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

Example 76 with DataAccessException

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

the class MergedData method getFunctions.

/**
 * Insert the method's description here.
 * Creation date: (10/11/00 5:16:06 PM)
 * @return cbit.vcell.math.Function
 * @param name java.lang.String
 */
public AnnotatedFunction[] getFunctions(OutputContext outputContext) {
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    ArrayList<AnnotatedFunction> functionsArr = new ArrayList<>();
    // Get the functions in annotatedFunctionsList
    for (int i = 0; i < annotatedFunctionList.size(); i++) {
        // AnnotatedFunction annotatedFunc = (AnnotatedFunction)annotatedFunctionList.elementAt(i);
        // functions[i] = new Function(annotatedFunc.getName(), annotatedFunc.getExpression());
        functionsArr.add((AnnotatedFunction) annotatedFunctionList.elementAt(i));
    }
    for (int i = 0; i < datasetsIDList.length; i++) {
        VCDataIdentifier vcdid = datasetsIDList[i];
        try {
            AnnotatedFunction[] myFuncs = getDatasetControllerImpl().getFunctions(outputContext, vcdid);
            for (int j = 0; j < myFuncs.length; j++) {
                AnnotatedFunction myfunc = new AnnotatedFunction(dataSetPrefix[i] + "." + myFuncs[j].getName(), myFuncs[j].getExpression(), myFuncs[j].getDomain(), myFuncs[j].getErrorString(), myFuncs[j].getFunctionType(), myFuncs[j].getFunctionCatogery());
                functionsArr.add(myfunc);
            }
        } catch (ExpressionBindingException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (DataAccessException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    return functionsArr.toArray(new AnnotatedFunction[0]);
}

Example 77 with DataAccessException

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

the class MergedData method getDataBlockTimeStamp.

/**
 * Insert the method's description here.
 * Creation date: (1/19/00 11:52:22 AM)
 * @return long
 * @param dataType int
 * @param timepoint double
 * @exception org.vcell.util.DataAccessException The exception description.
 */
public long getDataBlockTimeStamp(int dataType, double timepoint) throws DataAccessException {
    long latestTimeStamp = Long.MIN_VALUE;
    // use that value to find the max.
    try {
        for (int i = 0; i < datasetsIDList.length; i++) {
            VCData vcdata = getDatasetControllerImpl().getVCData(datasetsIDList[i]);
            double[] timeArray = getDatasetControllerImpl().getDataSetTimes(datasetsIDList[i]);
            boolean bTimesEqual = checkTimeArrays(timeArray);
            int timeArrayCounter = 0;
            long datatimeStamp;
            if (bTimesEqual) {
                datatimeStamp = vcdata.getDataBlockTimeStamp(dataType, timepoint);
            } else {
                while ((timeArrayCounter < timeArray.length - 2) && (timepoint > timeArray[timeArrayCounter + 1])) {
                    timeArrayCounter++;
                }
                datatimeStamp = vcdata.getDataBlockTimeStamp(dataType, timeArray[Math.min(timeArray.length - 1, timeArrayCounter + 1)]);
            }
            latestTimeStamp = Math.max(latestTimeStamp, datatimeStamp);
        }
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("\n Error computing Timestamp for CompositeData! " + e.getMessage());
    }
    return latestTimeStamp;
}

Example 78 with DataAccessException

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

the class PDEDataContext method setVariableNameAndTime.

public void setVariableNameAndTime(String varName, double timePoint) throws DataAccessException {
    DataIdentifier dataIdentifier = findDataIdentifier(varName);
    if (dataIdentifier == null) {
        throw new DataAccessException("Couldn't find DataIdentifier for variable name " + varName);
    }
    setVariableAndTime(dataIdentifier, timePoint);
}

Example 79 with DataAccessException

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

the class ParticleDataBlock method readParticleData.

private void readParticleData(List<String> lines) throws DataAccessException {
    String lastSpecies = null;
    List<Coordinate> working = null;
    for (String line : lines) {
        try {
            CommentStringTokenizer st = new CommentStringTokenizer(line);
            String sp = st.nextToken();
            if (!sp.equals(lastSpecies)) {
                lastSpecies = sp;
                working = fetch(sp);
            }
            double x = Double.parseDouble(st.nextToken());
            double y = Double.parseDouble(st.nextToken());
            double z = Double.parseDouble(st.nextToken());
            Coordinate c = new Coordinate(x, y, z);
            working.add(c);
        } catch (Exception exc) {
            throw new DataAccessException("Particle data file invalid. " + exc.getMessage());
        }
    }
}

Example 80 with DataAccessException

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

the class SimDataReader method getNextDataAtCurrentTime0.

private void getNextDataAtCurrentTime0(double[][] returnValues) throws IOException, DataAccessException {
    if (masterTimeIndex >= times.length) {
        throw new RuntimeException("No More Time Data");
    }
    try {
        // Setup the proper DataInputStream
        String currentSimDataFileName = simDataFileNames[masterTimeIndex];
        if (zipFilenNames != null && zipFilenNames[masterTimeIndex] != null) {
            if (currentZipFile == null || !currentZipFileName.equals(zipFilenNames[masterTimeIndex])) {
                if (currentZipFile != null) {
                    currentZipFile.close();
                    currentZipFileName = null;
                }
                currentZipFile = new org.apache.commons.compress.archivers.zip.ZipFile(zipFilenNames[masterTimeIndex]);
                currentZipFileName = zipFilenNames[masterTimeIndex];
            }
            if (dis != null) {
                dis.close();
                dis = null;
            }
            ZipEntry ze = currentZipFile.getEntry(currentSimDataFileName);
            if (wantsThisTime[masterTimeIndex]) {
                InputStream is = currentZipFile.getInputStream((ZipArchiveEntry) ze);
                // java.io.BufferedInputStream bis = new java.io.BufferedInputStream(is);
                dis = new java.io.DataInputStream(is);
            }
        } else if (wantsThisTime[masterTimeIndex]) {
            File file = new File(currentSimDataFileName);
            FileInputStream fis = new java.io.FileInputStream(file);
            dis = new java.io.DataInputStream(new java.io.BufferedInputStream(fis));
        }
        if (wantsThisTime[masterTimeIndex]) {
            masterStreamIndex = 0;
            // Read the SimDataHeader and SimdataBlock Info
            // This will fail if mis-aligned in stream
            FileHeader fileHeader = readFileHeader(dis);
            // System.out.println(currentSimDataFileName+" numBlocks="+fileHeader.numBlocks);
            DataBlock[] dataBlockList = new DataBlock[fileHeader.numBlocks];
            for (int j = 0; j < fileHeader.numBlocks; j++) {
                DataBlock dataBlock = new DataBlock();
                // This will fail if mis-aligned in stream
                incrementStreamCounts(dataBlock.readBlockHeader(dis));
                // System.out.println("varName="+dataBlock.getVarName()+" Offset="+dataBlock.getDataOffset()+" type="+dataBlock.getVariableTypeInteger());
                dataBlockList[j] = dataBlock;
            }
            // long blockTime = System.currentTimeMillis();
            // System.out.println("Time for Blocks="+(blockTime-entryTime));
            // Beginning of All SimData(Blocks) (All doubles) check DataBlocks in order (Always move forward in stream)
            int variableFoundCount = 0;
            for (int j = 0; j < dataBlockList.length; j += 1) {
                boolean isBlockIndexAligned = false;
                // See if current block is a variable we want
                for (int k = 0; k < varNames.length; k += 1) {
                    if (varNames[k].equals(dataBlockList[j].getVarName())) {
                        variableFoundCount += 1;
                        // Align to beginning of current block
                        if (!isBlockIndexAligned) {
                            skip(dis, dataBlockList[j].getDataOffset() - masterStreamIndex);
                            isBlockIndexAligned = true;
                        }
                        double val = 0;
                        for (int l = 0; l < varIndexes[k].length; l += 1) {
                            long skip = (sortedVarIndexes[k][l][INDEX_VALUE] - (l > 0 ? sortedVarIndexes[k][l - 1][INDEX_VALUE] : 0));
                            // If current data offset was same as last, re-use val
                            if ((l == 0) || (skip != 0)) {
                                // Align to desired data index
                                skip(dis, (l == 0 ? skip : skip - 1) * 8);
                                val = dis.readDouble();
                                incrementStreamCounts(8);
                            }
                            // Store value in original order
                            int unSortedVarIndex = (int) sortedVarIndexes[k][l][INDEX_ORIGINAL_POSITION];
                            int reMappedVarNameIndex = reMapper[k][unSortedVarIndex][0];
                            int reMappedVarIndexIndex = reMapper[k][unSortedVarIndex][1];
                            // System.out.println("k="+k+" l="+l+" uvi="+unSortedVarIndex+" rvni="+reMappedVarNameIndex+" rmvii="+reMappedVarIndexIndex);
                            returnValues[reMappedVarNameIndex][reMappedVarIndexIndex] = val;
                        // System.out.println("var="+varNames[k]+" sortindex="+l+
                        // " unsortindex="+sortedVarIndexes[k][l][INDEX_ORIGINAL_POSITION]+" index="+sortedVarIndexes[k][l][INDEX_VALUE]+" val="+val);
                        }
                    }
                }
            }
            if (variableFoundCount != varNames.length) {
                throw new DataAccessException(this.getClass().getName() + ".getNextDataAtCurrentTime: At least 1 variable name was not found in Datablock list");
            }
        // long dataTime = System.currentTimeMillis();
        // System.out.println("Time for data="+(dataTime-blockTime)+"\n");
        }
        if (dis != null) {
            dis.close();
            dis = null;
        }
        masterTimeIndex += 1;
        if (masterTimeIndex >= times.length) {
            close();
        }
    // long totalTime = System.currentTimeMillis();
    // System.out.println("Total Time="+(totalTime-beginTime));
    } catch (Throwable e) {
        close();
        throw new RuntimeException("Error reading SimData: " + (e.getMessage() != null ? e.getMessage() : e.getClass().getName()));
    }
}