Examples with Characteristic ubic.gemma.model.common.description.Characteristic used on opensource projects

Example 31 with Characteristic

use of ubic.gemma.model.common.description.Characteristic in project Gemma by PavlidisLab.

the class BatchInfoPopulationHelperServiceImpl method createBatchFactor.

@Override
@Transactional
public ExperimentalFactor createBatchFactor(ExpressionExperiment ee, Map<BioMaterial, Date> dates) {
    /*
         * Go through the dates and convert to factor values.
         */
    Collection<Date> allDates = new HashSet<>(dates.values());
    Map<String, Collection<Date>> datesToBatch = this.convertDatesToBatches(allDates);
    Map<Date, FactorValue> d2fv = new HashMap<>();
    ExperimentalFactor ef = null;
    if (datesToBatch == null || datesToBatch.size() < 2) {
        if (datesToBatch != null) {
            BatchInfoPopulationHelperServiceImpl.log.info("There is only one 'batch'");
        }
    // we still put the processing dates in, below.
    } else {
        ef = this.makeFactorForBatch(ee);
        for (String batchId : datesToBatch.keySet()) {
            FactorValue fv = FactorValue.Factory.newInstance();
            fv.setIsBaseline(false);
            /* we could set true for the first batch, but nobody cares. */
            fv.setValue(batchId);
            Collection<Characteristic> chars = new HashSet<>();
            VocabCharacteristic c = VocabCharacteristic.Factory.newInstance();
            c.setCategory(ExperimentalDesignUtils.BATCH_FACTOR_CATEGORY_NAME);
            c.setValue(batchId);
            c.setCategoryUri(ExperimentalDesignUtils.BATCH_FACTOR_CATEGORY_URI);
            c.setEvidenceCode(GOEvidenceCode.IIA);
            chars.add(c);
            fv.setCharacteristics(chars);
            fv.setExperimentalFactor(ef);
            /*
                 * persist
                 */
            fv.setCharacteristics(chars);
            experimentService.addFactorValue(ee, fv);
            for (Date d : datesToBatch.get(batchId)) {
                d2fv.put(d, fv);
            }
        }
    }
    bioMaterialService.associateBatchFactor(dates, d2fv);
    return ef;
}

Example 32 with Characteristic

use of ubic.gemma.model.common.description.Characteristic in project Gemma by PavlidisLab.

the class BatchInfoPopulationServiceImpl method isBatchFactor.

/**
 * @param ef ef
 * @return true if the factor seems to be a 'batch' factor.
 */
public static boolean isBatchFactor(ExperimentalFactor ef) {
    Characteristic c = ef.getCategory();
    boolean isBatchFactor = false;
    boolean looksLikeBatch = ef.getName().equals(ExperimentalDesignUtils.BATCH_FACTOR_NAME);
    if (c != null && c instanceof VocabCharacteristic) {
        VocabCharacteristic v = (VocabCharacteristic) c;
        if (v.getCategory() != null && v.getCategory().equals(ExperimentalDesignUtils.BATCH_FACTOR_CATEGORY_NAME)) {
            isBatchFactor = true;
        }
    } else if (looksLikeBatch) {
        isBatchFactor = true;
    }
    return isBatchFactor;
}

Example 33 with Characteristic

use of ubic.gemma.model.common.description.Characteristic in project Gemma by PavlidisLab.

the class DatabaseViewGeneratorImpl method generateDatasetTissueView.

private void generateDatasetTissueView(Integer limit, Collection<ExpressionExperiment> experiments) throws IOException {
    DatabaseViewGeneratorImpl.log.info("Generating dataset tissue view");
    /*
         * Get handle to output file
         */
    File file = this.getViewFile(DatabaseViewGeneratorImpl.DATASET_TISSUE_VIEW_BASENAME);
    DatabaseViewGeneratorImpl.log.info("Writing to " + file);
    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)))) {
        /*
             * For all of their annotations... if it's a tissue, print out a line
             */
        writer.write("GemmaDsId\tTerm\tTermURI\n");
        int i = 0;
        for (ExpressionExperiment ee : experiments) {
            ee = expressionExperimentService.thawLite(ee);
            DatabaseViewGeneratorImpl.log.info("Processing: " + ee.getShortName());
            Long gemmaId = ee.getId();
            for (Characteristic c : ee.getCharacteristics()) {
                if (StringUtils.isBlank(c.getValue())) {
                    continue;
                }
                if (c.getCategory().equals("OrganismPart")) {
                    // or tissue? check URI
                    String uri = "";
                    if (c instanceof VocabCharacteristic) {
                        VocabCharacteristic vocabCharacteristic = (VocabCharacteristic) c;
                        if (StringUtils.isNotBlank(vocabCharacteristic.getValueUri()))
                            uri = vocabCharacteristic.getValueUri();
                    }
                    writer.write(String.format("%d\t%s\t%s\n", gemmaId, c.getValue(), uri));
                }
            }
            if (limit != null && (limit > 0 && ++i > limit))
                break;
        }
    }
}

Example 34 with Characteristic

use of ubic.gemma.model.common.description.Characteristic in project Gemma by PavlidisLab.

the class SearchServiceTest method setup.

public void setup() throws Exception {
    try (InputStream is = this.getClass().getResourceAsStream("/data/loader/ontology/fma.test.owl")) {
        assert is != null;
        ontologyService.getFmaOntologyService().loadTermsInNameSpace(is);
    }
    ee = this.getTestPersistentBasicExpressionExperiment();
    VocabCharacteristic eeCharSpinalCord = VocabCharacteristic.Factory.newInstance();
    eeCharSpinalCord.setCategory(SearchServiceTest.SPINAL_CORD);
    eeCharSpinalCord.setCategoryUri(SearchServiceTest.SPINAL_CORD);
    eeCharSpinalCord.setValue(SearchServiceTest.SPINAL_CORD);
    eeCharSpinalCord.setValueUri(SearchServiceTest.SPINAL_CORD);
    characteristicService.create(eeCharSpinalCord);
    VocabCharacteristic eeCharGeneURI = VocabCharacteristic.Factory.newInstance();
    eeCharGeneURI.setCategory(SearchServiceTest.GENE_URI);
    eeCharGeneURI.setCategoryUri(SearchServiceTest.GENE_URI);
    eeCharGeneURI.setValue(SearchServiceTest.GENE_URI);
    eeCharGeneURI.setValueUri(SearchServiceTest.GENE_URI);
    characteristicService.create(eeCharGeneURI);
    VocabCharacteristic eeCharCortexURI = VocabCharacteristic.Factory.newInstance();
    eeCharCortexURI.setCategory(SearchServiceTest.BRAIN_CAVITY);
    eeCharCortexURI.setCategoryUri(SearchServiceTest.BRAIN_CAVITY);
    eeCharCortexURI.setValue(SearchServiceTest.BRAIN_CAVITY);
    eeCharCortexURI.setValueUri(SearchServiceTest.BRAIN_CAVITY);
    characteristicService.create(eeCharCortexURI);
    Collection<Characteristic> chars = new HashSet<>();
    chars.add(eeCharSpinalCord);
    chars.add(eeCharGeneURI);
    chars.add(eeCharCortexURI);
    ee.setCharacteristics(chars);
    eeService.update(ee);
    gene = this.getTestPersistentGene();
    this.geneNcbiId = RandomStringUtils.randomNumeric(8);
    gene.setNcbiGeneId(new Integer(geneNcbiId));
    geneService.update(gene);
    thePastUserQuery = UserQuery.Factory.newInstance();
    Calendar calendar = Calendar.getInstance();
    // the past
    calendar.set(Calendar.YEAR, 1979);
    calendar.set(Calendar.MONTH, 1);
    calendar.set(Calendar.DAY_OF_MONTH, 1);
    thePastUserQuery.setLastUsed(calendar.getTime());
    SearchSettings settings = SearchSettings.Factory.newInstance();
    settings.noSearches();
    // should hit 'cavity of brain'.
    settings.setQuery("Brain");
    settings.setSearchExperiments(true);
    settings.setUseCharacteristics(true);
    settings.setUseIndices(false);
    settings.setUseDatabase(false);
    thePastUserQuery.setSearchSettings(settings);
    thePastUserQuery.setUrl("someUrl");
    // the future
    calendar.add(Calendar.YEAR, 2000);
    theFutureUserQuery = UserQuery.Factory.newInstance();
    theFutureUserQuery.setLastUsed(calendar.getTime());
    SearchSettings futureSettings = SearchSettings.Factory.newInstance();
    futureSettings.noSearches();
    // should hit 'cavity of brain'.
    futureSettings.setQuery("Brain");
    futureSettings.setSearchExperiments(true);
    futureSettings.setUseCharacteristics(true);
    theFutureUserQuery.setSearchSettings(futureSettings);
    theFutureUserQuery.setUrl("someUrl");
    // save to db to load later to test if the pipes are clean
    userQueryService.create(thePastUserQuery);
    userQueryService.create(theFutureUserQuery);
}

Example 35 with Characteristic

use of ubic.gemma.model.common.description.Characteristic in project Gemma by PavlidisLab.

the class CharacteristicUpdateTaskImpl method doRemove.

private TaskResult doRemove() {
    Collection<AnnotationValueObject> chars = taskCommand.getAnnotationValueObjects();
    log.info("Delete " + chars.size() + " characteristics...");
    Collection<Characteristic> asChars = convertToCharacteristic(chars);
    if (asChars.size() == 0) {
        log.info("No characteristic objects were received");
        return new TaskResult(taskCommand, false);
    }
    Map<Characteristic, Object> charToParent = characteristicService.getParents(asChars);
    for (Characteristic cFromClient : asChars) {
        Characteristic cFromDatabase = characteristicService.load(cFromClient.getId());
        Object parent = charToParent.get(cFromDatabase);
        removeFromParent(cFromDatabase, parent);
        characteristicService.remove(cFromDatabase);
        log.info("Characteristic deleted: " + cFromDatabase + " (associated with " + parent + ")");
    }
    return new TaskResult(taskCommand, true);
}