Examples with TaxonTree org.openforis.collect.model.TaxonTree used on opensource projects

Example 6 with TaxonTree

use of org.openforis.collect.model.TaxonTree in project collect by openforis.

the class SpeciesManager method findByFamilyCode.

public List<TaxonOccurrence> findByFamilyCode(CollectTaxonomy taxonomy, String searchString, int maxResults, TaxonSearchParameters parameters) {
    List<TaxonOccurrence> result = new ArrayList<TaxonOccurrence>();
    TaxonTree taxonTree = loadTaxonTree(taxonomy);
    List<Taxon> families = taxonTree.findTaxaByCodeStartingWith(searchString, parameters.getHighestRank());
    result.addAll(fromTaxonomiesToTaxonOccurrences(families, parameters));
    for (Taxon familyTaxon : families) {
        List<TaxonOccurrence> descendants = taxonTree.getDescendantOccurrences(familyTaxon, parameters);
        result.addAll(descendants);
    }
    return result;
}

Example 7 with TaxonTree

use of org.openforis.collect.model.TaxonTree in project collect by openforis.

the class SpeciesBackupImportTask method createInternalVariables.

@Override
protected void createInternalVariables() throws Throwable {
    reader = new SpeciesBackupCSVReader(file);
    reader.init();
    List<String> infoColumnNames = reader.getInfoColumnNames();
    List<ReferenceDataDefinition.Attribute> attributes = ReferenceDataDefinition.Attribute.fromNames(infoColumnNames);
    TaxonomyDefinition taxonDefinition = new TaxonomyDefinition(taxonomyName);
    taxonDefinition.setAttributes(attributes);
    survey.getReferenceDataSchema().addTaxonomyDefinition(taxonDefinition);
    taxonTree = new TaxonTree(taxonDefinition);
    super.createInternalVariables();
}

Example 8 with TaxonTree

use of org.openforis.collect.model.TaxonTree in project collect by openforis.

the class SpeciesImportProcess method parseTaxonCSVLines.

protected void parseTaxonCSVLines(File file) {
    long currentRowNumber = 0;
    try {
        reader = new SpeciesCSVReader(file, csvFileOptions);
        reader.init();
        TaxonomyDefinition taxonomyDefinition = initializeTaxonomyDefinition();
        taxonTree = new TaxonTree(taxonomyDefinition);
        status.addProcessedRow(1);
        currentRowNumber = 2;
        while (status.isRunning()) {
            try {
                SpeciesLine line = reader.readNextLine();
                if (line != null) {
                    lines.add(line);
                }
                if (!reader.isReady()) {
                    break;
                }
            } catch (ParsingException e) {
                status.addParsingError(currentRowNumber, e.getError());
            } finally {
                currentRowNumber++;
            }
        }
        status.setTotal(reader.getLinesRead() + 1);
    } catch (ParsingException e) {
        status.error();
        status.addParsingError(1, e.getError());
    } catch (Exception e) {
        status.error();
        status.addParsingError(currentRowNumber, new ParsingError(ErrorType.IOERROR, e.getMessage()));
        LOG.error("Error importing species CSV file", e);
    } finally {
        IOUtils.closeQuietly(reader);
    }
}