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

Example 86 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project ORCID-Source by ORCID.

the class ActivityValidator method validateWork.

public void validateWork(Work work, SourceEntity sourceEntity, boolean createFlag, boolean isApiRequest, Visibility originalVisibility) {
    WorkTitle title = work.getWorkTitle();
    if (title == null || title.getTitle() == null || PojoUtil.isEmpty(title.getTitle().getContent())) {
        throw new ActivityTitleValidationException();
    }
    if (work.getCountry() != null) {
        if (work.getCountry().getValue() == null) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(Iso3166Country.values()).map(element -> element.value()).collect(Collectors.joining(", "));
            params.put("type", "country");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
    }
    // translated title language code
    if (title != null && title.getTranslatedTitle() != null) {
        String translatedTitle = title.getTranslatedTitle().getContent();
        String languageCode = title.getTranslatedTitle().getLanguageCode();
        if (PojoUtil.isEmpty(translatedTitle) && !PojoUtil.isEmpty(languageCode)) {
            throw new OrcidValidationException("Please specify a translated title or remove the language code");
        }
        // If translated title language code is null or invalid
        if (!PojoUtil.isEmpty(translatedTitle) && (PojoUtil.isEmpty(title.getTranslatedTitle().getLanguageCode()) || !Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).anyMatch(title.getTranslatedTitle().getLanguageCode()::equals))) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).collect(Collectors.joining(", "));
            params.put("type", "translated title -> language code");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
    }
    if (work.getWorkType() == null) {
        Map<String, String> params = new HashMap<String, String>();
        String values = Arrays.stream(WorkType.values()).map(element -> element.value()).collect(Collectors.joining(", "));
        params.put("type", "work type");
        params.put("values", values);
        throw new ActivityTypeValidationException(params);
    }
    if (!PojoUtil.isEmpty(work.getLanguageCode())) {
        if (!Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).anyMatch(work.getLanguageCode()::equals)) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).collect(Collectors.joining(", "));
            params.put("type", "language code");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
    }
    // publication date
    if (work.getPublicationDate() != null) {
        PublicationDate pd = work.getPublicationDate();
        Year year = pd.getYear();
        Month month = pd.getMonth();
        Day day = pd.getDay();
        if (year != null) {
            try {
                Integer.valueOf(year.getValue());
            } catch (NumberFormatException n) {
                Map<String, String> params = new HashMap<String, String>();
                params.put("type", "publication date -> year");
                params.put("values", "integers");
                throw new ActivityTypeValidationException(params);
            }
            if (year.getValue().length() != 4) {
                throw new OrcidValidationException("Invalid year " + year.getValue() + " please specify a four digits value");
            }
        }
        if (month != null) {
            try {
                Integer.valueOf(month.getValue());
            } catch (NumberFormatException n) {
                Map<String, String> params = new HashMap<String, String>();
                params.put("type", "publication date -> month");
                params.put("values", "integers");
                throw new ActivityTypeValidationException(params);
            }
            if (month.getValue().length() != 2) {
                throw new OrcidValidationException("Invalid month " + month.getValue() + " please specify a two digits value");
            }
        }
        if (day != null) {
            try {
                Integer.valueOf(day.getValue());
            } catch (NumberFormatException n) {
                Map<String, String> params = new HashMap<String, String>();
                params.put("type", "publication date -> day");
                params.put("values", "integers");
                throw new ActivityTypeValidationException(params);
            }
            if (day.getValue().length() != 2) {
                throw new OrcidValidationException("Invalid day " + day.getValue() + " please specify a two digits value");
            }
        }
        // Check the date is valid
        boolean isYearEmpty = (year == null || year.getValue() == null) ? true : false;
        boolean isMonthEmpty = (month == null || month.getValue() == null) ? true : false;
        boolean isDayEmpty = (day == null || day.getValue() == null) ? true : false;
        if (isYearEmpty && (!isMonthEmpty || !isDayEmpty)) {
            throw new OrcidValidationException("Invalid date, please specify a year element");
        } else if (!isYearEmpty && isMonthEmpty && !isDayEmpty) {
            throw new OrcidValidationException("Invalid date, please specify a month element");
        } else if (isYearEmpty && isMonthEmpty && !isDayEmpty) {
            throw new OrcidValidationException("Invalid date, please specify a year and month elements");
        }
    }
    // citation
    if (work.getWorkCitation() != null) {
        String citation = work.getWorkCitation().getCitation();
        CitationType type = work.getWorkCitation().getWorkCitationType();
        if (type == null) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(CitationType.values()).map(element -> element.value()).collect(Collectors.joining(", "));
            params.put("type", "citation type");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
        if (PojoUtil.isEmpty(citation)) {
            throw new OrcidValidationException("Please specify a citation or remove the parent tag");
        }
    }
    if (work.getWorkExternalIdentifiers() == null || work.getWorkExternalIdentifiers().getExternalIdentifier() == null || work.getExternalIdentifiers().getExternalIdentifier().isEmpty()) {
        throw new ActivityIdentifierValidationException();
    }
    if (work.getWorkContributors() != null) {
        WorkContributors contributors = work.getWorkContributors();
        if (!contributors.getContributor().isEmpty()) {
            for (Contributor contributor : contributors.getContributor()) {
                if (contributor.getContributorOrcid() != null) {
                    ContributorOrcid contributorOrcid = contributor.getContributorOrcid();
                    if (!PojoUtil.isEmpty(contributorOrcid.getUri())) {
                        if (!OrcidStringUtils.isValidOrcid2_1Uri(contributorOrcid.getUri())) {
                            throw new OrcidValidationException("Invalid contributor URI");
                        }
                    }
                    if (!PojoUtil.isEmpty(contributorOrcid.getPath())) {
                        if (!OrcidStringUtils.isValidOrcid(contributorOrcid.getPath())) {
                            throw new OrcidValidationException("Invalid contributor ORCID");
                        }
                    }
                }
                if (contributor.getCreditName() != null) {
                    if (PojoUtil.isEmpty(contributor.getCreditName().getContent())) {
                        throw new OrcidValidationException("Please specify a contributor credit name or remove the empty tag");
                    }
                }
                if (contributor.getContributorEmail() != null) {
                    if (PojoUtil.isEmpty(contributor.getContributorEmail().getValue())) {
                        throw new OrcidValidationException("Please specify a contributor email or remove the empty tag");
                    }
                }
            }
        }
    }
    if (work.getPutCode() != null && createFlag) {
        Map<String, String> params = new HashMap<String, String>();
        if (sourceEntity != null) {
            params.put("clientName", sourceEntity.getSourceName());
        }
        throw new InvalidPutCodeException(params);
    }
    // Check that we are not changing the visibility
    if (isApiRequest && !createFlag) {
        Visibility updatedVisibility = work.getVisibility();
        validateVisibilityDoesntChange(updatedVisibility, originalVisibility);
    }
    externalIDValidator.validateWorkOrPeerReview(work.getExternalIdentifiers());
}

Example 87 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project ORCID-Source by ORCID.

the class ActivityValidator method validateWork.

public void validateWork(Work work, SourceEntity sourceEntity, boolean createFlag, boolean isApiRequest, Visibility originalVisibility) {
    WorkTitle title = work.getWorkTitle();
    if (title == null || title.getTitle() == null || PojoUtil.isEmpty(title.getTitle().getContent())) {
        throw new ActivityTitleValidationException();
    }
    if (work.getCountry() != null) {
        if (work.getCountry().getValue() == null) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(Iso3166Country.values()).map(element -> element.value()).collect(Collectors.joining(", "));
            params.put("type", "country");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
    }
    // translated title language code
    if (title != null && title.getTranslatedTitle() != null) {
        String translatedTitle = title.getTranslatedTitle().getContent();
        String languageCode = title.getTranslatedTitle().getLanguageCode();
        if (PojoUtil.isEmpty(translatedTitle) && !PojoUtil.isEmpty(languageCode)) {
            throw new OrcidValidationException("Please specify a translated title or remove the language code");
        }
        // If translated title language code is null or invalid
        if (!PojoUtil.isEmpty(translatedTitle) && (PojoUtil.isEmpty(title.getTranslatedTitle().getLanguageCode()) || !Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).anyMatch(title.getTranslatedTitle().getLanguageCode()::equals))) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).collect(Collectors.joining(", "));
            params.put("type", "translated title -> language code");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
    }
    if (work.getWorkType() == null) {
        Map<String, String> params = new HashMap<String, String>();
        String values = Arrays.stream(WorkType.values()).map(element -> element.value()).collect(Collectors.joining(", "));
        params.put("type", "work type");
        params.put("values", values);
        throw new ActivityTypeValidationException(params);
    }
    if (!PojoUtil.isEmpty(work.getLanguageCode())) {
        if (!Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).anyMatch(work.getLanguageCode()::equals)) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(SiteConstants.AVAILABLE_ISO_LANGUAGES).collect(Collectors.joining(", "));
            params.put("type", "language code");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
    }
    // publication date
    if (work.getPublicationDate() != null) {
        PublicationDate pd = work.getPublicationDate();
        Year year = pd.getYear();
        Month month = pd.getMonth();
        Day day = pd.getDay();
        if (year != null) {
            try {
                Integer.valueOf(year.getValue());
            } catch (NumberFormatException n) {
                Map<String, String> params = new HashMap<String, String>();
                params.put("type", "publication date -> year");
                params.put("values", "integers");
                throw new ActivityTypeValidationException(params);
            }
            if (year.getValue().length() != 4) {
                throw new OrcidValidationException("Invalid year " + year.getValue() + " please specify a four digits value");
            }
        }
        if (month != null) {
            try {
                Integer.valueOf(month.getValue());
            } catch (NumberFormatException n) {
                Map<String, String> params = new HashMap<String, String>();
                params.put("type", "publication date -> month");
                params.put("values", "integers");
                throw new ActivityTypeValidationException(params);
            }
            if (month.getValue().length() != 2) {
                throw new OrcidValidationException("Invalid month " + month.getValue() + " please specify a two digits value");
            }
        }
        if (day != null) {
            try {
                Integer.valueOf(day.getValue());
            } catch (NumberFormatException n) {
                Map<String, String> params = new HashMap<String, String>();
                params.put("type", "publication date -> day");
                params.put("values", "integers");
                throw new ActivityTypeValidationException(params);
            }
            if (day.getValue().length() != 2) {
                throw new OrcidValidationException("Invalid day " + day.getValue() + " please specify a two digits value");
            }
        }
        // Check the date is valid
        boolean isYearEmpty = (year == null || year.getValue() == null) ? true : false;
        boolean isMonthEmpty = (month == null || month.getValue() == null) ? true : false;
        boolean isDayEmpty = (day == null || day.getValue() == null) ? true : false;
        if (isYearEmpty && (!isMonthEmpty || !isDayEmpty)) {
            throw new OrcidValidationException("Invalid date, please specify a year element");
        } else if (!isYearEmpty && isMonthEmpty && !isDayEmpty) {
            throw new OrcidValidationException("Invalid date, please specify a month element");
        } else if (isYearEmpty && isMonthEmpty && !isDayEmpty) {
            throw new OrcidValidationException("Invalid date, please specify a year and month elements");
        }
    }
    // citation
    if (work.getWorkCitation() != null) {
        String citation = work.getWorkCitation().getCitation();
        CitationType type = work.getWorkCitation().getWorkCitationType();
        if (type == null) {
            Map<String, String> params = new HashMap<String, String>();
            String values = Arrays.stream(CitationType.values()).map(element -> element.value()).collect(Collectors.joining(", "));
            params.put("type", "citation type");
            params.put("values", values);
            throw new ActivityTypeValidationException(params);
        }
        if (PojoUtil.isEmpty(citation)) {
            throw new OrcidValidationException("Please specify a citation or remove the parent tag");
        }
    }
    if (work.getWorkExternalIdentifiers() == null || work.getWorkExternalIdentifiers().getExternalIdentifier() == null || work.getExternalIdentifiers().getExternalIdentifier().isEmpty()) {
        throw new ActivityIdentifierValidationException();
    }
    if (work.getWorkContributors() != null) {
        WorkContributors contributors = work.getWorkContributors();
        if (!contributors.getContributor().isEmpty()) {
            for (Contributor contributor : contributors.getContributor()) {
                if (contributor.getContributorOrcid() != null) {
                    ContributorOrcid contributorOrcid = contributor.getContributorOrcid();
                    if (!PojoUtil.isEmpty(contributorOrcid.getUri())) {
                        if (!OrcidStringUtils.isValidOrcidUri(contributorOrcid.getUri())) {
                            throw new OrcidValidationException("Invalid contributor URI");
                        }
                    }
                    if (!PojoUtil.isEmpty(contributorOrcid.getPath())) {
                        if (!OrcidStringUtils.isValidOrcid(contributorOrcid.getPath())) {
                            throw new OrcidValidationException("Invalid contributor ORCID");
                        }
                    }
                }
                if (contributor.getCreditName() != null) {
                    if (PojoUtil.isEmpty(contributor.getCreditName().getContent())) {
                        throw new OrcidValidationException("Please specify a contributor credit name or remove the empty tag");
                    }
                }
                if (contributor.getContributorEmail() != null) {
                    if (PojoUtil.isEmpty(contributor.getContributorEmail().getValue())) {
                        throw new OrcidValidationException("Please specify a contributor email or remove the empty tag");
                    }
                }
            }
        }
    }
    if (work.getPutCode() != null && createFlag) {
        Map<String, String> params = new HashMap<String, String>();
        if (sourceEntity != null) {
            params.put("clientName", sourceEntity.getSourceName());
        }
        throw new InvalidPutCodeException(params);
    }
    // Check that we are not changing the visibility
    if (isApiRequest && !createFlag) {
        Visibility updatedVisibility = work.getVisibility();
        validateVisibilityDoesntChange(updatedVisibility, originalVisibility);
    }
    externalIDValidator.validateWorkOrPeerReview(work.getExternalIdentifiers());
}

Example 88 with EMPTY

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

the class AgreementUtils method makeStudy.

private static AgreementResult makeStudy(DiffResult aDiff, Collection<String> aUsers, String aType, String aFeature, boolean aExcludeIncomplete, boolean aNullLabelsAsEmpty, Map<String, List<JCas>> aCasMap) {
    List<String> users = new ArrayList<>(aUsers);
    Collections.sort(users);
    List<ConfigurationSet> completeSets = new ArrayList<>();
    List<ConfigurationSet> setsWithDifferences = new ArrayList<>();
    List<ConfigurationSet> incompleteSetsByPosition = new ArrayList<>();
    List<ConfigurationSet> incompleteSetsByLabel = new ArrayList<>();
    List<ConfigurationSet> pluralitySets = new ArrayList<>();
    List<ConfigurationSet> irrelevantSets = new ArrayList<>();
    CodingAnnotationStudy study = new CodingAnnotationStudy(users.size());
    // Check if the feature we are looking at is a primitive feature or a link feature
    // We do this by looking it up in the first available CAS. Mind that at this point all
    // CASes should have exactly the same typesystem.
    JCas someCas = findSomeCas(aCasMap);
    if (someCas == null) {
        // Well... there is NOTHING here!
        // All positions are irrelevant
        aDiff.getPositions().forEach(p -> irrelevantSets.add(aDiff.getConfigurtionSet(p)));
        return new AgreementResult(aType, aFeature, aDiff, study, users, completeSets, irrelevantSets, setsWithDifferences, incompleteSetsByPosition, incompleteSetsByLabel, pluralitySets, aExcludeIncomplete);
    }
    TypeSystem ts = someCas.getTypeSystem();
    // We should just do the right thing here which is: do nothing
    if (ts.getType(aType) == null) {
        // All positions are irrelevant
        aDiff.getPositions().forEach(p -> irrelevantSets.add(aDiff.getConfigurtionSet(p)));
        return new AgreementResult(aType, aFeature, aDiff, study, users, completeSets, irrelevantSets, setsWithDifferences, incompleteSetsByPosition, incompleteSetsByLabel, pluralitySets, aExcludeIncomplete);
    }
    // Check that the feature really exists instead of just getting a NPE later
    if (ts.getType(aType).getFeatureByBaseName(aFeature) == null) {
        throw new IllegalArgumentException("Type [" + aType + "] has no feature called [" + aFeature + "]");
    }
    boolean isPrimitiveFeature = ts.getType(aType).getFeatureByBaseName(aFeature).getRange().isPrimitive();
    nextPosition: for (Position p : aDiff.getPositions()) {
        ConfigurationSet cfgSet = aDiff.getConfigurtionSet(p);
        // Only calculate agreement for the given layer
        if (!cfgSet.getPosition().getType().equals(aType)) {
            // We don't even consider these as irrelevant, they are just filtered out
            continue;
        }
        // If the feature on a position is set, then it is a subposition
        boolean isSubPosition = p.getFeature() != null;
        // this is an inverted XOR!
        if (!(isPrimitiveFeature ^ isSubPosition)) {
            irrelevantSets.add(cfgSet);
            continue;
        }
        // feature
        if (isSubPosition && !aFeature.equals(cfgSet.getPosition().getFeature())) {
            irrelevantSets.add(cfgSet);
            continue nextPosition;
        }
        // If non of the current users has made any annotation at this position, then skip it
        if (users.stream().filter(u -> cfgSet.getCasGroupIds().contains(u)).count() == 0) {
            irrelevantSets.add(cfgSet);
            continue nextPosition;
        }
        Object[] values = new Object[users.size()];
        int i = 0;
        for (String user : users) {
            // this configuration set.
            if (!cfgSet.getCasGroupIds().contains(user)) {
                incompleteSetsByPosition.add(cfgSet);
                if (aExcludeIncomplete) {
                    // Record as incomplete
                    continue nextPosition;
                } else {
                    // Record as missing value
                    values[i] = null;
                    i++;
                    continue;
                }
            }
            // Make sure a single user didn't do multiple alternative annotations at a single
            // position. So there is currently no support for calculating agreement on stacking
            // annotations.
            List<Configuration> cfgs = cfgSet.getConfigurations(user);
            if (cfgs.size() > 1) {
                pluralitySets.add(cfgSet);
                continue nextPosition;
            }
            Configuration cfg = cfgs.get(0);
            // Check if source and/or targets of a relation are stacked
            if (cfg.getPosition() instanceof ArcPosition) {
                ArcPosition pos = (ArcPosition) cfg.getPosition();
                FeatureStructure arc = cfg.getFs(user, pos.getCasId(), aCasMap);
                ArcDiffAdapter adapter = (ArcDiffAdapter) aDiff.getDiffAdapter(pos.getType());
                // Check if the source of the relation is stacked
                AnnotationFS source = FSUtil.getFeature(arc, adapter.getSourceFeature(), AnnotationFS.class);
                List<AnnotationFS> sourceCandidates = CasUtil.selectAt(arc.getCAS(), source.getType(), source.getBegin(), source.getEnd());
                if (sourceCandidates.size() > 1) {
                    pluralitySets.add(cfgSet);
                    continue nextPosition;
                }
                // Check if the target of the relation is stacked
                AnnotationFS target = FSUtil.getFeature(arc, adapter.getTargetFeature(), AnnotationFS.class);
                List<AnnotationFS> targetCandidates = CasUtil.selectAt(arc.getCAS(), target.getType(), target.getBegin(), target.getEnd());
                if (targetCandidates.size() > 1) {
                    pluralitySets.add(cfgSet);
                    continue nextPosition;
                }
            }
            // Only calculate agreement for the given feature
            FeatureStructure fs = cfg.getFs(user, cfg.getPosition().getCasId(), aCasMap);
            // BEGIN PARANOIA
            assert fs.getType().getFeatureByBaseName(aFeature).getRange().isPrimitive() == isPrimitiveFeature;
            // should never have gotten here in the first place.
            assert !isPrimitiveFeature || !isSubPosition;
            if (isPrimitiveFeature && !isSubPosition) {
                // Primitive feature / primary position
                values[i] = getFeature(fs, aFeature);
            } else if (!isPrimitiveFeature && isSubPosition) {
                // Link feature / sub-position
                ArrayFS links = (ArrayFS) fs.getFeatureValue(fs.getType().getFeatureByBaseName(aFeature));
                FeatureStructure link = links.get(cfg.getAID(user).index);
                switch(cfg.getPosition().getLinkCompareBehavior()) {
                    case LINK_TARGET_AS_LABEL:
                        // FIXME The target feature name should be obtained from the feature
                        // definition!
                        AnnotationFS target = (AnnotationFS) link.getFeatureValue(link.getType().getFeatureByBaseName("target"));
                        values[i] = target.getBegin() + "-" + target.getEnd() + " [" + target.getCoveredText() + "]";
                        break;
                    case LINK_ROLE_AS_LABEL:
                        // FIXME The role feature name should be obtained from the feature
                        // definition!
                        String role = link.getStringValue(link.getType().getFeatureByBaseName("role"));
                        values[i] = role;
                        break;
                    default:
                        throw new IllegalStateException("Unknown link target comparison mode [" + cfg.getPosition().getLinkCompareBehavior() + "]");
                }
            } else {
                throw new IllegalStateException("Should never get here: primitive: " + fs.getType().getFeatureByBaseName(aFeature).getRange().isPrimitive() + "; subpos: " + isSubPosition);
            }
            // agreement calculation. The empty label is still a valid label.
            if (aNullLabelsAsEmpty && values[i] == null) {
                values[i] = "";
            }
            // "null" cannot be used in agreement calculations. We treat these as incomplete
            if (values[i] == null) {
                incompleteSetsByLabel.add(cfgSet);
                if (aExcludeIncomplete) {
                    continue nextPosition;
                }
            }
            i++;
        }
        if (ObjectUtils.notEqual(values[0], values[1])) {
            setsWithDifferences.add(cfgSet);
        }
        // are calculating agreement over
        assert cfgSet.getPosition().getFeature() == null || cfgSet.getPosition().getFeature().equals(aFeature);
        completeSets.add(cfgSet);
        study.addItemAsArray(values);
    }
    return new AgreementResult(aType, aFeature, aDiff, study, users, completeSets, irrelevantSets, setsWithDifferences, incompleteSetsByPosition, incompleteSetsByLabel, pluralitySets, aExcludeIncomplete);
}

Example 89 with EMPTY

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

the class OntologyServiceImpl method findTermsInexact.

@Override
public Collection<CharacteristicValueObject> findTermsInexact(String givenQueryString, Taxon taxon) {
    if (StringUtils.isBlank(givenQueryString))
        return null;
    StopWatch watch = new StopWatch();
    watch.start();
    String queryString = OntologySearch.stripInvalidCharacters(givenQueryString);
    if (StringUtils.isBlank(queryString)) {
        OntologyServiceImpl.log.warn("The query was not valid (ended up being empty): " + givenQueryString);
        return new HashSet<>();
    }
    if (OntologyServiceImpl.log.isDebugEnabled()) {
        OntologyServiceImpl.log.debug("starting findExactTerm for " + queryString + ". Timing information begins from here");
    }
    Collection<? extends OntologyResource> results;
    Collection<CharacteristicValueObject> searchResults = new HashSet<>();
    Map<String, CharacteristicValueObject> previouslyUsedInSystem = new HashMap<>();
    this.countOccurrences(queryString, previouslyUsedInSystem);
    this.searchForGenes(queryString, taxon, searchResults);
    for (AbstractOntologyService service : this.ontologyServices) {
        if (!service.isOntologyLoaded())
            continue;
        results = service.findResources(queryString);
        if (results.isEmpty())
            continue;
        if (OntologyServiceImpl.log.isDebugEnabled())
            OntologyServiceImpl.log.debug("found " + results.size() + " from " + service.getClass().getSimpleName() + " in " + watch.getTime() + " ms");
        searchResults.addAll(CharacteristicValueObject.characteristic2CharacteristicVO(this.termsToCharacteristics(results)));
        if (searchResults.size() > OntologyServiceImpl.MAX_TERMS_TO_FETCH) {
            break;
        }
    }
    this.countOccurrences(searchResults, previouslyUsedInSystem);
    // get GO terms, if we don't already have a lot of possibilities. (might have to adjust this)
    if (searchResults.size() < OntologyServiceImpl.MAX_TERMS_TO_FETCH && geneOntologyService.isReady()) {
        searchResults.addAll(CharacteristicValueObject.characteristic2CharacteristicVO(this.termsToCharacteristics(geneOntologyService.findTerm(queryString))));
    }
    // Sort the results rather elaborately.
    Collection<CharacteristicValueObject> sortedResults = this.sort(previouslyUsedInSystem, searchResults, queryString);
    if (watch.getTime() > 1000) {
        OntologyServiceImpl.log.info("Ontology term query for: " + givenQueryString + ": " + watch.getTime() + "ms");
    }
    return sortedResults;
}

Example 90 with EMPTY

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

the class DifferentialExpressionAnalyzerServiceImpl method persistAnalysis.

/**
 * Made public for testing purposes only.
 *
 * @param config               config
 * @param analysis             analysis
 * @param expressionExperiment the experiment
 * @return DEA
 */
@Override
public DifferentialExpressionAnalysis persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config) {
    this.deleteOldAnalyses(expressionExperiment, analysis, config.getFactorsToInclude());
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<ExpressionAnalysisResultSet> resultSets = analysis.getResultSets();
    analysis.setResultSets(new HashSet<ExpressionAnalysisResultSet>());
    // first transaction, gets us an ID
    DifferentialExpressionAnalysis persistentAnalysis = helperService.persistStub(analysis);
    // second set of transactions creates the empty resultSets.
    for (ExpressionAnalysisResultSet rs : resultSets) {
        Collection<DifferentialExpressionAnalysisResult> results = rs.getResults();
        rs.setResults(new HashSet<DifferentialExpressionAnalysisResult>());
        ExpressionAnalysisResultSet prs = helperService.create(rs);
        assert prs != null;
        for (DifferentialExpressionAnalysisResult r : results) {
            r.setResultSet(prs);
        }
        analysis.getResultSets().add(prs);
        rs.getResults().addAll(results);
        this.addPvalueDistribution(prs);
    }
    // third transaction - add results.
    DifferentialExpressionAnalyzerServiceImpl.log.info("Saving results");
    helperService.addResults(persistentAnalysis, resultSets);
    // get a clean copy of the analysis object from the DB.
    analysis = differentialExpressionAnalysisService.load(analysis.getId());
    // we do this here because now we have IDs for everything.
    try {
        expressionDataFileService.writeDiffExArchiveFile(expressionExperiment, analysis, config);
    } catch (IOException e) {
        DifferentialExpressionAnalyzerServiceImpl.log.error("Unable to save the data to a file: " + e.getMessage());
    }
    // final transaction: audit.
    try {
        auditTrailService.addUpdateEvent(expressionExperiment, DifferentialExpressionAnalysisEvent.Factory.newInstance(), persistentAnalysis.getDescription() + "; analysis id=" + persistentAnalysis.getId());
    } catch (Exception e) {
        DifferentialExpressionAnalyzerServiceImpl.log.error("Error while trying to add audit event: " + e.getMessage(), e);
        DifferentialExpressionAnalyzerServiceImpl.log.error("Continuing ...");
    /*
             * We shouldn't fail completely due to this.
             */
    }
    if (timer.getTime() > 5000) {
        DifferentialExpressionAnalyzerServiceImpl.log.info("Save results: " + timer.getTime() + "ms");
    }
    return persistentAnalysis;
}