Example usage for org.apache.poi.ss.usermodel WorkbookFactory create

List of usage examples for org.apache.poi.ss.usermodel WorkbookFactory create

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Introduction

In this page you can find the example usage for org.apache.poi.ss.usermodel WorkbookFactory create.

Prototype

public static Workbook create(File file) throws IOException, EncryptedDocumentException

Source Link

Document

Creates the appropriate HSSFWorkbook / XSSFWorkbook from the given File, which must exist and be readable.

Usage

From source file:org.cytoscape.tableimport.internal.LoadTableReaderTask.java

License:Open Source License

@Override
public void run(TaskMonitor tm) throws Exception {

    tm.setTitle("Loading table data");
    tm.setProgress(0.0);/* www  .j  av a 2s.  c  om*/
    tm.setStatusMessage("Loading table...");

    List<String> attrNameList = new ArrayList<String>();
    int colCount;
    int startLoadRowTemp;
    String[] attributeNames;

    Workbook workbook = null;
    // Load Spreadsheet data for preview.
    if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
            || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) {
        try {
            workbook = WorkbookFactory.create(isStart);
        } catch (InvalidFormatException e) {
            e.printStackTrace();
            throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?");
        } finally {
            if (isStart != null) {
                isStart.close();
            }
        }
    }
    if (startLoadRow > 0)
        startLoadRow--;
    startLoadRowTemp = startLoadRow;
    if (firstRowAsColumnNames)
        startLoadRowTemp = 0;

    previewPanel.setPreviewTable(workbook, fileType, inputName, isStart, delimiters.getSelectedValues(), null,
            50, null, startLoadRowTemp);

    colCount = previewPanel.getPreviewTable().getColumnModel().getColumnCount();
    importFlag = new boolean[colCount];
    Object curName = null;

    if (firstRowAsColumnNames) {
        setFirstRowAsColumnNames();
        startLoadRow++;
    }

    for (int i = 0; i < colCount; i++) {
        importFlag[i] = true;
        curName = previewPanel.getPreviewTable().getColumnModel().getColumn(i).getHeaderValue();

        if (attrNameList.contains(curName)) {
            int dupIndex = 0;

            for (int idx = 0; idx < attrNameList.size(); idx++) {
                if (curName.equals(attrNameList.get(idx))) {
                    dupIndex = idx;

                    break;
                }
            }

            if (importFlag[i] && importFlag[dupIndex]) {
                //TODO add message to user
                return;
            }
        }

        if (curName == null) {
            attrNameList.add("Column " + i);
        } else {
            attrNameList.add(curName.toString());
        }
    }
    attributeNames = attrNameList.toArray(new String[0]);

    final Byte[] test = previewPanel.getDataTypes(previewPanel.getSelectedSheetName());

    final Byte[] attributeTypes = new Byte[test.length];

    for (int i = 0; i < test.length; i++) {
        attributeTypes[i] = test[i];
    }

    if (keyColumnIndex > 0)
        keyColumnIndex--;

    amp = new AttributeMappingParameters(delimiters.getSelectedValues(),
            delimitersForDataList.getSelectedValue(), keyColumnIndex, attributeNames, attributeTypes,
            previewPanel.getCurrentListDataTypes(), importFlag, true, startLoadRow, null);

    if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
            || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {

        // Fixed bug# 1668, Only load data from the first sheet, ignore the rest sheets
        if (workbook.getNumberOfSheets() > 0) {
            final Sheet sheet = workbook.getSheetAt(0);
            this.reader = new ExcelAttributeSheetReader(sheet, amp);
            loadAnnotation(tm);
        }
    } else {
        this.reader = new DefaultAttributeTableReader(null, amp, this.isEnd);
        loadAnnotation(tm);
    }
}

From source file:org.cytoscape.tableimport.internal.task.ImportAttributeTableReaderTask.java

License:Open Source License

@Override
public void run(TaskMonitor tm) throws Exception {
    tm.setTitle("Loading table data");
    tm.setProgress(0.0);//from www .  jav a  2 s. c o m
    tm.setStatusMessage("Loading table...");

    Workbook workbook = null;

    // Load Spreadsheet data for preview.
    if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
            || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) {
        try {
            workbook = WorkbookFactory.create(is);
        } catch (InvalidFormatException e) {
            e.printStackTrace();
            throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?");
        } finally {
            if (is != null)
                is.close();
        }
    }

    if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
            || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {

        // Fixed bug# 1668, Only load data from the first sheet, ignore the rest sheets
        // UPDATE: From the user perspective it makes more sense to get the selected tab/sheet instead.
        String networkName = amp.getName();

        if (networkName == null)
            networkName = workbook.getSheetName(0);

        final Sheet sheet = workbook.getSheet(networkName);

        if (sheet != null) {
            reader = new ExcelAttributeSheetReader(sheet, amp, serviceRegistrar);
            loadAnnotation(tm);
        }
    } else {
        try {
            reader = new DefaultAttributeTableReader(null, amp, this.is, serviceRegistrar);
            loadAnnotation(tm);
        } catch (Exception ioe) {
            tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
        }
    }
}

From source file:org.cytoscape.tableimport.internal.task.ImportNetworkTableReaderTask.java

License:Open Source License

@Override
public void run(TaskMonitor tm) throws Exception {
    tm.setTitle("Loading network from table");
    tm.setProgress(0.0);//  ww  w. j  a va  2 s.  co m
    tm.setStatusMessage("Loading network...");

    Workbook workbook = null;

    // Load Spreadsheet data for preview.
    if (fileType != null && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
            || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) && workbook == null) {
        try {
            workbook = WorkbookFactory.create(is);
        } catch (InvalidFormatException e) {
            throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?", e);
        } finally {
            if (is != null)
                is.close();
        }
    }

    try {
        if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
                || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
            String networkName = ntmp.getName();

            if (networkName == null)
                networkName = workbook.getSheetName(0);

            final Sheet sheet = workbook.getSheet(networkName);

            reader = new ExcelNetworkSheetReader(networkName, sheet, ntmp, nMap, rootNetwork, serviceRegistrar);
        } else {
            reader = new NetworkTableReader(inputName, is, ntmp, nMap, rootNetwork, serviceRegistrar);
        }
    } catch (Exception ioe) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
        return;
    }

    loadNetwork(tm);
    tm.setProgress(1.0);
}

From source file:org.cytoscape.tableimport.internal.task.LoadNetworkReaderTask.java

License:Open Source License

@Override
public void run(final TaskMonitor tm) throws Exception {
    tm.setTitle("Loading network from table");
    tm.setProgress(0.0);/*w  w  w .j a v  a 2s .  c om*/
    tm.setStatusMessage("Loading network...");
    taskMonitor = tm;

    final List<String> attrNameList = new ArrayList<>();
    int colCount;
    String[] attributeNames;

    final CyNetworkReaderManager networkReaderManager = serviceRegistrar
            .getService(CyNetworkReaderManager.class);

    if (is != null)
        netReader = networkReaderManager.getReader(is, inputName);

    if (netReader == null)
        netReader = networkReaderManager.getReader(uri, inputName);

    if (netReader instanceof CombineReaderAndMappingTask) {
        Workbook workbook = null;

        // Load Spreadsheet data for preview.
        if (fileType != null
                && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
                        || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension()))
                && workbook == null) {
            try {
                workbook = WorkbookFactory.create(new FileInputStream(tempFile));
            } catch (InvalidFormatException e) {
                //e.printStackTrace();
                throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?", e);
            } finally {

            }
        }

        netReader = null;

        if (startLoadRow > 0)
            startLoadRow--;

        final int startLoadRowTemp = firstRowAsColumnNames ? 0 : startLoadRow;

        previewPanel.updatePreviewTable(workbook, fileType, tempFile.getAbsolutePath(),
                new FileInputStream(tempFile), delimiters.getSelectedValues(), null, startLoadRowTemp);

        colCount = previewPanel.getPreviewTable().getColumnModel().getColumnCount();
        Object curName = null;

        if (firstRowAsColumnNames) {
            previewPanel.setFirstRowAsColumnNames();
            startLoadRow++;
        }

        final SourceColumnSemantic[] types = previewPanel.getTypes();

        for (int i = 0; i < colCount; i++) {
            curName = previewPanel.getPreviewTable().getColumnModel().getColumn(i).getHeaderValue();

            if (attrNameList.contains(curName)) {
                int dupIndex = 0;

                for (int idx = 0; idx < attrNameList.size(); idx++) {
                    if (curName.equals(attrNameList.get(idx))) {
                        dupIndex = idx;

                        break;
                    }
                }

                if (!TypeUtil.allowsDuplicateName(ImportType.NETWORK_IMPORT, types[i], types[dupIndex])) {
                    // TODO add message to user (Duplicate Column Name Found)
                    return;
                }
            }

            if (curName == null)
                attrNameList.add("Column " + i);
            else
                attrNameList.add(curName.toString());
        }

        attributeNames = attrNameList.toArray(new String[attrNameList.size()]);

        final SourceColumnSemantic[] typesCopy = Arrays.copyOf(types, types.length);

        final AttributeDataType[] dataTypes = previewPanel.getDataTypes();
        final AttributeDataType[] dataTypesCopy = Arrays.copyOf(dataTypes, dataTypes.length);

        AttributeDataType[] tunableDataTypes = null;

        if (dataTypeList != null && !dataTypeList.trim().isEmpty())
            tunableDataTypes = TypeUtil.parseDataTypeList(dataTypeList);

        if (tunableDataTypes != null && tunableDataTypes.length > 0)
            System.arraycopy(tunableDataTypes, 0, dataTypesCopy, 0,
                    Math.min(tunableDataTypes.length, dataTypesCopy.length));

        String[] listDelimiters = previewPanel.getListDelimiters();

        if (listDelimiters == null || listDelimiters.length == 0) {
            listDelimiters = new String[dataTypes.length];

            if (delimitersForDataList.getSelectedValue() != null)
                Arrays.fill(listDelimiters, delimitersForDataList.getSelectedValue());
        }

        if (indexColumnSourceInteraction > 0)
            indexColumnSourceInteraction--;

        if (indexColumnTargetInteraction > 0)
            indexColumnTargetInteraction--;

        if (indexColumnTypeInteraction > 0)
            indexColumnTypeInteraction--;

        networkName = previewPanel.getSourceName();

        ntmp = new NetworkTableMappingParameters(networkName, delimiters.getSelectedValues(), listDelimiters,
                attributeNames, dataTypesCopy, typesCopy, indexColumnSourceInteraction,
                indexColumnTargetInteraction, indexColumnTypeInteraction, defaultInteraction, startLoadRow,
                null);

        try {
            if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
                    || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {
                final Sheet sheet = workbook.getSheet(networkName);

                reader = new ExcelNetworkSheetReader(networkName, sheet, ntmp, nMap, rootNetwork,
                        serviceRegistrar);
            } else {
                networkName = this.inputName;
                reader = new NetworkTableReader(networkName, new FileInputStream(tempFile), ntmp, nMap,
                        rootNetwork, serviceRegistrar);
            }
        } catch (Exception ioe) {
            tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read network: " + ioe.getMessage());
            return;
        }

        loadNetwork(tm);
        tm.setProgress(1.0);
    } else {
        networkName = this.inputName;
        insertTasksAfterCurrentTask(netReader);
    }
}

From source file:org.cytoscape.tableimport.internal.task.LoadTableReaderTask.java

License:Open Source License

@Override
public void run(final TaskMonitor tm) throws Exception {
    tm.setTitle("Loading table data");
    tm.setProgress(0.0);/*w  w w  . j a  va  2  s . co  m*/
    tm.setStatusMessage("Loading table...");

    List<String> attrNameList = new ArrayList<>();
    int colCount;
    String[] attributeNames;

    Workbook workbook = null;
    // Load Spreadsheet data for preview.
    try {
        if (fileType != null
                && (fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
                        || fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension()))
                && workbook == null) {
            try {
                workbook = WorkbookFactory.create(isStart);
            } catch (InvalidFormatException e) {
                e.printStackTrace();
                throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?");
            } finally {
                if (isStart != null)
                    isStart.close();
            }
        }
    } catch (Exception ioe) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Unable to read table: " + ioe.getMessage());
        return;
    }

    if (startLoadRow > 0)
        startLoadRow--;

    final int startLoadRowTemp = firstRowAsColumnNames ? 0 : startLoadRow;

    previewPanel.updatePreviewTable(workbook, fileType, inputName, isStart, delimiters.getSelectedValues(),
            null, startLoadRowTemp);

    colCount = previewPanel.getPreviewTable().getColumnModel().getColumnCount();
    Object curName = null;

    if (firstRowAsColumnNames) {
        previewPanel.setFirstRowAsColumnNames();
        startLoadRow++;
    }

    final String sourceName = previewPanel.getSourceName();
    final SourceColumnSemantic[] types = previewPanel.getTypes();

    for (int i = 0; i < colCount; i++) {
        curName = previewPanel.getPreviewTable().getColumnModel().getColumn(i).getHeaderValue();

        if (attrNameList.contains(curName)) {
            int dupIndex = 0;

            for (int idx = 0; idx < attrNameList.size(); idx++) {
                if (curName.equals(attrNameList.get(idx))) {
                    dupIndex = idx;

                    break;
                }
            }

            if (!TypeUtil.allowsDuplicateName(ImportType.TABLE_IMPORT, types[i], types[dupIndex])) {
                //TODO add message to user
                return;
            }
        }

        if (curName == null)
            attrNameList.add("Column " + i);
        else
            attrNameList.add(curName.toString());
    }

    attributeNames = attrNameList.toArray(new String[0]);

    final SourceColumnSemantic[] typesCopy = Arrays.copyOf(types, types.length);

    final AttributeDataType[] dataTypes = previewPanel.getDataTypes();
    final AttributeDataType[] dataTypesCopy = Arrays.copyOf(dataTypes, dataTypes.length);

    AttributeDataType[] tunableDataTypes = null;

    if (dataTypeList != null && !dataTypeList.trim().isEmpty())
        tunableDataTypes = TypeUtil.parseDataTypeList(dataTypeList);

    if (tunableDataTypes != null && tunableDataTypes.length > 0)
        System.arraycopy(tunableDataTypes, 0, dataTypesCopy, 0,
                Math.min(tunableDataTypes.length, dataTypesCopy.length));

    String[] listDelimiters = previewPanel.getListDelimiters();

    if (listDelimiters == null || listDelimiters.length == 0) {
        listDelimiters = new String[dataTypes.length];

        if (delimitersForDataList.getSelectedValue() != null)
            Arrays.fill(listDelimiters, delimitersForDataList.getSelectedValue());
    }

    if (keyColumnIndex > 0)
        keyColumnIndex--;

    amp = new AttributeMappingParameters(sourceName, delimiters.getSelectedValues(), listDelimiters,
            keyColumnIndex, attributeNames, dataTypesCopy, typesCopy, startLoadRow, null);

    if (this.fileType.equalsIgnoreCase(SupportedFileType.EXCEL.getExtension())
            || this.fileType.equalsIgnoreCase(SupportedFileType.OOXML.getExtension())) {

        // Fixed bug# 1668, Only load data from the first sheet, ignore the rest sheets
        // UPDATE: From the user perspective it makes more sense to get the selected tab/sheet than the first one.
        final Sheet sheet = workbook.getSheet(sourceName);

        if (sheet != null) {
            reader = new ExcelAttributeSheetReader(sheet, amp, serviceRegistrar);
            loadAnnotation(tm);
        }
    } else {
        reader = new DefaultAttributeTableReader(null, amp, this.isEnd, serviceRegistrar);
        loadAnnotation(tm);
    }
}

From source file:org.cytoscape.tableimport.internal.ui.ImportTablePanel.java

License:Open Source License

/**
 * Display preview table//from w w  w .j a  v  a  2 s .c om
 */
protected void readAnnotationForPreview(List<String> delimiters) throws IOException {
    /*
     * Load data from the given URL.
     */
    final String commentChar = getCommentLinePrefix();
    int startLine = getStartLineNumber();

    // creating the IS copy
    InputStream tempIs = null;

    if (tempFile != null)
        tempIs = new FileInputStream(tempFile);

    // Load Spreadsheet data for preview.
    if (isSpreadsheetFile() && workbook == null) {
        try {
            workbook = WorkbookFactory.create(tempIs);
        } catch (InvalidFormatException e) {
            tempIs.close();
            throw new IllegalArgumentException("Could not read Excel file.  Maybe the file is broken?", e);
        }
    }

    if (tempIs != null)
        tempIs.close();

    InputStream tempIs2 = null;

    if (tempFile != null)
        tempIs2 = new FileInputStream(tempFile);

    getPreviewPanel().updatePreviewTable(workbook, fileType, "", tempIs2, delimiters, commentChar,
            startLine - 1);

    if (tempIs2 != null)
        tempIs2.close();

    if (getPreviewPanel().getPreviewTable() == null)
        return;

    if (importType != NETWORK_IMPORT) {
        if (getPreviewPanel().getFileType() == FileType.GENE_ASSOCIATION_FILE) {
            final JTable table = getPreviewPanel().getPreviewTable();
            final TableModel previewModel = table.getModel();
            final String[] columnNames = new String[previewModel.getColumnCount()];

            for (int j = 0; j < columnNames.length; j++)
                columnNames[j] = previewModel.getColumnName(j);

            disableComponentsForGA();
        }

        /*
         * If this is not an Excel file, enable delimiter checkboxes.
         */
        if (fileType != null) {
            final FileType type = checkFileType();

            if (type == FileType.GENE_ASSOCIATION_FILE) {
                getPreviewPanel().setType(GO_ID.getPosition(), ONTOLOGY);
                disableComponentsForGA();
            } else if (!isSpreadsheetFile()) {
                nodeRadioButton.setEnabled(true);
                edgeRadioButton.setEnabled(true);
                networkRadioButton.setEnabled(true);
                getImportAllCheckBox().setEnabled(false);
            } else {
                getImportAllCheckBox().setEnabled(false);
            }
        }

        attributeRadioButtonActionPerformed(null);
    }

    getStartRowSpinner().setEnabled(true);

    final Window parent = SwingUtilities.getWindowAncestor(this);

    if (parent != null)
        parent.pack();
}

From source file:org.dash.valid.ars.AntigenRecognitionSiteLoader.java

License:Open Source License

private static HashMap<String, List<String>> loadARSData() throws InvalidFormatException, IOException {
    Workbook workbook = null;/*from   ww  w  .  ja va2 s  .  c o m*/

    workbook = WorkbookFactory
            .create(AntigenRecognitionSiteLoader.class.getClassLoader().getResourceAsStream(DEFAULT_ARS_FILE));

    // Return first sheet from the XLSX workbook
    Sheet mySheet = workbook.getSheetAt(0);

    // Get iterator to all the rows in current sheet
    Iterator<Row> rowIterator = mySheet.iterator();

    String gCode;
    String alleleString;
    List<String> alleles;
    HashMap<String, List<String>> arsMap = new HashMap<String, List<String>>();

    // Traversing over each row of XLSX file
    while (rowIterator.hasNext()) {
        alleles = new ArrayList<String>();
        Row row = rowIterator.next();
        gCode = row.getCell(0).getStringCellValue();
        if (gCode.contains(GLStringConstants.ASTERISK)) {
            alleleString = row.getCell(1).getStringCellValue();
            String[] parts = alleleString.split(GLStringConstants.COMMA);
            for (String part : parts) {
                alleles.add(GLStringConstants.HLA_DASH + part);
            }

            arsMap.put(GLStringConstants.HLA_DASH + gCode, alleles);
        }
    }

    workbook.close();

    return arsMap;
}

From source file:org.dash.valid.freq.HLAFrequenciesLoader.java

License:Open Source License

private List<DisequilibriumElement> loadNMDPLinkageReferenceData(String filename, Locus[] locusPositions)
        throws IOException, InvalidFormatException {
    List<DisequilibriumElement> disequilibriumElements = new ArrayList<DisequilibriumElement>();

    // Finds the workbook instance for XLSX file
    InputStream inStream = HLAFrequenciesLoader.class.getClassLoader().getResourceAsStream(filename);

    if (inStream == null) {
        throw new FileNotFoundException();
    }/*from w w w  .  j  a  va2 s.co  m*/

    Workbook workbook = WorkbookFactory.create(inStream);

    // Return first sheet from the XLSX workbook
    Sheet mySheet = workbook.getSheetAt(0);

    // Get iterator to all the rows in current sheet
    Iterator<Row> rowIterator = mySheet.iterator();

    int firstRow = mySheet.getFirstRowNum();

    List<String> raceHeaders = null;

    // Traversing over each row of XLSX file
    while (rowIterator.hasNext()) {
        Row row = rowIterator.next();

        if (row.getRowNum() == firstRow) {
            raceHeaders = readHeaderElementsByRace(row);
        } else {
            disequilibriumElements.add(readDiseqilibriumElementsByRace(row, raceHeaders, locusPositions));
        }
    }

    workbook.close();

    return disequilibriumElements;
}

From source file:org.dash.valid.freq.HLAFrequenciesLoader.java

License:Open Source License

private void loadIndividualLocusFrequency(Frequencies freq, Locus locus)
        throws IOException, InvalidFormatException {
    List<String> singleLocusFrequencies = new ArrayList<String>();
    String extension = freq.equals(Frequencies.NMDP) ? ".xlsx" : ".xls";
    InputStream inputStream = HLAFrequenciesLoader.class.getClassLoader().getResourceAsStream(
            "frequencies/" + freq.getShortName() + "/" + locus.getFrequencyName() + extension);

    if (inputStream == null)
        return;/*  w w w .  j a va2 s .c o  m*/

    Workbook workbook = WorkbookFactory.create(inputStream);

    // Return first sheet from the XLSX workbook
    Sheet mySheet = workbook.getSheetAt(0);

    // Get iterator to all the rows in current sheet
    Iterator<Row> rowIterator = mySheet.iterator();

    int firstRow = mySheet.getFirstRowNum();

    String cellValue = null;

    // Traversing over each row of XLSX file
    while (rowIterator.hasNext()) {
        Row row = rowIterator.next();

        if (row.getRowNum() == firstRow) {
            continue;
        } else {
            cellValue = row.getCell(0).getStringCellValue();
            if (!cellValue.contains(GLStringConstants.ASTERISK)) {
                cellValue = locus.getShortName() + GLStringConstants.ASTERISK + cellValue.substring(0, 2)
                        + GLStringUtilities.COLON + cellValue.substring(2);
            }
            singleLocusFrequencies.add(GLStringConstants.HLA_DASH + cellValue);
        }
    }

    individualLocusFrequencies.put(locus, singleLocusFrequencies);

    workbook.close();
}

From source file:org.databene.benerator.template.xmlanon.XmlAnonInputReader.java

License:Open Source License

private static AnonymizationSetup parseXls(String xlsUri) throws IOException, InvalidFormatException {
    Workbook workbook = WorkbookFactory.create(IOUtil.getInputStreamForURI(xlsUri));
    Sheet sheet = workbook.getSheetAt(0);

    // parse header information
    int varnameColumnIndex = -1;
    ArrayList<String> files = new ArrayList<String>();
    Row headerRow = sheet.getRow(0);/*ww  w  .  j  av  a  2  s.c om*/
    Assert.notNull(headerRow, "header row");
    for (int i = 0; i <= headerRow.getLastCellNum(); i++) {
        String header = headerRow.getCell(i).getStringCellValue();
        if ("varname".equals(header)) {
            varnameColumnIndex = i;
            break;
        } else {
            if (StringUtil.isEmpty(header))
                throw new ConfigurationError(
                        "Filename missing in column header #" + i + " of Excel document " + xlsUri);
            files.add(header);
        }
    }
    if (varnameColumnIndex == -1)
        throw new ConfigurationError("No 'varname' header defined in Excel document " + xlsUri);
    if (files.size() == 0)
        throw new ConfigurationError("No files specified in Excel document " + xlsUri);

    // parse anonymization rows
    List<Anonymization> anonymizations = new ArrayList<Anonymization>();
    for (int rownum = 1; rownum <= sheet.getLastRowNum(); rownum++) {
        Row row = sheet.getRow(rownum);
        if (XLSUtil.isEmpty(row))
            continue;
        Cell varnameCell = row.getCell(varnameColumnIndex);
        if (varnameCell == null || StringUtil.isEmpty(varnameCell.getStringCellValue()))
            throw new ConfigurationError("'varname' cell empty in table row #" + (rownum + 1));
        Anonymization anon = new Anonymization(varnameCell.getStringCellValue());
        // parse locators
        for (int colnum = 0; colnum < varnameColumnIndex; colnum++) {
            Cell cell = row.getCell(colnum);
            String path = (cell != null ? cell.getStringCellValue() : null);
            if (!StringUtil.isEmpty(path)) {
                List<String> tokens = XPathTokenizer.tokenize(path);
                String entityPath = XPathTokenizer.merge(tokens, 0, tokens.size() - 2);
                String entity = normalizeXMLPath(XPathTokenizer.nodeName(tokens.get(tokens.size() - 2)));
                String attribute = normalizeXMLPath(tokens.get(tokens.size() - 1));
                anon.addLocator(new Locator(files.get(colnum), path, entityPath, entity, attribute));
            }
        }
        // parse settings
        for (int colnum = varnameColumnIndex + 1; colnum < row.getLastCellNum() - 1; colnum += 2) {
            String key = row.getCell(colnum).getStringCellValue();
            String value = row.getCell(colnum + 1).getStringCellValue();
            if (!StringUtil.isEmpty(key) && !StringUtil.isEmpty(value))
                anon.addSetting(key, value);
        }
        anonymizations.add(anon);
    }
    return new AnonymizationSetup(files, anonymizations);
}