Examples with ExpressionExperimentSet ubic.gemma.model.analysis.expression.ExpressionExperimentSet used on opensource projects

Example 1 with ExpressionExperimentSet

use of ubic.gemma.model.analysis.expression.ExpressionExperimentSet in project Gemma by PavlidisLab.

the class DifferentialExpressionProbeResultEndpoint method invokeInternal.

/**
 * Reads the given <code>requestElement</code>, and sends a the response back.
 *
 * @param requestElement the contents of the SOAP message as DOM elements
 * @param document       a DOM document to be used for constructing <code>Node</code>s
 * @return the response element
 */
@Override
protected Element invokeInternal(Element requestElement, Document document) {
    StopWatch watch = new StopWatch();
    watch.start();
    setLocalName(LOCAL_NAME);
    // taxon input
    Collection<String> taxonInput = getSingleNodeValue(requestElement, "taxon_id");
    String taxonId = "";
    for (String id : taxonInput) {
        taxonId = id;
    }
    Taxon taxon = taxonService.load(Long.parseLong(taxonId));
    if (taxon == null) {
        String msg = "No taxon with id, " + taxonId + ", can be found.";
        return buildBadResponse(document, msg);
    }
    // gene ids input
    Collection<String> geneInput = getArrayValues(requestElement, "gene_ids");
    Collection<Long> geneIDLong = new HashSet<Long>();
    for (String id : geneInput) geneIDLong.add(Long.parseLong(id));
    Collection<Gene> rawGeneCol = geneService.loadThawed(geneIDLong);
    if (rawGeneCol.isEmpty()) {
        String msg = "None of the gene id's can be found.";
        return buildBadResponse(document, msg);
    }
    Collection<Gene> geneCol = retainGenesInCorrectTaxon(rawGeneCol, taxon);
    if (geneCol == null || geneCol.isEmpty()) {
        String msg = "Input genes do not match input taxon.";
        return buildBadResponse(document, msg);
    }
    // expression experiment set id input
    Collection<String> analysisInput = getSingleNodeValue(requestElement, "expression_experiment_set_id");
    String analysisId = "";
    for (String id : analysisInput) {
        analysisId = id;
    }
    ExpressionExperimentSet ees = expressionExperimentSetService.load(Long.parseLong(analysisId));
    if (ees == null) {
        String msg = "No matching expression experiment set can be found for id, " + analysisId;
        return buildBadResponse(document, msg);
    }
    if (!(ees.getTaxon().getId()).equals(taxon.getId())) {
        String msg = "Expression experiment set " + analysisId + " does not match input taxon " + taxon.getCommonName();
        return buildBadResponse(document, msg);
    }
    Collection<ExpressionExperiment> eeCol = getExperiments(ees);
    Collection<BioAssaySet> bioAssaySets = new HashSet<BioAssaySet>();
    bioAssaySets.addAll(eeCol);
    // threshold input
    Collection<String> thresholdInput = getSingleNodeValue(requestElement, "threshold");
    String threshold = "";
    for (String id : thresholdInput) {
        threshold = id;
    }
    log.info("XML input read: " + geneInput.size() + " gene ids,  & taxon id " + taxonId + ", & expression experiment set id " + analysisId + ", and threshold " + threshold);
    Element responseWrapper = document.createElementNS(NAMESPACE_URI, LOCAL_NAME);
    Element responseElement = document.createElementNS(NAMESPACE_URI, LOCAL_NAME + RESPONSE);
    responseWrapper.appendChild(responseElement);
    for (Gene gene : geneCol) {
        Map<ExpressionExperimentValueObject, List<DifferentialExpressionValueObject>> results = differentialExpressionResultService.find(gene, EntityUtils.getIds(bioAssaySets), Double.parseDouble(threshold), null);
        for (ExpressionExperimentValueObject ee : results.keySet()) {
            // main call to the DifferentialExpressionAnalysisService to retrieve
            // DifferentialExpressionAnalysisResultSet collection
            Collection<DifferentialExpressionValueObject> parCol = results.get(ee);
            // check that a DifferentialExpressionAnalysisResult is not null
            if (parCol == null || parCol.isEmpty()) {
                log.error("No probe analysis results can be found for gene: " + gene.getOfficialSymbol() + " & experiment: " + ee);
                buildXMLResponse(document, responseElement, gene.getId().toString(), ee.getId().toString(), null);
            } else
                buildXMLResponse(document, responseElement, gene.getId().toString(), ee.getId().toString(), parCol);
        }
    }
    watch.stop();
    Long time = watch.getTime();
    log.info("XML response for differential expression probe results built in " + time + "ms.");
    return responseWrapper;
}

Example 2 with ExpressionExperimentSet

use of ubic.gemma.model.analysis.expression.ExpressionExperimentSet in project Gemma by PavlidisLab.

the class ExpressionExperimentManipulatingCLI method experimentsFromEeSet.

private void experimentsFromEeSet(String optionValue) {
    if (StringUtils.isBlank(optionValue)) {
        throw new IllegalArgumentException("Please provide an eeset name");
    }
    ExpressionExperimentSetService expressionExperimentSetService = this.getBean(ExpressionExperimentSetService.class);
    Collection<ExpressionExperimentSet> sets = expressionExperimentSetService.findByName(optionValue);
    if (sets.size() > 1) {
        throw new IllegalArgumentException("More than on EE set has name '" + optionValue + "'");
    } else if (sets.size() == 0) {
        throw new IllegalArgumentException("No EE set has name '" + optionValue + "'");
    }
    ExpressionExperimentSet set = sets.iterator().next();
    this.expressionExperiments = new HashSet<>(set.getExperiments());
}

Example 3 with ExpressionExperimentSet

use of ubic.gemma.model.analysis.expression.ExpressionExperimentSet in project Gemma by PavlidisLab.

the class ExpressionExperimentServiceImpl method remove.

@Override
@Transactional
public void remove(Long id) {
    final ExpressionExperiment ee = this.load(id);
    if (!securityService.isEditable(ee)) {
        throw new SecurityException("Error performing 'ExpressionExperimentService.remove(ExpressionExperiment expressionExperiment)' --> " + " You do not have permission to edit this experiment.");
    }
    // Remove subsets
    Collection<ExpressionExperimentSubSet> subsets = this.getSubSets(ee);
    for (ExpressionExperimentSubSet subset : subsets) {
        expressionExperimentSubSetService.remove(subset);
    }
    // Remove differential expression analyses
    Collection<DifferentialExpressionAnalysis> diffAnalyses = this.differentialExpressionAnalysisDao.findByInvestigation(ee);
    for (DifferentialExpressionAnalysis de : diffAnalyses) {
        this.differentialExpressionAnalysisDao.remove(de);
    }
    // remove any sample coexpression matrices
    this.sampleCoexpressionAnalysisDao.removeForExperiment(ee);
    // Remove PCA
    Collection<PrincipalComponentAnalysis> pcas = this.principalComponentAnalysisService.findByExperiment(ee);
    for (PrincipalComponentAnalysis pca : pcas) {
        this.principalComponentAnalysisService.remove(pca);
    }
    /*
         * Delete any expression experiment sets that only have this one ee in it. If possible remove this experiment
         * from other sets, and update them. IMPORTANT, this section assumes that we already checked for gene2gene
         * analyses!
         */
    Collection<ExpressionExperimentSet> sets = this.expressionExperimentSetService.find(ee);
    for (ExpressionExperimentSet eeSet : sets) {
        if (eeSet.getExperiments().size() == 1 && eeSet.getExperiments().iterator().next().equals(ee)) {
            AbstractService.log.info("Removing from set " + eeSet);
            this.expressionExperimentSetService.remove(// remove the set because in only contains this experiment
            eeSet);
        } else {
            AbstractService.log.info("Removing " + ee + " from " + eeSet);
            eeSet.getExperiments().remove(ee);
            // update set to not reference this experiment.
            this.expressionExperimentSetService.update(eeSet);
        }
    }
    this.expressionExperimentDao.remove(ee);
}

Example 4 with ExpressionExperimentSet

use of ubic.gemma.model.analysis.expression.ExpressionExperimentSet in project Gemma by PavlidisLab.

the class ExpressionExperimentSetServiceImpl method findIds.

@Override
@Transactional(readOnly = true)
public Collection<Long> findIds(BioAssaySet bioAssaySet) {
    Collection<Long> ids = new ArrayList<>();
    Collection<ExpressionExperimentSet> eesets = this.expressionExperimentSetDao.find(bioAssaySet);
    for (ExpressionExperimentSet eeset : eesets) {
        ids.add(eeset.getId());
    }
    return ids;
}

Example 5 with ExpressionExperimentSet

use of ubic.gemma.model.analysis.expression.ExpressionExperimentSet in project Gemma by PavlidisLab.

the class AclAdviceTest method testExpressionExperimentAcls.

/*
     * Test of EE ACLs and also SecurityNotInherited on EE set.
     */
@Test
public void testExpressionExperimentAcls() {
    ExpressionExperiment ee = this.getTestPersistentCompleteExpressionExperiment(false);
    aclTestUtils.checkEEAcls(ee);
    /*
         * Make public, and then add a factor and factorvalue.
         */
    securityService.makePublic(ee);
    ExperimentalFactor ef = ExperimentalFactor.Factory.newInstance();
    VocabCharacteristic cat = VocabCharacteristic.Factory.newInstance();
    cat.setCategory("foo");
    cat.setCategoryUri("bar");
    ef.setName("TESTING ACLS");
    ef.setCategory(cat);
    ef.setType(FactorType.CATEGORICAL);
    ef = expressionExperimentService.addFactor(ee, ef);
    FactorValue fv = FactorValue.Factory.newInstance(ef);
    fv.setValue("ack");
    fv = FactorValue.Factory.newInstance(ef);
    fv.setValue("adddck");
    expressionExperimentService.addFactorValue(ee, fv);
    securityService.makePrivate(ee);
    aclTestUtils.checkEEAcls(ee);
    /*
         * Now associate with ee set, remove the set and then the ee, make sure things are done correctly!
         */
    ExpressionExperimentSet ees = ExpressionExperimentSet.Factory.newInstance();
    ees.getExperiments().add(ee);
    ees.setName(this.randomName());
    persisterHelper.persist(ees);
    // make sure the ACL for objects are there (throws an exception if not).
    Acl eeacl = aclService.readAclById(new AclObjectIdentity(ee));
    aclService.readAclById(new AclObjectIdentity(ees));
    assertNull(eeacl.getParentAcl());
    expressionExperimentSetService.remove(ees);
    // make sure ACL for ees is gone
    aclTestUtils.checkDeletedAcl(ees);
    // make sure the ACL for ee is still there
    aclTestUtils.checkHasAcl(ee);
    expressionExperimentService.remove(ee);
    aclTestUtils.checkDeleteEEAcls(ee);
}