Example usage for org.apache.poi.xssf.usermodel XSSFCell getBooleanCellValue

List of usage examples for org.apache.poi.xssf.usermodel XSSFCell getBooleanCellValue

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Introduction

In this page you can find the example usage for org.apache.poi.xssf.usermodel XSSFCell getBooleanCellValue.

Prototype

@Override
public boolean getBooleanCellValue()

Source Link

Document

Get the value of the cell as a boolean.

Usage

From source file:uk.ac.bbsrc.tgac.miso.core.util.FormUtils.java

License:Open Source License

private static List<Sample> processSampleInputXLSX(XSSFWorkbook wb, User u, RequestManager manager,
        MisoNamingScheme<Library> libraryNamingScheme) throws Exception {
    ((RequestManagerAwareNamingScheme) libraryNamingScheme).setRequestManager(manager);

    List<Sample> samples = new ArrayList<Sample>();
    XSSFSheet sheet = wb.getSheetAt(0);/*  w ww . j  a v a 2  s . co  m*/
    int rows = sheet.getPhysicalNumberOfRows();

    XSSFRow glrow = sheet.getRow(1);

    //process global headers
    XSSFCell pairedCell = glrow.getCell(0);
    boolean paired;
    if (getCellValueAsString(pairedCell) != null) {
        paired = pairedCell.getBooleanCellValue();
        log.info("Got paired: " + paired);
    } else {
        throw new InputFormException("'Paired' cell is empty. Please specify TRUE or FALSE.");
    }

    XSSFCell platformCell = glrow.getCell(1);
    PlatformType pt = null;
    if (getCellValueAsString(platformCell) != null) {
        pt = PlatformType.get(getCellValueAsString(platformCell));
    }
    if (pt == null) {
        throw new InputFormException(
                "Cannot resolve Platform type from: '" + getCellValueAsString(platformCell) + "'");
    } else {
        log.info("Got platform type: " + pt.getKey());
    }

    XSSFCell typeCell = glrow.getCell(2);
    LibraryType lt = null;
    if (getCellValueAsString(typeCell) != null) {
        String[] split = getCellValueAsString(typeCell).split("-");
        String plat = split[0];
        String type = split[1];
        if (getCellValueAsString(platformCell).equals(plat)) {
            lt = manager.getLibraryTypeByDescriptionAndPlatform(type, pt);
        } else {
            throw new InputFormException("Selected library type '" + getCellValueAsString(typeCell)
                    + "' doesn't match platform type: '" + getCellValueAsString(platformCell) + "'");
        }
    }
    if (lt == null) {
        throw new InputFormException(
                "Cannot resolve Library type from: '" + getCellValueAsString(typeCell) + "'");
    } else {
        log.info("Got library type: " + lt.getDescription());
    }

    XSSFCell selectionCell = glrow.getCell(3);
    LibrarySelectionType ls = null;
    if (getCellValueAsString(selectionCell) != null) {
        ls = manager.getLibrarySelectionTypeByName(getCellValueAsString(selectionCell));
    }
    if (ls == null) {
        throw new InputFormException(
                "Cannot resolve Library Selection type from: '" + getCellValueAsString(selectionCell) + "'");
    } else {
        log.info("Got library selection type: " + ls.getName());
    }

    XSSFCell strategyCell = glrow.getCell(4);
    LibraryStrategyType lst = null;
    if (getCellValueAsString(strategyCell) != null) {
        lst = manager.getLibraryStrategyTypeByName(getCellValueAsString(strategyCell));
    }
    if (lst == null) {
        throw new InputFormException(
                "Cannot resolve Library Strategy type from: '" + getCellValueAsString(strategyCell) + "'");
    } else {
        log.info("Got library strategy type: " + lst.getName());
    }

    //process entries
    Plate<LinkedList<Sample>, Sample> samplePlate = null;
    Map<String, Pool<Dilution>> pools = new HashMap<String, Pool<Dilution>>();

    for (int ri = 4; ri < rows; ri++) {
        XSSFRow row = sheet.getRow(ri);

        // Ax - plate position
        XSSFCell platePosCell = row.getCell(0);
        if (getCellValueAsString(platePosCell) != null && samplePlate == null) {
            //plated samples - process as plate
            samplePlate = new PlateImpl<Sample>();
        }

        //cell defs
        XSSFCell sampleAliasCell = row.getCell(2);

        Sample s = null;
        if (getCellValueAsString(sampleAliasCell) != null) {
            String salias = getCellValueAsString(sampleAliasCell);
            Collection<Sample> ss = manager.listSamplesByAlias(salias);
            if (!ss.isEmpty()) {
                if (ss.size() == 1) {
                    s = ss.iterator().next();
                    log.info("Got sample: " + s.getAlias());
                } else {
                    throw new InputFormException(
                            "Multiple samples retrieved with this alias: '" + salias + "'. Cannot process.");
                }
            } else {
                throw new InputFormException("No such sample '" + salias
                        + "'in database. Samples need to be created before using the form input functionality");
            }
        } else {
            log.info("Blank sample row found. Ending import.");
            break;
        }

        //sample OK - good to go
        if (s != null) {
            String projectAliasCell = getCellValueAsString(row.getCell(1));
            String poolNumberCell = getCellValueAsString(row.getCell(3));
            String sampleQcCell = getCellValueAsString(row.getCell(4));
            //String sampleAmountCell = getCellValueAsString(row.getCell(5));
            //String sampleWaterAmountCell = getCellValueAsString(row.getCell(6));
            String libraryDescriptionCell = getCellValueAsString(row.getCell(7));
            String barcodeKitCell = getCellValueAsString(row.getCell(8));
            String barcodeTagsCell = getCellValueAsString(row.getCell(9));
            String libraryQcCell = getCellValueAsString(row.getCell(10));
            String libraryQcInsertSizeCell = getCellValueAsString(row.getCell(11));
            String libraryQcMolarityCell = getCellValueAsString(row.getCell(12));
            String libraryQcPassFailCell = getCellValueAsString(row.getCell(13));
            //String libraryAmountCell = getCellValueAsString(row.getCell(14));
            //String libraryWaterAmountCell = getCellValueAsString(row.getCell(15));
            //String dilutionQcCell = getCellValueAsString(row.getCell(16));
            String dilutionMolarityCell = getCellValueAsString(row.getCell(17));
            //String dilutionAmountCell = getCellValueAsString(row.getCell(18));
            //String dilutionWaterAmountCell = getCellValueAsString(row.getCell(19));
            String poolQcCell = getCellValueAsString(row.getCell(20));
            //String poolAverageInsertSizeCell = getCellValueAsString(row.getCell(21));
            String poolConvertedMolarityCell = getCellValueAsString(row.getCell(22));

            //add pool, if any
            processPool(poolNumberCell, poolConvertedMolarityCell, pools);
            processSampleQC(sampleQcCell, s, u, manager);

            Library library = processLibrary(libraryQcCell, libraryDescriptionCell, libraryQcPassFailCell, s,
                    pt, lt, ls, lst, paired, libraryNamingScheme);
            if (library != null) {
                processLibraryQC(libraryQcCell, libraryQcMolarityCell, libraryQcInsertSizeCell, library, u,
                        manager);
                processBarcodes(barcodeKitCell, barcodeTagsCell, library, manager);
                processDilutions(dilutionMolarityCell, library, pools.get(poolNumberCell), u);
                log.info("Added library: " + library.toString());
                s.addLibrary(library);
            }
            samples.add(s);
        }
    }
    return samples;
}

From source file:uk.ac.bbsrc.tgac.miso.core.util.FormUtils.java

License:Open Source License

private static String getCellValueAsString(XSSFCell cell) {
    if (cell != null) {
        switch (cell.getCellType()) {
        case XSSFCell.CELL_TYPE_BLANK:
            return null;
        case XSSFCell.CELL_TYPE_BOOLEAN:
            return String.valueOf(cell.getBooleanCellValue());
        case XSSFCell.CELL_TYPE_ERROR:
            return cell.getErrorCellString();
        case XSSFCell.CELL_TYPE_FORMULA:
            return cell.getRawValue();
        case XSSFCell.CELL_TYPE_NUMERIC:
            return String.valueOf(cell.getNumericCellValue());
        case XSSFCell.CELL_TYPE_STRING:
            return cell.getStringCellValue();
        default:/*  w  ww.j  a va  2  s  . c o  m*/
            return null;
        }
    }
    return null;
}

From source file:uk.ac.bbsrc.tgac.miso.spring.util.FormUtils.java

License:Open Source License

private static List<Sample> processSampleInputXLSX(XSSFWorkbook wb, User u, SampleService sampleService,
        LibraryService libraryService, QualityControlService qcService, NamingScheme namingScheme,
        IndexService indexService) throws Exception {
    List<Sample> samples = new ArrayList<>();
    XSSFSheet sheet = wb.getSheetAt(0);//from ww w. j ava  2s . co m
    int rows = sheet.getPhysicalNumberOfRows();

    XSSFRow glrow = sheet.getRow(1);

    // process global headers
    XSSFCell pairedCell = glrow.getCell(0);
    boolean paired;
    if (getCellValueAsString(pairedCell) != null) {
        paired = pairedCell.getBooleanCellValue();
        log.info("Got paired: " + paired);
    } else {
        throw new InputFormException("'Paired' cell is empty. Please specify TRUE or FALSE.");
    }

    XSSFCell platformCell = glrow.getCell(1);
    PlatformType pt = null;
    if (getCellValueAsString(platformCell) != null) {
        pt = PlatformType.get(getCellValueAsString(platformCell));
    }
    if (pt == null) {
        throw new InputFormException(
                "Cannot resolve Platform type from: '" + getCellValueAsString(platformCell) + "'");
    } else {
        log.info("Got platform type: " + pt.getKey());
    }

    XSSFCell typeCell = glrow.getCell(2);
    LibraryType lt = null;
    if (getCellValueAsString(typeCell) != null) {
        String[] split = getCellValueAsString(typeCell).split("-");
        String plat = split[0];
        String type = split[1];
        if (getCellValueAsString(platformCell).equals(plat)) {
            lt = libraryService.getLibraryTypeByDescriptionAndPlatform(type, pt);
        } else {
            throw new InputFormException("Selected library type '" + getCellValueAsString(typeCell)
                    + "' doesn't match platform type: '" + getCellValueAsString(platformCell) + "'");
        }
    }
    if (lt == null) {
        throw new InputFormException(
                "Cannot resolve Library type from: '" + getCellValueAsString(typeCell) + "'");
    } else {
        log.info("Got library type: " + lt.getDescription());
    }

    XSSFCell selectionCell = glrow.getCell(3);
    LibrarySelectionType ls = null;
    if (getCellValueAsString(selectionCell) != null) {
        ls = libraryService.getLibrarySelectionTypeByName(getCellValueAsString(selectionCell));
    }
    if (ls == null) {
        throw new InputFormException(
                "Cannot resolve Library Selection type from: '" + getCellValueAsString(selectionCell) + "'");
    } else {
        log.info("Got library selection type: " + ls.getName());
    }

    XSSFCell strategyCell = glrow.getCell(4);
    LibraryStrategyType lst = null;
    if (getCellValueAsString(strategyCell) != null) {
        lst = libraryService.getLibraryStrategyTypeByName(getCellValueAsString(strategyCell));
    }
    if (lst == null) {
        throw new InputFormException(
                "Cannot resolve Library Strategy type from: '" + getCellValueAsString(strategyCell) + "'");
    } else {
        log.info("Got library strategy type: " + lst.getName());
    }

    // process entries
    Map<String, Pool> pools = new HashMap<>();

    for (int ri = 4; ri < rows; ri++) {
        XSSFRow row = sheet.getRow(ri);

        // cell defs
        XSSFCell sampleAliasCell = row.getCell(2);

        Sample s = null;
        if (getCellValueAsString(sampleAliasCell) != null) {
            String salias = getCellValueAsString(sampleAliasCell);
            Collection<Sample> ss = sampleService.getByAlias(salias);
            if (!ss.isEmpty()) {
                if (ss.size() == 1) {
                    s = ss.iterator().next();
                    log.info("Got sample: " + s.getAlias());
                } else {
                    throw new InputFormException(
                            "Multiple samples retrieved with this alias: '" + salias + "'. Cannot process.");
                }
            } else {
                throw new InputFormException("No such sample '" + salias
                        + "'in database. Samples need to be created before using the form input functionality");
            }
        } else {
            log.info("Blank sample row found. Ending import.");
            break;
        }

        // sample OK - good to go
        if (s != null) {
            String poolNumberCell = getCellValueAsString(row.getCell(3));
            String sampleQcCell = getCellValueAsString(row.getCell(4));
            String libraryDescriptionCell = getCellValueAsString(row.getCell(7));
            String indexKitCell = getCellValueAsString(row.getCell(8));
            String indexTagsCell = getCellValueAsString(row.getCell(9));
            String libraryQcCell = getCellValueAsString(row.getCell(10));
            String libraryQcInsertSizeCell = getCellValueAsString(row.getCell(11));
            String libraryQcMolarityCell = getCellValueAsString(row.getCell(12));
            String libraryQcPassFailCell = getCellValueAsString(row.getCell(13));
            String dilutionMolarityCell = getCellValueAsString(row.getCell(17));
            String poolConvertedMolarityCell = getCellValueAsString(row.getCell(22));

            // add pool, if any
            processPool(poolNumberCell, poolConvertedMolarityCell, pools);
            processSampleQC(sampleQcCell, s, u, qcService);

            Library library = processLibrary(libraryQcCell, libraryDescriptionCell, libraryQcPassFailCell, s,
                    pt, lt, ls, lst, paired, namingScheme);
            if (library != null) {
                processLibraryQC(libraryQcCell, libraryQcMolarityCell, libraryQcInsertSizeCell, library, u,
                        qcService);
                processIndices(indexKitCell, indexTagsCell, library, indexService);
                processDilutions(dilutionMolarityCell, library, pools.get(poolNumberCell), u);
                log.info("Added library: " + library.toString());
                s.addLibrary(library);
            }
            samples.add(s);
        }
    }
    return samples;
}