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

Example 31 with EMPTY

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

the class CycloBaseVisitor method visit.

@Override
public Object visit(ASTSwitchStatement node, Object data) {
    int childCount = node.jjtGetNumChildren();
    int lastIndex = childCount - 1;
    for (int n = 0; n < lastIndex; n++) {
        Node childNode = node.jjtGetChild(n);
        if (childNode instanceof ASTSwitchLabel) {
            // default is not considered a decision (same as "else")
            ASTSwitchLabel sl = (ASTSwitchLabel) childNode;
            if (!sl.isDefault()) {
                // check the label is not empty
                childNode = node.jjtGetChild(n + 1);
                if (childNode instanceof ASTBlockStatement) {
                    ((MutableInt) data).increment();
                }
            }
        }
    }
    super.visit(node, data);
    return data;
}

Example 32 with EMPTY

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

the class GeneralSearchControllerImpl method fillValueObjects.

@SuppressWarnings("unchecked")
private void fillValueObjects(Class<?> entityClass, List<SearchResult> results, SearchSettings settings) {
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<?> vos;
    if (ExpressionExperiment.class.isAssignableFrom(entityClass)) {
        vos = this.filterEE(expressionExperimentService.loadValueObjects(EntityUtils.getIds(results), false), settings);
        if (!SecurityUtil.isUserAdmin()) {
            auditableUtil.removeTroubledEes((Collection<ExpressionExperimentValueObject>) vos);
        }
    } else if (ArrayDesign.class.isAssignableFrom(entityClass)) {
        vos = this.filterAD(arrayDesignService.loadValueObjectsByIds(EntityUtils.getIds(results)), settings);
        if (!SecurityUtil.isUserAdmin()) {
            auditableUtil.removeTroubledArrayDesigns((Collection<ArrayDesignValueObject>) vos);
        }
    } else if (CompositeSequence.class.isAssignableFrom(entityClass)) {
        Collection<CompositeSequenceValueObject> css = new ArrayList<>();
        for (SearchResult sr : results) {
            CompositeSequenceValueObject csvo = compositeSequenceService.loadValueObject((CompositeSequence) sr.getResultObject());
            css.add(csvo);
        }
        vos = css;
    } else if (BibliographicReference.class.isAssignableFrom(entityClass)) {
        Collection<BibliographicReference> bss = bibliographicReferenceService.load(EntityUtils.getIds(results));
        bss = bibliographicReferenceService.thaw(bss);
        vos = bibliographicReferenceService.loadValueObjects(bss);
    } else if (Gene.class.isAssignableFrom(entityClass)) {
        Collection<Gene> genes = geneService.load(EntityUtils.getIds(results));
        genes = geneService.thawLite(genes);
        vos = geneService.loadValueObjects(genes);
    } else if (Characteristic.class.isAssignableFrom(entityClass)) {
        Collection<CharacteristicValueObject> cvos = new ArrayList<>();
        for (SearchResult sr : results) {
            Characteristic ch = (Characteristic) sr.getResultObject();
            cvos.add(new CharacteristicValueObject(ch));
        }
        vos = cvos;
    } else if (CharacteristicValueObject.class.isAssignableFrom(entityClass)) {
        Collection<CharacteristicValueObject> cvos = new ArrayList<>();
        for (SearchResult sr : results) {
            CharacteristicValueObject ch = (CharacteristicValueObject) sr.getResultObject();
            cvos.add(ch);
        }
        vos = cvos;
    } else if (BioSequenceValueObject.class.isAssignableFrom(entityClass)) {
        return;
    } else if (GeneSet.class.isAssignableFrom(entityClass)) {
        vos = geneSetService.getValueObjects(EntityUtils.getIds(results));
    } else if (ExpressionExperimentSet.class.isAssignableFrom(entityClass)) {
        vos = experimentSetService.loadValueObjects(experimentSetService.load(EntityUtils.getIds(results)));
    } else if (FactorValue.class.isAssignableFrom(entityClass)) {
        Collection<FactorValueValueObject> fvo = new ArrayList<>();
        for (SearchResult sr : results) {
            fvo.add(new FactorValueValueObject((FactorValue) sr.getResultObject()));
        }
        vos = fvo;
    } else {
        throw new UnsupportedOperationException("Don't know how to make value objects for class=" + entityClass);
    }
    if (vos == null || vos.isEmpty()) {
        // it causing front end errors, if vos is empty make sure to get rid of all search results
        for (Iterator<SearchResult> it = results.iterator(); it.hasNext(); ) {
            it.next();
            it.remove();
        }
        return;
    }
    // retained objects...
    Map<Long, Object> idMap = EntityUtils.getIdMap(vos);
    for (Iterator<SearchResult> it = results.iterator(); it.hasNext(); ) {
        SearchResult sr = it.next();
        if (!idMap.containsKey(sr.getId())) {
            it.remove();
            continue;
        }
        sr.setResultObject(idMap.get(sr.getId()));
    }
    if (timer.getTime() > 1000) {
        BaseFormController.log.info("Value object conversion after search: " + timer.getTime() + "ms");
    }
}

Example 33 with EMPTY

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

the class DifferentialExpressionResultDaoImpl method addToCache.

/**
 * This is to be called after a query for diff ex results is finished for a set of resultSets and genes. It assumes
 * that if a gene is missing from the results, there are none for that resultSet for that gene. It then stores a
 * dummy entry.
 *
 * @param results      - which might be empty.
 * @param resultSetids - the ones which we searched for in the database. Put in dummy results if we have to.
 */
private void addToCache(Map<Long, Map<Long, DiffExprGeneSearchResult>> results, Collection<Long> resultSetids, Collection<Long> geneIds) {
    StopWatch timer = new StopWatch();
    timer.start();
    int i = 0;
    for (Long resultSetId : resultSetids) {
        Map<Long, DiffExprGeneSearchResult> resultSetResults = results.get(resultSetId);
        for (Long geneId : geneIds) {
            if (resultSetResults != null && resultSetResults.containsKey(geneId)) {
                this.differentialExpressionResultCache.addToCache(resultSetResults.get(geneId));
            } else {
                // put in a dummy, so we don't bother searching for it later.
                this.differentialExpressionResultCache.addToCache(new MissingResult(resultSetId, geneId));
            }
            i++;
        }
    }
    if (timer.getTime() > 10) {
        AbstractDao.log.info("Add " + i + " results to cache: " + timer.getTime() + "ms");
    }
}

Example 34 with EMPTY

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

the class DEDVController method handleRequestInternal.

/**
 * Handle case of text export of the results.
 */
@RequestMapping("/downloadDEDV.html")
protected ModelAndView handleRequestInternal(HttpServletRequest request) {
    StopWatch watch = new StopWatch();
    watch.start();
    // might not be any
    Collection<Long> geneIds = ControllerUtils.extractIds(request.getParameter("g"));
    // might not be there
    Collection<Long> eeIds = ControllerUtils.extractIds(request.getParameter("ee"));
    ModelAndView mav = new ModelAndView(new TextView());
    if (eeIds == null || eeIds.isEmpty()) {
        mav.addObject("text", "Input empty for finding DEDVs: " + geneIds + " and " + eeIds);
        return mav;
    }
    String threshSt = request.getParameter("thresh");
    String resultSetIdSt = request.getParameter("rs");
    Double thresh = 100.0;
    if (StringUtils.isNotBlank(threshSt)) {
        try {
            thresh = Double.parseDouble(threshSt);
        } catch (NumberFormatException e) {
            throw new RuntimeException("Threshold was not a valid value: " + threshSt);
        }
    }
    Map<ExpressionExperimentValueObject, Map<Long, Collection<DoubleVectorValueObject>>> result;
    if (request.getParameter("pca") != null) {
        int component = Integer.parseInt(request.getParameter("component"));
        Long eeId = eeIds.iterator().next();
        Map<ProbeLoading, DoubleVectorValueObject> topLoadedVectors = this.svdService.getTopLoadedVectors(eeId, component, thresh.intValue());
        if (topLoadedVectors == null)
            return null;
        mav.addObject("text", format4File(topLoadedVectors.values()));
        return mav;
    }
    /*
         * The following should be set if we're viewing diff. ex results.
         */
    Long resultSetId = null;
    if (StringUtils.isNumeric(resultSetIdSt)) {
        resultSetId = Long.parseLong(resultSetIdSt);
    }
    if (resultSetId != null) {
        /*
             * Diff ex case.
             */
        Long eeId = eeIds.iterator().next();
        Collection<DoubleVectorValueObject> diffExVectors = processedExpressionDataVectorService.getDiffExVectors(resultSetId, thresh, MAX_RESULTS_TO_RETURN);
        if (diffExVectors == null || diffExVectors.isEmpty()) {
            mav.addObject("text", "No results");
            return mav;
        }
        /*
             * Organize the vectors in the same way expected by the ee+gene type of request.
             */
        ExpressionExperimentValueObject ee = expressionExperimentService.loadValueObject(expressionExperimentService.load(eeId));
        result = new HashMap<>();
        Map<Long, Collection<DoubleVectorValueObject>> gmap = new HashMap<>();
        for (DoubleVectorValueObject dv : diffExVectors) {
            for (Long g : dv.getGenes()) {
                if (!gmap.containsKey(g)) {
                    gmap.put(g, new HashSet<DoubleVectorValueObject>());
                }
                gmap.get(g).add(dv);
            }
        }
        result.put(ee, gmap);
    } else {
        // Generic listing.
        result = getDEDV(eeIds, geneIds);
    }
    if (result == null || result.isEmpty()) {
        mav.addObject("text", "No results");
        return mav;
    }
    mav.addObject("text", format4File(result));
    watch.stop();
    Long time = watch.getTime();
    if (time > 100) {
        log.info("Retrieved and Formated" + result.keySet().size() + " DEDVs for eeIDs: " + eeIds + " and GeneIds: " + geneIds + " in : " + time + " ms.");
    }
    return mav;
}

Example 35 with EMPTY

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

the class OpenstackAccountValidator method validate.

@Override
public void validate(ConfigProblemSetBuilder psBuilder, OpenstackAccount account) {
    DaemonTaskHandler.message("Validating " + account.getNodeName() + " with " + OpenstackAccountValidator.class.getSimpleName());
    String environment = account.getEnvironment();
    String accountType = account.getAccountType();
    String username = account.getUsername();
    String password = account.getPassword();
    String projectName = account.getPassword();
    String domainName = account.getDomainName();
    String authUrl = account.getAuthUrl();
    List<String> regions = account.getRegions();
    Boolean insecure = account.getInsecure();
    String heatTemplateLocation = account.getHeatTemplateLocation();
    OpenstackAccount.OpenstackLbaasOptions lbaas = account.getLbaas();
    ConsulConfig consulConfig = new ConsulConfig();
    String userDataFile = account.getUserDataFile();
    if (StringUtils.isEmpty(environment)) {
        psBuilder.addProblem(Problem.Severity.ERROR, "You must provide an environment name");
    }
    if (StringUtils.isEmpty(password) || StringUtils.isEmpty(username)) {
        psBuilder.addProblem(Problem.Severity.ERROR, "You must provide a both a username and a password");
    }
    if (StringUtils.isEmpty(projectName)) {
        psBuilder.addProblem(Problem.Severity.ERROR, "You must provide a project name");
    }
    if (!StringUtils.endsWith(authUrl, "/v3")) {
        psBuilder.addProblem(Problem.Severity.WARNING, "You must use Keystone v3. The default auth url will be of the format IP:5000/v3.");
    }
    if (StringUtils.isEmpty(domainName)) {
        psBuilder.addProblem(Problem.Severity.ERROR, "You must provide a domain name");
    }
    if (regions.size() == 0 || StringUtils.isEmpty(regions.get(0))) {
        psBuilder.addProblem(Problem.Severity.ERROR, "You must provide one region");
    }
    if (insecure) {
        psBuilder.addProblem(Problem.Severity.WARNING, "You've chosen to not validate SSL connections. This setup is not recommended in production deployments.");
    }
    if (heatTemplateLocation != null && heatTemplateLocation.isEmpty()) {
        psBuilder.addProblem(Problem.Severity.ERROR, "Not a valid Heat template location: ''");
    }
    if (lbaas.getPollInterval() < 0) {
        psBuilder.addProblem(Problem.Severity.ERROR, "Poll interval cannot be less than 0.").setRemediation("Update this value to be reasonable. Default is 5.");
    }
    if (lbaas.getPollTimeout() < 0) {
        psBuilder.addProblem(Problem.Severity.ERROR, "Poll timeout cannot be less than 0.").setRemediation("Update this value to be reasonable. Default is 60.");
    }
    boolean userDataProvided = userDataFile != null && !userDataFile.isEmpty();
    if (userDataProvided) {
        String resolvedUserData = ValidatingFileReader.contents(psBuilder, userDataFile);
        if (resolvedUserData == null) {
            return;
        } else if (resolvedUserData.isEmpty()) {
            psBuilder.addProblem(Problem.Severity.WARNING, "The supplied user data file is empty.").setRemediation("Please provide a non empty file, or remove the user data file.");
        }
        List<String> validTokens = Arrays.asList("account", "accounttype", "env", "region", "group", "autogrp", "cluster", "stack", "detail", "launchconfig");
        List<String> tokens = Arrays.asList(StringUtils.substringsBetween(resolvedUserData, "%%", "%%"));
        List<String> invalidTokens = tokens.stream().filter(t -> !validTokens.contains(t)).collect(Collectors.toList());
        if (invalidTokens.size() != 0) {
            psBuilder.addProblem(Problem.Severity.WARNING, "The supplied user data file contains tokens that won't be replaced. " + "Tokens \"" + StringUtils.join(invalidTokens, ", ") + "\" are not supported.").setRemediation("Please use only the supported tokens \"" + StringUtils.join(validTokens, ", ") + "\".");
        }
    }
    OpenstackConfigurationProperties.LbaasConfig lbaasConfig = new OpenstackConfigurationProperties.LbaasConfig();
    lbaasConfig.setPollInterval(lbaas.getPollInterval());
    lbaasConfig.setPollTimeout(lbaas.getPollTimeout());
    try {
        OpenstackNamedAccountCredentials openstackCredentials = new OpenstackNamedAccountCredentials.Builder().name(account.getName()).environment(environment).accountType(accountType).authUrl(authUrl).username(username).password(password).projectName(projectName).domainName(domainName).regions(regions).insecure(insecure).heatTemplateLocation(heatTemplateLocation).consulConfig(consulConfig).lbaasConfig(lbaasConfig).userDataFile(userDataFile).build();
        credentialsList.add(openstackCredentials);
    // TODO(emjburns) verify that these credentials can connect w/o error to the openstack instance
    } catch (Exception e) {
        psBuilder.addProblem(Problem.Severity.ERROR, "Failed to instantiate openstack credentials for account \"" + account.getName() + "\".");
    }
}