Example usage for org.apache.commons.lang3 StringUtils defaultIfBlank

Introduction

In this page you can find the example usage for org.apache.commons.lang3 StringUtils defaultIfBlank.

Prototype

public static <T extends CharSequence> T defaultIfBlank(final T str, final T defaultStr) 

Source Link

Document

Returns either the passed in CharSequence, or if the CharSequence is whitespace, empty ("") or null , the value of defaultStr .

 StringUtils.defaultIfBlank(null, "NULL")  = "NULL" StringUtils.defaultIfBlank("", "NULL")    = "NULL" StringUtils.defaultIfBlank(" ", "NULL")   = "NULL" StringUtils.defaultIfBlank("bat", "NULL") = "bat" StringUtils.defaultIfBlank("", null)      = null 

Usage

From source file:org.phenotips.data.permissions.internal.DefaultPermissionsConfiguration.java

@Override
public String getDefaultVisibility() {
    DocumentReference preferencesDocument = this.resolver.resolve(TEMPLATE_DOCUMENT);
    DocumentReference configurationClassDocument = this.resolver.resolve(Visibility.CLASS_REFERENCE);
    String visibilityName = (String) this.dab.getProperty(new ObjectPropertyReference("visibility",
            new BaseObjectReference(configurationClassDocument, 0, preferencesDocument)));
    return StringUtils.defaultIfBlank(visibilityName, null);
}

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From source file:org.phenotips.data.permissions.internal.RightsUpdateEventListener.java

private Visibility getVisibility(XWikiDocument doc) {
    String visibility = null;/*from   ww w . jav  a2 s . c om*/
    BaseObject visibilityObj = doc.getXObject(Visibility.CLASS_REFERENCE);
    if (visibilityObj != null) {
        visibility = visibilityObj.getStringValue("visibility");
    }
    return this.manager.resolveVisibility(StringUtils.defaultIfBlank(visibility, "private"));
}

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From source file:org.phenotips.ontology.internal.solr.AbstractOBOSolrOntologyService.java

/**
 * Add an ontology to the index./*w ww  .ja v  a2s . c o  m*/
 *
 * @param ontologyUrl the address from where to get the ontology file
 * @return {@code 0} if the indexing succeeded, {@code 1} if writing to the Solr server failed, {@code 2} if the
 *         specified URL is invalid
 */
protected int index(String ontologyUrl) {
    String realOntologyUrl = StringUtils.defaultIfBlank(ontologyUrl, getDefaultOntologyLocation());

    SolrUpdateGenerator generator = new SolrUpdateGenerator();
    Map<String, Double> fieldSelection = new HashMap<String, Double>();
    Map<String, TermData> data = generator.transform(realOntologyUrl, fieldSelection);
    if (data == null) {
        return 2;
    }
    try {
        Collection<SolrInputDocument> termBatch = new HashSet<SolrInputDocument>();
        Iterator<Map.Entry<String, TermData>> dataIterator = data.entrySet().iterator();
        int batchCounter = 0;
        while (dataIterator.hasNext()) {
            /* Resetting when the batch fills */
            if (batchCounter == getSolrDocsPerBatch()) {
                commitTerms(termBatch);
                termBatch = new HashSet<>();
                batchCounter = 0;
            }
            Map.Entry<String, TermData> item = dataIterator.next();
            SolrInputDocument doc = new SolrInputDocument();
            for (Map.Entry<String, Collection<String>> property : item.getValue().entrySet()) {
                String name = property.getKey();
                for (String value : property.getValue()) {
                    doc.addField(name, value, ParameterPreparer.DEFAULT_BOOST.floatValue());
                }
            }
            termBatch.add(doc);
            batchCounter++;
        }
        commitTerms(termBatch);
        return 0;
    } catch (SolrServerException ex) {
        this.logger.warn("Failed to index ontology: {}", ex.getMessage());
    } catch (IOException ex) {
        this.logger.warn("Failed to communicate with the Solr server while indexing ontology: {}",
                ex.getMessage());
    } catch (OutOfMemoryError ex) {
        this.logger.warn("Failed to add terms to the Solr. Ran out of memory. {}", ex.getMessage());
    }
    return 1;
}

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From source file:org.phenotips.ontology.internal.solr.HumanPhenotypeOntology.java

/**
 * Add an ontology to the index.//w w w .j av  a2s. c o  m
 *
 * @param ontologyUrl the address from where to get the ontology file
 * @return {@code 0} if the indexing succeeded, {@code 1} if writing to the Solr server failed, {@code 2} if the
 *         specified URL is invalid
 */
protected int index(String ontologyUrl) {
    String realOntologyUrl = StringUtils.defaultIfBlank(ontologyUrl, getDefaultOntologyLocation());

    SolrUpdateGenerator generator = new SolrUpdateGenerator();
    Map<String, Double> fieldSelection = new HashMap<String, Double>();
    Map<String, TermData> data = generator.transform(realOntologyUrl, fieldSelection);
    if (data == null) {
        return 2;
    }
    Collection<SolrInputDocument> allTerms = new HashSet<SolrInputDocument>();
    for (Map.Entry<String, TermData> item : data.entrySet()) {
        SolrInputDocument doc = new SolrInputDocument();
        for (Map.Entry<String, Collection<String>> property : item.getValue().entrySet()) {
            String name = property.getKey();
            for (String value : property.getValue()) {
                doc.addField(name, value, ParameterPreparer.DEFAULT_BOOST.floatValue());
            }
        }
        allTerms.add(doc);
    }
    try {
        this.externalServicesAccess.getServer().add(allTerms);
        this.externalServicesAccess.getServer().commit();
        this.externalServicesAccess.getCache().removeAll();
        return 0;
    } catch (SolrServerException ex) {
        this.logger.warn("Failed to index ontology: {}", ex.getMessage());
    } catch (IOException ex) {
        this.logger.warn("Failed to communicate with the Solr server while indexing ontology: {}",
                ex.getMessage());
    }
    return 1;
}

---

From source file:org.phenotips.tool.xarimporter.ImportMojo.java

private void toExtension(DefaultLocalExtension extension, Model model, ComponentManager componentManager)
        throws ComponentLookupException {
    extension.setName(getPropertyString(model, MPNAME_NAME, model.getName()));
    extension.setSummary(getPropertyString(model, MPNAME_SUMMARY, model.getDescription()));
    extension.setWebsite(getPropertyString(model, MPNAME_WEBSITE, model.getUrl()));

    // authors/*from   ww w  . j a v a 2 s . c o  m*/
    for (Developer developer : model.getDevelopers()) {
        URL authorURL = null;
        if (developer.getUrl() != null) {
            try {
                authorURL = new URL(developer.getUrl());
            } catch (MalformedURLException e) {
                this.getLog().warn(
                        "Invalid URL for developer [" + developer.getId() + "]: [" + developer.getUrl() + "]");
            }
        }

        extension.addAuthor(new DefaultExtensionAuthor(
                StringUtils.defaultIfBlank(developer.getName(), developer.getId()), authorURL));
    }

    // licenses
    ExtensionLicenseManager licenseManager = componentManager.getInstance(ExtensionLicenseManager.class);
    for (License license : model.getLicenses()) {
        extension.addLicense(getExtensionLicense(license, licenseManager));
    }

    // features
    String featuresString = getProperty(model, MPNAME_FEATURES);
    if (StringUtils.isNotBlank(featuresString)) {
        featuresString = featuresString.replaceAll("[\r\n]", "");
        ConverterManager converter = componentManager.getInstance(ConverterManager.class);
        extension.setFeatures(converter.<Collection<String>>convert(List.class, featuresString));
    }

    // dependencies
    for (Dependency mavenDependency : model.getDependencies()) {
        if (!mavenDependency.isOptional() && (mavenDependency.getScope().equals("compile")
                || mavenDependency.getScope().equals("runtime"))) {
            extension.addDependency(new DefaultExtensionDependency(
                    mavenDependency.getGroupId() + ':' + mavenDependency.getArtifactId(),
                    new DefaultVersionConstraint(mavenDependency.getVersion())));
        }
    }
}

---

From source file:org.phenotips.vocabulary.internal.GeneNomenclature.java

private SolrQuery produceDynamicSolrParams(Map<String, String> staticOptions, String originalQuery,
        Integer rows, String sort, String customFilter) {
    String escapedQuery = ClientUtils.escapeQueryChars(originalQuery.trim());

    SolrQuery params = new SolrQuery(escapedQuery);
    for (Map.Entry<String, String> option : staticOptions.entrySet()) {
        params.set(option.getKey(), option.getValue());
    }/*ww w  .j  a  va2  s.  c  o m*/
    params.setRows(rows);
    if (StringUtils.isNotBlank(sort)) {
        params.add(CommonParams.SORT, sort);
    }
    params.add(CommonParams.FQ, StringUtils.defaultIfBlank(customFilter, "status:Approved"));
    return params;
}

---

From source file:org.phenotips.vocabulary.internal.solr.AbstractCSVSolrVocabulary.java

/**
 * Add a vocabulary to the index.//from   ww w  . j a va2 s .  com
 *
 * @param sourceUrl the URL to be indexed
 * @return {@code 0} if the indexing succeeded, {@code 1} if writing to the Solr server failed, {@code 2} if the
 *         specified URL is invalid
 */
protected int index(String sourceUrl) {
    String url = StringUtils.defaultIfBlank(sourceUrl, getDefaultSourceLocation());
    Collection<SolrInputDocument> data = null;
    try {
        data = load(new URL(url));
    } catch (MalformedURLException e) {
        return 2;
    }
    if (data == null) {
        return 2;
    }
    try {
        Collection<SolrInputDocument> termBatch = new HashSet<>();
        Iterator<SolrInputDocument> dataIterator = data.iterator();
        int batchCounter = 0;
        while (dataIterator.hasNext()) {
            /* Resetting when the batch fills */
            if (batchCounter == getSolrDocsPerBatch()) {
                commitTerms(termBatch);
                termBatch = new HashSet<>();
                batchCounter = 0;
            }
            SolrInputDocument item = dataIterator.next();
            extendTerm(new SolrVocabularyInputTerm(item, this));
            termBatch.add(item);
            batchCounter++;
        }
        commitTerms(termBatch);
        return 0;
    } catch (SolrServerException ex) {
        this.logger.warn("Failed to index vocabulary: {}", ex.getMessage());
    } catch (IOException ex) {
        this.logger.warn("Failed to communicate with the Solr server while indexing vocabulary: {}",
                ex.getMessage());
    } catch (OutOfMemoryError ex) {
        this.logger.warn("Failed to add terms to the Solr. Ran out of memory. {}", ex.getMessage());
    }
    return 1;
}

---

From source file:org.phenotips.vocabulary.internal.solr.AbstractOBOSolrVocabulary.java

/**
 * Load vocabulary data from a provided source url.
 *
 * @param sourceUrl the address from where to get the vocabulary source file
 * @return vocabulary data, if exists/*w  ww.  j a  v  a 2s  . c o  m*/
 */
protected Map<String, TermData> load(final String sourceUrl) {
    String realOntologyUrl = StringUtils.defaultIfBlank(sourceUrl, getDefaultSourceLocation());

    SolrUpdateGenerator generator = new SolrUpdateGenerator();
    Map<String, Double> fieldSelection = new HashMap<>();
    return generator.transform(realOntologyUrl, fieldSelection);
}

---

From source file:org.phenotips.vocabulary.internal.solr.HumanPhenotypeOntology.java

private SolrQuery addDynamicQueryParameters(String originalQuery, Integer rows, String sort, String customFq,
        boolean isId, SolrQuery query) {
    String queryString = originalQuery.trim();
    String escapedQuery = ClientUtils.escapeQueryChars(queryString);
    if (isId) {/*  w  w w.  j av a  2s . co  m*/
        query.setFilterQueries(StringUtils.defaultIfBlank(customFq,
                new MessageFormat("id:{0} alt_id:{0}").format(new String[] { escapedQuery })));
    } else {
        query.setFilterQueries(StringUtils.defaultIfBlank(customFq, "term_category:HP\\:0000118"));
    }
    query.setQuery(escapedQuery);
    query.set(SpellingParams.SPELLCHECK_Q, queryString);
    query.setRows(rows);
    if (StringUtils.isNotBlank(sort)) {
        for (String sortItem : sort.split("\\s*,\\s*")) {
            query.addSort(StringUtils.substringBefore(sortItem, " "),
                    sortItem.endsWith(" desc") || sortItem.startsWith("-") ? ORDER.desc : ORDER.asc);
        }
    }
    return query;
}

---

From source file:org.phenotips.vocabulary.internal.solr.MendelianInheritanceInMan.java

private SolrQuery addDynamicQueryParameters(String originalQuery, Integer rows, String sort, String customFq,
        SolrQuery query) {/*from   w  w  w .j av  a2 s  .  c  om*/
    String queryString = originalQuery.trim();
    String escapedQuery = ClientUtils.escapeQueryChars(queryString);
    query.setFilterQueries(StringUtils.defaultIfBlank(customFq, "+type:disorder"));
    query.setQuery(escapedQuery);
    query.set(SpellingParams.SPELLCHECK_Q, queryString);
    String lastWord = StringUtils.substringAfterLast(escapedQuery, " ");
    if (StringUtils.isBlank(lastWord)) {
        lastWord = escapedQuery;
    }
    lastWord += "*";
    query.set(DisMaxParams.BQ,
            String.format(
                    "nameSpell:%1$s^20 short_name:%1$s^20 synonymSpell:%1$s^12 text:%1$s^1 textSpell:%1$s^2",
                    lastWord));
    query.setRows(rows);
    if (StringUtils.isNotBlank(sort)) {
        for (String sortItem : sort.split("\\s*,\\s*")) {
            query.addSort(StringUtils.substringBefore(sortItem, " "),
                    sortItem.endsWith(" desc") || sortItem.startsWith("-") ? ORDER.desc : ORDER.asc);
        }
    }
    return query;
}

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