Examples with CoexpressionValueObjectExt ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt used on opensource projects

Example 1 with CoexpressionValueObjectExt

use of ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt in project Gemma by PavlidisLab.

the class CoexpressionSearchController method doSearch.

/**
 * Important entry point - called by the CoexpressionSearchTask
 *
 * @param searchOptions search options
 * @return coexp. meta VO
 */
public CoexpressionMetaValueObject doSearch(CoexpressionSearchCommand searchOptions) {
    Collection<ExpressionExperiment> myEE = null;
    CoexpressionMetaValueObject result = new CoexpressionMetaValueObject();
    if (searchOptions.getGeneIds() == null || searchOptions.getGeneIds().isEmpty()) {
        if (searchOptions.getGeneSetId() != null) {
            searchOptions.setGeneIds(geneSetService.getGeneIdsInGroup(new GeneSetValueObject(searchOptions.getGeneSetId())));
        }
        if (searchOptions.getGeneIds().isEmpty()) {
            result.setErrorState("No genes were selected");
            return result;
        }
    }
    if (searchOptions.getGeneIds().size() > CoexpressionSearchController.MAX_GENES_FOR_QUERY_GENES_ONLY_QUERY) {
        result.setErrorState("Too many genes selected, please limit searches to " + CoexpressionSearchController.MAX_GENES_FOR_QUERY_GENES_ONLY_QUERY + " genes");
        return result;
    }
    if (searchOptions.getGeneIds().size() == 0) {
        result.setErrorState("Invalid gene id(s) - no genes found");
        return result;
    }
    // Add the user's datasets to the selected datasets
    if (searchOptions.isUseMyDatasets()) {
        myEE = expressionExperimentService.loadAll();
    }
    Collection<Long> eeIds = this.chooseExperimentsToQuery(searchOptions, result);
    if (StringUtils.isNotBlank(result.getErrorState()))
        return result;
    if (myEE != null && !myEE.isEmpty()) {
        eeIds.addAll(EntityUtils.getIds(myEE));
    } else {
        CoexpressionSearchController.log.info("No user data to add");
    }
    if (eeIds.isEmpty()) {
    // search all available experiments.
    } else {
        searchOptions.setEeIds(eeIds);
    }
    CoexpressionSearchController.log.info("Starting coexpression search: " + searchOptions);
    result = geneCoexpressionService.coexpressionSearch(searchOptions.getEeIds(), searchOptions.getGeneIds(), searchOptions.getStringency(), CoexpressionSearchController.MAX_RESULTS_PER_GENE, searchOptions.getQueryGenesOnly());
    // make sure to create an empty list instead of null for front-end
    if (result.getResults() == null) {
        List<CoexpressionValueObjectExt> res = new ArrayList<>();
        result.setResults(res);
    }
    if (result.getResults().isEmpty()) {
        result.setErrorState(CoexpressionSearchController.NOTHING_FOUND_MESSAGE);
        CoexpressionSearchController.log.info("No search results for query: " + searchOptions);
    }
    return result;
}

Example 2 with CoexpressionValueObjectExt

use of ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt in project Gemma by PavlidisLab.

the class GeneCoexpressionEndpoint 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) {
    try {
        StopWatch watch = new StopWatch();
        watch.start();
        this.setLocalName(GeneCoexpressionEndpoint.LOCAL_NAME);
        Collection<String> geneInput = this.getArrayValues(requestElement, "gene_ids");
        Collection<Long> geneIDLong = new HashSet<>();
        for (String id : geneInput) geneIDLong.add(Long.parseLong(id));
        Collection<String> taxonInput = this.getSingleNodeValue(requestElement, "taxon_id");
        String taxonId = "";
        for (String id : taxonInput) {
            taxonId = id;
        }
        // Collection<String> analysisInput = getSingleNodeValue( requestElement, "expression_experiment_set_id" );
        // String analysisId = "";
        // for ( String id : analysisInput ) {
        // analysisId = id;
        // }
        Collection<String> stringencyInput = this.getSingleNodeValue(requestElement, "stringency");
        String string = "";
        for (String id : stringencyInput) {
            string = id;
        }
        Collection<String> queryGenesOnlyInput = this.getSingleNodeValue(requestElement, "queryGenesOnly");
        String query = "";
        for (String id : queryGenesOnlyInput) {
            query = id;
        }
        boolean queryGenesOnly = false;
        if (query.endsWith("1"))
            queryGenesOnly = true;
        GeneCoexpressionEndpoint.log.debug("XML input read: " + geneInput.size() + " gene ids,  & taxon id, " + taxonId + " & stringency, " + string + " & queryGenesOnly=" + query);
        Taxon taxon = taxonService.load(Long.parseLong(taxonId));
        if (taxon == null) {
            String msg = "No taxon with id, " + taxonId + ", can be found.";
            return this.buildBadResponse(document, msg);
        }
        Collection<Gene> rawGeneCol = geneService.loadThawed(geneIDLong);
        if (rawGeneCol.isEmpty()) {
            String msg = "None of the gene id's can be found.";
            return this.buildBadResponse(document, msg);
        }
        Collection<Gene> geneCol = this.retainGenesInCorrectTaxon(rawGeneCol, taxon);
        if (geneCol == null || geneCol.isEmpty()) {
            String msg = "Input genes do not match input taxon.";
            return this.buildBadResponse(document, msg);
        }
        int stringency = Integer.parseInt(string);
        // get Gene2GeneCoexpression objects canned analysis
        Collection<CoexpressionValueObjectExt> coexpressedGenes = geneCoexpressionSearchService.coexpressionSearchQuick(null, EntityUtils.getIds(geneCol), stringency, GeneCoexpressionEndpoint.MAX_RESULTS, queryGenesOnly).getResults();
        if (coexpressedGenes.isEmpty()) {
            String msg = "No coexpressed genes found.";
            return this.buildBadResponse(document, msg);
        }
        final String QUERY_GENE_NAME = "query_gene";
        final String QUERY_GENE_ID = "query_id";
        final String FOUND_GENE_NAME = "found_gene";
        final String FOUND_GENE_ID = "found_id";
        final String SUPPORT_NAME = "support";
        final String SIGN_NAME = "sign";
        Element responseWrapper = document.createElementNS(AbstractGemmaEndpoint.NAMESPACE_URI, GeneCoexpressionEndpoint.LOCAL_NAME);
        Element responseElement = document.createElementNS(AbstractGemmaEndpoint.NAMESPACE_URI, GeneCoexpressionEndpoint.LOCAL_NAME + AbstractGemmaEndpoint.RESPONSE);
        responseWrapper.appendChild(responseElement);
        for (CoexpressionValueObjectExt cvo : coexpressedGenes) {
            // log.info( cvo );
            Element e1 = document.createElement(QUERY_GENE_NAME);
            e1.appendChild(document.createTextNode(cvo.getQueryGene().getOfficialSymbol()));
            responseElement.appendChild(e1);
            Element e2 = document.createElement(QUERY_GENE_ID);
            e2.appendChild(document.createTextNode(cvo.getQueryGene().getId().toString()));
            responseElement.appendChild(e2);
            Element e3 = document.createElement(FOUND_GENE_NAME);
            e3.appendChild(document.createTextNode(cvo.getFoundGene().getOfficialSymbol()));
            responseElement.appendChild(e3);
            Element e4 = document.createElement(FOUND_GENE_ID);
            e4.appendChild(document.createTextNode(cvo.getFoundGene().getId().toString()));
            responseElement.appendChild(e4);
            Integer support = 0;
            String sign = "";
            if (cvo.getPosSupp() > 0) {
                support = cvo.getPosSupp();
                sign = "+";
            } else if (cvo.getNegSupp() > 0) {
                support = cvo.getNegSupp();
                sign = "-";
            }
            // If it happens that a result has both neg and pos links, then the pos link and sign will be used
            // OLDTODO: Handle cases where a result can have both neg and pos links
            Element e5 = document.createElement(SUPPORT_NAME);
            e5.appendChild(document.createTextNode(support.toString()));
            responseElement.appendChild(e5);
            Element e6 = document.createElement(SIGN_NAME);
            e6.appendChild(document.createTextNode(sign));
            responseElement.appendChild(e6);
        // Element e7 = document.createElement( EEID_NAME );
        // e7.appendChild( document.createTextNode( encode( cvo.getSupportingExperiments().toArray() ) ) );
        // responseElement.appendChild( e7 );
        }
        watch.stop();
        Long time = watch.getTime();
        if (time > 1000) {
            GeneCoexpressionEndpoint.log.info("XML response for " + coexpressedGenes.size() + " results built in " + time + "ms.");
        }
        return responseWrapper;
    } catch (Exception e) {
        return this.buildBadResponse(document, e.getMessage());
    }
}

Example 3 with CoexpressionValueObjectExt

use of ubic.gemma.core.analysis.expression.coexpression.CoexpressionValueObjectExt in project Gemma by PavlidisLab.

the class GeneCoexpressionSearchEndpoint 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) {
    try {
        StopWatch watch = new StopWatch();
        watch.start();
        setLocalName(LOCAL_NAME);
        String queryGeneId = getNodeValue(requestElement, "query_gene_id");
        String pairQueryGeneId = getOptionalNodeValue(requestElement, "pair_query_gene_id");
        String stringency = getNodeValue(requestElement, "stringency");
        Collection<Gene> queryGenes = new LinkedList<>();
        Gene queryGene = geneService.findByNCBIId(Integer.parseInt(queryGeneId));
        if (queryGene == null) {
            String msg = "Query gene with id [" + queryGeneId + "] cannot be found.";
            return buildBadResponse(document, msg);
        }
        queryGenes.add(queryGene);
        if (pairQueryGeneId != null) {
            Gene queryGene2 = geneService.findByNCBIId(Integer.parseInt(pairQueryGeneId));
            if (queryGene2 == null) {
                String msg = "Query gene with id [" + pairQueryGeneId + "] cannot be found.";
                return buildBadResponse(document, msg);
            }
            queryGenes.add(queryGene2);
        }
        Collection<ExpressionExperimentSet> eeSets = expressionExperimentSetService.findByName("All mouse");
        // .load(5662l); // uses 'All mouse' by default.
        ExpressionExperimentSet eeSet = eeSets.iterator().next();
        Collection<BioAssaySet> experiments = eeSet.getExperiments();
        Collection<Long> inputEeIds = new ArrayList<>();
        for (BioAssaySet e : experiments) {
            inputEeIds.add(e.getId());
        }
        CoexpressionMetaValueObject metaVO;
        if (pairQueryGeneId == null) {
            metaVO = geneCoexpressionSearchService.coexpressionSearch(inputEeIds, EntityUtils.getIds(queryGenes), Integer.valueOf(stringency), MAX_RESULTS, false);
        } else {
            metaVO = geneCoexpressionSearchService.coexpressionSearch(inputEeIds, EntityUtils.getIds(queryGenes), Integer.valueOf(stringency), MAX_RESULTS, true);
        }
        Collection<CoexpressionValueObjectExt> coexpressedGenes = metaVO.getResults();
        if (coexpressedGenes.isEmpty()) {
            String msg = "No coexpressed genes found.";
            return buildBadResponse(document, msg);
        }
        Element responseWrapper = document.createElementNS(NAMESPACE_URI, LOCAL_NAME);
        Element responseElement = document.createElementNS(NAMESPACE_URI, LOCAL_NAME + RESPONSE);
        responseWrapper.appendChild(responseElement);
        for (CoexpressionValueObjectExt cvo : coexpressedGenes) {
            Element item = document.createElement("CoexpressionSearchResult");
            Element foundGeneElement = document.createElement("found_gene_id");
            foundGeneElement.appendChild(document.createTextNode(cvo.getFoundGene().getNcbiId() == null ? "" : cvo.getFoundGene().getNcbiId().toString()));
            item.appendChild(foundGeneElement);
            Element numExperimentsElement = document.createElement("num_experiments_tested");
            numExperimentsElement.appendChild(document.createTextNode(cvo.getNumTestedIn().toString()));
            item.appendChild(numExperimentsElement);
            Element numCoexpressedElement = document.createElement("num_experiments_coexpressed");
            numCoexpressedElement.appendChild(document.createTextNode(String.valueOf(cvo.getSupportingExperiments().size())));
            item.appendChild(numCoexpressedElement);
            Element gemmaURL = document.createElement("gemma_details_url");
            gemmaURL.appendChild(document.createTextNode(Settings.getBaseUrl() + "searchCoexpression.html?g=" + queryGene.getId() + "," + cvo.getFoundGene().getId() + "&s=" + stringency + "&t=2&q&a=5662&an=All%20mouse"));
            item.appendChild(gemmaURL);
            responseElement.appendChild(item);
        }
        watch.stop();
        Long time = watch.getTime();
        if (time > 1000) {
            log.info("XML response for " + coexpressedGenes.size() + " results built in " + time + "ms.");
        }
        return responseWrapper;
    } catch (Exception e) {
        return buildBadResponse(document, e.getMessage());
    }
}