Examples with DataAccessException org.vcell.util.DataAccessException used on opensource projects

Example 66 with DataAccessException

use of org.vcell.util.DataAccessException in project vcell by virtualcell.

the class DataSetControllerImpl method doDataOperation.

public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException {
    VCDataJobID vcDataJobID = null;
    try {
        if (dataOperation instanceof DataOperation.DataProcessingOutputTimeSeriesOP) {
            vcDataJobID = ((DataOperation.DataProcessingOutputTimeSeriesOP) dataOperation).getTimeSeriesJobSpec().getVcDataJobID();
        }
        if (!(getVCData(dataOperation.getVCDataIdentifier()) instanceof SimulationData)) {
            return null;
        }
        File dataProcessingOutputFileHDF5 = ((SimulationData) getVCData(dataOperation.getVCDataIdentifier())).getDataProcessingOutputSourceFileHDF5();
        DataOperationResults dataOperationResults = getDataProcessingOutput(dataOperation, dataProcessingOutputFileHDF5);
        if (vcDataJobID != null) {
            fireDataJobEventIfNecessary(vcDataJobID, MessageEvent.DATA_COMPLETE, dataOperation.getVCDataIdentifier(), new Double(0), ((DataOperationResults.DataProcessingOutputTimeSeriesValues) dataOperationResults).getTimeSeriesJobResults(), null);
        }
        return dataOperationResults;
    } catch (Exception e) {
        if (vcDataJobID != null) {
            fireDataJobEventIfNecessary(vcDataJobID, MessageEvent.DATA_FAILURE, dataOperation.getVCDataIdentifier(), new Double(0), null, e);
        }
        if (e instanceof DataAccessException) {
            throw (DataAccessException) e;
        } else {
            throw new DataAccessException("Datasetcontrollerimpl.doDataOperation error: " + e.getMessage(), e);
        }
    }
}

Example 67 with DataAccessException

use of org.vcell.util.DataAccessException in project vcell by virtualcell.

the class DataSetControllerImpl method getEmptyVtuMeshFiles.

public VtuFileContainer getEmptyVtuMeshFiles(ComsolSimFiles comsolSimFiles, VCDataIdentifier vcdataID, int timeIndex) throws DataAccessException {
    try {
        if (timeIndex > 0) {
            throw new RuntimeException("only time index 0 supported for comsol vtk mesh files");
        }
        ComsolVtkFileWriter comsolVTKFileWriter = new ComsolVtkFileWriter();
        File primaryDirectory = getPrimaryUserDir(vcdataID.getOwner(), false);
        VtuFileContainer vtuFiles = comsolVTKFileWriter.getEmptyVtuMeshFiles(comsolSimFiles, primaryDirectory);
        return vtuFiles;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK files: " + e.getMessage(), e);
    }
}

Example 68 with DataAccessException

use of org.vcell.util.DataAccessException in project vcell by virtualcell.

the class DataSetControllerImpl method getFunction.

public AnnotatedFunction getFunction(OutputContext outputContext, VCDataIdentifier vcdID, String variableName) throws DataAccessException {
    try {
        VCData vcData = getVCData(vcdID);
        AnnotatedFunction annotatedFunction = vcData.getFunction(outputContext, variableName);
        checkFieldDataExists(annotatedFunction, vcdID.getOwner());
        return annotatedFunction;
    } catch (IOException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 69 with DataAccessException

use of org.vcell.util.DataAccessException in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuMeshData.

public double[] getVtuMeshData(ChomboFiles chomboFiles, OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws DataAccessException {
    try {
        double[] times = getDataSetTimes(vcdataID);
        int timeIndex = -1;
        for (int i = 0; i < times.length; i++) {
            if (times[i] == time) {
                timeIndex = i;
                break;
            }
        }
        if (timeIndex < 0) {
            throw new DataAccessException("data for dataset " + vcdataID + " not found at time " + time);
        }
        ChomboVtkFileWriter chomboVTKFileWriter = new ChomboVtkFileWriter();
        double[] vtuData = chomboVTKFileWriter.getVtuMeshData(chomboFiles, outputContext, getUserDataDirectory(vcdataID), time, var, timeIndex);
        return vtuData;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK files: " + e.getMessage(), e);
    }
}

Example 70 with DataAccessException

use of org.vcell.util.DataAccessException in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuMeshData.

public double[] getVtuMeshData(ComsolSimFiles comsolSimFiles, OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws DataAccessException {
    try {
        double[] times = getVtuTimes(comsolSimFiles, vcdataID);
        int timeIndex = -1;
        for (int i = 0; i < times.length; i++) {
            if (times[i] == time) {
                timeIndex = i;
                break;
            }
        }
        if (timeIndex < 0) {
            throw new DataAccessException("data for dataset " + vcdataID + " not found at time " + time);
        }
        ComsolVtkFileWriter comsolVTKFileWriter = new ComsolVtkFileWriter();
        double[] vtuData = comsolVTKFileWriter.getVtuMeshData(comsolSimFiles, outputContext, getUserDataDirectory(vcdataID), time, var, timeIndex);
        return vtuData;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK files: " + e.getMessage(), e);
    }
}