Examples with Taxonomy org.obiba.opal.core.domain.taxonomy.Taxonomy used on opensource projects

Example 11 with Taxonomy

use of org.obiba.opal.core.domain.taxonomy.Taxonomy in project mica2 by obiba.

the class TaxonomyConfigServiceTest method validateRangeTaxonomyWithoutTerms.

@Test(expected = VocabularyMissingRangeTermsException.class)
public void validateRangeTaxonomyWithoutTerms() {
    Taxonomy taxonomy = new Taxonomy("tax001");
    taxonomy.addVocabulary(createVocabulary("voc001", null, AttributeBuilder.newBuilder().field("tax.voc").alias("tax-voc-range").range("true").type("integer").build()));
    new TaxonomyConfigService().validateTaxonomy(taxonomy);
}

Example 12 with Taxonomy

use of org.obiba.opal.core.domain.taxonomy.Taxonomy in project mica2 by obiba.

the class AbstractTaxonomySearchResource method filterTerms.

protected List<String> filterTerms(TaxonomyTarget target, String query, String locale, List<String> vocabularies) {
    try {
        if (vocabularies != null && vocabularies.size() > 0) {
            // filter on vocabulary names; remove taxonomy prefixes ('Mica_study:')
            String vocabulariesQuery = vocabularies.stream().map(v -> String.format("vocabularyName:%s", v.replaceAll("^([^\\:]+):", ""))).collect(Collectors.joining(" AND "));
            query = Strings.isNullOrEmpty(query) ? vocabulariesQuery : query + " " + vocabulariesQuery;
        }
        return esTaxonomyTermService.find(0, MAX_SIZE, DEFAULT_SORT, "asc", null, getTargettedQuery(target, query), getFields(locale, TERM_FIELDS)).getList();
    } catch (Exception e) {
        initTaxonomies();
        // for a 404 response
        throw new NoSuchElementException();
    }
}

Example 13 with Taxonomy

use of org.obiba.opal.core.domain.taxonomy.Taxonomy in project mica2 by obiba.

the class Mica220UpgradeTest method getWrapper.

private TaxonomyEntityWrapper getWrapper(String name) throws IOException {
    ObjectMapper mapper = new ObjectMapper();
    Taxonomy taxonomy = mapper.readValue(new File("src/test/resources/config/mica-" + name + ".json"), Taxonomy.class);
    TaxonomyEntityWrapper wrapper = new TaxonomyEntityWrapper();
    wrapper.setTarget(name);
    wrapper.setTaxonomy(taxonomy);
    return wrapper;
}

Example 14 with Taxonomy

use of org.obiba.opal.core.domain.taxonomy.Taxonomy in project mica2 by obiba.

the class TaxonomyConfigServiceTest method merge_taxonomy_with_one_having_same_vocabulary_but_extra_term.

@Test
public void merge_taxonomy_with_one_having_same_vocabulary_but_extra_term() {
    Taxonomy tax001 = new Taxonomy("tax001");
    tax001.addVocabulary(createVocabulary("voc001", null, null));
    Taxonomy tax002 = new Taxonomy("tax002");
    tax002.addVocabulary(createVocabulary("voc001", createTerms("term001"), null));
    new TaxonomyConfigService().mergeVocabulariesTerms(tax001, tax002);
    assert tax001.getVocabulary("voc001").hasTerm("term001");
}

Example 15 with Taxonomy

use of org.obiba.opal.core.domain.taxonomy.Taxonomy in project mica2 by obiba.

the class TaxonomyConfigServiceTest method merge_taxonomy_with_vocabulary_having_one_term_with_one_having_same_vocabulary_without_term.

@Test
public void merge_taxonomy_with_vocabulary_having_one_term_with_one_having_same_vocabulary_without_term() {
    Taxonomy tax001 = new Taxonomy("tax001");
    tax001.addVocabulary(createVocabulary("voc001", createTerms("term001"), null));
    Taxonomy tax002 = new Taxonomy("tax002");
    tax002.addVocabulary(createVocabulary("voc001", null, null));
    new TaxonomyConfigService().mergeVocabulariesTerms(tax001, tax002);
    assert tax001.getVocabulary("voc001").hasTerm("term001");
}