Examples with EMPTY org.apache.commons.lang3.StringUtils.EMPTY used on opensource projects

Example 91 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project Gemma by PavlidisLab.

the class GeneSearchServiceImpl method getGOGroupGenes.

@Override
public Collection<Gene> getGOGroupGenes(String goQuery, Taxon taxon) {
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<Taxon> taxaForPhenotypeAssoc = new ArrayList<>();
    Collection<Gene> genes = new ArrayList<>();
    // if taxon isn't set, get go groups for each possible taxon
    if (taxon == null) {
        taxaForPhenotypeAssoc.addAll(taxonService.loadAllTaxaWithGenes());
    } else {
        taxaForPhenotypeAssoc.add(taxon);
    }
    for (Taxon taxonForPA : taxaForPhenotypeAssoc) {
        for (GeneSet geneSet : geneSetSearch.findByGoTermName(goQuery, taxonForPA, GeneSearchServiceImpl.MAX_GO_TERMS_TO_PROCESS, GeneSearchServiceImpl.MAX_GO_GROUP_SIZE)) {
            // don't bother adding empty groups
            if (geneSet.getMembers() != null && geneSet.getMembers().size() != 0) {
                for (GeneSetMember geneMember : geneSet.getMembers()) {
                    genes.add(geneMember.getGene());
                }
            }
        }
    }
    GeneSearchServiceImpl.log.info("GO search: " + timer.getTime() + "ms");
    return genes;
}

Example 92 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project Gemma by PavlidisLab.

the class ExperimentalDesignVisualizationServiceImpl method sortVectorDataByDesign.

@Override
public Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs) {
    if (dedVs == null) {
        return new HashMap<>(0);
    }
    Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> returnedLayouts = new HashMap<>(dedVs.size());
    StopWatch timer = new StopWatch();
    timer.start();
    /*
         * This is shared across experiments that might show up in the dedVs; this should be okay...saves computation.
         * This is the only slow part.
         */
    this.prepare(dedVs);
    /*
         * This loop is not a performance issue.
         */
    Map<DoubleVectorValueObject, List<BioAssayValueObject>> newOrderingsForBioAssayDimensions = new HashMap<>();
    for (DoubleVectorValueObject vec : dedVs) {
        if (vec.isReorganized()) {
            continue;
        }
        assert !vec.getBioAssays().isEmpty();
        LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> layout = null;
        if (cachedLayouts.containsKey(vec.getExpressionExperiment().getId())) {
            layout = cachedLayouts.get(vec.getExpressionExperiment().getId());
        } else if (vec.getExpressionExperiment().getClass().isInstance(ExpressionExperimentSubsetValueObject.class)) {
            // subset.
            layout = cachedLayouts.get(((ExpressionExperimentSubsetValueObject) vec.getExpressionExperiment()).getSourceExperiment());
        }
        if (layout == null || layout.isEmpty()) {
            log.error("Did not find cached layout for " + vec.getId());
            continue;
        }
        List<BioAssayValueObject> newOrdering = new ArrayList<>(layout.keySet());
        newOrdering.retainAll(vec.getBioAssays());
        /*
             * This can happen if the vectors are out of whack with the bioassays - e.g. two platforms were used but
             * merging is not done. See bug 3775. Skipping the ordering is not the right thing to do.
             */
        if (newOrdering.isEmpty()) {
            boolean allNaN = this.allNaN(vec);
            if (allNaN) {
                // reordering will have no effect.
                continue;
            }
            /*
                 * Add to the layout.
                 */
            layout = this.extendLayout(vec, vec.getExpressionExperiment().getId());
            newOrdering = new ArrayList<>(layout.keySet());
            newOrdering.retainAll(vec.getBioAssays());
            assert !newOrdering.isEmpty();
        }
        newOrderingsForBioAssayDimensions.put(vec, newOrdering);
        Map<BioAssayValueObject, Integer> ordering = this.getOrdering(newOrdering);
        Long eeId;
        // might be subset id.
        eeId = vec.getExpressionExperiment().getId();
        if (!returnedLayouts.containsKey(eeId)) {
            if (vec.isSliced()) {
                LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> trimmedLayout = new LinkedHashMap<>();
                for (BioAssayValueObject baVo : newOrdering) {
                    trimmedLayout.put(baVo, layout.get(baVo));
                }
                returnedLayouts.put(eeId, trimmedLayout);
            } else {
                returnedLayouts.put(eeId, layout);
            }
        }
        /*
             * Might be a faster way.
             */
        double[] data = vec.getData();
        double[] dol = ArrayUtils.clone(data);
        // assert ordering.size() == data.length : "got " + ordering.size() + " expected " + data.length;
        List<BioAssayValueObject> oldOrdering = vec.getBioAssayDimension().getBioAssays();
        int j = 0;
        if (log.isTraceEnabled())
            log.trace("Old order: " + StringUtils.join(ArrayUtils.toObject(data), ","));
        for (BioAssayValueObject ba : oldOrdering) {
            if (ordering.get(ba) == null) {
                assert Double.isNaN(dol[j]);
                j++;
                continue;
            }
            assert ordering.containsKey(ba);
            assert ordering.get(ba) != null;
            Integer targetIndex = ordering.get(ba);
            data[targetIndex] = dol[j++];
        }
        if (log.isTraceEnabled())
            log.trace("New order: " + StringUtils.join(ArrayUtils.toObject(data), ","));
        vec.setReorganized(true);
    }
    for (DoubleVectorValueObject vec : dedVs) {
        if (vec.getBioAssayDimension().isReordered())
            continue;
        List<BioAssayValueObject> newOrdering = newOrderingsForBioAssayDimensions.get(vec);
        if (newOrdering == null)
            // data was empty, etc.
            continue;
        vec.getBioAssayDimension().reorder(newOrdering);
    }
    if (timer.getTime() > 1500) {
        log.info("Sort vectors by design: " + timer.getTime() + "ms");
    }
    return returnedLayouts;
}

Example 93 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project Gemma by PavlidisLab.

the class CoexpressionDaoImpl method getCoexpressionFromDbViaGenes2.

/**
 * Alternative method: query twice, once to get the coexpression basics and then again to get the support details,
 * instead of using a join.
 *
 * @param populateTestedInDetails populate tested in details
 * @param stringency              stringency
 * @param geneIds                 gene IDs
 * @param t                       taxon
 */
private Map<Long, List<CoexpressionValueObject>> getCoexpressionFromDbViaGenes2(Collection<Long> geneIds, Taxon t, int stringency, boolean populateTestedInDetails) {
    StopWatch timer = new StopWatch();
    timer.start();
    List<Object[]> q1results = this.getRawCoexpressionFromDbViaGenes(geneIds, t, stringency);
    CoexpressionDaoImpl.log.debug(q1results.size() + " raw coexpression results for " + geneIds.size() + " genes at support>=" + stringency + " " + timer.getTime() + "ms");
    if (q1results.isEmpty()) {
        return new HashMap<>();
    }
    List<Object[]> supportDetails = new ArrayList<>();
    /*
         * Because we are not trimming the results at all here, this can be a lot of data to iterate over, even at
         * high stringencies. For example, for 20 genes at a stringency of 5, because the query above does not
         * constrain to data sets, there can be >500 per gene, or >100k links in total. Fetching the support details
         * here is rather wasteful if we are not retaining the results, but we don't know that until we know which
         * data sets are supporting.
         */
    BatchIterator<Object[]> batches = BatchIterator.batches(q1results, CoexpressionDaoImpl.BATCH_SIZE);
    int n = 1;
    for (Collection<Object[]> batch : batches) {
        StopWatch timer2 = new StopWatch();
        timer2.start();
        List<Long> supportDetailsIds = new ArrayList<>();
        for (Object[] oa : batch) {
            Long supportDetailsId = ((BigInteger) oa[5]).longValue();
            supportDetailsIds.add(supportDetailsId);
        }
        // Note: should never be empty
        String sqlQuery2 = "select ID,BYTES from " + CoexpressionQueryUtils.getSupportDetailsTableName(t) + " where ID in (:ids)";
        SQLQuery query2 = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery2);
        query2.setParameterList("ids", supportDetailsIds.toArray());
        supportDetails.addAll(query2.list());
        if (timer2.getTime() > 1000) {
            CoexpressionDaoImpl.log.debug("Fetch batch " + n + " of support details: " + timer2.getTime() + "ms");
        }
        n++;
    }
    CoexpressionDaoImpl.log.debug("Fetched details for " + supportDetails.size() + " coexpressions, " + n + " batches");
    if (timer.getTime() > 5000) {
        CoexpressionDaoImpl.log.info("Coexpression query: " + geneIds.size() + " genes took " + timer.getTime() + "ms: " + q1results.size() + " results");
    }
    timer.reset();
    timer.start();
    // it might be better to do this in the loop above, incrementally per batch.
    Map<Long, List<CoexpressionValueObject>> results = this.convertToValueObjects(q1results, supportDetails, geneIds);
    if (timer.getTime() > 100) {
        CoexpressionDaoImpl.log.info("Convert to value objects " + q1results.size() + " results: " + timer.getTime() + "ms");
    }
    timer.reset();
    timer.start();
    for (Long g : results.keySet()) {
        List<CoexpressionValueObject> gc = results.get(g);
        Collections.sort(gc);
        if (populateTestedInDetails) {
            this.populateTestedInDetails(gc);
        }
    }
    if (timer.getTime() > 100) {
        CoexpressionDaoImpl.log.info("Filter, sort and finish " + q1results.size() + " results: " + timer.getTime() + "ms");
    }
    return results;
}

Example 94 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project molgenis by molgenis.

the class SortaController method retrieveSortaJobResults.

@PostMapping("/match/retrieve")
@ResponseBody
public EntityCollectionResponse retrieveSortaJobResults(@RequestBody SortaServiceRequest sortaServiceRequest) {
    List<Map<String, Object>> entityMaps = new ArrayList<>();
    String sortaJobExecutionId = sortaServiceRequest.getSortaJobExecutionId();
    String filterQuery = sortaServiceRequest.getFilterQuery();
    String ontologyIri = sortaServiceRequest.getOntologyIri();
    EntityPager entityPager = sortaServiceRequest.getEntityPager();
    SortaJobExecution sortaJobExecution = findSortaJobExecution(sortaJobExecutionId);
    String resultEntityName = sortaJobExecution.getResultEntityName();
    double threshold = sortaJobExecution.getThreshold();
    boolean isMatched = sortaServiceRequest.isMatched();
    QueryRule queryRuleInputEntities = new QueryRule(Arrays.asList(new QueryRule(VALIDATED, EQUALS, isMatched), new QueryRule(isMatched ? OR : AND), new QueryRule(SCORE, isMatched ? GREATER_EQUAL : LESS, threshold)));
    List<QueryRule> queryRuleInputEntitiesInOneMatchingTask = singletonList(queryRuleInputEntities);
    // Add filter to the query if query string is not empty
    if (isNotEmpty(filterQuery)) {
        Iterable<String> filteredInputTermIds = dataService.findAll(sortaJobExecution.getSourceEntityName(), new QueryImpl<>().search(filterQuery)).map(inputEntity -> inputEntity.getString(SortaServiceImpl.DEFAULT_MATCHING_IDENTIFIER)).collect(Collectors.toList());
        QueryRule previousQueryRule = new QueryRule(queryRuleInputEntitiesInOneMatchingTask);
        QueryRule queryRuleFilterInput = new QueryRule(MatchingTaskContentMetaData.INPUT_TERM, Operator.IN, filteredInputTermIds);
        queryRuleInputEntitiesInOneMatchingTask = Arrays.asList(previousQueryRule, new QueryRule(Operator.AND), queryRuleFilterInput);
    }
    Query<Entity> query = new QueryImpl<>(queryRuleInputEntitiesInOneMatchingTask);
    long count = dataService.count(resultEntityName, query);
    int start = entityPager.getStart();
    int num = entityPager.getNum();
    Stream<Entity> findAll = dataService.findAll(sortaJobExecution.getResultEntityName(), query.offset(start).pageSize(num).sort(new Sort().on(VALIDATED, DESC).on(SCORE, DESC)));
    findAll.forEach(mappingEntity -> {
        Map<String, Object> outputEntity = new HashMap<>();
        outputEntity.put("inputTerm", getEntityAsMap(mappingEntity.getEntity(INPUT_TERM)));
        outputEntity.put("matchedTerm", getEntityAsMap(mappingEntity));
        Object matchedTerm = mappingEntity.get(MATCHED_TERM);
        if (matchedTerm != null) {
            outputEntity.put("ontologyTerm", SortaServiceUtil.getEntityAsMap(sortaService.getOntologyTermEntity(matchedTerm.toString(), ontologyIri)));
        }
        entityMaps.add(outputEntity);
    });
    EntityPager pager = new EntityPager(start, num, count, null);
    return new EntityCollectionResponse(pager, entityMaps, "/match/retrieve", ontologyTermMetaData, permissionService, dataService);
}

Example 95 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project xwiki-platform by xwiki.

the class ExecutionContextCopier method copy.

@Override
public ExecutionContext copy(ExecutionContext originalExecutionContext) throws CloneFailedException {
    try {
        ExecutionContext clonedExecutionContext = this.executionContextManager.clone(originalExecutionContext);
        // XWikiContext
        // The above clone just creates and initializes an empty XWiki Context, so it needs special handling.
        XWikiContext xwikiContext = (XWikiContext) originalExecutionContext.getProperty(XWikiContext.EXECUTIONCONTEXT_KEY);
        XWikiContext clonedXWikiContext = xwikiContextCloner.copy(xwikiContext);
        clonedExecutionContext.setProperty(XWikiContext.EXECUTIONCONTEXT_KEY, clonedXWikiContext);
        // VelocityContext
        // Reset the VelocityContext from the EC by removing it and calling the Velocity ECInitializer which is
        // normally called by the execution of the ECInitializers by ECManager.clone(). This ensures a clean new
        // VC is created. It'll get filled when VelocityContextManager.getVelocityContext() is called by whatever
        // code need the VC.
        clonedExecutionContext.removeProperty(VelocityExecutionContextInitializer.VELOCITY_CONTEXT_ID);
        this.velocityExecutionContextInitializer.initialize(clonedExecutionContext);
        return clonedExecutionContext;
    } catch (Exception e) {
        throw new CloneFailedException(String.format("Failed to clone [%s]", originalExecutionContext), e);
    }
}