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

Example 6 with Vocabulary

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

the class DatasetDtos method asDto.

private Mica.TermAttributesDto asDto(Taxonomy taxonomy, Attributes attributes, String locale) {
    Mica.TermAttributesDto.Builder builder = // 
    Mica.TermAttributesDto.newBuilder().setTaxonomy(taxonomyDtos.asDto(taxonomy, locale));
    Map<String, Mica.TermAttributeDto.Builder> terms = Maps.newHashMap();
    attributes.getAttributes(taxonomy.getName()).forEach(attr -> {
        if (taxonomy.hasVocabulary(attr.getName())) {
            Vocabulary vocabulary = taxonomy.getVocabulary(attr.getName());
            String termStr = attr.getValues().getUndetermined();
            if (!Strings.isNullOrEmpty(termStr) && vocabulary.hasTerm(termStr)) {
                Mica.TermAttributeDto.Builder termBuilder;
                if (terms.containsKey(vocabulary.getName())) {
                    termBuilder = terms.get(vocabulary.getName());
                } else {
                    termBuilder = Mica.TermAttributeDto.newBuilder();
                    terms.put(vocabulary.getName(), termBuilder);
                    termBuilder.setVocabulary(taxonomyDtos.asDto(vocabulary, locale));
                }
                Term term = vocabulary.getTerm(termStr);
                termBuilder.addTerms(taxonomyDtos.asDto(term, locale));
            }
        }
    });
    // keep vocabulary order
    taxonomy.getVocabularies().forEach(vocabulary -> {
        if (terms.containsKey(vocabulary.getName())) {
            builder.addVocabularyTerms(terms.get(vocabulary.getName()));
        }
    });
    return builder.build();
}

Example 7 with Vocabulary

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

the class Mica220Upgrade method updateFixWrongKeysInStudyTaxonomy.

private void updateFixWrongKeysInStudyTaxonomy() {
    TaxonomyEntityWrapper studyTaxonomy = taxonomyConfigRepository.findOne("study");
    if (studyTaxonomy == null)
        return;
    List<Vocabulary> vocabularies = studyTaxonomy.getTaxonomy().getVocabularies();
    vocabularies.stream().filter(vocabulary -> vocabulary.getName().equals("numberOfParticipants-sample-number") || vocabulary.getName().equals("numberOfParticipants-sample-range")).map(TaxonomyEntity::getAttributes).forEach(attributes -> {
        attributes.put("field", "model." + attributes.get("field"));
        attributes.put("alias", "model-" + attributes.get("alias"));
    });
    taxonomyConfigRepository.save(studyTaxonomy);
}

Example 8 with Vocabulary

use of org.obiba.opal.core.domain.taxonomy.Vocabulary 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 9 with Vocabulary

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

the class TaxonomyConfigService method mergeVocabulariesTerms.

void mergeVocabulariesTerms(Taxonomy taxonomy, Taxonomy defaultTaxonomy) {
    defaultTaxonomy.getVocabularies().forEach(v -> {
        if (!taxonomy.hasVocabulary(v.getName())) {
            taxonomy.addVocabulary(v);
        } else {
            Vocabulary defaultTaxonomyVocabulary = defaultTaxonomy.getVocabulary(v.getName());
            Vocabulary taxonomyVocabulary = taxonomy.getVocabulary(v.getName());
            if (defaultTaxonomyVocabulary.hasTerms()) {
                defaultTaxonomyVocabulary.getTerms().forEach(t -> {
                    if (!taxonomyVocabulary.hasTerm(t.getName()))
                        taxonomyVocabulary.addTerm(t);
                });
            }
        }
    });
}

Example 10 with Vocabulary

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

the class VocabularyDuplicateAliasExceptionMapper method getErrorDto.

@Override
protected GeneratedMessage.ExtendableMessage<?> getErrorDto(VocabularyDuplicateAliasException e) {
    Vocabulary vocabulary = e.getVocabulary();
    ErrorDtos.ClientErrorDto.Builder builder = ErrorDtos.ClientErrorDto.newBuilder().setCode(getStatus().getStatusCode());
    if (vocabulary != null) {
        builder.setMessageTemplate("server.error.taxonomy.duplicate-criterion-alias");
        String field = vocabulary.getAttributeValue("field");
        builder.addArguments(Strings.isNullOrEmpty(field) ? vocabulary.getName() : field);
    }
    return builder.build();
}