from.setReadOnly(true);
        con_to.setReadOnly(false);
        // 
        // get Last key in target table (using the "to" connection) - NULL if no records.
        // 
        String sql = "SELECT ID FROM " + table.getTableName() + " ORDER BY ID DESC LIMIT 1";
        System.out.println(sql);
        // 
        // should disable self-referential reference in vc_struct table (field "parentRef")
        // 
        KeyValue lastkey = null;
        try (Statement stmt_to_init = con_to.createStatement();
            ResultSet rset_to_init = stmt_to_init.executeQuery(sql)) {
            if (rset_to_init.next()) {
                BigDecimal keyBigDecimal = rset_to_init.getBigDecimal(1);
                if (!rset_to_init.wasNull()) {
                    lastkey = new KeyValue(keyBigDecimal);
                }
            }
        }
        // 
        // gather fields to copy
        // 
        ArrayList<Field> fieldsToCopy = new ArrayList<Field>();
        for (Field f : table.getFields()) {
            // if (f.getSqlDataType() == SQLDataType.clob_text || f.getSqlDataType() == SQLDataType.blob_bytea){
            // continue; // insert in another pass
            // }
            fieldsToCopy.add(f);
        }
        // 
        // form the query using the "from" connection
        // 
        StringBuffer selectBuffer = new StringBuffer();
        selectBuffer.append("SELECT ");
        for (int i = 0; i < fieldsToCopy.size(); i++) {
            selectBuffer.append(fieldsToCopy.get(i).getUnqualifiedColName());
            if (i < fieldsToCopy.size() - 1) {
                selectBuffer.append(",");
            }
        }
        selectBuffer.append(" FROM " + table.getTableName());
        if (lastkey != null) {
            selectBuffer.append(" WHERE id > " + lastkey + " ");
        }
        selectBuffer.append(" ORDER BY id");
        System.out.println(selectBuffer.toString());
        // 
        // form the prepared INSERT statement for the "to" connection
        // 
        StringBuffer insertBuffer = new StringBuffer();
        insertBuffer.append("INSERT INTO " + table.getTableName() + " values (");
        for (int i = 0; i < fieldsToCopy.size(); i++) {
            insertBuffer.append("?");
            if (i < fieldsToCopy.size() - 1) {
                insertBuffer.append(",");
            }
        }
        insertBuffer.append(")");
        System.out.println(insertBuffer.toString());
        try (Statement stmt_from = con_from.createStatement();
            ResultSet rset_from = stmt_from.executeQuery(selectBuffer.toString());
            PreparedStatement stmt_to = con_to.prepareStatement(insertBuffer.toString())) {
            long rowCount = 0;
            long batchCount = 0;
            while (rset_from.next()) {
                for (int i = 0; i < fieldsToCopy.size(); i++) {
                    Field f = fieldsToCopy.get(i);
                    switch(f.getSqlDataType().basicDataType) {
                        case BLOB:
                            {
                                boolean found = false;
                                Object lob_object = rset_from.getObject(i + 1);
                                if (!rset_from.wasNull()) {
                                    if (lob_object instanceof java.sql.Blob) {
                                        java.sql.Blob blob_object = (java.sql.Blob) lob_object;
                                        byte[] bytes = blob_object.getBytes((long) 1, (int) blob_object.length());
                                        stmt_to.setBytes(i + 1, bytes);
                                        found = true;
                                    }
                                }
                                if (!found) {
                                    stmt_to.setNull(i + 1, java.sql.Types.LONGVARBINARY);
                                }
                                break;
                            }
                        case CLOB:
                            {
                                boolean found = false;
                                Object lob_object = rset_from.getObject(i + 1);
                                if (!rset_from.wasNull()) {
                                    if (lob_object instanceof java.sql.Clob) {
                                        java.sql.Clob clob_object = (java.sql.Clob) lob_object;
                                        byte[] ins = new byte[(int) clob_object.length()];
                                        try {
                                            clob_object.getAsciiStream().read(ins);
                                            String str = new String(ins);
                                            stmt_to.setString(i + 1, str);
                                            found = true;
                                        } catch (IOException e) {
                                            e.printStackTrace();
                                        }
                                    }
                                }
                                if (!found) {
                                    stmt_to.setNull(i + 1, java.sql.Types.LONGVARCHAR);
                                }
                                break;
                            }
                        case CHAR:
                            {
                                String str = rset_from.getString(i + 1);
                                if (!rset_from.wasNull()) {
                                    stmt_to.setString(i + 1, str);
                                } else {
                                    stmt_to.setNull(i + 1, java.sql.Types.CHAR);
                                }
                                break;
                            }
                        case VARCHAR:
                            {
                                String str = rset_from.getString(i + 1);
                                if (!rset_from.wasNull()) {
                                    stmt_to.setString(i + 1, str);
                                } else {
                                    stmt_to.setNull(i + 1, java.sql.Types.VARCHAR);
                                }
                                break;
                            }
                        case DATE:
                            {
                                Date date = rset_from.getDate(i + 1);
                                if (!rset_from.wasNull()) {
                                    stmt_to.setDate(i + 1, date);
                                } else {
                                    stmt_to.setNull(i + 1, java.sql.Types.DATE);
                                }
                                break;
                            }
                        case BIGINT:
                            {
                                BigDecimal bigDecimal = rset_from.getBigDecimal(i + 1);
                                if (!rset_from.wasNull()) {
                                    stmt_to.setBigDecimal(i + 1, bigDecimal);
                                } else {
                                    stmt_to.setNull(i + 1, java.sql.Types.BIGINT);
                                }
                                break;
                            }
                        case NUMERIC:
                            {
                                BigDecimal bigDecimal = rset_from.getBigDecimal(i + 1);
                                if (!rset_from.wasNull()) {
                                    stmt_to.setBigDecimal(i + 1, bigDecimal);
                                } else {
                                    stmt_to.setNull(i + 1, java.sql.Types.NUMERIC);
                                }
                                break;
                            }
                        default:
                            {
                                throw new RuntimeException("support for JDBC Type " + f.getSqlDataType().basicDataType + " not yet supported");
                            }
                    }
                }
                stmt_to.addBatch();
                rowCount++;
                batchCount++;
                if (batchCount >= 300) {
                    System.out.println("writing " + batchCount + " of " + rowCount + " records into table " + table.getTableName());
                    batchCount = 0;
                    stmt_to.executeBatch();
                    con_to.commit();
                }
            }
            if (batchCount > 0) {
                stmt_to.executeBatch();
                con_to.commit();
            }
        }
        // end try
        System.out.println("starting migration of table " + table.getTableName());
    } finally {
        if (con_from != null)
            con_from.close();
        if (con_to != null)
            con_to.close();
    }
}