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

Example 1 with Treatment

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

the class SearchServiceImpl method characteristicExpressionExperimentSearch.

private Collection<SearchResult> characteristicExpressionExperimentSearch(final SearchSettings settings) {
    Collection<SearchResult> results = new HashSet<>();
    // this is a collection because of the API
    Collection<Class<?>> classToSearch = new ArrayList<>(1);
    // for characteristicService; could add
    // findByUri(Class<?>...)
    // order matters.
    Queue<Class<?>> orderedClassesToSearch = new LinkedList<>();
    orderedClassesToSearch.add(ExpressionExperiment.class);
    orderedClassesToSearch.add(FactorValue.class);
    orderedClassesToSearch.add(BioMaterial.class);
    orderedClassesToSearch.add(Treatment.class);
    Collection<SearchResult> characterSearchResults = new HashSet<>();
    while (characterSearchResults.size() < SearchServiceImpl.SUFFICIENT_EXPERIMENT_RESULTS_FROM_CHARACTERISTICS && !orderedClassesToSearch.isEmpty()) {
        classToSearch.clear();
        classToSearch.add(orderedClassesToSearch.poll());
        // We handle the OR clauses here.
        String[] subclauses = settings.getQuery().split(" OR ");
        for (String subclause : subclauses) {
            /*
                 * Note that the AND is applied only within one entity type. The fix would be to apply AND at this
                 * level.
                 */
            Collection<SearchResult> classResults = this.characteristicSearchWithChildren(classToSearch, subclause);
            if (!classResults.isEmpty()) {
                String msg = "Found " + classResults.size() + " " + classToSearch.iterator().next().getSimpleName() + " results from characteristic search.";
                if (characterSearchResults.size() >= SearchServiceImpl.SUFFICIENT_EXPERIMENT_RESULTS_FROM_CHARACTERISTICS) {
                    msg += " Total found > " + SearchServiceImpl.SUFFICIENT_EXPERIMENT_RESULTS_FROM_CHARACTERISTICS + ", will not search for more entities.";
                }
                SearchServiceImpl.log.info(msg);
            }
            characterSearchResults.addAll(classResults);
        }
    }
    StopWatch watch = new StopWatch();
    watch.start();
    // filter and get parents...
    int numEEs = 0;
    Collection<BioMaterial> biomaterials = new HashSet<>();
    Collection<FactorValue> factorValues = new HashSet<>();
    Collection<Treatment> treatments = new HashSet<>();
    for (SearchResult sr : characterSearchResults) {
        Class<?> resultClass = sr.getResultClass();
        // highlightedText.put( sr.getResultObject(), sr.getHighlightedText() );
        if (ExpressionExperiment.class.isAssignableFrom(resultClass)) {
            sr.setHighlightedText(sr.getHighlightedText() + " (characteristic)");
            results.add(sr);
            numEEs++;
        } else if (BioMaterial.class.isAssignableFrom(resultClass)) {
            biomaterials.add((BioMaterial) sr.getResultObject());
        } else if (FactorValue.class.isAssignableFrom(resultClass)) {
            factorValues.add((FactorValue) sr.getResultObject());
        } else if (Treatment.class.isAssignableFrom(resultClass)) {
            treatments.add((Treatment) sr.getResultObject());
        }
    }
    /*
         * Much faster to batch it...but we loose track of which search result came from which, so we put generic
         * highlighted text.
         */
    if (biomaterials.size() > 0) {
        Collection<ExpressionExperiment> ees = expressionExperimentService.findByBioMaterials(biomaterials);
        for (ExpressionExperiment ee : ees) {
            results.add(new SearchResult(ee, SearchServiceImpl.INDIRECT_DB_HIT_PENALTY, "BioMaterial characteristic"));
        }
    }
    this.addEEeByFactorvalues(results, factorValues);
    if (treatments.size() > 0) {
        SearchServiceImpl.log.info("Not processing treatments, but hits were found");
    }
    if (SearchServiceImpl.log.isDebugEnabled()) {
        SearchServiceImpl.log.debug("ExpressionExperiment search: " + settings + " -> " + results.size() + " characteristic hits");
    }
    if (watch.getTime() > 1000) {
        SearchServiceImpl.log.info("Retrieving " + results.size() + " experiments from " + characterSearchResults.size() + " retrieved characteristics took " + watch.getTime() + " ms");
        SearchServiceImpl.log.info("Breakdown: " + numEEs + " via direct association with EE; " + biomaterials.size() + " via association with Biomaterial; " + factorValues.size() + " via experimental design");
    }
    return results;
}

Example 2 with Treatment

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

the class AuditAdviceTest method checkEEAuditTrails.

private void checkEEAuditTrails(ExpressionExperiment ee, Collection<Long> trailIds, Collection<Long> eventIds) {
    this.checkAuditTrail(ee, trailIds, eventIds);
    for (BioAssay ba : ee.getBioAssays()) {
        this.checkAuditTrail(ba, trailIds, eventIds);
        BioMaterial bm = ba.getSampleUsed();
        this.checkAuditTrail(bm, trailIds, eventIds);
        for (Characteristic c : bm.getCharacteristics()) {
            this.checkAuditTrail(c, trailIds, eventIds);
        }
        for (Treatment t : bm.getTreatments()) {
            this.checkAuditTrail(t, trailIds, eventIds);
            this.checkAuditTrail(t.getAction(), trailIds, eventIds);
        // for ( CompoundMeasurement cm : t.getCompoundMeasurements() ) {
        // checkAuditTrail( cm.getCompound().getCompoundIndices(), trailIds, eventIds );
        // }
        }
    }
    Collection<ExperimentalFactor> experimentalFactors = ee.getExperimentalDesign().getExperimentalFactors();
    assertTrue(experimentalFactors.size() > 0);
    for (ExperimentalFactor ef : experimentalFactors) {
        this.checkAuditTrail(ef, trailIds, eventIds);
        for (FactorValue fv : ef.getFactorValues()) {
            for (Characteristic c : fv.getCharacteristics()) {
                this.checkAuditTrail(c, trailIds, eventIds);
            }
        }
    }
}

Example 3 with Treatment

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

the class GeoConverterImpl method convertChannel.

/**
 * GEO does not keep track of 'biomaterials' that make up different channels. Therefore the two channels effectively
 * make up a single biomaterial, as far as we're concerned. We're losing information here.
 *
 * @param sample      sample
 * @param channel     channel
 * @param bioMaterial BA
 */
private void convertChannel(GeoSample sample, GeoChannel channel, BioMaterial bioMaterial) {
    if (bioMaterial == null)
        return;
    GeoConverterImpl.log.debug("Sample: " + sample.getGeoAccession() + " - Converting channel " + channel.getSourceName());
    bioMaterial.setDescription((bioMaterial.getDescription() == null ? "" : bioMaterial.getDescription() + ";") + "Channel " + channel.getChannelNumber());
    if (!StringUtils.isBlank(channel.getGrowthProtocol())) {
        Treatment treatment = Treatment.Factory.newInstance();
        treatment.setName(sample.getGeoAccession() + " channel " + channel.getChannelNumber() + " treatment");
        treatment.setDescription(channel.getGrowthProtocol());
        bioMaterial.getTreatments().add(treatment);
    }
    if (!StringUtils.isBlank(channel.getTreatmentProtocol())) {
        Treatment treatment = Treatment.Factory.newInstance();
        treatment.setName(sample.getGeoAccession() + " channel " + channel.getChannelNumber() + " growth");
        treatment.setDescription(channel.getTreatmentProtocol());
        bioMaterial.getTreatments().add(treatment);
    }
    if (!StringUtils.isBlank(channel.getExtractProtocol())) {
        Treatment treatment = Treatment.Factory.newInstance();
        treatment.setName(sample.getGeoAccession() + " channel " + channel.getChannelNumber() + " extraction");
        treatment.setDescription(channel.getExtractProtocol());
        bioMaterial.getTreatments().add(treatment);
    }
    if (!StringUtils.isBlank(channel.getLabelProtocol())) {
        Treatment treatment = Treatment.Factory.newInstance();
        treatment.setName(sample.getGeoAccession() + " channel " + channel.getChannelNumber() + " labeling");
        treatment.setDescription(channel.getLabelProtocol());
        bioMaterial.getTreatments().add(treatment);
    }
    for (String characteristic : channel.getCharacteristics()) {
        characteristic = this.trimString(characteristic);
        /*
             * Sometimes values are like Age:8 weeks, so we can try to convert them.
             */
        String[] fields = characteristic.split(":");
        String defaultDescription = "GEO Sample characteristic";
        if (fields.length == 2) {
            String category = fields[0].trim();
            String value = fields[1].trim();
            try {
                Characteristic gemmaChar = Characteristic.Factory.newInstance();
                this.convertVariableType(gemmaChar, GeoVariable.convertStringToType(category));
                if (gemmaChar.getCategory() == null) {
                    continue;
                }
                gemmaChar.setDescription(defaultDescription);
                gemmaChar.setValue(value);
                gemmaChar.setEvidenceCode(GOEvidenceCode.IIA);
                bioMaterial.getCharacteristics().add(gemmaChar);
            } catch (Exception e) {
                // conversion didn't work, fall back.
                this.doFallback(bioMaterial, characteristic, defaultDescription);
            }
        } else {
            // no colon, just use raw (same as fallback above)
            this.doFallback(bioMaterial, characteristic, defaultDescription);
        }
    }
    if (StringUtils.isNotBlank(channel.getSourceName())) {
        Characteristic sourceChar = Characteristic.Factory.newInstance();
        sourceChar.setDescription("GEO Sample source");
        String characteristic = this.trimString(channel.getSourceName());
        sourceChar.setCategory("BioSource");
        sourceChar.setCategoryUri("http://www.ebi.ac.uk/efo/EFO_0000635");
        sourceChar.setValue(characteristic);
        sourceChar.setEvidenceCode(GOEvidenceCode.IIA);
        bioMaterial.getCharacteristics().add(sourceChar);
    }
    if (StringUtils.isNotBlank(channel.getOrganism())) {
        // if we have a case where the two channels have different taxon throw an exception.
        String currentChannelTaxon = channel.getOrganism();
        if (bioMaterial.getSourceTaxon() != null) {
            String previousChannelTaxon = bioMaterial.getSourceTaxon().getScientificName();
            if (previousChannelTaxon != null && !(previousChannelTaxon.equals(currentChannelTaxon))) {
                throw new IllegalArgumentException("Channel 1 taxon is " + bioMaterial.getSourceTaxon().getScientificName() + " Channel 2 taxon is " + currentChannelTaxon + " Check that is expected for sample " + sample.getGeoAccession());
            }
        } else {
            // get it from the channel.
            Taxon taxon = Taxon.Factory.newInstance();
            taxon.setIsSpecies(true);
            taxon.setScientificName(channel.getOrganism());
            // plausible default, doesn't matter.
            taxon.setIsGenesUsable(true);
            bioMaterial.setSourceTaxon(taxon);
        }
    }
    if (channel.getMolecule() != null) {
        // this we can convert automatically pretty easily.
        Characteristic c = channel.getMoleculeAsCharacteristic();
        bioMaterial.getCharacteristics().add(c);
    }
    if (StringUtils.isNotBlank(channel.getLabel())) {
        String characteristic = this.trimString(channel.getLabel());
        // This is typically something like "biotin-labeled nucleotides", which we can convert later.
        Characteristic labelChar = Characteristic.Factory.newInstance();
        labelChar.setDescription("GEO Sample label");
        labelChar.setCategory("LabelCompound");
        labelChar.setCategoryUri("http://www.ebi.ac.uk/efo/EFO_0000562");
        labelChar.setValue(characteristic);
        labelChar.setEvidenceCode(GOEvidenceCode.IIA);
        bioMaterial.getCharacteristics().add(labelChar);
    }
}

Example 4 with Treatment

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

the class ExpressionPersister method persistBioMaterial.

private BioMaterial persistBioMaterial(BioMaterial entity) {
    if (entity == null)
        return null;
    AbstractPersister.log.debug("Persisting " + entity);
    if (!this.isTransient(entity))
        return entity;
    assert entity.getSourceTaxon() != null;
    AbstractPersister.log.debug("Persisting " + entity);
    this.fillInDatabaseEntry(entity.getExternalAccession());
    AbstractPersister.log.debug("db entry done");
    entity.setSourceTaxon(this.persistTaxon(entity.getSourceTaxon()));
    AbstractPersister.log.debug("taxon done");
    for (Treatment treatment : entity.getTreatments()) {
        Characteristic action = treatment.getAction();
        AbstractPersister.log.debug(treatment + " action: " + action);
        AbstractPersister.log.debug("treatment done");
    }
    AbstractPersister.log.debug("start save");
    BioMaterial bm = bioMaterialDao.findOrCreate(entity);
    AbstractPersister.log.debug("save biomaterial done");
    return bm;
}