Examples with ExternalIdentifiers org.orcid.jaxb.model.message.ExternalIdentifiers used on opensource projects

Example 6 with ExternalIdentifiers

use of org.orcid.jaxb.model.message.ExternalIdentifiers in project ORCID-Source by ORCID.

the class T2OrcidApiServiceDelegatorTest method testAddDuplicatedExtIdsWhenThereIsNonPublicCountry.

@Test
public void testAddDuplicatedExtIdsWhenThereIsNonPublicCountry() {
    String userOrcid = "0000-0000-0000-0003";
    OrcidMessage message = new OrcidMessage();
    message.setMessageVersion("1.2_rc6");
    message.setOrcidProfile(new OrcidProfile());
    message.getOrcidProfile().setOrcidBio(new OrcidBio());
    ExternalIdentifiers extIds = new ExternalIdentifiers();
    ExternalIdentifier extId1 = new ExternalIdentifier();
    String commonName = "common-name-1-" + System.currentTimeMillis();
    extId1.setExternalIdCommonName(new ExternalIdCommonName(commonName));
    extId1.setExternalIdReference(new ExternalIdReference("ext-id-reference-1"));
    extId1.setExternalIdUrl(new ExternalIdUrl("http://test.orcid.org/" + System.currentTimeMillis()));
    extIds.getExternalIdentifier().add(extId1);
    message.getOrcidProfile().getOrcidBio().setExternalIdentifiers(extIds);
    // Add for client 1
    SecurityContextTestUtils.setUpSecurityContext(userOrcid, "APP-5555555555555555", ScopePathType.PERSON_UPDATE, ScopePathType.PERSON_READ_LIMITED);
    Response r = t2OrcidApiServiceDelegator.addExternalIdentifiers(null, userOrcid, message);
    assertNotNull(r);
    OrcidMessage newMessage1 = (OrcidMessage) r.getEntity();
    assertNotNull(newMessage1);
    assertNotNull(newMessage1.getOrcidProfile());
    assertNotNull(newMessage1.getOrcidProfile().getOrcidBio());
    assertNotNull(newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers());
    assertNotNull(newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier());
    assertEquals(4, newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().size());
    assertEquals(commonName, newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(3).getExternalIdCommonName().getContent());
    assertEquals("APP-5555555555555555", newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(3).getSource().retrieveSourcePath());
}

Example 7 with ExternalIdentifiers

use of org.orcid.jaxb.model.message.ExternalIdentifiers in project ORCID-Source by ORCID.

the class T2OrcidApiServiceDelegatorTest method testAddDuplicatedExtIdsWithDifferentClientWorks.

@Test
public void testAddDuplicatedExtIdsWithDifferentClientWorks() {
    String orcid = "0000-0000-0000-0002";
    OrcidMessage message = new OrcidMessage();
    message.setMessageVersion("1.2_rc6");
    message.setOrcidProfile(new OrcidProfile());
    message.getOrcidProfile().setOrcidBio(new OrcidBio());
    ExternalIdentifiers extIds = new ExternalIdentifiers();
    ExternalIdentifier extId1 = new ExternalIdentifier();
    String commonName = "common-name-1-" + System.currentTimeMillis();
    extId1.setExternalIdCommonName(new ExternalIdCommonName(commonName));
    extId1.setExternalIdReference(new ExternalIdReference("ext-id-reference-1"));
    extId1.setExternalIdUrl(new ExternalIdUrl("http://test.orcid.org/" + System.currentTimeMillis()));
    extIds.getExternalIdentifier().add(extId1);
    message.getOrcidProfile().getOrcidBio().setExternalIdentifiers(extIds);
    // Add for client 1
    SecurityContextTestUtils.setUpSecurityContext("0000-0000-0000-0002", "APP-5555555555555555", ScopePathType.PERSON_UPDATE, ScopePathType.PERSON_READ_LIMITED);
    Response r = t2OrcidApiServiceDelegator.addExternalIdentifiers(null, orcid, message);
    assertNotNull(r);
    OrcidMessage newMessage1 = (OrcidMessage) r.getEntity();
    assertNotNull(newMessage1);
    assertNotNull(newMessage1.getOrcidProfile());
    assertNotNull(newMessage1.getOrcidProfile().getOrcidBio());
    assertNotNull(newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers());
    assertNotNull(newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier());
    assertEquals(1, newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().size());
    assertEquals(commonName, newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(0).getExternalIdCommonName().getContent());
    assertEquals("APP-5555555555555555", newMessage1.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(0).getSource().retrieveSourcePath());
    // Reset message for source # 2
    message = new OrcidMessage();
    message.setMessageVersion("1.2_rc6");
    message.setOrcidProfile(new OrcidProfile());
    message.getOrcidProfile().setOrcidBio(new OrcidBio());
    extId1.setSource(null);
    message.getOrcidProfile().getOrcidBio().setExternalIdentifiers(extIds);
    SecurityContextTestUtils.setUpSecurityContext("0000-0000-0000-0002", "APP-5555555555555556", ScopePathType.PERSON_UPDATE, ScopePathType.PERSON_READ_LIMITED);
    r = t2OrcidApiServiceDelegator.addExternalIdentifiers(null, orcid, message);
    OrcidMessage newMessage2 = (OrcidMessage) r.getEntity();
    assertNotNull(newMessage2);
    assertNotNull(newMessage2.getOrcidProfile());
    assertNotNull(newMessage2.getOrcidProfile().getOrcidBio());
    assertNotNull(newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers());
    assertNotNull(newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier());
    assertEquals(2, newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().size());
    assertEquals(commonName, newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(0).getExternalIdCommonName().getContent());
    assertEquals("APP-5555555555555555", newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(0).getSource().retrieveSourcePath());
    assertEquals(commonName, newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(1).getExternalIdCommonName().getContent());
    assertEquals("APP-5555555555555556", newMessage2.getOrcidProfile().getOrcidBio().getExternalIdentifiers().getExternalIdentifier().get(1).getSource().retrieveSourcePath());
}

Example 8 with ExternalIdentifiers

use of org.orcid.jaxb.model.message.ExternalIdentifiers in project ORCID-Source by ORCID.

the class T2OrcidApiServiceDelegatorImpl method addExternalIdentifiers.

/**
 * Add new external identifiers to the profile. As with all calls, if the
 * message contains any other elements, a 400 Bad Request will be returned.
 *
 * @param orcidMessage
 *            the message congtaining the external ids
 * @return If successful, returns a 200 OK with the updated content.
 */
@Override
@AccessControl(requiredScope = ScopePathType.ORCID_BIO_EXTERNAL_IDENTIFIERS_CREATE)
public Response addExternalIdentifiers(UriInfo uriInfo, String orcid, OrcidMessage orcidMessage) {
    OrcidProfile orcidProfile = orcidMessage.getOrcidProfile();
    try {
        ExternalIdentifiers updatedExternalIdentifiers = orcidProfile.getOrcidBio().getExternalIdentifiers();
        // Get the client profile information
        Authentication authentication = SecurityContextHolder.getContext().getAuthentication();
        String clientId = null;
        if (OAuth2Authentication.class.isAssignableFrom(authentication.getClass())) {
            OAuth2Request authorizationRequest = ((OAuth2Authentication) authentication).getOAuth2Request();
            clientId = authorizationRequest.getClientId();
        }
        for (ExternalIdentifier ei : updatedExternalIdentifiers.getExternalIdentifier()) {
            // Set the client profile to each external identifier
            if (ei.getSource() == null) {
                Source source = new Source();
                source.setSourceClientId(new SourceClientId(clientId));
                ei.setSource(source);
            } else {
                // Check if the provided external orcid exists
                Source source = ei.getSource();
                String sourceOrcid = source.retrieveSourcePath();
                if (sourceOrcid != null) {
                    if (StringUtils.isBlank(sourceOrcid) || (!profileEntityManager.orcidExists(sourceOrcid) && !clientDetailsManager.exists(sourceOrcid))) {
                        Map<String, String> params = new HashMap<String, String>();
                        params.put("orcid", sourceOrcid);
                        throw new OrcidNotFoundException(params);
                    }
                }
            }
        }
        orcidProfile = orcidProfileManager.addExternalIdentifiers(orcidProfile);
        return getOrcidMessageResponse(orcidProfile, orcid);
    } catch (DataAccessException e) {
        throw new OrcidBadRequestException(localeManager.resolveMessage("apiError.badrequest_createorcid.exception"));
    }
}

Example 9 with ExternalIdentifiers

use of org.orcid.jaxb.model.message.ExternalIdentifiers in project ORCID-Source by ORCID.

the class OrcidApiAuthorizationSecurityAspect method visibilityResponseFilter.

@AfterReturning(pointcut = "@annotation(accessControl)", returning = "response")
public void visibilityResponseFilter(Response response, AccessControl accessControl) {
    if (accessControl.requestComesFromInternalApi()) {
        return;
    }
    Object entity = response.getEntity();
    if (entity != null && OrcidMessage.class.isAssignableFrom(entity.getClass())) {
        OrcidMessage orcidMessage = (OrcidMessage) entity;
        // If it is search results, don't filter them, just return them
        if (orcidMessage.getOrcidSearchResults() != null) {
            return;
        }
        // get the client id
        Object authentication = getAuthentication();
        Set<Visibility> visibilities = new HashSet<Visibility>();
        if (allowAnonymousAccess((Authentication) authentication, accessControl)) {
            visibilities.add(Visibility.PUBLIC);
        } else {
            visibilities = permissionChecker.obtainVisibilitiesForAuthentication(getAuthentication(), accessControl.requiredScope(), orcidMessage);
        }
        // If the message contains a bio, and the given name is filtered, restore it as an empty space
        boolean setEmptyGivenNameIfFiltered = false;
        if (orcidMessage.getOrcidProfile() != null) {
            if (orcidMessage.getOrcidProfile() != null && orcidMessage.getOrcidProfile().getOrcidBio() != null) {
                setEmptyGivenNameIfFiltered = true;
            }
        }
        ScopePathType requiredScope = accessControl.requiredScope();
        // If the required scope is */read-limited or */update
        if (isUpdateOrReadScope(requiredScope)) {
            // if it should be able to
            if (OrcidOAuth2Authentication.class.isAssignableFrom(authentication.getClass())) {
                OrcidOAuth2Authentication orcidAuth = (OrcidOAuth2Authentication) getAuthentication();
                OAuth2Request authorization = orcidAuth.getOAuth2Request();
                String clientId = authorization.getClientId();
                // #1: Get the user orcid
                String userOrcid = getUserOrcidFromOrcidMessage(orcidMessage);
                // #2: Evaluate the scope to know which field to filter
                boolean allowWorks = false;
                boolean allowFunding = false;
                boolean allowAffiliations = false;
                // Get the update equivalent scope, if it is reading, but,
                // doesnt have the read permissions, check if it have the
                // update permissions
                ScopePathType equivalentUpdateScope = getEquivalentUpdateScope(requiredScope);
                if (requiredScope.equals(ScopePathType.READ_LIMITED)) {
                    if (hasScopeEnabled(clientId, userOrcid, ScopePathType.ORCID_WORKS_READ_LIMITED.getContent(), ScopePathType.ORCID_WORKS_UPDATE.getContent()))
                        allowWorks = true;
                    if (hasScopeEnabled(clientId, userOrcid, ScopePathType.FUNDING_READ_LIMITED.getContent(), ScopePathType.FUNDING_UPDATE.getContent()))
                        allowFunding = true;
                    if (hasScopeEnabled(clientId, userOrcid, ScopePathType.AFFILIATIONS_READ_LIMITED.getContent(), ScopePathType.AFFILIATIONS_UPDATE.getContent()))
                        allowAffiliations = true;
                } else if (requiredScope.equals(ScopePathType.ORCID_WORKS_UPDATE) || requiredScope.equals(ScopePathType.ORCID_WORKS_READ_LIMITED)) {
                    // works
                    if (hasScopeEnabled(clientId, userOrcid, requiredScope.getContent(), equivalentUpdateScope == null ? null : equivalentUpdateScope.getContent()))
                        // If so, allow him to see private works
                        allowWorks = true;
                } else if (requiredScope.equals(ScopePathType.FUNDING_UPDATE) || requiredScope.equals(ScopePathType.FUNDING_READ_LIMITED)) {
                    // funding
                    if (hasScopeEnabled(clientId, userOrcid, requiredScope.getContent(), equivalentUpdateScope == null ? null : equivalentUpdateScope.getContent()))
                        // If so, allow him to see private funding
                        allowFunding = true;
                } else if (requiredScope.equals(ScopePathType.AFFILIATIONS_UPDATE) || requiredScope.equals(ScopePathType.AFFILIATIONS_READ_LIMITED)) {
                    // affiliations
                    if (hasScopeEnabled(clientId, userOrcid, requiredScope.getContent(), equivalentUpdateScope == null ? null : equivalentUpdateScope.getContent()))
                        // If so, allow him to see private affiliations
                        allowAffiliations = true;
                }
                visibilityFilter.filter(orcidMessage, clientId, allowWorks, allowFunding, allowAffiliations, visibilities.toArray(new Visibility[visibilities.size()]));
            } else {
                visibilityFilter.filter(orcidMessage, null, false, false, false, visibilities.toArray(new Visibility[visibilities.size()]));
            }
        } else {
            visibilityFilter.filter(orcidMessage, null, false, false, false, visibilities.toArray(new Visibility[visibilities.size()]));
        }
        // If the given name was set at the beginning and now is filtered, it means we should restore it as an empty field
        if (setEmptyGivenNameIfFiltered) {
            if (orcidMessage.getOrcidProfile() != null) {
                if (orcidMessage.getOrcidProfile().getOrcidBio() == null) {
                    orcidMessage.getOrcidProfile().setOrcidBio(new OrcidBio());
                }
                if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails() == null) {
                    orcidMessage.getOrcidProfile().getOrcidBio().setPersonalDetails(new PersonalDetails());
                }
            }
        }
        // Filter given or family names visibility
        if (orcidMessage.getOrcidProfile() != null) {
            if (orcidMessage.getOrcidProfile().getOrcidBio() != null) {
                if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails() != null) {
                    if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getGivenNames() != null) {
                        orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getGivenNames().setVisibility(null);
                    } else {
                        // Null given names could break client integrations, so, lets return an empty string
                        GivenNames empty = new GivenNames();
                        empty.setContent(StringUtils.EMPTY);
                        orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().setGivenNames(empty);
                    }
                    if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getFamilyName() != null) {
                        orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getFamilyName().setVisibility(null);
                    }
                }
            }
        }
        // replace section visibilities now we may have filtered items
        if (orcidMessage.getOrcidProfile() != null) {
            if (orcidMessage.getOrcidProfile().getOrcidBio() != null) {
                if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails() != null) {
                    OtherNames n = orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getOtherNames();
                    if (n != null) {
                        n.setVisibility(getMostFromCollection(n.getOtherName()));
                    }
                }
                ExternalIdentifiers ids = orcidMessage.getOrcidProfile().getOrcidBio().getExternalIdentifiers();
                if (ids != null) {
                    ids.setVisibility(getMostFromCollection(ids.getExternalIdentifier()));
                }
                Keywords kws = orcidMessage.getOrcidProfile().getOrcidBio().getKeywords();
                if (kws != null) {
                    kws.setVisibility(getMostFromCollection(kws.getKeyword()));
                }
                ResearcherUrls urls = orcidMessage.getOrcidProfile().getOrcidBio().getResearcherUrls();
                if (urls != null) {
                    urls.setVisibility(getMostFromCollection(urls.getResearcherUrl()));
                }
            }
        }
    }
}

Example 10 with ExternalIdentifiers

use of org.orcid.jaxb.model.message.ExternalIdentifiers in project ORCID-Source by ORCID.

the class OrcidProfileManagerImpl method addExternalIdentifiers.

/**
 * Add new external identifiers to an existing profile
 *
 * @param updatedOrcidProfile
 * @return
 */
@Override
public OrcidProfile addExternalIdentifiers(OrcidProfile updatedOrcidProfile) {
    OrcidProfile existingProfile = retrieveOrcidProfile(updatedOrcidProfile.getOrcidIdentifier().getPath());
    if (existingProfile != null && existingProfile.getOrcidBio() != null) {
        OrcidBio orcidBio = existingProfile.getOrcidBio();
        ExternalIdentifiers externalIdentifiers = orcidBio.getExternalIdentifiers();
        if (externalIdentifiers == null) {
            orcidBio.setExternalIdentifiers(new ExternalIdentifiers());
        }
        ExternalIdentifiers externalIdentifier = updatedOrcidProfile.getOrcidBio().getExternalIdentifiers();
        List<ExternalIdentifier> updatedExternalIdentifiers = externalIdentifier.getExternalIdentifier();
        List<ExternalIdentifier> existingExternalIdentifiers = orcidBio.getExternalIdentifiers().getExternalIdentifier();
        // Copy all the existing external identifiers to the updated profile
        for (ExternalIdentifier ei : existingExternalIdentifiers) {
            updatedExternalIdentifiers.add(ei);
        }
        orcidJaxbCopyManager.copyUpdatedExternalIdentifiersToExistingPreservingVisibility(orcidBio, updatedOrcidProfile.getOrcidBio());
        OrcidProfile profileToReturn = updateOrcidProfile(existingProfile);
        notificationManager.sendAmendEmail(updatedOrcidProfile.getOrcidIdentifier().getPath(), AmendedSection.EXTERNAL_IDENTIFIERS, null);
        return profileToReturn;
    } else {
        return null;
    }
}