Examples with BioMaterial ubic.gemma.model.expression.biomaterial.BioMaterial used on opensource projects

Example 86 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class BioMaterialServiceImpl method associateBatchFactor.

@Override
public void associateBatchFactor(final Map<BioMaterial, Date> dates, final Map<Date, FactorValue> d2fv) {
    for (final BioMaterial bm : dates.keySet()) {
        final BioMaterial toUpdate = this.bioMaterialDao.load(bm.getId());
        if (!d2fv.isEmpty()) {
            toUpdate.getFactorValues().add(d2fv.get(dates.get(toUpdate)));
        }
        for (final BioAssay ba : toUpdate.getBioAssaysUsedIn()) {
            if (ba.getProcessingDate() != null) {
                if (!ba.getProcessingDate().equals(dates.get(toUpdate))) {
                    ba.setProcessingDate(dates.get(toUpdate));
                    bioAssayDao.update(ba);
                }
            } else {
                ba.setProcessingDate(dates.get(toUpdate));
                bioAssayDao.update(ba);
            }
        }
        bioMaterialDao.update(toUpdate);
    }
}

Example 87 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class BioMaterialServiceImpl method getBioMaterialIdList.

@Override
public String getBioMaterialIdList(Collection<BioMaterial> bioMaterials) {
    StringBuilder buf = new StringBuilder();
    for (BioMaterial bm : bioMaterials) {
        buf.append(bm.getId());
        buf.append(",");
    }
    return buf.toString().replaceAll(",$", "");
}

Example 88 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial 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 89 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class ExpressionExperimentDaoImpl method thaw.

private ExpressionExperiment thaw(ExpressionExperiment ee, boolean vectorsAlso) {
    if (ee == null) {
        return null;
    }
    if (ee.getId() == null)
        throw new IllegalArgumentException("id cannot be null, cannot be thawed: " + ee);
    /*
         * Trying to do everything fails miserably, so we still need a hybrid approach. But returning the thawed object,
         * as opposed to thawing the one passed in, solves problems.
         */
    String thawQuery = "select distinct e from ExpressionExperiment e " + " left join fetch e.accession acc left join fetch acc.externalDatabase where e.id=:eeId";
    List res = this.getSessionFactory().getCurrentSession().createQuery(thawQuery).setParameter("eeId", ee.getId()).list();
    if (res.size() == 0) {
        throw new IllegalArgumentException("No experiment with id=" + ee.getId() + " could be loaded.");
    }
    ExpressionExperiment result = (ExpressionExperiment) res.iterator().next();
    Hibernate.initialize(result.getMeanVarianceRelation());
    Hibernate.initialize(result.getQuantitationTypes());
    Hibernate.initialize(result.getCharacteristics());
    Hibernate.initialize(result.getRawDataFile());
    Hibernate.initialize(result.getPrimaryPublication());
    Hibernate.initialize(result.getOtherRelevantPublications());
    Hibernate.initialize(result.getBioAssays());
    Hibernate.initialize(result.getAuditTrail());
    Hibernate.initialize(result.getGeeq());
    if (result.getAuditTrail() != null)
        Hibernate.initialize(result.getAuditTrail().getEvents());
    Hibernate.initialize(result.getCurationDetails());
    for (BioAssay ba : result.getBioAssays()) {
        Hibernate.initialize(ba.getArrayDesignUsed());
        Hibernate.initialize(ba.getArrayDesignUsed().getDesignProvider());
        Hibernate.initialize(ba.getDerivedDataFiles());
        Hibernate.initialize(ba.getSampleUsed());
        BioMaterial bm = ba.getSampleUsed();
        if (bm != null) {
            Hibernate.initialize(bm.getFactorValues());
            Hibernate.initialize(bm.getTreatments());
        }
    }
    ExperimentalDesign experimentalDesign = result.getExperimentalDesign();
    if (experimentalDesign != null) {
        Hibernate.initialize(experimentalDesign);
        Hibernate.initialize(experimentalDesign.getExperimentalFactors());
        experimentalDesign.getTypes().size();
        for (ExperimentalFactor factor : experimentalDesign.getExperimentalFactors()) {
            Hibernate.initialize(factor.getAnnotations());
            for (FactorValue f : factor.getFactorValues()) {
                Hibernate.initialize(f.getCharacteristics());
                if (f.getMeasurement() != null) {
                    Hibernate.initialize(f.getMeasurement());
                    if (f.getMeasurement().getUnit() != null) {
                        Hibernate.initialize(f.getMeasurement().getUnit());
                    }
                }
            }
        }
    }
    this.thawReferences(result);
    this.thawMeanVariance(result);
    if (vectorsAlso) {
        /*
             * Optional because this could be slow.
             */
        Hibernate.initialize(result.getRawExpressionDataVectors());
        Hibernate.initialize(result.getProcessedExpressionDataVectors());
    }
    return result;
}

Example 90 with BioMaterial

use of ubic.gemma.model.expression.biomaterial.BioMaterial in project Gemma by PavlidisLab.

the class ExpressionExperimentDaoImpl method remove.

@Override
public void remove(final ExpressionExperiment ee) {
    if (ee == null)
        throw new IllegalArgumentException();
    Session session = this.getSessionFactory().getCurrentSession();
    try {
        // Note that links and analyses are deleted separately - see the ExpressionExperimentService.
        // At this point, the ee is probably still in the session, as the service already has gotten it
        // in this transaction.
        session.flush();
        session.clear();
        session.buildLockRequest(LockOptions.NONE).lock(ee);
        Hibernate.initialize(ee.getAuditTrail());
        Set<BioAssayDimension> dims = new HashSet<>();
        Set<QuantitationType> qts = new HashSet<>();
        Collection<RawExpressionDataVector> designElementDataVectors = ee.getRawExpressionDataVectors();
        Hibernate.initialize(designElementDataVectors);
        ee.setRawExpressionDataVectors(null);
        /*
             * We don't remove the investigators, just breaking the association.
             */
        ee.getInvestigators().clear();
        int count = 0;
        if (designElementDataVectors != null) {
            count = this.removeDataVectors(session, dims, qts, designElementDataVectors, count);
        }
        Collection<ProcessedExpressionDataVector> processedVectors = ee.getProcessedExpressionDataVectors();
        Hibernate.initialize(processedVectors);
        if (processedVectors != null && processedVectors.size() > 0) {
            ee.setProcessedExpressionDataVectors(null);
            this.removeProcessedVectors(session, dims, qts, count, processedVectors);
        }
        session.flush();
        session.clear();
        session.update(ee);
        AbstractDao.log.info("Removing BioAssay Dimensions ...");
        for (BioAssayDimension dim : dims) {
            dim.getBioAssays().clear();
            session.update(dim);
            session.delete(dim);
        }
        dims.clear();
        session.flush();
        AbstractDao.log.info("Removing Bioassays and biomaterials ...");
        // keep to put back in the object.
        Map<BioAssay, BioMaterial> copyOfRelations = new HashMap<>();
        Collection<BioMaterial> bioMaterialsToDelete = new HashSet<>();
        Collection<BioAssay> bioAssays = ee.getBioAssays();
        this.removeBioAssays(session, copyOfRelations, bioMaterialsToDelete, bioAssays);
        AbstractDao.log.info("Last bits ...");
        // We remove them here in case they are associated to more than one bioassay-- no cascade is possible.
        for (BioMaterial bm : bioMaterialsToDelete) {
            session.delete(bm);
        }
        for (QuantitationType qt : qts) {
            session.delete(qt);
        }
        session.flush();
        session.delete(ee);
        /*
             * Put transient instances back. This is possibly useful for clearing ACLS.
             */
        ee.setProcessedExpressionDataVectors(processedVectors);
        ee.setRawExpressionDataVectors(designElementDataVectors);
        for (BioAssay ba : ee.getBioAssays()) {
            ba.setSampleUsed(copyOfRelations.get(ba));
        }
        AbstractDao.log.info("Deleted " + ee);
    } catch (Exception e) {
        AbstractDao.log.error(e);
    } finally {
        AbstractDao.log.info("Finalising remove method.");
    }
}