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

Example 11 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project pyramid by cheng-li.

the class ESIndex method getTermStats.

/**
     * df is from one shard!!!
     * @param id
     * @return term statistics from one doc
     * @throws IOException
     */
public Set<TermStat> getTermStats(String field, String id) throws IOException {
    StopWatch stopWatch = null;
    if (logger.isDebugEnabled()) {
        stopWatch = new StopWatch();
        stopWatch.start();
    }
    TermVectorResponse response = client.prepareTermVector(indexName, documentType, id).setOffsets(false).setPositions(false).setFieldStatistics(false).setTermStatistics(true).setSelectedFields(field).execute().actionGet();
    Terms terms = response.getFields().terms(field);
    Set<TermStat> set = new HashSet<>();
    // if the field is empty, terms==null
    if (terms == null) {
        return set;
    }
    TermsEnum iterator = terms.iterator(null);
    for (int i = 0; i < terms.size(); i++) {
        String term = iterator.next().utf8ToString();
        int tf = iterator.docsAndPositions(null, null).freq();
        int df = iterator.docFreq();
        DefaultSimilarity defaultSimilarity = new DefaultSimilarity();
        /**
             * from lucene
             */
        /**
             * tf is just tf, not square root of tf as in lucene
             */
        /** Implemented as <code>log(numDocs/(docFreq+1)) + 1</code>. */
        float tfidf = tf * defaultSimilarity.idf(df, this.numDocs);
        TermStat termStat = new TermStat(term);
        termStat.setTf(tf).setDf(df).setTfidf(tfidf);
        set.add(termStat);
    }
    if (logger.isDebugEnabled()) {
        logger.debug("time spent on getNgramInfos for " + id + " = " + stopWatch);
    }
    return set;
}

Example 12 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project API by ca-cwds.

the class ScreeningToReferralService method processReferralAddress.

private gov.ca.cwds.rest.api.domain.Address processReferralAddress(ScreeningToReferral scr, Set<ErrorMessage> messages) throws ServiceException {
    gov.ca.cwds.rest.api.domain.Address address = scr.getAddress();
    if (address == null || address.getZip() == null || address.getStreetAddress() == null || address.getType() == null) {
        String message = " Screening address is null or empty";
        ServiceException se = new ServiceException(message);
        logError(message, se, messages);
        return address;
    }
    try {
        Address domainAddress = Address.createWithDefaults(address, DEFAULT_STATE_CODE);
        buildErrors(messages, validator.validate(domainAddress));
        PostedAddress postedAddress = (PostedAddress) this.addressService.create(domainAddress);
        address.setLegacyId(postedAddress.getExistingAddressId());
        address.setLegacySourceTable("ADDRS_T");
    } catch (Exception e) {
        logError(e.getMessage(), e, messages);
    }
    return address;
}

Example 13 with EMPTY

use of org.apache.commons.lang3.StringUtils.EMPTY in project gatk-protected by broadinstitute.

the class EvaluateCopyNumberTriStateCalls method buildAndAnnotateTruthOverlappingGenotype.

private Genotype buildAndAnnotateTruthOverlappingGenotype(final String sample, final VariantContext truth, final List<VariantContext> calls, final TargetCollection<Target> targets) {
    final Genotype truthGenotype = truth.getGenotype(sample);
    // if there is no truth genotype for that sample, we output the "empty" genotype.
    if (truthGenotype == null) {
        return GenotypeBuilder.create(sample, Collections.emptyList());
    }
    final int truthCopyNumber = GATKProtectedVariantContextUtils.getAttributeAsInt(truthGenotype, GS_COPY_NUMBER_FORMAT_KEY, truthNeutralCopyNumber);
    final CopyNumberTriStateAllele truthAllele = copyNumberToTrueAllele(truthCopyNumber);
    final List<Pair<VariantContext, Genotype>> allCalls = calls.stream().map(vc -> new ImmutablePair<>(vc, vc.getGenotype(sample))).filter(pair -> pair.getRight() != null).filter(pair -> GATKProtectedVariantContextUtils.getAttributeAsString(pair.getRight(), XHMMSegmentGenotyper.DISCOVERY_KEY, XHMMSegmentGenotyper.DISCOVERY_FALSE).equals(XHMMSegmentGenotyper.DISCOVERY_TRUE)).collect(Collectors.toList());
    final List<Pair<VariantContext, Genotype>> qualifiedCalls = composeQualifyingCallsList(targets, allCalls);
    return buildAndAnnotateTruthOverlappingGenotype(sample, targets, truthGenotype, truthCopyNumber, truthAllele, qualifiedCalls);
}

Example 14 with EMPTY

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

the class EvaluateCopyNumberTriStateCalls method buildAndAnnotateTruthOverlappingGenotype.

private Genotype buildAndAnnotateTruthOverlappingGenotype(final String sample, final VariantContext truth, final List<VariantContext> calls, final TargetCollection<Target> targets) {
    final Genotype truthGenotype = truth.getGenotype(sample);
    // if there is no truth genotype for that sample, we output the "empty" genotype.
    if (truthGenotype == null) {
        return GenotypeBuilder.create(sample, Collections.emptyList());
    }
    final int truthCopyNumber = GATKProtectedVariantContextUtils.getAttributeAsInt(truthGenotype, GS_COPY_NUMBER_FORMAT_KEY, truthNeutralCopyNumber);
    final CopyNumberTriStateAllele truthAllele = copyNumberToTrueAllele(truthCopyNumber);
    final List<Pair<VariantContext, Genotype>> allCalls = calls.stream().map(vc -> new ImmutablePair<>(vc, vc.getGenotype(sample))).filter(pair -> pair.getRight() != null).filter(pair -> GATKProtectedVariantContextUtils.getAttributeAsString(pair.getRight(), XHMMSegmentGenotyper.DISCOVERY_KEY, XHMMSegmentGenotyper.DISCOVERY_FALSE).equals(XHMMSegmentGenotyper.DISCOVERY_TRUE)).collect(Collectors.toList());
    final List<Pair<VariantContext, Genotype>> qualifiedCalls = composeQualifyingCallsList(targets, allCalls);
    return buildAndAnnotateTruthOverlappingGenotype(sample, targets, truthGenotype, truthCopyNumber, truthAllele, qualifiedCalls);
}

Example 15 with EMPTY

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

the class WithdrawalView method setAddressColumnCellFactory.

///////////////////////////////////////////////////////////////////////////////////////////
// ColumnCellFactories
///////////////////////////////////////////////////////////////////////////////////////////
private void setAddressColumnCellFactory() {
    addressColumn.setCellValueFactory((addressListItem) -> new ReadOnlyObjectWrapper<>(addressListItem.getValue()));
    addressColumn.setCellFactory(new Callback<TableColumn<WithdrawalListItem, WithdrawalListItem>, TableCell<WithdrawalListItem, WithdrawalListItem>>() {

        @Override
        public TableCell<WithdrawalListItem, WithdrawalListItem> call(TableColumn<WithdrawalListItem, WithdrawalListItem> column) {
            return new TableCell<WithdrawalListItem, WithdrawalListItem>() {

                private HyperlinkWithIcon hyperlinkWithIcon;

                @Override
                public void updateItem(final WithdrawalListItem item, boolean empty) {
                    super.updateItem(item, empty);
                    if (item != null && !empty) {
                        String address = item.getAddressString();
                        hyperlinkWithIcon = new HyperlinkWithIcon(address, AwesomeIcon.EXTERNAL_LINK);
                        hyperlinkWithIcon.setOnAction(event -> openBlockExplorer(item));
                        hyperlinkWithIcon.setTooltip(new Tooltip("Open external blockchain explorer for " + "address: " + address));
                        setGraphic(hyperlinkWithIcon);
                    } else {
                        setGraphic(null);
                        if (hyperlinkWithIcon != null)
                            hyperlinkWithIcon.setOnAction(null);
                    }
                }
            };
        }
    });
}