SiLeBAT/FSK-Lab

package metadata;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNull;

import java.io.InputStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.time.LocalDate;

import org.apache.poi.ss.usermodel.Sheet;
import org.apache.poi.ss.usermodel.Workbook;
import org.apache.poi.ss.usermodel.WorkbookFactory;
import org.junit.Test;

import de.bund.bfr.knime.fsklab.metadata.model.tests.TestUtils;
import de.bund.bfr.knime.fsklab.nodes.Variable;
import de.bund.bfr.knime.pmm.fskx.FskMetaData;
import de.bund.bfr.pmfml.ModelClass;

@SuppressWarnings("static-method")
public class LegacyMetadataImporterTest {

    @Test
    public void test() throws Exception {
        Sheet sheet0;

        final Path path = Paths.get("files/Duarte_MetaData.xlsx");
        try (InputStream stream = Files.newInputStream(path)) {
            final Workbook workbook = WorkbookFactory.create(stream);
            sheet0 = workbook.getSheetAt(0);
        }

        final LegacyMetadataImporter importer = new LegacyMetadataImporter();
        final FskMetaData metadata = importer.processSpreadsheet(sheet0);

        assertEquals("Duarte_R", metadata.modelId);
        assertEquals("Duarte_FittingDistributionToMicrobialCounts", metadata.modelName);
        assertEquals("generic_broth", metadata.organism);
        assertNull(metadata.organismDetails);
        assertEquals("lab experiment", metadata.matrix);
        assertEquals("This method fits a zero-inflated Poisson", metadata.matrixDetails);
        assertEquals("Duarte, A.S.R.; Filter, M.", metadata.creator);
        assertEquals("asrd@food.dtu.dk", metadata.referenceDescription);

        final LocalDate creationDate = TestUtils.toLocalDate(metadata.createdDate);
        assertEquals(LocalDate.of(2016, 11, 9), creationDate);

        final LocalDate modificationDate = TestUtils.toLocalDate(metadata.modifiedDate);
        assertEquals(LocalDate.of(2016,  11,  9), modificationDate);

        assertEquals("Public", metadata.rights);
        assertNull(metadata.type);
        assertEquals(ModelClass.UNKNOWN, metadata.subject);
        assertEquals("This method fits a zero-inflated Poisson", metadata.notes);

        assertEquals("expected.temp", metadata.dependentVariable.name);
        assertEquals("log10(CFU)", metadata.dependentVariable.unit);
        assertEquals("0.0", metadata.dependentVariable.min);
        assertEquals("12.0", metadata.dependentVariable.max);

        // Check first independent variable: mu.init
        final Variable muInit = metadata.independentVariables.get(0);
        assertEquals("mu.init", muInit.name);
        assertEquals("log10(CFU)", muInit.unit);
        assertEquals("0", muInit.min);
        assertEquals("1000", muInit.max);

        // Check second independent variable: sd.init
        final Variable sdInit = metadata.independentVariables.get(1);
        assertEquals("sd.init", sdInit.name);
        assertEquals("log10(CFU)", sdInit.unit);
        assertEquals("0", sdInit.min);
        assertEquals("1000", sdInit.max);

        // Check third independent variable: mu.start
        final Variable muStart = metadata.independentVariables.get(2);
        assertEquals("mu.start", muStart.name);
        assertEquals("log10(CFU)", muStart.unit);
        assertEquals("0", muStart.min);
        assertEquals("1000", muStart.max);

        // Check fourth independent variable: sd.start
        final Variable sdStart = metadata.independentVariables.get(3);
        assertEquals("sd.start", sdStart.name);
        assertEquals("log10(CFU)", sdStart.unit);
        assertEquals("0", sdStart.min);
        assertEquals("1000", sdStart.max);

        assertFalse(metadata.hasData);
    }
}