Examples with TaxonImpl org.eol.globi.domain.TaxonImpl used on opensource projects

Example 61 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class NonResolvingTaxonIndexTest method createNullTaxon.

@Test
public final void createNullTaxon() throws NodeFactoryException {
    Taxon taxon1 = new TaxonImpl(null, "EOL:1234");
    taxon1.setPath(null);
    TaxonNode taxon = taxonService.getOrCreateTaxon(taxon1);
    assertThat(taxon, is(notNullValue()));
    assertEquals("no name", taxon.getName());
}

Example 62 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class GlobalNamesService method noMatch.

private void noMatch(TermMatchListener termMatchListener, JsonNode data) {
    String suppliedNameString = getSuppliedNameString(data);
    termMatchListener.foundTaxonForName(requestId(data), suppliedNameString, new TaxonImpl(suppliedNameString), NameType.NONE);
}

Example 63 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class GlobalNamesService method parseClassification.

protected void parseClassification(TermMatchListener termMatchListener, JsonNode data, JsonNode aResult, TaxonomyProvider provider) {
    Taxon taxon = new TaxonImpl();
    String classificationPath = aResult.get("classification_path").asText();
    taxon.setPath(parseList(classificationPath));
    if (aResult.has("classification_path_ids")) {
        String classificationPathIds = aResult.get("classification_path_ids").asText();
        taxon.setPathIds(parseList(classificationPathIds, provider.getIdPrefix()));
    }
    String pathRanks = aResult.get("classification_path_ranks").asText();
    taxon.setPathNames(parseList(pathRanks));
    String[] ranks = pathRanks.split("\\|");
    if (ranks.length > 0) {
        String rank = ranks[ranks.length - 1];
        taxon.setRank(rank);
    }
    String[] taxonNames = classificationPath.split("\\|");
    if (ranks.length > 0 && taxonNames.length > 0) {
        String taxonName = taxonNames[taxonNames.length - 1];
        taxon.setName(taxonName);
    } else {
        taxon.setName(aResult.get("canonical_form").asText());
    }
    String taxonIdLabel = aResult.has("current_taxon_id") ? "current_taxon_id" : "taxon_id";
    String taxonIdValue = aResult.get(taxonIdLabel).asText();
    // see https://github.com/GlobalNamesArchitecture/gni/issues/35
    if (!StringUtils.startsWith(taxonIdValue, "gn:")) {
        String externalId = provider.getIdPrefix() + taxonIdValue;
        taxon.setExternalId(externalId);
        String suppliedNameString = getSuppliedNameString(data);
        boolean isExactMatch = aResult.has("match_type") && aResult.get("match_type").getIntValue() < 3;
        NameType nameType = isExactMatch ? NameType.SAME_AS : NameType.SIMILAR_TO;
        if (isExactMatch && aResult.has("current_name_string")) {
            nameType = NameType.SYNONYM_OF;
        }
        // related to https://github.com/GlobalNamesArchitecture/gni/issues/48
        if (!pathTailRepetitions(taxon)) {
            termMatchListener.foundTaxonForName(requestId(data), suppliedNameString, taxon, nameType);
        }
    }
    if (aResult.has("vernaculars")) {
        List<String> commonNames = new ArrayList<String>();
        JsonNode vernaculars = aResult.get("vernaculars");
        for (JsonNode vernacular : vernaculars) {
            if (vernacular.has("name") && vernacular.has("language")) {
                String name = vernacular.get("name").asText();
                String language = vernacular.get("language").asText();
                if (!StringUtils.equals(name, "null") && !StringUtils.equals(language, "null")) {
                    commonNames.add(vernacular.get("name").asText() + " @" + language);
                }
            }
        }
        if (commonNames.size() > 0) {
            taxon.setCommonNames(StringUtils.join(commonNames, CharsetConstant.SEPARATOR));
        }
    }
}

Example 64 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class EOLTaxonImageService method lookupImage.

private TaxonImage lookupImage(String externalId) throws PropertyEnricherException {
    TaxonImage image;
    Map<String, String> enrich = new EOLService().enrich(TaxonUtil.taxonToMap(new TaxonImpl(null, externalId)));
    Taxon taxon = TaxonUtil.mapToTaxon(enrich);
    image = taxonToTaxonImage(taxon);
    return image;
}

Example 65 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForBlewett method addPreyForPredator.

private List<Specimen> addPreyForPredator(String[] header, String[] line, Study study) throws NodeFactoryException {
    List<Specimen> preyItems = new ArrayList<Specimen>();
    int preyColumn = 4;
    for (int i = preyColumn; i < header.length; i++) {
        if (i < line.length) {
            String preyCountString = line[i];
            if (preyCountString.trim().length() > 0) {
                try {
                    int preyCount = Integer.parseInt(preyCountString);
                    String preyName = header[i];
                    for (int j = 0; j < preyCount; j++) {
                        Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(preyName, null));
                        preyItems.add(preySpecimen);
                    }
                } catch (NumberFormatException e) {
                    getLogger().warn(study, "failed to parse prey count line/column:");
                }
            }
        }
    }
    return preyItems;
}