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

Example 56 with StringUtils.isBlank

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

the class SalesForceManagerImpl method createContact.

@Override
public void createContact(Contact contact) {
    String accountId = contact.getAccountId();
    if (StringUtils.isBlank(contact.getEmail())) {
        String contactOrcid = contact.getOrcid();
        Email primaryEmail = emailManager.getEmails(contactOrcid).getEmails().stream().filter(e -> e.isPrimary()).findFirst().get();
        contact.setEmail(primaryEmail.getEmail());
    }
    List<Contact> existingContacts = salesForceDao.retrieveAllContactsByAccountId(accountId);
    Optional<Contact> existingContact = existingContacts.stream().filter(c -> {
        if ((contact.getOrcid() != null && contact.getOrcid().equals(c.getOrcid())) || (contact.getEmail() != null && contact.getEmail().equals(c.getEmail()))) {
            return true;
        }
        return false;
    }).findFirst();
    String contactId = existingContact.isPresent() ? existingContact.get().getId() : salesForceDao.createContact(contact);
    List<Contact> existingContactsWithRoles = salesForceDao.retrieveContactsWithRolesByAccountId(accountId, true);
    Optional<ContactRole> existingContactRole = existingContactsWithRoles.stream().filter(c -> contactId.equals(c.getId()) && ContactRoleType.OTHER_CONTACT.equals(c.getRole().getRoleType())).map(c -> c.getRole()).findFirst();
    if (existingContactRole.isPresent()) {
        ContactRole contactRole = existingContactRole.get();
        if (!contactRole.isCurrent()) {
            contactRole.setCurrent(true);
            salesForceDao.updateContactRole(contactRole);
        }
    } else {
        ContactRole contactRole = new ContactRole();
        contactRole.setContactId(contactId);
        contactRole.setRoleType(ContactRoleType.OTHER_CONTACT);
        contactRole.setAccountId(contact.getAccountId());
        salesForceDao.createContactRole(contactRole);
    }
    addSalesForceConnection(accountId, contact);
    salesForceContactsCache.remove(accountId);
}

Example 57 with StringUtils.isBlank

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

the class GeneSetDaoImpl method findByName.

@Override
public Collection<GeneSet> findByName(String name, Taxon taxon) {
    StopWatch timer = new StopWatch();
    timer.start();
    if (StringUtils.isBlank(name))
        return new HashSet<>();
    assert taxon != null;
    // slow? would it be faster to just findByName and then restrict taxon?
    List result = this.getSessionFactory().getCurrentSession().createQuery("select gs from GeneSet gs join gs.members gm join gm.gene g where g.taxon = :taxon and gs.name like :query order by gs.name").setParameter("query", name + "%").setParameter("taxon", taxon).list();
    if (timer.getTime() > 500)
        AbstractDao.log.info("Find geneSets by name took " + timer.getTime() + "ms query=" + name + " taxon=" + taxon);
    // noinspection unchecked
    return (Collection<GeneSet>) result;
}

Example 58 with StringUtils.isBlank

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

the class ArrayDesignSequenceProcessingServiceImpl method parseAccessionFile.

/**
 * @param sequenceIdentifierFile with two columns: first is probe id, second is genbank accession.
 */
private Map<String, String> parseAccessionFile(InputStream sequenceIdentifierFile) throws IOException {
    try (BufferedReader br = new BufferedReader(new InputStreamReader(sequenceIdentifierFile))) {
        String line;
        StopWatch timer = new StopWatch();
        timer.start();
        Map<String, String> probe2acc = new HashMap<>();
        int count = 0;
        int totalLines = 0;
        while ((line = br.readLine()) != null) {
            String[] fields = line.split("\t");
            ++totalLines;
            if (fields.length < 2) {
                continue;
            }
            String probeName = fields[0];
            String seqAcc = fields[1];
            if (StringUtils.isBlank(seqAcc)) {
                continue;
            }
            probe2acc.put(probeName, seqAcc);
            if (++count % 2000 == 0 && timer.getTime() > 10000) {
                ArrayDesignSequenceProcessingServiceImpl.log.info(count + " / " + totalLines + " probes read so far have identifiers");
            }
        }
        ArrayDesignSequenceProcessingServiceImpl.log.info(count + " / " + totalLines + " probes have accessions");
        return probe2acc;
    }
}

Example 59 with StringUtils.isBlank

use of org.apache.commons.lang3.StringUtils.isBlank 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 60 with StringUtils.isBlank

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

the class GeneralSearchControllerImpl method ajaxSearch.

@Override
public JsonReaderResponse<SearchResult> ajaxSearch(SearchSettingsValueObject settingsValueObject) {
    SearchSettings settings = SearchSettingsValueObject.toEntity(settingsValueObject);
    List<SearchResult> finalResults = new ArrayList<>();
    if (settings == null || StringUtils.isBlank(settings.getQuery()) || StringUtils.isBlank(settings.getQuery().replaceAll("\\*", ""))) {
        // FIXME validate input better, and return error.
        BaseFormController.log.info("No query or invalid.");
        // return new ListRange( finalResults );
        throw new IllegalArgumentException("Query '" + settings + "' was invalid");
    }
    StopWatch watch = new StopWatch();
    watch.start();
    ((SearchSettingsImpl) settings).setDoHighlighting(true);
    Map<Class<?>, List<SearchResult>> searchResults = searchService.search(settings);
    watch.stop();
    if (watch.getTime() > 500) {
        BaseFormController.log.info("Search service work on: " + settings + " took " + watch.getTime() + " ms");
    }
    /*
         * FIXME sort by the number of hits per class, so smallest number of hits is at the top.
         */
    watch.reset();
    watch.start();
    if (searchResults != null) {
        for (Class<?> clazz : searchResults.keySet()) {
            List<SearchResult> results = searchResults.get(clazz);
            if (results.size() == 0)
                continue;
            BaseFormController.log.info("Search for: " + settings + "; result: " + results.size() + " " + clazz.getSimpleName() + "s");
            /*
                 * Now put the valueObjects inside the SearchResults in score order.
                 */
            Collections.sort(results);
            this.fillValueObjects(clazz, results, settings);
            finalResults.addAll(results);
        }
    }
    if (watch.getTime() > 500) {
        BaseFormController.log.info("Final unpacking of results for query:" + settings + " took " + watch.getTime() + " ms");
    }
    return new JsonReaderResponse<>(finalResults);
}