Examples with CharacteristicValueObject ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject used on opensource projects

Example 6 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class OntologyServiceImpl method findExperimentsCharacteristicTags.

/**
 * Using the ontology and values in the database, for a search searchQuery given by the client give an ordered list
 * of possible choices
 */
@Override
public Collection<CharacteristicValueObject> findExperimentsCharacteristicTags(String searchQueryString, boolean useNeuroCartaOntology) {
    String searchQuery = OntologySearch.stripInvalidCharacters(searchQueryString);
    if (searchQuery.length() < 3) {
        return new HashSet<>();
    }
    // this will do like %search%
    Collection<CharacteristicValueObject> characteristicsFromDatabase = CharacteristicValueObject.characteristic2CharacteristicVO(this.characteristicService.findByValue("%" + searchQuery));
    Map<String, CharacteristicValueObject> characteristicFromDatabaseWithValueUri = new HashMap<>();
    Collection<CharacteristicValueObject> characteristicFromDatabaseFreeText = new HashSet<>();
    for (CharacteristicValueObject characteristicInDatabase : characteristicsFromDatabase) {
        // flag to let know that it was found in the database
        characteristicInDatabase.setAlreadyPresentInDatabase(true);
        if (characteristicInDatabase.getValueUri() != null && !characteristicInDatabase.getValueUri().equals("")) {
            characteristicFromDatabaseWithValueUri.put(characteristicInDatabase.getValueUri(), characteristicInDatabase);
        } else {
            // free txt, no value uri
            characteristicFromDatabaseFreeText.add(characteristicInDatabase);
        }
    }
    // search the ontology for the given searchTerm, but if already found in the database dont add it again
    Collection<CharacteristicValueObject> characteristicsFromOntology = this.findCharacteristicsFromOntology(searchQuery, useNeuroCartaOntology, characteristicFromDatabaseWithValueUri);
    // order to show the the term: 1-exactMatch, 2-startWith, 3-substring and 4- no rule
    // order to show values for each List : 1-From database with Uri, 2- from Ontology, 3- from from database with
    // no Uri
    Collection<CharacteristicValueObject> characteristicsWithExactMatch = new ArrayList<>();
    Collection<CharacteristicValueObject> characteristicsStartWithQuery = new ArrayList<>();
    Collection<CharacteristicValueObject> characteristicsSubstring = new ArrayList<>();
    Collection<CharacteristicValueObject> characteristicsNoRuleFound = new ArrayList<>();
    // from the database with a uri
    this.putCharacteristicsIntoSpecificList(searchQuery, characteristicFromDatabaseWithValueUri.values(), characteristicsWithExactMatch, characteristicsStartWithQuery, characteristicsSubstring, characteristicsNoRuleFound);
    // from the ontology
    this.putCharacteristicsIntoSpecificList(searchQuery, characteristicsFromOntology, characteristicsWithExactMatch, characteristicsStartWithQuery, characteristicsSubstring, characteristicsNoRuleFound);
    // from the database with no uri
    this.putCharacteristicsIntoSpecificList(searchQuery, characteristicFromDatabaseFreeText, characteristicsWithExactMatch, characteristicsStartWithQuery, characteristicsSubstring, characteristicsNoRuleFound);
    List<CharacteristicValueObject> allCharacteristicsFound = new ArrayList<>();
    allCharacteristicsFound.addAll(characteristicsWithExactMatch);
    allCharacteristicsFound.addAll(characteristicsStartWithQuery);
    allCharacteristicsFound.addAll(characteristicsSubstring);
    allCharacteristicsFound.addAll(characteristicsNoRuleFound);
    // limit the size of the returned phenotypes to 100 terms
    if (allCharacteristicsFound.size() > 100) {
        return allCharacteristicsFound.subList(0, 100);
    }
    return allCharacteristicsFound;
}

Example 7 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class OntologyServiceTest method test.

@Test
public void test() {
    os.getDiseaseOntologyService().loadTermsInNameSpace(this.getClass().getResourceAsStream("/data/loader/ontology/dotest.owl.xml"));
    Collection<CharacteristicValueObject> name = os.findTermsInexact("diarrhea", null);
    assertTrue(name.size() > 0);
    OntologyTerm t1 = os.getTerm("http://purl.obolibrary.org/obo/DOID_0050001");
    assertNotNull(t1);
    // Actinomadura madurae infectious disease
    assertTrue(os.isObsolete("http://purl.obolibrary.org/obo/DOID_0050001"));
    // inflammatory diarrhea, not obsolete as of May 2012.
    assertNotNull(os.getTerm("http://purl.obolibrary.org/obo/DOID_0050132"));
    assertTrue(!os.isObsolete("http://purl.obolibrary.org/obo/DOID_0050132"));
}

Example 8 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class PhenotypeAssoOntologyHelperImpl method ontology2CharacteristicValueObject.

/**
 * Ontology term to CharacteristicValueObject
 *
 * @return collection of the input, converted to 'shell' CharacteristicValueObjects (which have other slots we want
 * to use)
 */
private Set<CharacteristicValueObject> ontology2CharacteristicValueObject(Collection<OntologyTerm> ontologyTerms) {
    Set<CharacteristicValueObject> characteristicsVO = new HashSet<>();
    for (OntologyTerm ontologyTerm : ontologyTerms) {
        CharacteristicValueObject phenotype = new CharacteristicValueObject(-1L, ontologyTerm.getLabel().toLowerCase(), ontologyTerm.getUri());
        characteristicsVO.add(phenotype);
    }
    return characteristicsVO;
}

Example 9 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class GeneralSearchControllerImpl method fillValueObjects.

@SuppressWarnings("unchecked")
private void fillValueObjects(Class<?> entityClass, List<SearchResult> results, SearchSettings settings) {
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<?> vos;
    if (ExpressionExperiment.class.isAssignableFrom(entityClass)) {
        vos = this.filterEE(expressionExperimentService.loadValueObjects(EntityUtils.getIds(results), false), settings);
        if (!SecurityUtil.isUserAdmin()) {
            auditableUtil.removeTroubledEes((Collection<ExpressionExperimentValueObject>) vos);
        }
    } else if (ArrayDesign.class.isAssignableFrom(entityClass)) {
        vos = this.filterAD(arrayDesignService.loadValueObjectsByIds(EntityUtils.getIds(results)), settings);
        if (!SecurityUtil.isUserAdmin()) {
            auditableUtil.removeTroubledArrayDesigns((Collection<ArrayDesignValueObject>) vos);
        }
    } else if (CompositeSequence.class.isAssignableFrom(entityClass)) {
        Collection<CompositeSequenceValueObject> css = new ArrayList<>();
        for (SearchResult sr : results) {
            CompositeSequenceValueObject csvo = compositeSequenceService.loadValueObject((CompositeSequence) sr.getResultObject());
            css.add(csvo);
        }
        vos = css;
    } else if (BibliographicReference.class.isAssignableFrom(entityClass)) {
        Collection<BibliographicReference> bss = bibliographicReferenceService.load(EntityUtils.getIds(results));
        bss = bibliographicReferenceService.thaw(bss);
        vos = bibliographicReferenceService.loadValueObjects(bss);
    } else if (Gene.class.isAssignableFrom(entityClass)) {
        Collection<Gene> genes = geneService.load(EntityUtils.getIds(results));
        genes = geneService.thawLite(genes);
        vos = geneService.loadValueObjects(genes);
    } else if (Characteristic.class.isAssignableFrom(entityClass)) {
        Collection<CharacteristicValueObject> cvos = new ArrayList<>();
        for (SearchResult sr : results) {
            Characteristic ch = (Characteristic) sr.getResultObject();
            cvos.add(new CharacteristicValueObject(ch));
        }
        vos = cvos;
    } else if (CharacteristicValueObject.class.isAssignableFrom(entityClass)) {
        Collection<CharacteristicValueObject> cvos = new ArrayList<>();
        for (SearchResult sr : results) {
            CharacteristicValueObject ch = (CharacteristicValueObject) sr.getResultObject();
            cvos.add(ch);
        }
        vos = cvos;
    } else if (BioSequenceValueObject.class.isAssignableFrom(entityClass)) {
        return;
    } else if (GeneSet.class.isAssignableFrom(entityClass)) {
        vos = geneSetService.getValueObjects(EntityUtils.getIds(results));
    } else if (ExpressionExperimentSet.class.isAssignableFrom(entityClass)) {
        vos = experimentSetService.loadValueObjects(experimentSetService.load(EntityUtils.getIds(results)));
    } else if (FactorValue.class.isAssignableFrom(entityClass)) {
        Collection<FactorValueValueObject> fvo = new ArrayList<>();
        for (SearchResult sr : results) {
            fvo.add(new FactorValueValueObject((FactorValue) sr.getResultObject()));
        }
        vos = fvo;
    } else {
        throw new UnsupportedOperationException("Don't know how to make value objects for class=" + entityClass);
    }
    if (vos == null || vos.isEmpty()) {
        // it causing front end errors, if vos is empty make sure to get rid of all search results
        for (Iterator<SearchResult> it = results.iterator(); it.hasNext(); ) {
            it.next();
            it.remove();
        }
        return;
    }
    // retained objects...
    Map<Long, Object> idMap = EntityUtils.getIdMap(vos);
    for (Iterator<SearchResult> it = results.iterator(); it.hasNext(); ) {
        SearchResult sr = it.next();
        if (!idMap.containsKey(sr.getId())) {
            it.remove();
            continue;
        }
        sr.setResultObject(idMap.get(sr.getId()));
    }
    if (timer.getTime() > 1000) {
        BaseFormController.log.info("Value object conversion after search: " + timer.getTime() + "ms");
    }
}

Example 10 with CharacteristicValueObject

use of ubic.gemma.model.genome.gene.phenotype.valueObject.CharacteristicValueObject in project Gemma by PavlidisLab.

the class PhenotypeAssociationDaoImpl method findEvidenceCategoryTerms.

/**
 * find category terms currently used in the database by evidence
 */
@Override
public Collection<CharacteristicValueObject> findEvidenceCategoryTerms() {
    Collection<CharacteristicValueObject> mgedCategory = new TreeSet<>();
    String queryString = "SELECT DISTINCT CATEGORY_URI, category FROM PHENOTYPE_ASSOCIATION " + "JOIN INVESTIGATION ON PHENOTYPE_ASSOCIATION.EXPERIMENT_FK = INVESTIGATION.ID " + "JOIN CHARACTERISTIC ON CHARACTERISTIC.INVESTIGATION_FK= INVESTIGATION.ID";
    org.hibernate.SQLQuery queryObject = this.getSessionFactory().getCurrentSession().createSQLQuery(queryString);
    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    while (results.next()) {
        CharacteristicValueObject characteristicValueObject = new CharacteristicValueObject(-1L);
        characteristicValueObject.setCategoryUri((String) results.get(0));
        characteristicValueObject.setCategory((String) results.get(1));
        mgedCategory.add(characteristicValueObject);
    }
    results.close();
    return mgedCategory;
}