OpenBISScreeningML.java

     *         plate space code, plate code, row, column }</code>
     */
    public static Object[][][] getGeneMappingForPlates(String[] platesCodes)
    {
        checkLoggedIn();
        final List<PlateWellMaterialMapping> mappingList =
                openbis.listPlateMaterialMapping(toPlates(platesCodes), MaterialTypeIdentifier.GENE);
        int size = 0;
        for (PlateWellMaterialMapping mapping : mappingList)
        {
            size +=
                    mapping.getPlateGeometry().getNumberOfRows()
                            * mapping.getPlateGeometry().getNumberOfColumns();
        }
        final Object[][][] result = new Object[2][size][];
        int resultIdx = 0;
        for (PlateWellMaterialMapping mapping : mappingList)
        {
            for (int row = 1; row <= mapping.getPlateGeometry().getNumberOfRows(); ++row)
            {
                for (int col = 1; col <= mapping.getPlateGeometry().getNumberOfColumns(); ++col)
                {
                    final List<MaterialIdentifier> genes = mapping.getMaterialsForWell(row, col);
                    result[0][resultIdx] = new Object[genes.size()];
                    for (int i = 0; i < genes.size(); ++i)
                    {
                        result[0][resultIdx][i] = genes.get(i).getMaterialCode();
                    }
                    final PlateIdentifier plate = mapping.getPlateIdentifier();
                    result[1][resultIdx] =
                            new Object[]
                                { createPlateWellDescription(plate, row, col),
                                        plate.getAugmentedCode(), plate.getPermId(),
                                        plate.tryGetSpaceCode(), plate.getPlateCode(), row, col, };
                    ++resultIdx;
                }
            }
        }
        return result;
    }

    //
    // Helper methods
    //

    private static List<PlateIdentifier> toPlates(String[] augmentedPlateCodes)
    {
        final List<PlateIdentifier> result =
                new ArrayList<PlateIdentifier>(augmentedPlateCodes.length);
        for (String plateCode : augmentedPlateCodes)
        {
            result.add(PlateIdentifier.createFromAugmentedCode(plateCode));
        }
        return result;
    }

    private static Object[][] listProperties(Map<String, String> properties)
    {
        if (properties == null || properties.isEmpty())
        {
            return new Object[0][];
        }

        List<Map.Entry<String, String>> list =
                new ArrayList<Map.Entry<String, String>>(properties.entrySet());
        Object[][] result = new Object[list.size()][2];
        for (int i = 0; i < list.size(); i++)
        {
            result[i] = new Object[]
                { list.get(i).getKey(), list.get(i).getValue() };
        }
        return result;
    }

    private static Plate getPlate(String augmentedPlateCode)
    {
        Plate plateIdentifier = plateCodeToPlateMap.get(augmentedPlateCode);
        if (plateIdentifier == null)
        {
            throw new RuntimeException("No plate with that code '" + augmentedPlateCode
                    + "' found.");
        }
        return plateIdentifier;
    }

    private static ExperimentIdentifier getExperimentIdentifierOrFail(String experiment)
    {
        ExperimentIdentifier experimentIdentifier = experimentCodeToExperimentMap.get(experiment);
        if (experimentIdentifier == null)
        {
            String errorMessage = String.format("No experiment with code '%s' found.", experiment);
            throw new RuntimeException(errorMessage);
        }
        return experimentIdentifier;
    }

    private static String createPlateWellDescription(PlateIdentifier p, FeatureVector f)
    {
        return createPlateWellDescription(p, f.getWellPosition().getWellRow(), f.getWellPosition()
                .getWellColumn());
    }

    private static String createPlateWellDescription(PlateIdentifier p, int row, int col)
    {
        return p.getPlateCode() + ":" + translateRowNumberIntoLetterCode(row) + col;
    }

    /**
     * Translates a row number into letter code. Thus, 1 -> A, 2 -> B, 26 -> Z, 27 -> AA, 28 -> AB,
     * etc.
     */
    private static String translateRowNumberIntoLetterCode(int rowNumber)
    {
        int rowIndex = rowNumber - 1;
        String code = "";
        while (rowIndex >= 0)
        {
            code = (char) (rowIndex % 26 + 'A') + code;
            rowIndex = rowIndex / 26 - 1;
        }
        return code;
    }

    private static void checkLoggedIn()
    {
        if (openbis == null)
        {
            if (Login.OPENBIS_TOKEN_FILE.exists())
            {
                BufferedReader br = null;
                try
                {
                    br = new BufferedReader(new FileReader(Login.OPENBIS_TOKEN_FILE));
                    final String token = br.readLine();
                    br.close();
                    br = new BufferedReader(new FileReader(Login.OPENBIS_SERVER_URL_FILE));
                    final String serverUrl = br.readLine();
                    br.close();
                    br = null;
                    IScreeningOpenbisServiceFacade facade =
                            facadeFactory.tryToCreate(token, serverUrl);
                    if (facade == null)
                    {
                        throw new RuntimeException("Login failed.");
                    }
                    init(facade);
                } catch (IOException ex)
                {
                    if (openbis == null)
                    {
                        throw new RuntimeException("Login failed.", ex);
                    }
                } finally
                {
                    if (br != null)
                    {
                        try
                        {
                            br.close();
                        } catch (IOException ex)
                        {
                            // Silence this.
                        }
                    }
                }
            }
            if (openbis == null)
            {
                throw new RuntimeException("Not logged in.");
            }
        }
    }

}