Example usage for org.apache.poi.hssf.usermodel HSSFWorkbook getSheetAt

List of usage examples for org.apache.poi.hssf.usermodel HSSFWorkbook getSheetAt

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Introduction

In this page you can find the example usage for org.apache.poi.hssf.usermodel HSSFWorkbook getSheetAt.

Prototype

@Override
public HSSFSheet getSheetAt(int index)

Source Link

Document

Get the HSSFSheet object at the given index.

Usage

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

License:Open Source License

/**
 * @param treeDef/*www  .j  a v a  2  s .  co m*/
 * @return
 */
public Geography convertGeographyFromXLS(final GeographyTreeDef treeDef) {
    frame.setDesc("Building Geography Tree...");

    Hashtable<String, Geography> geoHash = new Hashtable<String, Geography>();

    geoHash.clear();

    String fileName = "Geography.xls";
    File file = XMLHelper.getConfigDir("../demo_files/" + fileName);
    if (!file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir");
        file = XMLHelper.getConfigDir(fileName);
        if (!file.exists()) {
            file = new File("Specify/demo_files/" + fileName);
        }
    }

    if (file == null || !file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "]");
        return null;
    }

    // setup the root Geography record (planet Earth)
    Geography earth = new Geography();
    earth.initialize();
    earth.setName(getResourceString("Earth"));
    earth.setFullName(earth.getName());
    earth.setNodeNumber(1);
    earth.setHighestChildNodeNumber(1);
    earth.setRankId(0);
    earth.setDefinition(treeDef);
    GeographyTreeDefItem defItem = treeDef.getDefItemByRank(0);
    earth.setDefinitionItem(defItem);

    int counter = 0;

    try {
        startTx();

        persist(earth);

        String[] cells = new String[4];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        int lastRowNum = sheet.getLastRowNum();
        if (frame != null) {
            final int mx = lastRowNum;
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    frame.setProcess(0, mx);
                }
            });
        }

        while (rows.hasNext()) {
            if (counter == 0) {
                counter = 1;
                rows.next();
                continue;
            }
            if (counter % 100 == 0) {
                if (frame != null)
                    frame.setProcess(counter);
                log.info("Converted " + counter + " Geography records");
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            int i = 0;
            while (cellsIter.hasNext() && i < 4) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString());
                    i++;
                }
            }
            // Sets nulls to unused cells
            for (int j = i; j < 4; j++) {
                cells[j] = null;
            }
            //System.out.println();
            @SuppressWarnings("unused")
            Geography newGeo = convertGeographyRecord(cells[0], cells[1], cells[2], cells[3], earth);

            counter++;
        }

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

    if (frame != null)
        frame.setProcess(counter);

    log.info("Converted " + counter + " Geography records");

    frame.setDesc("Saving Geography Tree...");
    frame.getProcessProgress().setIndeterminate(true);

    TreeHelper.fixFullnameForNodeAndDescendants(earth);
    earth.setNodeNumber(1);
    fixNodeNumbersFromRoot(earth);

    commitTx();

    /*startTx();
    TreeHelper.fixFullnameForNodeAndDescendants(earth);
    earth.setNodeNumber(1);
    fixNodeNumbersFromRoot(earth);
            
    printTree(earth, 0);
    saveTree(earth);
            
    commitTx();*/

    log.info("Converted " + counter + " Stratigraphy records");

    // set up Geography foreign key mapping for locality
    geoHash.clear();

    return earth;
}

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

License:Open Source License

/**
 * @param fileName// ww  w  . j  a va2s  .  com
 * @return
 */
public HashSet<String> getColumnNamesFromXLS(final String fileName, final boolean doUserProvidedFile) {
    File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile);
    if (file == null) {
        return null;
    }

    HashSet<String> nameHash = new HashSet<String>();
    try {
        String[] cells = new String[35];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        rows = sheet.rowIterator();
        if (rows.hasNext()) {
            for (int i = 0; i < cells.length; i++) {
                cells[i] = null;
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            while (cellsIter.hasNext()) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    nameHash.add(StringUtils.trim(cell.getRichStringCellValue().getString()));
                }
            }
        }

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

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

License:Open Source License

/**
 * @param treeDef/*  w  w  w  .  j  ava2s .  co m*/
 * @param fileName
 * @param doUserProvidedFile
 * @return
 */
public Taxon convertTaxonFromXLS(final TaxonTreeDef treeDef, final String fileName,
        final boolean doUserProvidedFile) {
    Hashtable<String, Taxon> taxonHash = new Hashtable<String, Taxon>();

    taxonHash.clear();

    File file = TaxonLoadSetupPanel.getFileForTaxon(fileName, doUserProvidedFile);
    if (file == null) {
        return null;
    }

    Vector<TaxonTreeDefItem> rankedItems = new Vector<TaxonTreeDefItem>();
    Hashtable<String, Boolean> colNames = new Hashtable<String, Boolean>();
    for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) {
        colNames.put(item.getName().toLowerCase(), true);
        rankedItems.add(item);
    }

    Collections.sort(rankedItems, new Comparator<TaxonTreeDefItem>() {
        @Override
        public int compare(TaxonTreeDefItem o1, TaxonTreeDefItem o2) {
            return o1.getRankId().compareTo(o2.getRankId());
        }
    });

    Connection conn = null;
    Statement stmt = null;

    TaxonTreeDefItem rootTreeDefItem = rankedItems.get(0);
    Set<Taxon> rootKids = rootTreeDefItem.getTreeEntries();
    Taxon root = rootKids.iterator().next();

    Vector<Pair<String, Integer>> nodeList = new Vector<Pair<String, Integer>>();
    Pair<String, Integer> rootNode = new Pair<String, Integer>(root.getName(), root.getId());
    nodeList.add(rootNode);

    int counter = 0;
    int numDataCols = 0;
    try {
        startTx();

        for (TaxonTreeDefItem item : treeDef.getTreeDefItems()) {
            persist(item);
        }

        persist(root);

        commitTx();

        String[] cells = new String[35];
        String[] header = new String[35];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        int lastRowNum = sheet.getLastRowNum();
        if (frame != null) {
            final int mx = lastRowNum;
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    frame.setProcess(0, mx);
                }
            });
        }

        conn = DBConnection.getInstance().createConnection();
        //conn.setAutoCommit(false);
        stmt = conn.createStatement();

        rows = sheet.rowIterator();
        while (rows.hasNext()) {
            for (int i = 0; i < cells.length; i++) {
                cells[i] = null;
            }

            if (counter == 0) {
                HSSFRow row = (HSSFRow) rows.next();
                Iterator<?> cellsIter = row.cellIterator();
                int i = 0;
                while (cellsIter.hasNext()) {
                    HSSFCell cell = (HSSFCell) cellsIter.next();
                    if (cell != null) {
                        cells[i] = getXLSCellValueAsStr(cell);
                        header[i] = cells[i];
                        i++;
                    }
                }
                for (i = 0; i < cells.length; i++) {
                    if (cells[i] == null)
                        break;

                    if (colNames.get(cells[i].toLowerCase()) != null) {
                        numDataCols = i + 1;
                    } else {
                        for (String key : colNames.keySet()) {
                            System.err.println("key[" + key + "]");
                        }
                        System.err.println("Not Found: [" + cells[i].toLowerCase() + "]");
                        break;
                    }
                }
                loadIndexes(cells);
                counter = 1;

                for (String hdr : header) {
                    if (hdr == null)
                        break;

                    int inx = 0;
                    for (TaxonTreeDefItem item : rankedItems) {
                        if (hdr.equalsIgnoreCase(item.getName())) {
                            log.debug("Header: " + hdr + " -> " + inx);
                            taxonIndexes.put(hdr, inx);
                            item.setIsInFullName(item.getRankId() >= TaxonTreeDef.GENUS);

                        } else {
                            log.debug("Header: " + hdr + " -> skipped.");
                        }
                        inx++;
                    }
                }
                continue;
            }

            if (counter % 100 == 0) {
                if (frame != null)
                    frame.setProcess(counter);
                //log.info("Converted " + counter + " of "+lastRowNum+" Taxon records");
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            int i = 0;
            while (cellsIter.hasNext() && i < cells.length) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    cells[i] = getXLSCellValueAsStr(cell);
                    i++;
                }
            }

            convertTaxonNodes(conn, stmt, header, cells, numDataCols, rootNode, nodeList, rankedItems,
                    root.getDefinition().getId());

            counter++;
        }

        stmt.executeUpdate(
                "UPDATE taxon SET IsAccepted = true WHERE IsAccepted IS NULL and AcceptedID IS NULL AND TaxonTReeDefID = "
                        + treeDef.getId());

        // Clear all GUIDs in Taxon.
        stmt.executeUpdate("UPDATE taxon SET GUID = NULL WHERE TaxonTreeDefID = " + treeDef.getId());

        conn.close();

        input.close();

        if (frame != null)
            frame.setProcess(lastRowNum);

        root = (Taxon) session.createQuery("FROM Taxon WHERE id = " + root.getId()).list().get(0);

    } catch (Exception ex) {
        ex.printStackTrace();
        edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount();
        edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(BackupServiceFactory.class, ex);

    } finally {
        try {
            if (stmt != null) {
                stmt.close();
            }
            if (conn != null) {
                conn.close();
            }
        } catch (Exception ex) {
            ex.printStackTrace();
        }
    }

    if (frame != null) {
        frame.setDesc("Saving Taxon Tree...");
        frame.getProcessProgress().setIndeterminate(true);
    }

    NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem> nodeNumberer = new NodeNumberer<Taxon, TaxonTreeDef, TaxonTreeDefItem>(
            root.getDefinition());
    nodeNumberer.doInBackground();

    //startTx();
    //TreeHelper.fixFullnameForNodeAndDescendants(root);
    //root.setNodeNumber(1);
    //fixNodeNumbersFromRoot(root);
    //commitTx();

    log.info("Converted " + counter + " Taxon records");

    // set up Taxon foreign key mapping for locality
    taxonHash.clear();

    return root;
}

From source file:edu.ku.brc.specify.utilapps.BuildSampleDatabase.java

License:Open Source License

/**
 * @param treeDef/*from  w w w. ja  v  a 2s . c o  m*/
 * @return
 */
public GeologicTimePeriod convertChronoStratFromXLS(final GeologicTimePeriodTreeDef treeDef,
        final Agent userAgent) {
    startTx();

    GeologicTimePeriodTreeDefItem root = createGeologicTimePeriodTreeDefItem(null, treeDef, "Root", 0);
    GeologicTimePeriodTreeDefItem era = createGeologicTimePeriodTreeDefItem(root, treeDef, "Erathem/Era", 100);
    GeologicTimePeriodTreeDefItem period = createGeologicTimePeriodTreeDefItem(era, treeDef, "System/Period",
            200);
    GeologicTimePeriodTreeDefItem series = createGeologicTimePeriodTreeDefItem(period, treeDef, "Series/Epoch",
            300);
    @SuppressWarnings("unused")
    GeologicTimePeriodTreeDefItem member = createGeologicTimePeriodTreeDefItem(series, treeDef, "Stage/Age",
            400);
    persist(root);
    commitTx();

    series.setIsInFullName(true);

    frame.setDesc("Building ChronoStratigraphy Tree...");

    Hashtable<String, GeologicTimePeriod> chronoHash = new Hashtable<String, GeologicTimePeriod>();

    chronoHash.clear();

    String fileName = "chronostrat_tree.xls";
    File file = XMLHelper.getConfigDir("../demo_files/" + fileName);
    if (!file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "] checking the config dir");
        file = XMLHelper.getConfigDir(fileName);
        if (!file.exists()) {
            file = new File("Specify/demo_files/" + fileName);
        }
    }

    if (file == null || !file.exists()) {
        log.error("Couldn't file[" + file.getAbsolutePath() + "]");
        return null;
    }

    // setup the root ChronoStrat record (planet Earth)
    GeologicTimePeriod rootNode = new GeologicTimePeriod();
    rootNode.initialize();
    rootNode.setName(getResourceString("Root"));
    rootNode.setFullName(rootNode.getName());
    rootNode.setRankId(0);
    rootNode.setDefinition(treeDef);
    rootNode.setDefinitionItem(root);
    rootNode.setCreatedByAgent(userAgent);

    int counter = 0;

    try {
        startTx();

        persist(rootNode);

        String[] cells = new String[4];
        InputStream input = new FileInputStream(file);
        POIFSFileSystem fs = new POIFSFileSystem(input);
        HSSFWorkbook workBook = new HSSFWorkbook(fs);
        HSSFSheet sheet = workBook.getSheetAt(0);
        Iterator<?> rows = sheet.rowIterator();

        int lastRowNum = sheet.getLastRowNum();
        if (frame != null) {
            final int mx = lastRowNum;
            SwingUtilities.invokeLater(new Runnable() {
                public void run() {
                    frame.setProcess(0, mx);
                }
            });
        }

        while (rows.hasNext()) {
            if (counter == 0) {
                counter = 1;
                continue;
            }
            if (counter % 100 == 0) {
                if (frame != null)
                    frame.setProcess(counter);
                log.info("Converted " + counter + " ChronoStrat records");
            }

            HSSFRow row = (HSSFRow) rows.next();
            Iterator<?> cellsIter = row.cellIterator();
            int i = 0;
            while (cellsIter.hasNext() && i < 4) {
                HSSFCell cell = (HSSFCell) cellsIter.next();
                if (cell != null) {
                    cells[i] = StringUtils.trim(cell.getRichStringCellValue().getString());
                    i++;
                }
            }
            for (int j = i; j < 4; j++) {
                cells[j] = null;
            }
            //System.out.println();
            @SuppressWarnings("unused")
            GeologicTimePeriod newGeo = convertChronoStratRecord(cells[0], cells[1], cells[2], cells[3],
                    rootNode, userAgent);

            counter++;
        }

        input.close();

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

    if (frame != null)
        frame.setProcess(counter);

    log.info("Converted " + counter + " ChronoStrat records");

    TreeHelper.fixFullnameForNodeAndDescendants(rootNode);
    rootNode.setNodeNumber(1);
    fixNodeNumbersFromRoot(rootNode);

    commitTx();

    log.info("Converted " + counter + " Stratigraphy records");

    // set up ChronoStrat foreign key mapping for locality
    chronoHash.clear();

    return rootNode;
}

From source file:edu.rice.rems.Scheduler.java

License:Open Source License

/**
 * Extract shift schedule data from excel file
 *
 * @param xlsFile/*from w  ww. jav  a  2s .  c om*/
 * @return data
 */
private static ArrayList<ArrayList<String>> extractData(File xlsFile) {
    ArrayList<ArrayList<String>> data = new ArrayList<>();

    try {
        FileInputStream file = new FileInputStream(xlsFile);

        HSSFWorkbook workbook = new HSSFWorkbook(file);
        HSSFSheet sheet = workbook.getSheetAt(0);

        //Iterate through each rows from first sheet
        Iterator<Row> rowIterator = sheet.iterator();
        while (rowIterator.hasNext()) {
            Row row = rowIterator.next();
            ArrayList<String> newRow = new ArrayList<String>();

            //For each row, iterate through each columns
            Iterator<Cell> cellIterator = row.cellIterator();
            while (cellIterator.hasNext()) {
                Cell cell = cellIterator.next();
                newRow.add(cell.getStringCellValue());
            }
            data.add(newRow);
        }
        file.close();
    } catch (Exception e) {
        e.printStackTrace();
        return null;
    }
    return data;
}

From source file:edu.tum.cs.conqat.quamoco.ExcelUtils.java

License:Apache License

/**
 * Read Excel sheet. Returns first sheet in the file.
 * /*ww w.j a va2  s .c  o  m*/
 * @throws ConQATException
 *             if file cannot be read
 */
public static HSSFSheet readFirstSheet(File file) throws ConQATException {
    try {
        InputStream myxls = new FileInputStream(file);
        HSSFWorkbook workbook = new HSSFWorkbook(myxls);
        return workbook.getSheetAt(0);
    } catch (IOException e) {
        throw new ConQATException("Could not read Excel file: " + e.getMessage(), e);
    }
}

From source file:edu.ucsd.bioeng.coreplugin.tableImport.tests.ExcelAttributeSheetReaderTest.java

License:Open Source License

/**
 *  DOCUMENT ME!/*  w  ww  .  j a v a  2 s.c o  m*/
 *
 * @throws Exception DOCUMENT ME!
 */
public void testReadTable() throws Exception {
    /*
     * Load test network
     */
    CyNetwork net = Cytoscape.createNetworkFromURL(getClass().getResource(NETWORK_FILE), true);

    /*
     * Single Sheet Test
     */
    InputStream is = null;
    POIFSFileSystem excelIn;
    try {
        is = getClass().getResource(WORKBOOK1).openStream();
        excelIn = new POIFSFileSystem(is);
    } finally {
        if (is != null) {
            is.close();
        }
    }

    HSSFWorkbook wb = new HSSFWorkbook(excelIn);

    HSSFSheet sheet = wb.getSheetAt(0);

    List<String> delimiters = new ArrayList<String>();
    delimiters.add(TextFileDelimiters.TAB.toString());

    List<Integer> aliasList = new ArrayList<Integer>();
    aliasList.add(2);

    String[] galAttrName = { "ID", "ID in SGD", "Synonyms", "Description of Genes", "Date",
            "Sample Boolean Attr2", "gal1RGexp", "gal1RGsig", "String List" };
    Byte[] galAttrTypes = { CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
            CyAttributes.TYPE_STRING, CyAttributes.TYPE_INTEGER, CyAttributes.TYPE_BOOLEAN,
            CyAttributes.TYPE_FLOATING, CyAttributes.TYPE_FLOATING, CyAttributes.TYPE_SIMPLE_LIST };

    for (int i = 0; i < galAttrTypes.length; i++) {
        System.out.println("GAL Data Type " + i + " = " + galAttrTypes[i]);
    }

    AttributeMappingParameters mapping = new AttributeMappingParameters(TextTableReader.ObjectType.NODE, null,
            COMMA.toString(), 0, "ID", aliasList, galAttrName, galAttrTypes, null, null);

    TextTableReader rd = new ExcelAttributeSheetReader(sheet, mapping, 0);
    rd.readTable();

    assertEquals("ribosomal protein S28A (S33A) (YS27)",
            Cytoscape.getNodeAttributes().getStringAttribute("YOR167C", "Description of Genes"));
    assertEquals(new Integer(20010118), Cytoscape.getNodeAttributes().getIntegerAttribute("YHR141C", "Date"));
    //assertEquals(4, Cytoscape.getNodeAttributes().getListAttribute("YER112W", "alias").size());

    /*
     * Multiple sheet test (not yet supported)
     */
    Cytoscape.destroyNetwork(net);
}

From source file:edu.ucsd.bioeng.coreplugin.tableImport.tests.ExcelNetworkSheetReaderTest.java

License:Open Source License

/**
 *  DOCUMENT ME!/*from  w ww. j a v  a  2s . com*/
 *
 * @throws Exception DOCUMENT ME!
 */
public void testReadTable() throws Exception {

    InputStream is = null;
    POIFSFileSystem excelIn;

    try {
        is = getClass().getResource(NETWORK_FILE).openStream();
        excelIn = new POIFSFileSystem(is);
    } finally {
        if (is != null) {
            is.close();
        }
    }

    HSSFWorkbook wb = new HSSFWorkbook(excelIn);

    HSSFSheet sheet = wb.getSheetAt(0);

    List<String> delimiters = new ArrayList<String>();
    delimiters.add(TextFileDelimiters.TAB.toString());

    String[] galAttrName = { "Source", "Target", "Interaction", "edge bool attr", "edge string attr",
            "edge float attr" };
    Byte[] galAttrTypes = { CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
            CyAttributes.TYPE_BOOLEAN, CyAttributes.TYPE_STRING, CyAttributes.TYPE_FLOATING };
    NetworkTableMappingParameters mapping = new NetworkTableMappingParameters(delimiters,
            TextFileDelimiters.PIPE.toString(), galAttrName, galAttrTypes, null, null, 0, 1, 2, null);

    reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping);

    CyNetwork net = Cytoscape.createNetwork(reader, false, null);

    /*
     * test cases
     */
    assertEquals("Yeast Network Sheet 1", net.getTitle());
    assertEquals(331, net.getNodeCount());
    assertEquals(362, net.getEdgeCount());

    CyAttributes attr = Cytoscape.getEdgeAttributes();
    assertTrue(attr.getBooleanAttribute("YGL122C (pp) YOL123W", "edge bool attr"));
    assertFalse(attr.getBooleanAttribute("YKR026C (pp) YGL122C", "edge bool attr"));

    assertEquals(1.2344543, attr.getDoubleAttribute("YBL026W (pp) YOR167C", "edge float attr"));
    assertEquals("abcd12706", attr.getStringAttribute("YBL026W (pp) YOR167C", "edge string attr"));
    assertEquals("abcd12584", attr.getStringAttribute("YPL248C (pd) ?", "edge string attr"));

    Cytoscape.destroyNetwork(net);
}

From source file:edu.ucsd.bioeng.coreplugin.tableImport.tests.ExcelNetworkSheetReaderTest.java

License:Open Source License

public void testReadTableWithEmptyRows() throws Exception {
    String network = "/empty_attr_row.xls";

    InputStream is = null;/*from w w w  . j a  v a 2 s  .  c  om*/
    POIFSFileSystem excelIn;

    try {
        is = getClass().getResource(network).openStream();
        excelIn = new POIFSFileSystem(is);
    } finally {
        if (is != null) {
            is.close();
        }
    }

    HSSFWorkbook wb = new HSSFWorkbook(excelIn);

    HSSFSheet sheet = wb.getSheetAt(0);

    List<String> delimiters = new ArrayList<String>();
    delimiters.add(TextFileDelimiters.TAB.toString());

    String[] galAttrName = { "Gene 1", "Gene 2", "Interaction Type", "Gene", "GO Group" };
    Byte[] galAttrTypes = { CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
            CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING };
    NetworkTableMappingParameters mapping = new NetworkTableMappingParameters(delimiters,
            TextFileDelimiters.PIPE.toString(), galAttrName, galAttrTypes, null, null, 0, 1, 2, null);

    CyNetwork net = null;
    try {
        reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping, 1);
        net = Cytoscape.createNetwork(reader, false, null);
    } catch (Exception ee) {
        ee.printStackTrace();
        fail("Caught exception");
    }

    assertEquals(222, net.getNodeCount());
    assertEquals(443, net.getEdgeCount());

    CyAttributes attr = Cytoscape.getEdgeAttributes();

    // test some random edges
    assertEquals("cc", attr.getStringAttribute("YDR459C (cc) YNL271C", "interaction"));
    assertEquals("Transport", attr.getStringAttribute("YDR459C (cc) YNL271C", "GO Group"));
    assertEquals("YPR011C", attr.getStringAttribute("YDR459C (cc) YNL271C", "Gene"));

    assertNull(attr.getStringAttribute("YEL040W (cc) YER016W", "GO Group"));
    assertNull(attr.getStringAttribute("YEL040W (cc) YER016W", "Gene"));

    Cytoscape.destroyNetwork(net);
}

From source file:edu.wustl.catissuecore.webservice.util.ExcelFileReader.java

License:BSD License

/**
 * Method to perform initialization tasks for the class
 * @throws IOException//  ww  w  .  j  av a 2 s . c  o m
 */
private void init() throws IOException {
    File excelSheet = new File(this.fileName);
    InputStream s = new FileInputStream(excelSheet);
    HSSFWorkbook workbook = new HSSFWorkbook(s);
    sheet = workbook.getSheetAt(0);
}