Examples with ExternalID org.orcid.jaxb.model.record_v2.ExternalID used on opensource projects

Example 21 with ExternalID

use of org.orcid.jaxb.model.record_v2.ExternalID in project ORCID-Source by ORCID.

the class ValidateV2_1SamplesTest method testUnmarshallWorks.

@Test
public void testUnmarshallWorks() throws JAXBException, SAXException, URISyntaxException {
    Works works = (Works) unmarshallFromPath("/record_2.1/samples/read_samples/works-2.1.xml", Works.class, "/record_2.1/activities-2.1.xsd");
    assertNotNull(works);
    assertNotNull(works.getLastModifiedDate());
    assertNotNull(works.getLastModifiedDate().getValue());
    assertEquals(3, works.getWorkGroup().size());
    boolean foundWorkWithNoExtIds = false;
    for (WorkGroup group : works.getWorkGroup()) {
        assertNotNull(group.getLastModifiedDate().getValue());
        assertNotNull(group.getIdentifiers().getExternalIdentifier());
        if (group.getIdentifiers().getExternalIdentifier().isEmpty()) {
            WorkSummary summary = group.getWorkSummary().get(0);
            validateSourceInHttps(summary.getSource());
            assertEquals("1", summary.getDisplayIndex());
            assertEquals(1, summary.getExternalIdentifiers().getExternalIdentifier().size());
            assertEquals("doi", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getType());
            assertEquals("https://doi.org/123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getUrl().getValue());
            assertEquals("123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getValue());
            assertEquals("/8888-8888-8888-8880/work/3356", summary.getPath());
            assertEquals("03", summary.getPublicationDate().getDay().getValue());
            assertEquals("03", summary.getPublicationDate().getMonth().getValue());
            assertEquals("2017", summary.getPublicationDate().getYear().getValue());
            assertEquals("Work # 0", summary.getTitle().getTitle().getContent());
            assertEquals(WorkType.CONFERENCE_PAPER, summary.getType());
            assertEquals(Visibility.PUBLIC, summary.getVisibility());
            foundWorkWithNoExtIds = true;
        } else {
            assertEquals(1, group.getIdentifiers().getExternalIdentifier().size());
            ExternalID extId = group.getIdentifiers().getExternalIdentifier().get(0);
            if (extId.getType().equals("arxiv")) {
                assertEquals(Relationship.SELF, extId.getRelationship());
                assertEquals("http://arxiv.org/abs/123456", extId.getUrl().getValue());
                assertEquals("123456", extId.getValue());
            } else if (extId.getType().equals("bibcode")) {
                assertEquals(Relationship.SELF, extId.getRelationship());
                assertEquals("http://adsabs.harvard.edu/abs/4567", extId.getUrl().getValue());
                assertEquals("4567", extId.getValue());
            } else {
                fail("Invalid ext id type " + extId.getType());
            }
            assertEquals(1, group.getWorkSummary().size());
            WorkSummary summary = group.getWorkSummary().get(0);
            validateSourceInHttps(summary.getSource());
            if (summary.getPutCode().equals(Long.valueOf(3357))) {
                assertEquals("1", summary.getDisplayIndex());
                assertEquals(1, summary.getExternalIdentifiers().getExternalIdentifier().size());
                assertEquals("arxiv", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getType());
                assertEquals("http://arxiv.org/abs/123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getUrl().getValue());
                assertEquals("123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getValue());
                assertEquals("/8888-8888-8888-8880/work/3357", summary.getPath());
                assertEquals("02", summary.getPublicationDate().getDay().getValue());
                assertEquals("02", summary.getPublicationDate().getMonth().getValue());
                assertEquals("2017", summary.getPublicationDate().getYear().getValue());
                assertEquals("Work # 1", summary.getTitle().getTitle().getContent());
                assertEquals(WorkType.CONFERENCE_PAPER, summary.getType());
                assertEquals(Visibility.PUBLIC, summary.getVisibility());
            } else if (summary.getPutCode().equals(Long.valueOf(3358))) {
                assertEquals("1", summary.getDisplayIndex());
                assertEquals(1, summary.getExternalIdentifiers().getExternalIdentifier().size());
                assertEquals("bibcode", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getType());
                assertEquals("http://adsabs.harvard.edu/abs/4567", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getUrl().getValue());
                assertEquals("4567", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getValue());
                assertEquals("/8888-8888-8888-8880/work/3358", summary.getPath());
                assertEquals("03", summary.getPublicationDate().getDay().getValue());
                assertEquals("03", summary.getPublicationDate().getMonth().getValue());
                assertEquals("2017", summary.getPublicationDate().getYear().getValue());
                assertEquals("Work # 2", summary.getTitle().getTitle().getContent());
                assertEquals(WorkType.JOURNAL_ARTICLE, summary.getType());
                assertEquals(Visibility.PUBLIC, summary.getVisibility());
            } else {
                fail("Invalid put code " + summary.getPutCode());
            }
        }
    }
    assertTrue(foundWorkWithNoExtIds);
}

Example 22 with ExternalID

use of org.orcid.jaxb.model.record_v2.ExternalID in project ORCID-Source by ORCID.

the class ValidateV2_1IdentifiersTest method testPeerReview.

/** Test both types of identifier here
     * 
     * @throws SAXException
     * @throws IOException
     * @throws JAXBException
     * @throws ParserConfigurationException
     */
@Test
public void testPeerReview() throws SAXException, IOException, JAXBException, ParserConfigurationException {
    PeerReview peerReview = unmarshallFromPath("/record_2.1/samples/read_samples/peer-review-2.1.xml", PeerReview.class);
    ExternalID id = peerReview.getExternalIdentifiers().getExternalIdentifier().get(0);
    assertEquals("source-work-id", id.getType());
    assertEquals("work:external-identifier-id", id.getValue());
    assertEquals(new Url("http://orcid.org"), id.getUrl());
    assertEquals(Relationship.SELF, id.getRelationship());
    ExternalID subjectid = peerReview.getSubjectExternalIdentifier();
    assertEquals("doi", subjectid.getType());
    assertEquals("peer-review:subject-external-identifier-id", subjectid.getValue());
    assertEquals(new Url("http://orcid.org"), subjectid.getUrl());
    assertEquals(Relationship.SELF, subjectid.getRelationship());
    Validator validator = getValidator("peer-review");
    validator.validate(marshall(PeerReview.class, peerReview));
    validator.validate(marshallToDOM(PeerReview.class, peerReview));
    //do the full record too
    peerReview = unmarshallFromPath("/record_2.1/samples/read_samples/peer-review-full-2.1.xml", PeerReview.class);
    id = peerReview.getExternalIdentifiers().getExternalIdentifier().get(0);
    assertEquals("source-work-id", id.getType());
    assertEquals("work:external-identifier-id", id.getValue());
    assertEquals(new Url("http://orcid.org"), id.getUrl());
    assertEquals(Relationship.SELF, id.getRelationship());
    subjectid = peerReview.getSubjectExternalIdentifier();
    assertEquals("doi", subjectid.getType());
    assertEquals("peer-review:subject-external-identifier-id", subjectid.getValue());
    assertEquals(new Url("http://orcid.org"), subjectid.getUrl());
    assertEquals(Relationship.SELF, subjectid.getRelationship());
}

Example 23 with ExternalID

use of org.orcid.jaxb.model.record_v2.ExternalID in project ORCID-Source by ORCID.

the class WorkToCiteprocTranslatorTest method testBibtexWorkTranslationHyperAuthorLiteralAndMissingDOI.

@Test
public void testBibtexWorkTranslationHyperAuthorLiteralAndMissingDOI() {
    Work w = makeWork(bibtexHyperLiteral);
    ExternalIDs wei = new ExternalIDs();
    ExternalID eid = new ExternalID();
    eid.setType(WorkExternalIdentifierType.DOI.name());
    //WorkExternalIdentifierId id = new WorkExternalIdentifierId();
    eid.setValue("10.1234/1234");
    wei.getExternalIdentifier().add(eid);
    w.setWorkExternalIdentifiers(wei);
    WorkToCiteprocTranslator t = new WorkToCiteprocTranslator();
    CSLItemData d = t.toCiteproc(w, null, true);
    Assert.assertEquals(d.getAuthor().length, 1);
    Assert.assertEquals(d.getAuthor()[0].getLiteral(), "Altshuler, D.M. and Durbin, R.M. and Abecasis, G.R. and Bentley, D.R. and Chakravarti, A. and Clark, A.G. and Donnelly, P. and Eichler, E.E. and Flicek, P. and Gabriel, S.B. and Gibbs, R.A. and Gre...");
    Assert.assertEquals(d.getDOI(), "10.1234/1234");
}

Example 24 with ExternalID

use of org.orcid.jaxb.model.record_v2.ExternalID in project ORCID-Source by ORCID.

the class MemberV2ApiServiceDelegator_PeerReviewsTest method testAddPeerReviewWithSameExtIdValueButDifferentExtIdType.

@Test
public void testAddPeerReviewWithSameExtIdValueButDifferentExtIdType() {
    SecurityContextTestUtils.setUpSecurityContext("4444-4444-4444-4444", ScopePathType.READ_LIMITED, ScopePathType.ACTIVITIES_UPDATE);
    PeerReview peerReview1 = new PeerReview();
    ExternalIDs weis1 = new ExternalIDs();
    ExternalID wei1 = new ExternalID();
    wei1.setRelationship(null);
    wei1.setValue("same_but_different_type");
    wei1.setType(WorkExternalIdentifierType.DOI.value());
    weis1.getExternalIdentifier().add(wei1);
    peerReview1.setExternalIdentifiers(weis1);
    peerReview1.setGroupId("issn:0000003");
    peerReview1.setOrganization(Utils.getOrganization());
    peerReview1.setRole(Role.CHAIR);
    peerReview1.setSubjectContainerName(new Title("subject-container-name"));
    peerReview1.setSubjectExternalIdentifier(wei1);
    WorkTitle workTitle1 = new WorkTitle();
    workTitle1.setTitle(new Title("work-title"));
    peerReview1.setSubjectName(workTitle1);
    peerReview1.setSubjectType(WorkType.DATA_SET);
    peerReview1.setType(PeerReviewType.EVALUATION);
    Response response1 = serviceDelegator.createPeerReview("4444-4444-4444-4444", peerReview1);
    assertNotNull(response1);
    assertEquals(Response.Status.CREATED.getStatusCode(), response1.getStatus());
    Map<?, ?> map = response1.getMetadata();
    assertNotNull(map);
    assertTrue(map.containsKey("Location"));
    List<?> resultWithPutCode = (List<?>) map.get("Location");
    Long putCode1 = Long.valueOf(String.valueOf(resultWithPutCode.get(0)));
    PeerReview peerReview2 = new PeerReview();
    ExternalIDs weis2 = new ExternalIDs();
    ExternalID wei2 = new ExternalID();
    wei2.setRelationship(null);
    // Same value
    wei2.setValue("same_but_different_type");
    // But different
    wei2.setType(WorkExternalIdentifierType.ARXIV.value());
    // type
    weis2.getExternalIdentifier().add(wei2);
    peerReview2.setExternalIdentifiers(weis2);
    peerReview2.setGroupId("issn:0000003");
    peerReview2.setOrganization(Utils.getOrganization());
    peerReview2.setRole(Role.CHAIR);
    peerReview2.setSubjectContainerName(new Title("subject-container-name"));
    peerReview2.setSubjectExternalIdentifier(wei2);
    WorkTitle workTitle2 = new WorkTitle();
    workTitle2.setTitle(new Title("work-title"));
    peerReview2.setSubjectName(workTitle2);
    peerReview2.setSubjectType(WorkType.DATA_SET);
    peerReview2.setType(PeerReviewType.EVALUATION);
    Response response2 = serviceDelegator.createPeerReview("4444-4444-4444-4444", peerReview2);
    assertNotNull(response2);
    assertEquals(Response.Status.CREATED.getStatusCode(), response2.getStatus());
    map = response2.getMetadata();
    assertNotNull(map);
    assertTrue(map.containsKey("Location"));
    resultWithPutCode = (List<?>) map.get("Location");
    Long putCode2 = Long.valueOf(String.valueOf(resultWithPutCode.get(0)));
    // Delete new peer reviews so they don't affect other tests
    serviceDelegator.deletePeerReview("4444-4444-4444-4444", putCode1);
    serviceDelegator.deletePeerReview("4444-4444-4444-4444", putCode2);
}

Example 25 with ExternalID

use of org.orcid.jaxb.model.record_v2.ExternalID in project ORCID-Source by ORCID.

the class OrcidSecurityManagerImpl method filterExternalIdentifiers.

/**
     * Filter the group external identifiers to match the external identifiers
     * that belongs to the activities it have after filtering
     * 
     * @param group
     *            The group we want to filter the external identifiers
     */
private void filterExternalIdentifiers(Group group) {
    // Iterate over every external identifier and check if it is still
    // present in the list of filtered elements
    ExternalIDs extIds = group.getIdentifiers();
    Iterator<ExternalID> extIdsIt = extIds.getExternalIdentifier().iterator();
    while (extIdsIt.hasNext()) {
        ExternalID extId = extIdsIt.next();
        boolean found = false;
        for (GroupableActivity summary : group.getActivities()) {
            if (summary.getExternalIdentifiers() != null) {
                if (summary.getExternalIdentifiers().getExternalIdentifier().contains(extId)) {
                    found = true;
                    break;
                }
            }
        }
        // If the ext id is not found, remove it from the list of ext ids
        if (!found) {
            extIdsIt.remove();
        }
    }
}