SiLeBAT/FSK-Lab

package metadata;

import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Sheet;

import de.bund.bfr.knime.fsklab.nodes.Variable;
import de.bund.bfr.knime.pmm.fskx.FskMetaData;
import de.bund.bfr.pmfml.ModelClass;
import de.bund.bfr.pmfml.ModelType;

public class LegacyMetadataImporter {

    // Rows
    private final int ID = 2;
    private final int NAME = 1;
    private final int ORGANISM = 3;
    private final int ORGANISM_DETAIL = 4;
    private final int MATRIX = 5;
    private final int MATRIX_DETAIL = 6;
    private final int CREATOR = 7;
    private final int REFERENCE_DESCRIPTION = 8;
    private final int CREATED_DATE = 9;
    private final int MODIFIED_DATE = 10;
    private final int RIGHTS = 11;
    private final int TYPE = 13;
    private final int SUBJECT = 14;
    private final int NOTES = 12;
    private final int DEPVAR = 21;
    private final int DEPVAR_UNIT = 22;
    private final int DEPVAR_MIN = 23;
    private final int DEPVAR_MAX = 24;
    private final int INDEPVAR = 25;
    private final int INDEPVAR_UNIT = 26;
    private final int INDEPVAR_MIN = 27;
    private final int INDEPVAR_MAX = 28;

    public FskMetaData processSpreadsheet(final Sheet sheet) {

        final FskMetaData template = new FskMetaData();

        final Cell modelNameCell = sheet.getRow(NAME).getCell(5);
        if (modelNameCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.modelName = modelNameCell.getStringCellValue();
        }

        final Cell modelIdCell = sheet.getRow(ID).getCell(5);
        if (modelIdCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.modelId = modelIdCell.getStringCellValue();
        }

        // model link

        final Cell organismCell = sheet.getRow(ORGANISM).getCell(5);
        if (organismCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.organism = organismCell.getStringCellValue();
        }

        final Cell organismDetailCell = sheet.getRow(ORGANISM_DETAIL).getCell(5);
        if (organismDetailCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.organismDetails = organismDetailCell.getStringCellValue();
        }

        final Cell matrixCell = sheet.getRow(MATRIX).getCell(5);
        if (matrixCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.matrix = matrixCell.getStringCellValue();
        }

        final Cell matrixDetailCell = sheet.getRow(MATRIX_DETAIL).getCell(5);
        if (matrixDetailCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.matrixDetails = matrixDetailCell.getStringCellValue();
        }

        final Cell creatorCell = sheet.getRow(CREATOR).getCell(5);
        if (creatorCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.creator = creatorCell.getStringCellValue();
        }

        // There is no family name, contact or software in the spreadsheet.

        final Cell referenceDescriptionCell = sheet.getRow(REFERENCE_DESCRIPTION).getCell(5);
        if (referenceDescriptionCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.referenceDescription = referenceDescriptionCell.getStringCellValue();
        }

        // reference description link

        final Cell creationDateCell = sheet.getRow(CREATED_DATE).getCell(5);
        if (creationDateCell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
            template.createdDate = creationDateCell.getDateCellValue();
        }

        final Cell modificationCell = sheet.getRow(MODIFIED_DATE).getCell(5);
        if (modificationCell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
            template.modifiedDate = modificationCell.getDateCellValue();
        }

        final Cell rightsCell = sheet.getRow(RIGHTS).getCell(5);
        if (rightsCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.rights = rightsCell.getStringCellValue();
        }

        final Cell notesCell = sheet.getRow(NOTES).getCell(5);
        if (notesCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.notes = notesCell.getStringCellValue();
        }

        // curated

        try {
            final Cell typeCell = sheet.getRow(TYPE).getCell(5);
            if (typeCell.getCellType() == Cell.CELL_TYPE_STRING) {
                template.type = ModelType.valueOf(typeCell.getStringCellValue());
            }
        } catch (final IllegalArgumentException e) {
        }

        try {
            final Cell subjectCell = sheet.getRow(SUBJECT).getCell(5);
            if (subjectCell.getCellType() == Cell.CELL_TYPE_STRING) {
                template.subject = ModelClass.valueOf(subjectCell.getStringCellValue());
            }
        } catch (final IllegalArgumentException e) {
            template.subject = ModelClass.UNKNOWN;
        }

        // food process

        // dependent variable
        final Cell depVarNameCell = sheet.getRow(DEPVAR).getCell(5);
        if (depVarNameCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.dependentVariable.name = depVarNameCell.getStringCellValue();
        }

        final Cell depVarUnitCell = sheet.getRow(DEPVAR_UNIT).getCell(5);
        if (depVarUnitCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.dependentVariable.unit = depVarUnitCell.getStringCellValue();
        }

        final Cell depVarMinCell = sheet.getRow(DEPVAR_MIN).getCell(5);
        if (depVarMinCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.dependentVariable.min = depVarMinCell.getStringCellValue();
        } else if (depVarMinCell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
            template.dependentVariable.min = Double.toString(depVarMinCell.getNumericCellValue());
        }

        final Cell depVarMaxCell = sheet.getRow(DEPVAR_MAX).getCell(5);
        if (depVarMaxCell.getCellType() == Cell.CELL_TYPE_STRING) {
            template.dependentVariable.max = depVarMaxCell.getStringCellValue();
        } else if (depVarMaxCell.getCellType() == Cell.CELL_TYPE_NUMERIC) {
            template.dependentVariable.max = Double.toString(depVarMaxCell.getNumericCellValue());
        }

        // independent variables *
        String[] indepVars = null;
        final Cell indepVarCell = sheet.getRow(INDEPVAR).getCell(5);
        if (indepVarCell.getCellType() == Cell.CELL_TYPE_STRING) {
            indepVars = indepVarCell.getStringCellValue().split("\\|\\|");
        }

        String[] indepVarUnits = null;
        final Cell indepVarUnitCell = sheet.getRow(INDEPVAR_UNIT).getCell(5);
        if (indepVarUnitCell.getCellType() == Cell.CELL_TYPE_STRING) {
            indepVarUnits = indepVarUnitCell.getStringCellValue().split("\\|\\|");
        }

        String[] mins = null;
        final Cell indepVarMinCell = sheet.getRow(INDEPVAR_MIN).getCell(5);
        if (indepVarMinCell.getCellType() == Cell.CELL_TYPE_STRING) {
            mins = indepVarMinCell.getStringCellValue().split("\\|\\|");
        }

        String[] maxs = null;
        final Cell indepVarMaxCell = sheet.getRow(INDEPVAR_MAX).getCell(5);
        if (indepVarMaxCell.getCellType() == Cell.CELL_TYPE_STRING) {
            maxs = indepVarMaxCell.getStringCellValue().split("\\|\\|");
        }

        if (indepVars != null && indepVarUnits != null && mins != null && maxs != null) {
            for (int i = 0; i < indepVars.length; i++) {
                final Variable variable = new Variable();
                variable.name = indepVars[i].trim();
                variable.unit = indepVarUnits[i].trim();
                variable.min = mins[i].trim();
                variable.max = maxs[i].trim();
                // no values or types in the spreadsheet
                variable.value = "";
                template.independentVariables.add(variable);
            }
        }

        template.hasData = false;

        return template;
    }
}