Examples with ExternalID org.orcid.jaxb.model.v3.dev1.record.ExternalID used on opensource projects

Example 61 with ExternalID

use of org.orcid.jaxb.model.v3.dev1.record.ExternalID in project ORCID-Source by ORCID.

the class WorkManagerImpl method createWorks.

/**
 * Add a list of works to the given profile
 *
 * @param works
 *            The list of works that want to be added
 * @param orcid
 *            The id of the user we want to add the works to
 *
 * @return the work bulk with the put codes of the new works or the error
 *         that indicates why a work can't be added
 */
@Override
@Transactional
public WorkBulk createWorks(String orcid, WorkBulk workBulk) {
    SourceEntity sourceEntity = sourceManager.retrieveSourceEntity();
    List<Work> existingWorks = this.findWorks(orcid);
    if (workBulk.getBulk() != null && !workBulk.getBulk().isEmpty()) {
        List<BulkElement> bulk = workBulk.getBulk();
        Set<ExternalID> existingExternalIdentifiers = buildExistingExternalIdsSet(existingWorks, sourceEntity.getSourceId());
        if ((existingWorks.size() + bulk.size()) > this.maxNumOfActivities) {
            throw new ExceedMaxNumberOfElementsException();
        }
        // Check bulk size
        if (bulk.size() > maxBulkSize) {
            Locale locale = localeManager.getLocale();
            throw new IllegalArgumentException(messageSource.getMessage("apiError.validation_too_many_elements_in_bulk.exception", new Object[] { maxBulkSize }, locale));
        }
        for (int i = 0; i < bulk.size(); i++) {
            if (Work.class.isAssignableFrom(bulk.get(i).getClass())) {
                Work work = (Work) bulk.get(i);
                try {
                    activityValidator.validateWork(work, sourceEntity, true, true, null);
                    // Validate it is not duplicated
                    if (work.getExternalIdentifiers() != null) {
                        for (ExternalID extId : work.getExternalIdentifiers().getExternalIdentifier()) {
                            // normalise the provided ID
                            extId.setNormalized(new TransientNonEmptyString(norm.normalise(extId.getType(), extId.getValue())));
                            // If the external id exists and is a SELF identifier, then mark it as duplicated
                            if (existingExternalIdentifiers.contains(extId) && Relationship.SELF.equals(extId.getRelationship())) {
                                Map<String, String> params = new HashMap<String, String>();
                                params.put("clientName", sourceEntity.getSourceName());
                                throw new OrcidDuplicatedActivityException(params);
                            }
                        }
                    }
                    // Save the work
                    WorkEntity workEntity = jpaJaxbWorkAdapter.toWorkEntity(work);
                    ProfileEntity profile = profileEntityCacheManager.retrieve(orcid);
                    workEntity.setOrcid(orcid);
                    workEntity.setAddedToProfileDate(new Date());
                    // Set source id
                    if (sourceEntity.getSourceProfile() != null) {
                        workEntity.setSourceId(sourceEntity.getSourceProfile().getId());
                    }
                    if (sourceEntity.getSourceClient() != null) {
                        workEntity.setClientSourceId(sourceEntity.getSourceClient().getId());
                    }
                    setIncomingWorkPrivacy(workEntity, profile);
                    DisplayIndexCalculatorHelper.setDisplayIndexOnNewEntity(workEntity, true);
                    workDao.persist(workEntity);
                    // Update the element in the bulk
                    Work updatedWork = jpaJaxbWorkAdapter.toWork(workEntity);
                    bulk.set(i, updatedWork);
                    // Add the work extIds to the list of existing external identifiers
                    addExternalIdsToExistingSet(updatedWork, existingExternalIdentifiers);
                } catch (Exception e) {
                    // Get the exception
                    OrcidError orcidError = orcidCoreExceptionMapper.getV3OrcidError(e);
                    bulk.set(i, orcidError);
                }
            }
        }
        workDao.flush();
    }
    return workBulk;
}

Example 62 with ExternalID

use of org.orcid.jaxb.model.v3.dev1.record.ExternalID in project ORCID-Source by ORCID.

the class ExternalIDNormalizedValueTest method testEqualsAndHashcode.

@Test
public void testEqualsAndHashcode() {
    ExternalID id1 = new ExternalID();
    id1.setType("doi");
    id1.setValue("VALUE");
    id1.setNormalized(new TransientNonEmptyString("value"));
    ExternalID id2 = new ExternalID();
    id2.setType("doi");
    id2.setValue("value");
    id2.setNormalized(new TransientNonEmptyString("value"));
    assertEquals(id1, id2);
    assertEquals(id1.hashCode(), id2.hashCode());
    Set<ExternalID> set1 = new HashSet<ExternalID>();
    id1.getNormalized().setValue("value");
    set1.add(id1);
    set1.add(id2);
    assertEquals(1, set1.size());
    id1.getNormalized().setValue("VALUE");
    assertNotEquals(id1, id2);
    assertNotEquals(id1.hashCode(), id2.hashCode());
    Set<ExternalID> set2 = new HashSet<ExternalID>();
    set2.add(id1);
    set2.add(id2);
    assertEquals(2, set2.size());
}

Example 63 with ExternalID

use of org.orcid.jaxb.model.v3.dev1.record.ExternalID in project ORCID-Source by ORCID.

the class TransientNonEmptyStringTest method testMarshal.

/**
 *    <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 *    <common:external-ids xmlns:internal="http://www.orcid.org/ns/internal" xmlns:address="http://www.orcid.org/ns/address" xmlns:email="http://www.orcid.org/ns/email" xmlns:history="http://www.orcid.org/ns/history" xmlns:employment="http://www.orcid.org/ns/employment" xmlns:person="http://www.orcid.org/ns/person" xmlns:education="http://www.orcid.org/ns/education" xmlns:other-name="http://www.orcid.org/ns/other-name" xmlns:personal-details="http://www.orcid.org/ns/personal-details" xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:common="http://www.orcid.org/ns/common" xmlns:record="http://www.orcid.org/ns/record" xmlns:keyword="http://www.orcid.org/ns/keyword" xmlns:activities="http://www.orcid.org/ns/activities" xmlns:deprecated="http://www.orcid.org/ns/deprecated" xmlns:external-identifier="http://www.orcid.org/ns/external-identifier" xmlns:funding="http://www.orcid.org/ns/funding" xmlns:error="http://www.orcid.org/ns/error" xmlns:preferences="http://www.orcid.org/ns/preferences" xmlns:work="http://www.orcid.org/ns/work" xmlns:researcher-url="http://www.orcid.org/ns/researcher-url" xmlns:peer-review="http://www.orcid.org/ns/peer-review">
 *        <common:external-id>
 *            <common:external-id-type>doi</common:external-id-type>
 *            <common:external-id-value>value</common:external-id-value>
 *            <common:external-id-normalized transient="true">normalized-value</common:external-id-normalized>
 *        </common:external-id>
 *    </common:external-ids>
 * @throws JAXBException
 * @throws SAXException
 * @throws IOException
 */
@Test
public void testMarshal() throws JAXBException, SAXException, IOException {
    ExternalIDs ids = new ExternalIDs();
    ExternalID id = new ExternalID();
    id.setType("doi");
    id.setValue("value");
    id.setNormalized(new TransientNonEmptyString("normalized-value"));
    ids.getExternalIdentifier().add(id);
    JAXBContext context = JAXBContext.newInstance(ExternalIDs.class);
    Marshaller marshaller = context.createMarshaller();
    StringWriter sw = new StringWriter();
    marshaller.marshal(ids, sw);
    assertTrue(sw.toString().contains("<common:external-id-normalized transient=\"true\">normalized-value</common:external-id-normalized>"));
    SchemaFactory factory = SchemaFactory.newInstance("http://www.w3.org/2001/XMLSchema");
    Schema schema = factory.newSchema(getClass().getResource("/common_3.0_dev1/common-3.0_dev1.xsd"));
    Validator validator = schema.newValidator();
    validator.validate(new JAXBSource(context, ids));
}

Example 64 with ExternalID

use of org.orcid.jaxb.model.v3.dev1.record.ExternalID in project ORCID-Source by ORCID.

the class ActivitiesGroupGenerator_GroupingWorksTest method testNormalizedGrouping.

@Test
public void testNormalizedGrouping() {
    ActivitiesGroupGenerator generator = new ActivitiesGroupGenerator();
    List<WorkSummary> sums = new ArrayList<WorkSummary>();
    for (int i = 0; i < 2; i++) {
        String title = "work-" + i;
        WorkSummary work = new WorkSummary();
        // Set title
        WorkTitle workTitle = new WorkTitle();
        workTitle.setTitle(new Title(title));
        work.setTitle(workTitle);
        ExternalIDs wei = new ExternalIDs();
        ExternalID e1 = new ExternalID();
        e1.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.DOI.value());
        e1.setValue("a");
        e1.setNormalized(new TransientNonEmptyString("a"));
        wei.getExternalIdentifier().add(e1);
        work.setExternalIdentifiers(wei);
        sums.add(work);
    }
    sums.get(0).getExternalIdentifiers().getExternalIdentifier().get(0).setValue("A");
    generator.group(sums.get(0));
    generator.group(sums.get(1));
    assertEquals(1, generator.getGroups().size());
    checkActivitiesBelongsToTheSameGroup(generator.getGroups(), sums.get(0), sums.get(1));
    for (int i = 2; i < 4; i++) {
        String title = "work-" + i;
        WorkSummary work = new WorkSummary();
        // Set title
        WorkTitle workTitle = new WorkTitle();
        workTitle.setTitle(new Title(title));
        work.setTitle(workTitle);
        ExternalIDs wei = new ExternalIDs();
        ExternalID e1 = new ExternalID();
        e1.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
        e1.setValue("https://dx.doi.org/10/UPPER");
        e1.setNormalized(new TransientNonEmptyString("10/upper"));
        wei.getExternalIdentifier().add(e1);
        work.setExternalIdentifiers(wei);
        sums.add(work);
    }
    sums.get(0).getExternalIdentifiers().getExternalIdentifier().get(0).setValue("http://doi.org/10/upper");
    generator.group(sums.get(2));
    generator.group(sums.get(3));
    assertEquals(2, generator.getGroups().size());
    checkActivitiesBelongsToTheSameGroup(generator.getGroups(), sums.get(0), sums.get(1));
    checkActivitiesBelongsToTheSameGroup(generator.getGroups(), sums.get(2), sums.get(3));
}

Example 65 with ExternalID

use of org.orcid.jaxb.model.v3.dev1.record.ExternalID in project ORCID-Source by ORCID.

the class ActivitiesGroupGenerator_GroupingWorksTest method generateWorks.

/**
 * work-1 -> ARG(A), ARG(B), ARG(C)
 * work-2 -> ARG(C), ARG(D), ARG(E)
 * work-3 -> ARG(X), ARG(Y), ARG(Z)
 * work-4 -> ARG(Y), ARG(B), ARG(1)
 * work-5 -> ARG(M), ARG(N), ARG(O)
 * work-6 -> ARXIV(A), ARXIV(B), ARXIV(C)
 * work-7 -> DOI(1), DOI(2), ARIXV(B)
 * work-8 -> No external identifiers
 * work-9 -> No external identifiers
 * work-10 -> ISSN(1), ISSN(2), ISSN(3)
 * work-11 -> ISSN(3), ISSN(4), ISSN(5)
 * work-12 -> DOI(1), ISSN(1)
 * work-13 -> DOI(1), ISSN(4)
 */
private Map<String, WorkSummary> generateWorks() {
    Map<String, WorkSummary> result = new HashMap<String, WorkSummary>();
    for (int i = 1; i < 14; i++) {
        String title = "work-" + i;
        WorkSummary work = new WorkSummary();
        // Set title
        WorkTitle workTitle = new WorkTitle();
        workTitle.setTitle(new Title(title));
        work.setTitle(workTitle);
        ExternalIDs wei = new ExternalIDs();
        switch(i) {
            case 1:
                ExternalID e1 = new ExternalID();
                e1.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e1.setValue("A");
                ExternalID e2 = new ExternalID();
                e2.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e2.setValue("B");
                ExternalID e3 = new ExternalID();
                e3.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e3.setValue("C");
                wei.getExternalIdentifier().add(e1);
                wei.getExternalIdentifier().add(e2);
                wei.getExternalIdentifier().add(e3);
                break;
            case 2:
                ExternalID e4 = new ExternalID();
                e4.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e4.setValue("C");
                ExternalID e5 = new ExternalID();
                e5.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e5.setValue("D");
                ExternalID e6 = new ExternalID();
                e6.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e6.setValue("E");
                wei.getExternalIdentifier().add(e4);
                wei.getExternalIdentifier().add(e5);
                wei.getExternalIdentifier().add(e6);
                break;
            case 3:
                ExternalID e7 = new ExternalID();
                e7.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e7.setValue("X");
                ExternalID e8 = new ExternalID();
                e8.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e8.setValue("Y");
                ExternalID e9 = new ExternalID();
                e9.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e9.setValue("Z");
                wei.getExternalIdentifier().add(e7);
                wei.getExternalIdentifier().add(e8);
                wei.getExternalIdentifier().add(e9);
                break;
            case 4:
                ExternalID e10 = new ExternalID();
                e10.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e10.setValue("Y");
                ExternalID e11 = new ExternalID();
                e11.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e11.setValue("B");
                ExternalID e12 = new ExternalID();
                e12.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e12.setValue("1");
                wei.getExternalIdentifier().add(e10);
                wei.getExternalIdentifier().add(e11);
                wei.getExternalIdentifier().add(e12);
                break;
            case 5:
                ExternalID e13 = new ExternalID();
                e13.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e13.setValue("M");
                ExternalID e14 = new ExternalID();
                e14.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e14.setValue("N");
                ExternalID e15 = new ExternalID();
                e15.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.AGR.value());
                e15.setValue("O");
                wei.getExternalIdentifier().add(e13);
                wei.getExternalIdentifier().add(e14);
                wei.getExternalIdentifier().add(e15);
                break;
            case 6:
                ExternalID e16 = new ExternalID();
                e16.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ARXIV.value());
                e16.setValue("A");
                ExternalID e17 = new ExternalID();
                e17.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ARXIV.value());
                e17.setValue("B");
                ExternalID e18 = new ExternalID();
                e18.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ARXIV.value());
                e18.setValue("C");
                wei.getExternalIdentifier().add(e16);
                wei.getExternalIdentifier().add(e17);
                wei.getExternalIdentifier().add(e18);
                break;
            case 7:
                ExternalID e19 = new ExternalID();
                e19.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.DOI.value());
                e19.setValue("1");
                ExternalID e20 = new ExternalID();
                e20.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.DOI.value());
                e20.setValue("2");
                ExternalID e21 = new ExternalID();
                e21.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ARXIV.value());
                e21.setValue("B");
                wei.getExternalIdentifier().add(e19);
                wei.getExternalIdentifier().add(e20);
                wei.getExternalIdentifier().add(e21);
                break;
            case 10:
                ExternalID e22 = new ExternalID();
                e22.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e22.setValue("1");
                ExternalID e23 = new ExternalID();
                e23.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e23.setValue("2");
                ExternalID e24 = new ExternalID();
                e24.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e24.setValue("3");
                wei.getExternalIdentifier().add(e22);
                wei.getExternalIdentifier().add(e23);
                wei.getExternalIdentifier().add(e24);
                break;
            case 11:
                ExternalID e25 = new ExternalID();
                e25.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e25.setValue("3");
                ExternalID e26 = new ExternalID();
                e26.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e26.setValue("3");
                ExternalID e27 = new ExternalID();
                e27.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e27.setValue("3");
                wei.getExternalIdentifier().add(e25);
                wei.getExternalIdentifier().add(e26);
                wei.getExternalIdentifier().add(e27);
                break;
            case 12:
                ExternalID e28 = new ExternalID();
                e28.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.DOI.value());
                e28.setValue("1");
                ExternalID e29 = new ExternalID();
                e29.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e29.setValue("1");
                wei.getExternalIdentifier().add(e28);
                wei.getExternalIdentifier().add(e29);
                break;
            case 13:
                ExternalID e30 = new ExternalID();
                e30.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.DOI.value());
                e30.setValue("1");
                ExternalID e31 = new ExternalID();
                e31.setType(org.orcid.jaxb.model.message.WorkExternalIdentifierType.ISSN.value());
                e31.setValue("4");
                wei.getExternalIdentifier().add(e30);
                wei.getExternalIdentifier().add(e31);
                break;
        }
        work.setExternalIdentifiers(wei);
        result.put(title, work);
    }
    return result;
}