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

Example 31 with FactorValue

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

the class CharacteristicUpdateTaskImpl method removeFromParent.

private void removeFromParent(Characteristic c, Object parent) {
    if (parent instanceof ExpressionExperiment) {
        ExpressionExperiment ee = (ExpressionExperiment) parent;
        ee = expressionExperimentService.thawLite(ee);
        ee.getCharacteristics().remove(c);
        expressionExperimentService.update(ee);
    } else if (parent instanceof BioMaterial) {
        BioMaterial bm = (BioMaterial) parent;
        bm.getCharacteristics().remove(c);
        bioMaterialService.update(bm);
    } else if (parent instanceof FactorValue) {
        FactorValue fv = (FactorValue) parent;
        fv.getCharacteristics().remove(c);
        factorValueService.update(fv);
    }
}

Example 32 with FactorValue

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

the class BioAssayDimensionValueObject method makeDummyBioAssayDimension.

private BioAssayDimension makeDummyBioAssayDimension() {
    assert this.id == null;
    BioAssayDimension fakeBd = BioAssayDimension.Factory.newInstance("Placeholder representing: " + name, description, new ArrayList<BioAssay>());
    Map<Long, ExperimentalFactor> fakeEfs = new HashMap<>();
    for (BioAssayValueObject bav : this.bioAssays) {
        BioAssay ba = BioAssay.Factory.newInstance();
        ba.setId(bav.getId());
        ba.setName(bav.getName());
        ba.setDescription("Fake placeholder");
        BioMaterial sampleUsed = BioMaterial.Factory.newInstance();
        BioMaterialValueObject bmVo = bav.getSample();
        assert bmVo != null;
        sampleUsed.setId(bmVo.getId());
        sampleUsed.setName(bmVo.getName());
        sampleUsed.setDescription("Fake placeholder");
        for (IdentifiableValueObject iVo : bmVo.getFactorValueObjects()) {
            FactorValueValueObject fvVo = (FactorValueValueObject) iVo;
            FactorValue fv = FactorValue.Factory.newInstance();
            assert fvVo.getId() != null;
            fv.setId(fvVo.getId());
            assert fvVo.getValue() != null;
            fv.setValue(fvVo.getValue());
            Long efId = fvVo.getFactorId();
            ExperimentalFactor ef;
            if (fakeEfs.containsKey(efId)) {
                ef = fakeEfs.get(efId);
            } else {
                ef = ExperimentalFactor.Factory.newInstance();
                ef.setId(efId);
                ef.setName(fvVo.getCategory());
                ef.setType(fvVo.isMeasurement() ? FactorType.CONTINUOUS : FactorType.CATEGORICAL);
                fakeEfs.put(efId, ef);
            }
            ef.getFactorValues().add(fv);
            fv.setExperimentalFactor(ef);
            sampleUsed.getFactorValues().add(fv);
        }
        ba.setSampleUsed(sampleUsed);
        ArrayDesign ad = ArrayDesign.Factory.newInstance();
        ArrayDesignValueObject adVo = bav.getArrayDesign();
        assert adVo != null;
        ad.setId(adVo.getId());
        ad.setShortName(adVo.getShortName());
        ad.setDescription("Fake placeholder");
        ba.setArrayDesignUsed(ad);
        fakeBd.getBioAssays().add(ba);
    }
    return fakeBd;
}

Example 33 with FactorValue

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

the class ExpressionExperimentSubSetDaoImpl method getFactorValuesUsed.

@Override
public Collection<FactorValueValueObject> getFactorValuesUsed(Long subSetId, Long experimentalFactor) {
    // noinspection unchecked
    List<FactorValue> list = this.getSessionFactory().getCurrentSession().createQuery("select distinct fv from ExpressionExperimentSubSet es join es.bioAssays ba join ba.sampleUsed bm " + "join bm.factorValues fv where es.id=:es and fv.experimentalFactor.id = :ef ").setParameter("es", subSetId).setParameter("ef", experimentalFactor).list();
    Collection<FactorValueValueObject> result = new HashSet<>();
    for (FactorValue fv : list) {
        result.add(new FactorValueValueObject(fv));
    }
    return result;
}

Example 34 with FactorValue

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

the class BioMaterialServiceImpl method update.

private BioMaterial update(BioMaterialValueObject bmvo) {
    BioMaterial bm = this.load(bmvo.getId());
    Collection<FactorValue> updatedFactorValues = new HashSet<>();
    // all of them.
    Map<String, String> factorIdToFactorValueId = bmvo.getFactorIdToFactorValueId();
    for (String factorIdString : factorIdToFactorValueId.keySet()) {
        String factorValueString = factorIdToFactorValueId.get(factorIdString);
        assert factorIdString.matches("factor\\d+");
        Long factorId = Long.parseLong(factorIdString.substring(6));
        // noinspection StatementWithEmptyBody // no value provided, that's okay, the curator can fill it in later.
        if (StringUtils.isBlank(factorValueString)) {
        } else if (factorValueString.matches("fv\\d+")) {
            // categorical
            long fvId = Long.parseLong(factorValueString.substring(2));
            FactorValue fv = factorValueDao.load(fvId);
            if (fv == null) {
                throw new RuntimeException("No such factorValue with id=" + fvId);
            }
            updatedFactorValues.add(fv);
        } else {
            // continuous, the value send is the actual value, not an id. This will only make sense if the value is
            // a measurement.
            boolean found = false;
            // find the right factor value to update.
            for (FactorValue fv : bm.getFactorValues()) {
                if (fv.getExperimentalFactor().getId().equals(factorId)) {
                    if (fv.getMeasurement() == null) {
                        throw new IllegalStateException("Should have been a measurement associated with fv=" + fv + ", cannot update.");
                    } else if (!fv.getMeasurement().getValue().equals(factorValueString)) {
                        AbstractService.log.debug("Updating continuous value on biomaterial:" + bmvo + ", factor=" + fv.getExperimentalFactor() + " value= '" + factorValueString + "'");
                        fv.getMeasurement().setValue(factorValueString);
                    } else {
                        AbstractService.log.debug("Value unchanged from " + fv.getMeasurement().getValue());
                    }
                    // always add...
                    updatedFactorValues.add(fv);
                    found = true;
                    break;
                }
            }
            if (!found) {
                /*
                     * Have to load the factor, create a factor value.
                     */
                ExperimentalFactor ef = experimentalFactorDao.load(factorId);
                // note that this type of factorvalues are not reused for continuous ones.
                AbstractService.log.info("Adding factor value for " + ef + ": " + factorValueString + " to " + bm);
                FactorValue fv = FactorValue.Factory.newInstance();
                fv.setExperimentalFactor(ef);
                fv.setValue(factorValueString);
                Measurement m = Measurement.Factory.newInstance();
                m.setType(MeasurementType.ABSOLUTE);
                m.setValue(fv.getValue());
                try {
                    // noinspection ResultOfMethodCallIgnored // check if it is a number, don't need the value.
                    Double.parseDouble(fv.getValue());
                    m.setRepresentation(PrimitiveType.DOUBLE);
                } catch (NumberFormatException e) {
                    m.setRepresentation(PrimitiveType.STRING);
                }
                fv.setMeasurement(m);
                fv = factorValueDao.create(fv);
                updatedFactorValues.add(fv);
                ef.getFactorValues().add(fv);
                experimentalFactorDao.update(ef);
            }
        }
    }
    // this is not valid, because it's possible that we are removing a factor value.
    // assert bm.getFactorValues().size() <= updatedFactorValues.size();
    bm.getFactorValues().clear();
    bm.getFactorValues().addAll(updatedFactorValues);
    assert !bm.getFactorValues().isEmpty();
    this.update(bm);
    assert !bm.getFactorValues().isEmpty();
    return bm;
}

Example 35 with FactorValue

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

the class ExperimentalDesignUtils method extractFactorValueForSample.

private static Object extractFactorValueForSample(Map<ExperimentalFactor, FactorValue> baselines, BioMaterial samp, ExperimentalFactor factor) {
    FactorValue baseLineFV = baselines.get(factor);
    /*
         * Find this biomaterial's value for the current factor.
         */
    Object value = null;
    boolean found = false;
    for (FactorValue fv : samp.getFactorValues()) {
        if (fv.getExperimentalFactor().equals(factor)) {
            if (found) {
                // not unique
                throw new IllegalStateException("Biomaterial had more than one value for factor: " + factor);
            }
            boolean isBaseline = baseLineFV != null && fv.equals(baseLineFV);
            if (ExperimentalDesignUtils.isContinuous(factor)) {
                Measurement measurement = fv.getMeasurement();
                assert measurement != null;
                try {
                    value = Double.parseDouble(measurement.getValue());
                } catch (NumberFormatException e) {
                    value = Double.NaN;
                }
            } else {
                /*
                     * We always use a dummy value. It's not as human-readable but at least we're sure it is unique and
                     * R-compliant. (assuming the fv is persistent!)
                     */
                value = ExperimentalDesignUtils.nameForR(fv, isBaseline);
            }
            found = true;
        // could break here but nice to check for uniqueness.
        }
    }
    if (!found) {
        return null;
    }
    return value;
}