Examples with Taxon org.openforis.idm.model.species.Taxon used on opensource projects

Example 16 with Taxon

use of org.openforis.idm.model.species.Taxon in project collect by openforis.

the class SpeciesImportProcess method createTaxonGenus.

protected Taxon createTaxonGenus(SpeciesLine line) throws ParsingException {
    String genus = line.getGenus();
    if (genus == null) {
        ParsingError error = new ParsingError(ErrorType.INVALID_VALUE, line.getLineNumber(), SpeciesFileColumn.SCIENTIFIC_NAME.getColumnName(), INVALID_GENUS_NAME_ERROR_MESSAGE_KEY);
        throw new ParsingException(error);
    }
    Taxon taxonFamily = createTaxonFamily(line);
    String normalizedScientificName = StringUtils.join(genus, " ", GENUS_SUFFIX);
    return createTaxon(line, GENUS, taxonFamily, normalizedScientificName);
}

Example 17 with Taxon

use of org.openforis.idm.model.species.Taxon in project collect by openforis.

the class TaxonDao method insert.

/**
 * Inserts the items in batch.
 */
public void insert(CollectTaxonomy taxonomy, List<Taxon> items) {
    if (items != null && !items.isEmpty()) {
        TaxonDSLContext dsl = dsl(taxonomy);
        int id = dsl.nextId(OFC_TAXON.ID, OFC_TAXON_ID_SEQ);
        int maxId = id;
        Insert<OfcTaxonRecord> query = dsl.createInsertStatement();
        BatchBindStep batch = dsl.batch(query);
        for (Taxon item : items) {
            if (item.getSystemId() == null) {
                item.setSystemId(id++);
            }
            Object[] values = dsl.extractValues(item);
            batch.bind(values);
            maxId = Math.max(maxId, item.getSystemId());
        }
        batch.execute();
        dsl.restartSequence(OFC_TAXON_ID_SEQ, maxId + 1);
    }
}

Example 18 with Taxon

use of org.openforis.idm.model.species.Taxon in project collect by openforis.

the class SpeciesBackupImportJobIntegrationTest method findTaxonByCode.

protected Taxon findTaxonByCode(String code) {
    CollectTaxonomy taxonomy = taxonomyDao.loadByName(survey, TEST_TAXONOMY_NAME);
    List<Taxon> results = taxonDao.findByCode(taxonomy, FAMILY, code, 10);
    assertNotNull(results);
    assertEquals(1, results.size());
    Taxon taxon = results.get(0);
    return taxon;
}

Example 19 with Taxon

use of org.openforis.idm.model.species.Taxon in project collect by openforis.

the class SurveyManagerIntegrationTest method insertTestTaxonomy.

private void insertTestTaxonomy() {
    CollectTaxonomy taxonomy = new CollectTaxonomy();
    taxonomy.setName("tree");
    taxonomy.setSurvey(survey);
    speciesManager.save(taxonomy);
    Taxon taxon = new Taxon();
    taxon.setTaxonomyId(taxonomy.getId());
    taxon.setCode("ALB/GLA");
    taxon.setScientificName("Albizia glaberrima");
    taxon.setTaxonRank(TaxonRank.GENUS);
    speciesManager.save(taxon);
    {
        TaxonVernacularName vernacularName = new TaxonVernacularName();
        vernacularName.setTaxonSystemId(taxon.getSystemId());
        vernacularName.setVernacularName("Mgerenge");
        vernacularName.setLanguageCode("swh");
        speciesManager.save(vernacularName);
    }
    {
        TaxonVernacularName vernacularName = new TaxonVernacularName();
        vernacularName.setTaxonSystemId(taxon.getSystemId());
        vernacularName.setVernacularName("Mchani");
        vernacularName.setLanguageCode("swh");
        speciesManager.save(vernacularName);
    }
}

Example 20 with Taxon

use of org.openforis.idm.model.species.Taxon in project collect by openforis.

the class SpeciesDaoIntegrationTest method testFindCode.

private void testFindCode(String match, int maxResults, int expectedResults) {
    // Create taxonomy
    CollectTaxonomy taxonomy1 = testInsertAndLoadTaxonomy("it_bamboo");
    testUpdateAndLoadTaxonomy(taxonomy1, "it_trees");
    Taxon family1 = testInsertAndLoadTaxon(taxonomy1, -1, "JUGLANDACAE", "Juglandaceae", FAMILY, 9, null);
    Taxon genus1 = testInsertAndLoadTaxon(taxonomy1, -2, "JUG", "Juglans sp.", GENUS, 9, family1);
    testInsertAndLoadTaxon(taxonomy1, -3, "JUG/REG", "Juglans regia", SPECIES, 9, genus1);
    List<Taxon> results = taxonDao.findByCode(taxonomy1, FAMILY, match, maxResults);
    assertEquals(expectedResults, results.size());
    match = match.toUpperCase();
    for (Taxon taxon : results) {
        String code = taxon.getCode();
        code = (code == null) ? "" : code.toUpperCase();
        assertTrue(code.startsWith(match));
    }
}