Example usage for org.apache.poi.poifs.filesystem POIFSFileSystem POIFSFileSystem

List of usage examples for org.apache.poi.poifs.filesystem POIFSFileSystem POIFSFileSystem

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Introduction

In this page you can find the example usage for org.apache.poi.poifs.filesystem POIFSFileSystem POIFSFileSystem.

Prototype


public POIFSFileSystem(InputStream stream) throws IOException

Source Link

Document

Create a POIFSFileSystem from an InputStream.

Usage

From source file:gov.nih.nci.evs.app.neopl.XLSXMetadataUtils.java

License:Open Source License

public static String getSummaryData(String filename, String key) {
    String value = null;/*from   w  ww .j  a va2  s .co m*/
    FileInputStream stream = null;
    try {
        stream = new FileInputStream(new File(filename));
        POIFSFileSystem poifs = null;
        try {
            poifs = new POIFSFileSystem(stream);
        } catch (Exception e) {
            stream.close();
            return getPOISummaryData(filename, key);
        }
        DirectoryEntry dir = poifs.getRoot();
        DocumentEntry siEntry = (DocumentEntry) dir.getEntry(SummaryInformation.DEFAULT_STREAM_NAME);
        if (siEntry != null) {
            DocumentInputStream dis = new DocumentInputStream(siEntry);
            PropertySet ps = new PropertySet(dis);
            SummaryInformation si = new SummaryInformation(ps);

            if (key.compareTo(SUMMARY_DATA_AUTHOR) == 0) {
                value = si.getAuthor();
            } else if (key.compareTo(SUMMARY_DATA_KEYWORDS) == 0) {
                value = si.getKeywords();
            } else if (key.compareTo(SUMMARY_DATA_TITLE) == 0) {
                value = si.getTitle();
            } else if (key.compareTo(SUMMARY_DATA_SUBJECT) == 0) {
                value = si.getSubject();
            }
        }
    } catch (Exception ex) {
        ex.getStackTrace();
    } finally {
        try {
            stream.close();
        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }
    return value;
}

From source file:gov.nih.nci.evs.app.neopl.XLSXMetadataUtils.java

License:Open Source License

public static void setSummaryData(String filename, String[] keys, String[] values) {
    String size = getFileSize(filename);
    FileInputStream stream = null;
    try {//w ww  .j a v a  2s  . com
        stream = new FileInputStream(new File(filename));
        POIFSFileSystem poifs = null;
        boolean passed = false;
        try {
            poifs = new POIFSFileSystem(stream);
            passed = true;
        } catch (Exception e) {
            passed = false;
        }
        if (!passed) {
            setPOISummaryData(filename, keys, values);
            stream.close();
            return;
        }

        HSSFWorkbook workbook = null;
        SummaryInformation summaryInfo = null;
        FileInputStream fis = null;
        try {
            System.out.println(filename);
            fis = new FileInputStream(filename);

            workbook = new HSSFWorkbook(fis);
            summaryInfo = workbook.getSummaryInformation();
            if (summaryInfo == null) {
                workbook.createInformationProperties();
                summaryInfo = workbook.getSummaryInformation();

                for (int i = 0; i < keys.length; i++) {
                    String key = keys[i];
                    String value = values[i];

                    System.out.println(key + " -> " + value);

                    if (key.compareTo(SUMMARY_DATA_AUTHOR) == 0) {
                        summaryInfo.setAuthor(value);
                    } else if (key.compareTo(SUMMARY_DATA_KEYWORDS) == 0) {
                        summaryInfo.setKeywords(value);
                    } else if (key.compareTo(SUMMARY_DATA_TITLE) == 0) {
                        summaryInfo.setTitle(value);
                    } else if (key.compareTo(SUMMARY_DATA_SUBJECT) == 0) {
                        summaryInfo.setSubject(value);
                    }
                }

            }
        } catch (Exception ex) {
            ex.printStackTrace();
        } finally {
            try {
                fis.close();
            } catch (Exception ex) {

            }
        }
        FileOutputStream fos = null;

        try {
            fos = new FileOutputStream(new File(filename));
            workbook.write(fos);
            fos.flush();
        } catch (Exception ex) {
            ex.printStackTrace();
        } finally {
            fos.close();
        }

    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

From source file:gov.nih.nci.evs.app.neopl.XLSXMetadataUtils.java

License:Open Source License

public static String getAuthor(File file) {
    String author = null;//from  w  w  w  . ja va 2 s  .  c o  m
    try {
        FileInputStream stream = new FileInputStream(file);
        POIFSFileSystem poifs = null;
        try {
            poifs = new POIFSFileSystem(stream);
        } catch (Exception e) {
            stream.close();
            return getCreator(file);
        }
        DirectoryEntry dir = null;
        try {
            dir = poifs.getRoot();
        } catch (Exception ex) {
            System.out.println("DirectoryEntry is NULL???");
            return null;
        }
        DocumentEntry siEntry = (DocumentEntry) dir.getEntry(SummaryInformation.DEFAULT_STREAM_NAME);
        if (siEntry != null) {
            DocumentInputStream dis = new DocumentInputStream(siEntry);
            PropertySet ps = new PropertySet(dis);
            SummaryInformation si = new SummaryInformation(ps);
            author = si.getAuthor();
        }
        stream.close();
    } catch (Exception ex) {
        ex.getStackTrace();
    }
    return author;
}

From source file:gov.nih.nci.evs.app.neopl.XLSXMetadataUtils.java

License:Open Source License

public static void setAuthor(String filename, String author) {
    try {/*from   w w w  .  j  a  v a2  s  .  com*/
        FileInputStream stream = new FileInputStream(new File(filename));
        POIFSFileSystem poifs = new POIFSFileSystem(stream);
        DirectoryEntry dir = poifs.getRoot();

        System.out.println("SummaryInformation.DEFAULT_STREAM_NAME: " + SummaryInformation.DEFAULT_STREAM_NAME);

        DocumentEntry siEntry = (DocumentEntry) dir.getEntry(SummaryInformation.DEFAULT_STREAM_NAME);
        DocumentInputStream dis = new DocumentInputStream(siEntry);
        PropertySet ps = new PropertySet(dis);
        SummaryInformation si = new SummaryInformation(ps);

        System.out.println("SummaryInformation setAuthor: " + author);

        si.setAuthor(author);

        OutputStream outStream = null;
        outStream = new FileOutputStream(new File(filename));
        byte[] buffer = new byte[1024];
        int length;

        while ((length = stream.read(buffer)) > 0) {
            outStream.write(buffer, 0, length);
        }
        outStream.close();
        stream.close();

    } catch (Exception ex) {
        ex.getStackTrace();
    }
}

From source file:gov.nih.nci.evs.app.neopl.XLSXMetadataUtils.java

License:Open Source License

public static void setAuthor(File file, String author) {
    try {// ww  w  .  j a v a  2  s  . c  o  m
        FileInputStream stream = new FileInputStream(file);
        POIFSFileSystem poifs = null;
        try {
            poifs = new POIFSFileSystem(stream);
        } catch (Exception e) {
            stream.close();
            setCreator(file, author);
            return;
        }
        DirectoryEntry dir = poifs.getRoot();
        DocumentEntry siEntry = (DocumentEntry) dir.getEntry(SummaryInformation.DEFAULT_STREAM_NAME);
        if (siEntry != null) {
            DocumentInputStream dis = new DocumentInputStream(siEntry);
            PropertySet ps = new PropertySet(dis);
            SummaryInformation si = new SummaryInformation(ps);
            si.setAuthor(author);
        }
        stream.close();
    } catch (Exception ex) {
        ex.getStackTrace();
    }
}

From source file:gr.abiss.calipso.domain.ExcelFile.java

License:Open Source License

public ExcelFile(InputStream is) {
    POIFSFileSystem fs = null;/*from   ww  w. j a  v  a 2 s  .co m*/
    HSSFWorkbook wb = null;
    try {
        fs = new POIFSFileSystem(is);
        wb = new HSSFWorkbook(fs);
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
    HSSFSheet sheet = wb.getSheetAt(0);
    HSSFRow r = null;
    HSSFCell c = null;
    int row = 0;
    int col = 0;
    columns = new ArrayList<Column>();
    //========================== HEADER ====================================
    r = sheet.getRow(row);
    while (true) {
        c = r.getCell((short) col);
        if (c == null) {
            break;
        }
        String value = c.getStringCellValue();
        if (value == null || value.trim().length() == 0) {
            break;
        }
        Column column = new Column(value.trim());
        columns.add(column);
        col++;
    }
    //============================ DATA ====================================
    rows = new ArrayList<List<Cell>>();
    while (true) {
        row++;
        r = sheet.getRow(row);
        if (r == null) {
            break;
        }
        List rowData = new ArrayList(columns.size());
        boolean isEmptyRow = true;
        for (col = 0; col < columns.size(); col++) {
            c = r.getCell((short) col);
            Object value = null;
            switch (c.getCellType()) {
            case (HSSFCell.CELL_TYPE_STRING):
                value = c.getStringCellValue();
                break;
            case (HSSFCell.CELL_TYPE_NUMERIC):
                // value = c.getDateCellValue();
                value = c.getNumericCellValue();
                break;
            case (HSSFCell.CELL_TYPE_BLANK):
                break;
            default: // do nothing
            }
            if (value != null && value.toString().length() > 0) {
                isEmptyRow = false;
                rowData.add(new Cell(value));
            } else {
                rowData.add(null);
            }
        }
        if (isEmptyRow) {
            break;
        }
        rows.add(rowData);
    }
}

From source file:guineu.data.parser.impl.ParserXLS.java

License:Open Source License

public HSSFWorkbook openExcel(String file_name) throws IOException {
    FileInputStream fileIn = null;
    try {//from w  w w  .j a va  2 s .co  m
        HSSFWorkbook wb;
        POIFSFileSystem fs;
        fileIn = new FileInputStream(file_name);
        fs = new POIFSFileSystem(fileIn);
        wb = new HSSFWorkbook(fs);
        return wb;
    } finally {
        if (fileIn != null) {
            fileIn.close();
        }
    }
}

From source file:guineu.database.intro.impl.WriteFile.java

License:Open Source License

/**
 * Writes the LC-MS data set into an excel file.
 *
 * @param dataset LC-MS data set//  w  ww.  j  ava 2 s  .c  o  m
 * @param path Path where the new file will be created
 * @param parameters Parameters for saving the file (columns saved in the new file)
 */
public void WriteExcelFileLCMS(Dataset dataset, String path, SimpleParameterSet parameters) {
    FileOutputStream fileOut = null;
    try {
        // Prepares sheet                   
        HSSFSheet sheet;
        try {
            FileInputStream fileIn = new FileInputStream(path);
            POIFSFileSystem fs = new POIFSFileSystem(fileIn);
            wb = new HSSFWorkbook(fs);
            int NumberOfSheets = wb.getNumberOfSheets();
            sheet = wb.createSheet(String.valueOf(NumberOfSheets));
        } catch (Exception exception) {
            wb = new HSSFWorkbook();
            sheet = wb.createSheet("Normalized");
        }
        HSSFRow row = sheet.getRow(0);
        if (row == null) {
            row = sheet.createRow(0);
        }

        LCMSColumnName elementsObjects[] = parameters.getParameter(SaveLCMSParameters.exportLCMS).getValue();

        // Writes head
        int fieldsNumber = elementsObjects.length;
        int cont = 0;
        for (LCMSColumnName p : elementsObjects) {
            this.setCell(row, cont++, p.getColumnName(), null);
        }
        int c = fieldsNumber;
        for (String experimentName : dataset.getAllColumnNames()) {
            this.setCell(row, c++, experimentName, null);
        }

        // Writes content
        for (int i = 0; i < dataset.getNumberRows(); i++) {
            SimplePeakListRowLCMS lipid = (SimplePeakListRowLCMS) dataset.getRow(i);
            row = sheet.getRow(i + 1);
            if (row == null) {
                row = sheet.createRow(i + 1);
            }

            cont = 0;
            for (LCMSColumnName p : elementsObjects) {
                try {
                    this.setCell(row, cont++, lipid.getVar(p.getGetFunctionName()), null);
                } catch (Exception ee) {
                }

            }
            c = fieldsNumber;
            for (String experimentName : dataset.getAllColumnNames()) {
                this.setCell(row, c++, lipid.getPeak(experimentName), null);
            }
        }
        //Writes the output to a file
        fileOut = new FileOutputStream(path);
        wb.write(fileOut);
        fileOut.close();
    } catch (Exception exception) {
    }
}

From source file:guineu.database.intro.impl.WriteFile.java

License:Open Source License

/**
 * Writes the basic data set into an excel file.
 *
 * @param dataset basic data set/*from   w ww.  j av  a2 s .c  om*/
 * @param path Path where the new file will be created
 */
public void WriteXLSFileBasicDataset(Dataset dataset, String path) {
    FileOutputStream fileOut = null;
    try {
        HSSFSheet sheet;
        try {
            FileInputStream fileIn = new FileInputStream(path);
            POIFSFileSystem fs = new POIFSFileSystem(fileIn);
            wb = new HSSFWorkbook(fs);
            int NumberOfSheets = wb.getNumberOfSheets();
            sheet = wb.createSheet(String.valueOf(NumberOfSheets));
        } catch (Exception exception) {
            wb = new HSSFWorkbook();
            sheet = wb.createSheet("Page 1");
        }
        HSSFRow row = sheet.getRow(0);
        if (row == null) {
            row = sheet.createRow(0);
        }
        int cont = 0;
        for (String experimentName : dataset.getAllColumnNames()) {
            this.setCell(row, cont++, experimentName, null);

        }

        HSSFPalette palette = wb.getCustomPalette();
        Color[] colors = dataset.getRowColor();
        if (colors.length > 0) {
            for (int i = 0; i < dataset.getNumberRows(); i++) {
                palette.setColorAtIndex((short) 0x12, (byte) colors[i].getRed(), (byte) colors[i].getGreen(),
                        (byte) colors[i].getBlue());
                HSSFColor mycolor = palette.getColor((short) 0x12); //unmodified
                SimplePeakListRowOther lipid = (SimplePeakListRowOther) dataset.getRow(i);

                row = sheet.getRow(i + 1);
                if (row == null) {
                    row = sheet.createRow(i + 1);
                }
                int c = 0;
                for (String experimentName : dataset.getAllColumnNames()) {
                    if (lipid.getPeak(experimentName) == null) {
                        this.setCell(row, c++, "", mycolor);
                    } else {
                        this.setCell(row, c++, lipid.getPeak(experimentName), mycolor);
                    }
                }

            }
        } else {

            List<String> names = dataset.getAllColumnNames();
            for (int i = 0; i < dataset.getNumberRows(); i++) {
                SimplePeakListRowOther lipid = (SimplePeakListRowOther) dataset.getRow(i);
                row = sheet.getRow(i + 1);
                if (row == null) {
                    row = sheet.createRow(i + 1);
                }
                for (int j = 0; j < names.size(); j++) {
                    Color c = dataset.getCellColor(i, j + 1);
                    HSSFColor mycolor = null;
                    if (c != null) {
                        mycolor = palette.findColor((byte) c.getRed(), (byte) c.getGreen(), (byte) c.getBlue());
                    }
                    if (lipid.getPeak(names.get(j)) == null) {
                        this.setCell(row, j, "", null);
                    } else {
                        this.setCell(row, j, lipid.getPeak(names.get(j)), mycolor);
                    }
                }
            }
        }

        //Write the output to a file
        fileOut = new FileOutputStream(path);
        wb.write(fileOut);
        fileOut.close();
    } catch (Exception exception) {
    }
}

From source file:guineu.database.intro.impl.WriteFile.java

License:Open Source License

/**
 * Writes the GCxGC-MS data set into an excel file.
 *
 * @param dataset GCxGC-MS data set/*  w w  w  . j  a  v  a2 s.co  m*/
 * @param path Path where the new file will be created
 * @param parameters Parameters for saving the file (columns saved in the new file)
 */
public void WriteExcelFileGCGC(Dataset dataset, String path, SimpleParameterSet parameters) {
    FileOutputStream fileOut = null;
    try {
        HSSFSheet sheet;
        try {
            FileInputStream fileIn = new FileInputStream(path);
            POIFSFileSystem fs = new POIFSFileSystem(fileIn);
            wb = new HSSFWorkbook(fs);
            int NumberOfSheets = wb.getNumberOfSheets();
            sheet = wb.createSheet(String.valueOf(NumberOfSheets));
        } catch (Exception exception) {
            wb = new HSSFWorkbook();
            sheet = wb.createSheet("Normalized");
        }
        HSSFRow row = sheet.getRow(0);
        if (row == null) {
            row = sheet.createRow(0);
        }

        GCGCColumnName elementsObjects[] = parameters.getParameter(SaveGCGCParameters.exportGCGC).getValue();

        // Write head
        int fieldsNumber = elementsObjects.length;
        int cont = 0;
        for (GCGCColumnName p : elementsObjects) {
            this.setCell(row, cont++, p.getColumnName(), null);
        }
        int c = fieldsNumber;
        for (String experimentName : dataset.getAllColumnNames()) {
            this.setCell(row, c++, experimentName, null);
        }

        // Write content
        for (int i = 0; i < dataset.getNumberRows(); i++) {
            SimplePeakListRowGCGC metabolite = (SimplePeakListRowGCGC) dataset.getRow(i);
            row = sheet.getRow(i + 1);
            if (row == null) {
                row = sheet.createRow(i + 1);
            }
            cont = 0;

            for (GCGCColumnName p : elementsObjects) {
                try {
                    this.setCell(row, cont++, metabolite.getVar(p.getGetFunctionName()), null);
                } catch (Exception ee) {
                }

            }
            c = fieldsNumber;
            for (String experimentName : dataset.getAllColumnNames()) {
                try {
                    this.setCell(row, c++, metabolite.getPeak(experimentName), null);
                } catch (Exception e) {
                    this.setCell(row, c, "NA", null);
                }
            }
        }
        //Write the output to a file
        fileOut = new FileOutputStream(path);
        wb.write(fileOut);
        fileOut.close();
    } catch (Exception e) {
        System.out.println("Inoracle2.java --> WriteExcelFileGCGC() " + e);
    }
}