Examples with SpeciesImportProcess org.openforis.collect.manager.speciesimport.SpeciesImportProcess used on opensource projects

Example 6 with SpeciesImportProcess

use of org.openforis.collect.manager.speciesimport.SpeciesImportProcess in project collect by openforis.

the class SpeciesImportProcessIntegrationTest method testVernacularNamesImport.

@Test
public void testVernacularNamesImport() throws Exception {
    SpeciesImportProcess process = importCSVFile(VALID_TEST_CSV);
    SpeciesImportStatus status = process.getStatus();
    assertTrue(status.isComplete());
    CollectTaxonomy taxonomy = speciesManager.loadTaxonomyByName(survey, TEST_TAXONOMY_NAME);
    TaxonSearchParameters taxonSearchParameters = new TaxonSearchParameters();
    taxonSearchParameters.setHighestRank(FAMILY);
    {
        List<TaxonOccurrence> occurrences = speciesManager.findByVernacularName(taxonomy, null, "Mbamba", 10, taxonSearchParameters);
        assertNotNull(occurrences);
        assertEquals(1, occurrences.size());
        TaxonOccurrence stored = occurrences.get(0);
        TaxonOccurrence expected = new TaxonOccurrence(8, "AFZ/QUA", "Afzelia quanzensis", "Mbambakofi", "swh", null);
        expected.setTaxonRank(SPECIES);
        assertEquals(expected, stored);
    }
    {
        List<TaxonOccurrence> occurrences = speciesManager.findByVernacularName(taxonomy, null, "Mshai-mamba", 10, taxonSearchParameters);
        assertNotNull(occurrences);
        assertEquals(1, occurrences.size());
        TaxonOccurrence stored = occurrences.get(0);
        TaxonOccurrence expected = new TaxonOccurrence(10, "ALB/ADI", "Albizia adianthifolia", "Mshai-mamba", "ksb", null);
        expected.setTaxonRank(SPECIES);
        assertEquals(expected, stored);
    }
    {
        Taxon taxon = findTaxonByCode("ALB/ADI");
        Integer taxonId = taxon.getSystemId();
        List<TaxonVernacularName> vernacularNames = taxonVernacularNameDao.findByTaxon(taxonId);
        assertTrue(contains(vernacularNames, "ksb", "Mchao"));
        assertTrue(contains(vernacularNames, "ksb", "Mkengemshaa"));
        assertTrue(contains(vernacularNames, "ksb", "Msai"));
        assertTrue(contains(vernacularNames, "ksb", "Mshai"));
        assertTrue(contains(vernacularNames, "ksb", "Mshai-mamba"));
        assertFalse(contains(vernacularNames, "eng", "Mahogany"));
        assertFalse(contains(vernacularNames, "ksb", "Mahogany"));
    }
    {
        Taxon taxon = findTaxonByCode("BOU/PET");
        assertEquals("Bourreria petiolaris", taxon.getScientificName());
        Integer taxonId = taxon.getSystemId();
        List<TaxonVernacularName> vernacularNames = taxonVernacularNameDao.findByTaxon(taxonId);
        assertEquals(1, vernacularNames.size());
        assertTrue(contains(vernacularNames, "swh", "Mpanda jongoo"));
    }
    {
        Taxon taxon = findTaxonByCode("BOM/RHO");
        assertEquals("Bombax rhodognaphalon", taxon.getScientificName());
        Integer taxonId = taxon.getSystemId();
        List<TaxonVernacularName> vernacularNames = taxonVernacularNameDao.findByTaxon(taxonId);
        assertEquals(1, vernacularNames.size());
        assertTrue(contains(vernacularNames, "swh", "Msufi mwitu"));
    }
}

Example 7 with SpeciesImportProcess

use of org.openforis.collect.manager.speciesimport.SpeciesImportProcess in project collect by openforis.

the class SpeciesImportProcessIntegrationTest method testHierarchyImport.

@Test
public void testHierarchyImport() throws Exception {
    SpeciesImportProcess process = importCSVFile(VALID_TEST_CSV);
    SpeciesImportStatus status = process.getStatus();
    assertTrue(status.isComplete());
    CollectTaxonomy taxonomy = taxonomyDao.loadByName(survey, TEST_TAXONOMY_NAME);
    {
        Taxon variety = findTaxonByCode("ALB/SCH/amaniensis");
        assertNotNull(variety);
        assertEquals(VARIETY, variety.getTaxonRank());
        Integer speciesId = variety.getParentId();
        assertNotNull(speciesId);
        Taxon species = taxonDao.loadById(taxonomy, speciesId);
        assertNotNull(species);
        assertNull(species.getCode());
        assertEquals(SPECIES, species.getTaxonRank());
        assertEquals("Albizia schimperiana", species.getScientificName());
        Integer genusId = species.getParentId();
        assertNotNull(genusId);
        Taxon genus = taxonDao.loadById(taxonomy, genusId);
        assertNotNull(genus);
        assertEquals("ALB", genus.getCode());
        assertEquals(GENUS, genus.getTaxonRank());
        assertEquals("Albizia sp.", genus.getScientificName());
        Integer familyId = genus.getParentId();
        assertNotNull(familyId);
        Taxon family = taxonDao.loadById(taxonomy, familyId);
        assertNotNull(family);
        assertNull(family.getParentId());
        assertEquals(FAMILY, family.getTaxonRank());
        assertEquals("Fabaceae", family.getScientificName());
    }
    {
        Taxon subspecies = findTaxonByCode("OLE/EUR/cuspidata");
        assertNotNull(subspecies);
        assertEquals(SUBSPECIES, subspecies.getTaxonRank());
        Integer speciesId = subspecies.getParentId();
        assertNotNull(speciesId);
        Taxon species = taxonDao.loadById(taxonomy, speciesId);
        assertNotNull(species);
        assertEquals(SPECIES, species.getTaxonRank());
        assertEquals("OLE/EUR", species.getCode());
        assertEquals("Olea europaea", species.getScientificName());
    }
}

Example 8 with SpeciesImportProcess

use of org.openforis.collect.manager.speciesimport.SpeciesImportProcess in project collect by openforis.

the class SpeciesImportProcessIntegrationTest method testErrorHandling.

@Test
public void testErrorHandling() throws Exception {
    SpeciesImportProcess process = importCSVFile(INVALID_TEST_CSV);
    SpeciesImportStatus status = process.getStatus();
    List<ParsingError> errors = status.getErrors();
    assertEquals(7, errors.size());
    assertTrue(status.isRowProcessed(1));
    assertTrue(status.isRowProcessed(2));
    assertTrue(status.isRowProcessed(4));
    assertTrue(status.isRowProcessed(5));
    assertFalse(status.isRowProcessed(3));
    assertFalse(status.isRowProcessed(6));
    assertFalse(status.isRowProcessed(7));
    assertFalse(status.isRowProcessed(8));
    assertFalse(status.isRowProcessed(9));
    assertFalse(status.isRowProcessed(10));
    assertFalse(status.isRowProcessed(11));
    // unexisting row
    assertFalse(status.isRowProcessed(12));
    assertTrue(containsError(errors, 3, SpeciesFileColumn.CODE, ErrorType.EMPTY));
    assertTrue(containsError(errors, 6, SpeciesFileColumn.CODE, ErrorType.DUPLICATE_VALUE));
    assertTrue(containsError(errors, 7, SpeciesFileColumn.FAMILY, ErrorType.EMPTY));
    assertTrue(containsError(errors, 8, SpeciesFileColumn.NO, ErrorType.DUPLICATE_VALUE));
    assertTrue(containsError(errors, 9, SpeciesFileColumn.SCIENTIFIC_NAME, ErrorType.DUPLICATE_VALUE));
    assertTrue(containsError(errors, 10, SpeciesFileColumn.SCIENTIFIC_NAME, ErrorType.DUPLICATE_VALUE));
    assertTrue(containsError(errors, 11, "swh", ErrorType.INVALID_VALUE));
}

Example 9 with SpeciesImportProcess

use of org.openforis.collect.manager.speciesimport.SpeciesImportProcess in project collect by openforis.

the class SpeciesImportProcessIntegrationTest method importCSVFile.

public SpeciesImportProcess importCSVFile(String fileName) throws Exception {
    File file = getTestFile(fileName);
    CollectTaxonomy taxonomy = new CollectTaxonomy();
    taxonomy.setSurvey(survey);
    taxonomy.setName(TEST_TAXONOMY_NAME);
    speciesManager.save(taxonomy);
    SpeciesImportProcess process = new SpeciesImportProcess(surveyManager, speciesManager, survey, taxonomy.getId(), file, new CSVFileOptions(), true);
    process.call();
    return process;
}