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

Example 11 with Taxon

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

the class SpeciesManager method loadAncestorTaxons.

private void loadAncestorTaxons(Taxon taxon, TaxonOccurrence o) {
    Taxon currentTaxon = taxon;
    while (currentTaxon.getParentId() != null) {
        Taxon parentTaxon = taxonDao.loadById((CollectTaxonomy) currentTaxon.getTaxonomy(), currentTaxon.getParentId());
        TaxonOccurrence parentTaxonOccurrence = new TaxonOccurrence(parentTaxon);
        o.addAncestorTaxon(parentTaxonOccurrence);
        currentTaxon = parentTaxon;
    }
}

Example 12 with Taxon

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

the class SpeciesManager method findByFamilyScientificName.

public List<TaxonOccurrence> findByFamilyScientificName(CollectTaxonomy taxonomy, String searchString, int maxResults, TaxonSearchParameters parameters) {
    List<TaxonOccurrence> result = new ArrayList<TaxonOccurrence>();
    TaxonTree taxonTree = loadTaxonTree(taxonomy);
    List<Taxon> families = taxonTree.findTaxaByScientificNameStartingWith(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 13 with Taxon

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

the class SpeciesManager method loadTaxonTree.

public TaxonTree loadTaxonTree(CollectTaxonomy taxonomy) {
    TaxonTree tree = taxonTreeByTaxonomyIdCache.get(taxonomy.getId());
    if (tree == null) {
        String taxonomyName = taxonomy.getName();
        TaxonomyDefinition taxonDefinition = taxonomy.getSurvey().getReferenceDataSchema().getTaxonomyDefinition(taxonomyName);
        List<Taxon> taxons = taxonDao.loadTaxonsForTreeBuilding(taxonomy);
        tree = new TaxonTree(taxonDefinition);
        Map<Integer, Taxon> idToTaxon = new HashMap<Integer, Taxon>();
        for (Taxon taxon : taxons) {
            Integer systemId = taxon.getSystemId();
            Integer parentId = taxon.getParentId();
            Taxon parent = parentId == null ? null : idToTaxon.get(parentId);
            Node newNode = tree.addNode(parent, taxon);
            List<TaxonVernacularName> vernacularNames = taxonVernacularNameDao.findByTaxon(systemId);
            tree.addVernacularNames(newNode, vernacularNames);
            idToTaxon.put(systemId, taxon);
        }
        taxonTreeByTaxonomyIdCache.put(taxonomy.getId(), tree);
    }
    return tree;
}

Example 14 with Taxon

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

the class SpeciesImportProcess method findParentTaxon.

private Taxon findParentTaxon(SpeciesLine line) throws ParsingException {
    TaxonRank rank = line.getRank();
    TaxonRank parentRank = rank.getParent();
    String scientificName;
    switch(parentRank) {
        case FAMILY:
            scientificName = line.getFamilyName();
            break;
        case GENUS:
            scientificName = line.getGenus();
            break;
        case SPECIES:
            scientificName = line.getSpeciesName();
            break;
        default:
            throw new RuntimeException("Unsupported rank");
    }
    Taxon result = taxonTree.findTaxonByScientificName(scientificName);
    return result;
}

Example 15 with Taxon

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

the class SpeciesImportProcess method createTaxon.

protected Taxon createTaxon(SpeciesLine line, TaxonRank rank, Taxon parent, String normalizedScientificName) throws ParsingException {
    boolean mostSpecificRank = line.getRank() == rank;
    Taxon taxon = taxonTree.findTaxonByScientificName(normalizedScientificName);
    boolean newTaxon = taxon == null;
    if (newTaxon) {
        taxon = new Taxon();
        taxon.setTaxonRank(rank);
        taxon.setScientificName(normalizedScientificName);
        Node node = taxonTree.addNode(parent, taxon);
        node.addMetadata(LINE_NUMBER_TREE_NODE_METADATA, line.getLineNumber());
        node.addMetadata(RAW_SCIENTIFIC_NAME_TREE_NODE_METADATA, line.getRawScientificName());
    } else if (mostSpecificRank) {
        checkDuplicateScientificName(line, parent, normalizedScientificName);
    }
    if (mostSpecificRank) {
        String code = line.getCode();
        Integer taxonId = line.getTaxonId();
        checkDuplicates(line, code, taxonId);
        taxon.setCode(code);
        taxon.setTaxonId(taxonId);
        TaxonomyDefinition taxonDefinition = survey.getReferenceDataSchema().getTaxonomyDefinition(taxonomyName);
        List<Attribute> taxonAttributes = taxonDefinition.getAttributes();
        for (Attribute attribute : taxonAttributes) {
            String value = line.getInfoAttribute(attribute.getName());
            taxon.addInfoAttribute(value);
        }
        taxonTree.updateNodeInfo(taxon);
        processVernacularNames(line, taxon);
    }
    return taxon;
}