Examples with FactorValue ubic.gemma.model.expression.experiment.FactorValue used on opensource projects

Example 11 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class ContinuousVariableDiffExTest method test.

@Test
public void test() {
    AnalysisType aa = analysisService.determineAnalysis(ee, ee.getExperimentalDesign().getExperimentalFactors(), null, true);
    assertEquals(AnalysisType.GENERICLM, aa);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    Collection<ExperimentalFactor> factors = ee.getExperimentalDesign().getExperimentalFactors();
    assertEquals(1, factors.size());
    config.setAnalysisType(aa);
    config.setFactorsToInclude(factors);
    analyzer = this.getBean(DiffExAnalyzer.class);
    Collection<DifferentialExpressionAnalysis> result = analyzer.run(ee, config);
    assertEquals(1, result.size());
    DifferentialExpressionAnalysis analysis = result.iterator().next();
    assertNotNull(analysis);
    Map<ExperimentalFactor, FactorValue> baselineLevels = ExpressionDataMatrixColumnSort.getBaselineLevels(ee.getExperimentalDesign().getExperimentalFactors());
    assertEquals(1, baselineLevels.size());
    FactorValue fv = baselineLevels.values().iterator().next();
    assertEquals(24.0, Double.parseDouble(fv.getMeasurement().getValue()), 0.0001);
// checkResults( analysis );
}

Example 12 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class ExpressionDataMatrixColumnSortTest method testOrderByExperimentalDesignB.

@Test
public void testOrderByExperimentalDesignB() {
    BioAssayDimension bad = BioAssayDimension.Factory.newInstance();
    /*
         * Five factors. Factor4 is a measurmeent.
         */
    Collection<ExperimentalFactor> factors = new HashSet<>();
    for (int i = 0; i < 5; i++) {
        ExperimentalFactor ef = ExperimentalFactor.Factory.newInstance();
        ef.setType(FactorType.CATEGORICAL);
        ef.setName("factor" + i);
        if (i == 4) {
            ef.setName("mfact" + i);
        }
        ef.setId((long) i);
        for (int j = 0; j < 3; j++) {
            FactorValue fv = FactorValue.Factory.newInstance();
            fv.setValue("fv" + (j + 1) * (i + 1));
            fv.setId((long) (j + 1) * (i + 1));
            fv.setExperimentalFactor(ef);
            ef.getFactorValues().add(fv);
            if (j == 2 && i != 4) {
                fv.setValue("control_group");
            }
            if (i == 4) {
                ef.setType(FactorType.CONTINUOUS);
                Measurement m = Measurement.Factory.newInstance();
                m.setId((long) j * (i + 1));
                m.setValue(j + ".00");
                m.setRepresentation(PrimitiveType.DOUBLE);
                fv.setMeasurement(m);
            }
        }
        factors.add(ef);
    }
    Random random = new Random();
    for (int i = 0; i < 100; i++) {
        BioAssay ba = BioAssay.Factory.newInstance();
        ba.setName("ba" + i);
        ba.setId((long) i);
        bad.getBioAssays().add(ba);
        BioMaterial bm = BioMaterial.Factory.newInstance();
        bm.setId((long) i);
        bm.setName("bm" + i);
        ba.setSampleUsed(bm);
        for (ExperimentalFactor ef : factors) {
            /*
                 * Note: if we use 4, then some of the biomaterials will not have a factorvalue for each factor. This is
                 * realistic. Use 3 to fill it in completely.
                 */
            int k = random.nextInt(4);
            int m = 0;
            FactorValue toUse = null;
            for (FactorValue fv : ef.getFactorValues()) {
                if (m == k) {
                    toUse = fv;
                    break;
                }
                m++;
            }
            if (toUse != null)
                bm.getFactorValues().add(toUse);
        // log.info( ba + " -> " + bm + " -> " + ef + " -> " + toUse );
        }
    }
    EmptyExpressionMatrix mat = new EmptyExpressionMatrix(bad);
    assertEquals(100, mat.columns());
    List<BioMaterial> ordered = ExpressionDataMatrixColumnSort.orderByExperimentalDesign(mat);
    assertEquals(100, ordered.size());
// for ( BioMaterial bioMaterial : ordered ) {
// log.info( bioMaterial + " .... " + StringUtils.join( bioMaterial.getFactorValues(), "  --- " ) );
// }
}

Example 13 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class ExperimentalDesignUtils method getBaselineConditions.

public static Map<ExperimentalFactor, FactorValue> getBaselineConditions(List<BioMaterial> samplesUsed, List<ExperimentalFactor> factors) {
    Map<ExperimentalFactor, FactorValue> baselineConditions = ExpressionDataMatrixColumnSort.getBaselineLevels(samplesUsed, factors);
    /*
         * For factors that don't have an obvious baseline, use the first factorvalue.
         */
    Collection<FactorValue> factorValuesOfFirstSample = samplesUsed.iterator().next().getFactorValues();
    for (ExperimentalFactor factor : factors) {
        if (!baselineConditions.containsKey(factor)) {
            for (FactorValue biomf : factorValuesOfFirstSample) {
                /*
                     * the first biomaterial has the values used as baseline
                     */
                if (biomf.getExperimentalFactor().equals(factor)) {
                    baselineConditions.put(factor, biomf);
                }
            }
        }
    }
    return baselineConditions;
}

Example 14 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue 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 15 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class FactorValueDaoImpl method find.

@Override
public FactorValue find(FactorValue factorValue) {
    try {
        Criteria queryObject = this.getSessionFactory().getCurrentSession().createCriteria(FactorValue.class);
        BusinessKey.checkKey(factorValue);
        BusinessKey.createQueryObject(queryObject, factorValue);
        java.util.List<?> results = queryObject.list();
        Object result = null;
        if (results != null) {
            if (results.size() > 1) {
                this.debug(results);
                throw new org.springframework.dao.InvalidDataAccessResourceUsageException(results.size() + " instances of '" + FactorValue.class.getName() + "' was found when executing query for " + factorValue);
            } else if (results.size() == 1) {
                result = results.iterator().next();
            }
        }
        return (FactorValue) result;
    } catch (org.hibernate.HibernateException ex) {
        throw super.convertHibernateAccessException(ex);
    }
}