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

Example 6 with NameType

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

the class GlobalNamesServiceTest method createTaxaListFromNameList.

@Test
public void createTaxaListFromNameList() throws PropertyEnricherException {
    GlobalNamesService service = new GlobalNamesService(GlobalNamesSources.ITIS);
    final List<Taxon> foundTaxa = new ArrayList<Taxon>();
    service.findTermsForNames(Arrays.asList("1|Homo sapiens", "2|Ariopsis felis"), new TermMatchListener() {

        @Override
        public void foundTaxonForName(Long nodeId, String name, Taxon taxon, NameType nameType) {
            assertNotNull(nodeId);
            foundTaxa.add(taxon);
        }
    });
    assertThat(foundTaxa.size(), is(2));
}

Example 7 with NameType

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

the class TaxonEnricherImpl method findTerms.

@Override
public void findTerms(List<Term> terms, TermMatchListener termMatchListener) throws PropertyEnricherException {
    for (Term name : terms) {
        Map<String, String> enriched = enrich(new TreeMap<String, String>() {

            {
                put(PropertyAndValueDictionary.NAME, name.getName());
                put(PropertyAndValueDictionary.EXTERNAL_ID, name.getId());
            }
        });
        if (enriched != null) {
            NameType nameMatchType = TaxonUtil.isResolved(enriched) ? NameType.SAME_AS : NameType.NONE;
            termMatchListener.foundTaxonForName(null, name.getName(), TaxonUtil.mapToTaxon(enriched), nameMatchType);
        }
    }
}

Example 8 with NameType

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

the class GlobalNamesServiceTest method lookupMultipleSources.

@Test
public void lookupMultipleSources() throws PropertyEnricherException {
    GlobalNamesService service = new GlobalNamesService(Arrays.asList(GlobalNamesSources.GBIF, GlobalNamesSources.ITIS));
    final List<Taxon> taxa = new ArrayList<Taxon>();
    service.findTermsForNames(Collections.singletonList("Homo sapiens"), new TermMatchListener() {

        @Override
        public void foundTaxonForName(Long nodeId, String name, Taxon taxon, NameType nameType) {
            taxa.add(taxon);
        }
    });
    assertThat(taxa.size(), is(2));
}

Example 9 with NameType

use of org.eol.globi.domain.NameType 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 10 with NameType

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

the class GlobalNamesServiceTest method createTaxaListFromNameWithSpecialCharacter.

@Test
public void createTaxaListFromNameWithSpecialCharacter() throws PropertyEnricherException {
    GlobalNamesService service = new GlobalNamesService(GlobalNamesSources.IF);
    final List<Taxon> foundTaxa = new ArrayList<Taxon>();
    service.findTermsForNames(Collections.singletonList("4594386|Epichloë"), new TermMatchListener() {

        @Override
        public void foundTaxonForName(Long nodeId, String name, Taxon taxon, NameType nameType) {
            assertNotNull(nodeId);
            foundTaxa.add(taxon);
        }
    });
    assertThat(foundTaxa.size(), is(1));
}