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

Example 16 with Taxonomy

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

the class TaxonomyConfigServiceTest method validateRangeTaxonomyWithoutRangeAttribute.

@Test(expected = VocabularyMissingRangeAttributeException.class)
public void validateRangeTaxonomyWithoutRangeAttribute() {
    Taxonomy taxonomy = new Taxonomy("tax001");
    taxonomy.addVocabulary(createVocabulary("voc001", createTerms("term001", "term002"), AttributeBuilder.newBuilder().field("tax.voc").alias("tax-voc-range").type("integer").build()));
    new TaxonomyConfigService().validateTaxonomy(taxonomy);
}

Example 17 with Taxonomy

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

the class Mica310Upgrade method addDefaultFacets.

private void addDefaultFacets() {
    logger.info("Add default facets in study taxonomy");
    ImmutableList<String> vocabulariesWithFacet = ImmutableList.<String>builder().add("methods-design").add("start").add("end").add("populations-selectionCriteria-countriesIso").add("populations-selectionCriteria-ageMin").add("populations-selectionCriteria-ageMax").add("populations-selectionCriteria-gender").add("populations-selectionCriteria-pregnantWomen").add("populations-selectionCriteria-newborn").add("populations-selectionCriteria-twins").add("numberOfParticipants-participant-number").add("numberOfParticipants-sample-number").add("methods-recruitments").add("populations-recruitment-dataSources").add("populations-dataCollectionEvents-dataSources").add("populations-dataCollectionEvents-bioSamples").add("access", "19").build();
    Taxonomy studyTaxonomy = taxonomyConfigService.findByTarget(TaxonomyTarget.STUDY);
    for (Vocabulary vocabulary : studyTaxonomy.getVocabularies()) {
        if (vocabulariesWithFacet.contains(vocabulary.getName())) {
            vocabulary.addAttribute("facet", "true");
            vocabulary.addAttribute("facetPosition", "0");
            vocabulary.addAttribute("facetExpanded", "false");
        }
    }
    taxonomyConfigService.update(TaxonomyTarget.STUDY, studyTaxonomy);
}

Example 18 with Taxonomy

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

the class TaxonomyConfigService method mergeWithDefault.

public void mergeWithDefault(TaxonomyTarget target) {
    Taxonomy targetTaxonomy = findByTarget(target);
    mergeVocabulariesTerms(targetTaxonomy, getDefault(target));
    updateInternal(target, targetTaxonomy);
}

Example 19 with Taxonomy

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

the class OpalServiceHelper method getTaxonomies.

// opal root url as key
@Cacheable(value = "opal-taxonomies", key = "#opalJavaClient.newUri().build()")
public Map<String, Taxonomy> getTaxonomies(OpalJavaClient opalJavaClient) {
    log.info("Fetching opal taxonomies");
    URI uri = opalJavaClient.newUri().segment("system", "conf", "taxonomies").build();
    List<Opal.TaxonomyDto> taxonomies = opalJavaClient.getResources(Opal.TaxonomyDto.class, uri, Opal.TaxonomyDto.newBuilder());
    ConcurrentMap<String, Taxonomy> taxonomiesList = taxonomies.stream().collect(Collectors.toConcurrentMap(Opal.TaxonomyDto::getName, this::fromDto));
    eventBus.post(new OpalTaxonomiesUpdatedEvent(taxonomiesList));
    return taxonomiesList;
}

Example 20 with Taxonomy

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

the class TaxonomyAggregationMetaDataProvider method getVocabulary.

private Optional<Vocabulary> getVocabulary(String aggregation) {
    String key = aggregation.replaceAll("^attributes-", "").replaceAll("-und$", "");
    AttributeKey attrKey = AttributeKey.from(key);
    String targetTaxonomy = attrKey.hasNamespace(null) ? "Default" : attrKey.getNamespace();
    String targetVocabulary = attrKey.getName();
    return // 
    getTaxonomies().stream().filter(// 
    taxonomy -> !Strings.isNullOrEmpty(targetTaxonomy) && taxonomy.getName().equals(targetTaxonomy)).map(// 
    Taxonomy::getVocabularies).flatMap(// 
    Collection::stream).filter(// 
    vocabulary -> vocabulary.getName().equals(targetVocabulary)).findFirst();
}