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:gda.hrpd.data.ExcelReader.java

License:Open Source License

/**
 * open or reopen the specified spreadsheet file for work sheet 0.
 * //from w  w  w. ja  va2s.  co  m
 * @param filename
 */
public void openSpreadsheet(String filename) {
    if (filename == null) {
        filename = this.filename;
    }
    if (!filename.equalsIgnoreCase(this.filename)) {
        close();
        try {
            fin = new FileInputStream(filename);
        } catch (FileNotFoundException e) {
            logger.warn("Cannot find sample information file {}.", filename);
            JythonServerFacade.getInstance().print("please specify the URL for the sample information file.");
        }
    }
    if (fin != null) {

        try {
            fs = new POIFSFileSystem(fin);
            wb = new HSSFWorkbook(fs);
            sheet = wb.getSheetAt(0);
        } catch (IOException e) {
            logger.error("Error opening spreadsheet", e);
        }
    }
}

From source file:gda.hrpd.data.ExcelWorkbook.java

License:Open Source License

/**
 * Constructor - opens a file input stream object, creates a workbook for accessing to the content of the Excel
 * file.//from ww w. j a v a2s  . com
 * 
 * @param filename
 * @throws InstantiationException
 */
public ExcelWorkbook(String filename) throws InstantiationException {
    if (filename != null) {
        this.filename = filename;
    } else {
        throw new InstantiationException("Filename is null");
    }
    if (fileInput != null) {
        // close existing file input stream to ensure only one stream available
        try {
            fileInput.close();
        } catch (IOException e) {
            throw new InstantiationException("Can not close existing file input stream");
        }
    }

    // check file permission
    File file = new File(this.filename);

    readable = file.canRead();
    if (readable) {
        logger.info("GDA can read from the file: {}", this.filename);
    } else {
        logger.warn(
                "GDA cannot read from the file: {}. Please make sure file permission is correct for GDA to read.",
                this.filename);
    }

    writeable = file.canWrite();
    if (writeable) {
        logger.info("GDA can write to the file: {}", this.filename);
    } else {
        logger.warn(
                "GDA cannot write to the file: {}. Please make sure file permission is correct for GDA to write.",
                this.filename);
    }

    // open a new file input stream
    try {
        fileInput = new FileInputStream(this.filename);
    } catch (FileNotFoundException e) {
        logger.error("Cannot find sample information file {}.", filename);
        JythonServerFacade.getInstance().print("please specify the URL for file.");
        throw new InstantiationException(e.getMessage());
    }
    // open the workbook
    if (fileInput != null) {
        try {
            fs = new POIFSFileSystem(fileInput);
            wb = new HSSFWorkbook(fs);
        } catch (IOException e) {
            logger.error("failed to open Excel file {}.", this.filename);
            throw new InstantiationException("can not open Excel file: " + this.filename);
        }
    }
}

From source file:gda.hrpd.data.HSSF.java

License:Apache License

/**
 * Constructor HSSF - creates an HSSFStream from an InputStream. The HSSFStream reads in the records allowing
 * modification.//from  w w  w  . j a  va 2s . co  m
 *
 * @param filename
 * @exception IOException
 */

public HSSF(String filename) throws IOException {
    this.filename = filename;
    POIFSFileSystem fs = new POIFSFileSystem(new FileInputStream(filename));

    hssfworkbook = new HSSFWorkbook(fs);

    // records = RecordFactory.createRecords(stream);
}

From source file:gda.hrpd.data.HSSF.java

License:Apache License

/**
 * Constructor HSSF - takes in file - attempts to read it then reconstruct it
 *
 * @param infile// w  w w  .  ja  v a  2  s  .  c om
 * @param outfile
 * @param write
 * @exception IOException
 */

public HSSF(String infile, @SuppressWarnings("unused") String outfile,
        @SuppressWarnings("unused") boolean write) throws IOException {
    this.filename = infile;
    POIFSFileSystem fs = new POIFSFileSystem(new FileInputStream(filename));

    hssfworkbook = new HSSFWorkbook(fs);

    // HSSFWorkbook book = hssfstream.getWorkbook();
}

From source file:gda.hrpd.data.SampleExperimentSummary.java

License:Open Source License

/**
 * @throws InstantiationException/*from   ww  w  .  j  a va  2  s  .  com*/
 */
public SampleExperimentSummary() throws InstantiationException {
    // check if the data directory has been defined
    dataDir = PathConstructor.createFromDefaultProperty();

    if (this.dataDir == null) {
        // this java property is compulsory - stop the scan
        String error = "java property gda.data.scan.datawriter.datadir not defined - cannot create a new data file";
        logger.error(error);
        throw new InstantiationException(error);
    }
    String sampleInfoFile = LocalProperties.get("gda.hrpd.data.sample.info", "Sample.xls");
    // check if the sample information file is available
    filename = dataDir + File.separator + sampleInfoFile;

    try {
        fin = new FileInputStream(filename);
    } catch (FileNotFoundException e) {
        logger.warn("Cannot find sample information file {}.", filename);
    }

    if (fin != null) {

        try {
            fs = new POIFSFileSystem(fin);
            wb = new HSSFWorkbook(fs);
            sheet = wb.getSheetAt(1);
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
}

From source file:gov.nih.nci.cabig.caaers.dataimport.AgentSpecificTermsImporter.java

License:BSD License

public Map<String, Object> importFile() throws Exception {

    POIFSFileSystem poifs;/*from ww w  .j a v  a2s. c o  m*/
    HSSFWorkbook wb;
    HSSFSheet sh = null;

    boolean isExcel = file.getName().endsWith(".xls");
    boolean isCSV = file.getName().endsWith(".csv");

    Map<String, Object> results = new HashMap<String, Object>();
    int rowCount = 0;
    int columnsCount = 0;
    Map<String, Agent> agents = new HashMap<String, Agent>();
    Map<String, Agent> missingAgents = new HashMap<String, Agent>();
    Set<String> missingTerms = new HashSet<String>();
    Map<String, String> asaelCache = new HashMap<String, String>();
    int asael;

    // wipe out the table
    agentSpecificTermDao.deleteAll();
    studyDao.deleteAllExpectedTerms();
    // if (true) return null;

    // get needed headers
    if (isExcel) {
        poifs = new POIFSFileSystem(new FileInputStream(file));
        wb = new HSSFWorkbook(poifs);
        sh = wb.getSheetAt(0);
        rowCount = sh.getLastRowNum();
        columnsCount = sh.getRow(0).getLastCellNum();

        for (byte i = 0; i < columnsCount; i++) {
            HSSFCell cell = sh.getRow(0).getCell(i);
            if (headers.containsKey(cell.getStringCellValue())) {
                headers.remove(cell.getStringCellValue());
                headers.put(cell.getStringCellValue(), Short.valueOf(i));
            }
        }
    }

    InputStream ir = null;
    Reader r = null;
    BufferedReader br = null;

    if (isCSV) {
        // readLines
        rowCount = 0;
        ir = new FileInputStream(file);
        r = new InputStreamReader(ir);
        br = new BufferedReader(r);
        String s = br.readLine();
        while (s != null) {
            if (rowCount == 0) {
                String[] _s = s.split("[\\|]{1}");
                for (byte j = 0; j < _s.length; j++) {
                    // System.out.println(_s[j]);
                    if (headers.containsKey(_s[j])) {
                        headers.remove(_s[j]);
                        headers.put(_s[j], Short.valueOf(j));
                    }
                }
            }
            rowCount++;
            s = br.readLine();
        }
        br.close();
        r.close();
        ir.close();

        ir = new FileInputStream(file);
        r = new InputStreamReader(ir);
        br = new BufferedReader(r);
    }

    /*
            System.out.println(rowCount);
            for (Map.Entry e : headers.entrySet()) {
    System.out.println(e.getKey() + "=>" + e.getValue());
            }
    */

    agents.clear();
    missingTerms.clear();
    missingAgents.clear();
    asael = 0;
    int duplicateAgentTerms = 0;

    //
    String nsc = "";
    String ctcae_category = "";
    String ctcae_version = "0.0";
    String ae_term = "";
    String other_toxicity = "";

    // Loading ASAE list
    // if (true) {  return null; }

    int i = 1;
    while (i <= rowCount) {

        nsc = "";

        if (isExcel) {
            HSSFRow row = sh.getRow(i);
            if (row != null) {
                nsc = getCellData("", i, row.getCell((short) headers.get("NSC")));
                ctcae_category = getCellData("", i, row.getCell((short) headers.get("CTCAE_CATEGORY")));
                ctcae_version = getCellData("", i, row.getCell((short) headers.get("CTCAE_VERSION")));
                ae_term = getCellData("", i, row.getCell((short) headers.get("AE_TERM")));
                other_toxicity = getCellData("", i, row.getCell((short) headers.get("OTHER_TOXICITY")));
            }
        } else {
            String s;
            s = br.readLine();
            if (s != null) {
                String[] _s = s.split("[\\|]{1}");
                if (i > 1 && _s.length > 1) {
                    nsc = _s[headers.get("NSC")];
                    ctcae_category = _s[headers.get("CTCAE_CATEGORY")];
                    try {
                        ctcae_version = _s[headers.get("CTCAE_VERSION")].trim();
                    } catch (NumberFormatException e) {
                        //                                System.out.println(s);
                        return null;
                    }
                    ae_term = _s[headers.get("AE_TERM")];
                    if (_s.length - 1 >= headers.get("OTHER_TOXICITY"))
                        other_toxicity = _s[headers.get("OTHER_TOXICITY")];
                    else
                        other_toxicity = "";
                }
            }
        }

        if (nsc.trim().equals("")) {
            i++;
            continue;
        } else {
            // System.out.println(String.format("%s). NSC:%s,   V:%s,   C:%s,   T:%s", i, nsc, ctcae_version, ctcae_category, ae_term));
        }

        Agent a = agents.get(nsc);
        if (a == null) {
            a = agentDao.getByNscNumber(nsc);
            // System.out.println(asael + ". OK. Found agent [" + a.getName() + "] for NSC: [" + nsc + "]");
            agents.put(nsc, a);
        }

        if (a != null) {
            AgentSpecificCtcTerm t = new AgentSpecificCtcTerm();
            t.setAgent(a);
            t.setOtherToxicity(other_toxicity);

            List<CtcTerm> list = terminologyRepository.getCtcTerm(ctcae_category, ctcae_version, ae_term);
            if (list.size() == 0) {
                // System.out.println("<ERROR>: Term not found: " + ae_term + ", Category: " + ctcae_category + ", CTCAE Version: " + ctcae_version);
                missingTerms.add("Term not found: " + ae_term + ", Category: " + ctcae_category
                        + ", CTCAE Version: " + ctcae_version);
            } else {
                t.setCtcTerm(list.get(0));
                if (persistASAE(t))
                    asael++;
                else
                    duplicateAgentTerms++;
            }

            agentSpecificTermDao.evict(t);

        } else {
            if (!missingAgents.containsKey(nsc)) {
                // System.out.println("<ERROR>: The agent was not found by its NSC: " + nsc);
                missingAgents.put(nsc, null);
            }
        }

        i++;
    }

    if (isCSV) {
        br.close();
        r.close();
        ir.close();
    }

    results.put(KEY_MISSING_TERMS, missingTerms);
    results.put(KEY_PROCESSED_AGENTS, agents.size() - missingAgents.size());
    results.put(KEY_PROCESSED_AGENTTERMS, asael);
    results.put(KEY_MISSING_AGENTS, missingAgents);
    results.put(KEY_DUPLICATE_AGENT_TERMS, duplicateAgentTerms);

    return results;
}

From source file:gov.nih.nci.cabig.caaers.tools.ExcelProcessor.java

License:BSD License

private void bootstrap(File inputFile) throws Exception {

    poifs = new POIFSFileSystem(new FileInputStream(inputFile));

    // create a workbook out of the input stream
    wb = new HSSFWorkbook(poifs);
    studyInfoSheet = getSheet(STUDY_SHEET_NAME);
    agentInfoSheet = getSheet(AGENT_SHEET_NAME);
    diseaseInfoSheet = getSheet(DISEASE_SHEET_NAME);
    tacInfoSheet = getSheet(TAC_SHEET_NAME);
    orgInfoSheet = getSheet(ORG_SHEET_NAME);
    investigatorInfoSheet = getSheet(INVESTIGATOR_SHEET_NAME);
    therapyInfoSheet = getSheet(THERAPY_SHEET_NAME);
    rowCount = studyInfoSheet.getLastRowNum();
}

From source file:gov.nih.nci.cananolab.util.ExcelParser.java

License:BSD License

/**
 * Vertically parse the Excel file into a 2-D matrix represented as a map of map.
 * Key is Column header, value is a map, whose key is Row header and value is
 * the cell./*  w  ww.j  a va2 s  .c o m*/
 * 
 * @return
 * @throws IOException
 */
public SortedMap<String, SortedMap<String, Double>> verticalParse(String fileName) throws IOException {
    InputStream inputStream = null;
    SortedMap<String, SortedMap<String, Double>> dataMatrix = new TreeMap<String, SortedMap<String, Double>>();
    try {
        inputStream = new BufferedInputStream(new FileInputStream(fileName));
        POIFSFileSystem fs = new POIFSFileSystem(inputStream);
        Workbook wb = new HSSFWorkbook(fs);
        Sheet sheet1 = wb.getSheetAt(0);
        //printSheet(sheet1);
        Row firstRow = sheet1.getRow(0);
        int rowIndex = 0;
        for (Row row : sheet1) {
            int colIndex = 0;
            String rowHeader = row.getCell(0).getStringCellValue();
            for (Cell cell : row) {
                if (rowIndex > 0 && colIndex > 0) { //skipping first row/column
                    String columnHeader = firstRow.getCell(colIndex).getStringCellValue();
                    SortedMap<String, Double> columnData = null;
                    if (dataMatrix.get(columnHeader) != null) {
                        columnData = dataMatrix.get(columnHeader);
                    } else {
                        columnData = new TreeMap<String, Double>();
                    }
                    if (cell != null) {
                        columnData.put(rowHeader, cell.getNumericCellValue());
                        dataMatrix.put(columnHeader, columnData);
                    }
                }
                colIndex++;
            }
            rowIndex++;
        }
    } finally {
        if (inputStream != null) {
            try {
                inputStream.close();
            } catch (Exception e) {
            }
        }
    }
    return dataMatrix;
}

From source file:gov.nih.nci.cananolab.util.ExcelParser.java

License:BSD License

/**
 * Horizontally parse the Excel file into a 2-D matrix represented as a map of map.
 * Key is Row header, value is a map, whose key is Column header and value is
 * the cell.//from  w  w w  .ja v a2s  .c  om
 * 
 * @return
 * @throws IOException
 */
public SortedMap<String, SortedMap<String, Double>> horizontalParse(String fileName) throws IOException {
    InputStream inputStream = null;
    SortedMap<String, SortedMap<String, Double>> dataMatrix = new TreeMap<String, SortedMap<String, Double>>();
    try {
        inputStream = new BufferedInputStream(new FileInputStream(fileName));
        POIFSFileSystem fs = new POIFSFileSystem(inputStream);
        Workbook wb = new HSSFWorkbook(fs);
        Sheet sheet1 = wb.getSheetAt(0);
        //printSheet(sheet1);
        Row firstRow = sheet1.getRow(0);
        int rowIndex = 0;
        for (Row row : sheet1) {
            int colIndex = 0;
            String rowHeader = row.getCell(0).getStringCellValue();
            for (Cell cell : row) {
                if (rowIndex > 0 && colIndex > 0) { //skipping first row/column
                    String columnHeader = firstRow.getCell(colIndex).getStringCellValue();
                    SortedMap<String, Double> rowData = null;
                    if (dataMatrix.get(rowHeader) != null) {
                        rowData = dataMatrix.get(rowHeader);
                    } else {
                        rowData = new TreeMap<String, Double>();
                    }
                    if (cell != null) {
                        rowData.put(columnHeader, cell.getNumericCellValue());
                        dataMatrix.put(rowHeader, rowData);
                    }
                }
                colIndex++;
            }
            rowIndex++;
        }
    } finally {
        if (inputStream != null) {
            try {
                inputStream.close();
            } catch (Exception e) {
            }
        }
    }
    return dataMatrix;
}

From source file:gov.nih.nci.cananolab.util.ExcelParser.java

License:BSD License

/**
 * Parse secondary StanShaw Excel spreadsheet and store data in a 3-layer map.
 * 1st layer: sample map, key is sample name (261-13-4), value is the 2nd layer map.
 * 2nd layer: assay map, key is assay name (Aorta 1), value is the 3rd layer map.
 * 3rd layer: datum map, there are always 3 entries in this map, for example,  
 *            key is datum name Median (M), value is 9.02194E-08.
 *            key is datum name Mean (M), value is 7.96025E-08.
 *            key is datum name SEM (M), value is 6.12968E-09.
 *  //from ww w.  java 2  s .  c  o m
 * @param fileName
 * @return a 3-layer map
 * @throws IOException
 */
public SortedMap<String, SortedMap<String, SortedMap<String, Double>>> twoWayParse(String fileName)
        throws IOException {
    InputStream inputStream = null;
    SortedMap<String, SortedMap<String, SortedMap<String, Double>>> dataMatrix = new TreeMap<String, SortedMap<String, SortedMap<String, Double>>>();
    try {
        inputStream = new BufferedInputStream(new FileInputStream(fileName));
        POIFSFileSystem fs = new POIFSFileSystem(inputStream);
        Workbook wb = new HSSFWorkbook(fs);
        Sheet sheet1 = wb.getSheetAt(0);
        //printSheet(sheet1);
        // Sheet must contain >= 2 rows (header + data).
        if (sheet1.getLastRowNum() < 1) {
            return dataMatrix;
        }
        // Sheet must contain >= 5 columns (assay, sample + 3 datums).   
        Row firstRow = sheet1.getRow(0);
        if (firstRow.getLastCellNum() < 4) {
            return dataMatrix;
        }
        // Iterate sheet from 2nd row and populate the data matrix.
        for (int rowIndex = 1; rowIndex <= sheet1.getLastRowNum(); rowIndex++) {
            Row row = sheet1.getRow(rowIndex);

            //1.get sampleName key for 1st layer map, assayName key for 2 layer map.
            String sampleName = row.getCell(1).getStringCellValue();
            String assayName = row.getCell(0).getStringCellValue();

            //2.find sampleMap in dataMatrix, if null create & store new sampleMap.
            SortedMap<String, SortedMap<String, Double>> sampleMap = dataMatrix.get(sampleName);
            if (sampleMap == null) {
                sampleMap = new TreeMap<String, SortedMap<String, Double>>();
                dataMatrix.put(sampleName, sampleMap);
            }

            //3.find assayMap in sampleMap, if null create & store new assayMap.
            SortedMap<String, Double> assayMap = sampleMap.get(assayName);
            if (assayMap == null) {
                assayMap = new TreeMap<String, Double>();
                sampleMap.put(assayName, assayMap);
            }

            //4.iterate row from col-2 to last column, store datum value.
            for (int colIndex = 2; colIndex <= row.getLastCellNum(); colIndex++) {
                Cell cell = row.getCell(colIndex);
                if (cell != null && cell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
                    String datumName = firstRow.getCell(colIndex).getStringCellValue();
                    assayMap.put(datumName, cell.getNumericCellValue());
                }
            }
        }
    } finally {
        if (inputStream != null) {
            try {
                inputStream.close();
            } catch (Exception e) {
            }
        }
        //this.print2ndMatrix(dataMatrix);
    }
    return dataMatrix;
}