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

Example 11 with OrcidBio

use of org.orcid.jaxb.model.message.OrcidBio 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 12 with OrcidBio

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

the class EmailMessageSenderTest method testCreateDigest.

@Test
public void testCreateDigest() throws IOException {
    OrcidProfile orcidProfile = new OrcidProfile();
    OrcidBio orcidBio = new OrcidBio();
    orcidProfile.setOrcidBio(orcidBio);
    PersonalDetails personalDetails = new PersonalDetails();
    orcidBio.setPersonalDetails(personalDetails);
    personalDetails.setGivenNames(new GivenNames("John"));
    personalDetails.setFamilyName(new FamilyName("Watson"));
    OrcidInternal orcidInternal = new OrcidInternal();
    Preferences preferences = new Preferences();
    orcidProfile.setOrcidInternal(orcidInternal);
    orcidInternal.setPreferences(preferences);
    preferences.setSendEmailFrequencyDays("7.0");
    List<Notification> notifications = new ArrayList<>();
    NotificationPermission notification1 = new NotificationPermission();
    notification1.setPutCode(1L);
    Items activities1 = new Items();
    notification1.setItems(activities1);
    activities1.getItems().add(createActivity(ItemType.WORK, "Work 1", "123446/67654"));
    activities1.getItems().add(createActivity(ItemType.WORK, "Work 2", "http://dx.doi.org/123446/67655"));
    notification1.setCreatedDate(DateUtils.convertToXMLGregorianCalendar("2014-07-10T13:39:31"));
    notification1.setAuthorizationUrl(new AuthorizationUrl("https://thirdparty.com/add-to-orcid/12345"));
    Source source1 = new Source();
    source1.setSourceName(new SourceName("Super Institution 1"));
    source1.setSourceClientId(new SourceClientId("APP-5555-5555-5555-5555"));
    notification1.setSource(source1);
    notifications.add(notification1);
    NotificationPermission notification2 = new NotificationPermission();
    notification2.setPutCode(2L);
    Items activities2 = new Items();
    notification2.setItems(activities2);
    activities2.getItems().add(createActivity(ItemType.EMPLOYMENT, "Employment 1 ", "12345/abc"));
    notification2.setCreatedDate(DateUtils.convertToXMLGregorianCalendar("2014-08-17T10:22:15"));
    notification2.setAuthorizationUrl(new AuthorizationUrl("https://thirdparty.com/add-to-orcid/abc"));
    Source source2 = new Source();
    source2.setSourceName(new SourceName("Super Institution 1"));
    source2.setSourceClientId(new SourceClientId("APP-5555-5555-5555-5555"));
    notification2.setSource(source2);
    notifications.add(notification2);
    NotificationPermission notification3 = new NotificationPermission();
    notification3.setPutCode(3L);
    Items activities3 = new Items();
    notification3.setItems(activities3);
    activities3.getItems().add(createActivity(ItemType.WORK, "Work 3", "12345/def"));
    activities3.getItems().add(createActivity(ItemType.WORK, "Work 4", "12345/ghi"));
    notification3.setCreatedDate(DateUtils.convertToXMLGregorianCalendar("2014-07-10T08:53:56"));
    notification3.setAuthorizationUrl(new AuthorizationUrl("https://thirdparty.com/add-to-orcid/def"));
    Source source3 = new Source();
    source3.setSourceName(new SourceName("Lovely Publisher 1"));
    notification3.setSource(source3);
    source3.setSourceClientId(new SourceClientId("APP-ABCD-ABCD-ABCD-ABCD"));
    notifications.add(notification3);
    NotificationCustom notification4 = new NotificationCustom();
    notification4.setPutCode(4L);
    notification4.setSubject("We have release a new messaging feature");
    notification4.setCreatedDate(DateUtils.convertToXMLGregorianCalendar("2014-07-10T08:53:56"));
    notifications.add(notification4);
    NotificationCustom notification5 = new NotificationCustom();
    notification5.setPutCode(5L);
    notification5.setSubject("The ORCID registry is now available in Orc");
    notification5.setCreatedDate(DateUtils.convertToXMLGregorianCalendar("2014-07-11T06:42:18"));
    notifications.add(notification5);
    NotificationAmended notification6 = new NotificationAmended();
    notification6.setPutCode(6L);
    notification6.setSubject("Amended by member");
    notification6.setAmendedSection(AmendedSection.FUNDING);
    notification6.setCreatedDate(DateUtils.convertToXMLGregorianCalendar("2014-07-12T18:44:36"));
    notification6.setSource(source3);
    notifications.add(notification6);
    EmailMessage emailMessage = emailMessageSender.createDigest(orcidProfile, notifications, Locale.ENGLISH);
    assertNotNull(emailMessage);
    String expectedBodyText = IOUtils.toString(getClass().getResourceAsStream("example_digest_email_body.txt"));
    String expectedBodyHtml = IOUtils.toString(getClass().getResourceAsStream("example_digest_email_body.html"));
    assertTrue(expectedBodyText.contains("Lovely Publisher 1 has updated recent funding on your ORCID record."));
    assertTrue(expectedBodyHtml.contains("Lovely Publisher 1 has updated recent funding on your ORCID record."));
    assertTrue(expectedBodyText.contains("Super Institution 1: Request to add items"));
    assertTrue(expectedBodyHtml.contains("Super Institution 1: Request to add items"));
    assertTrue(expectedBodyText.contains("/action"));
    assertTrue(expectedBodyHtml.contains("/action"));
    assertEquals("[ORCID] John Watson you have 6 new notifications", emailMessage.getSubject());
}

Example 13 with OrcidBio

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

the class OrcidProfileManagerImplTest method testUpdateOrcidBioKeepTheUserVisibility.

@Test
@Transactional
public void testUpdateOrcidBioKeepTheUserVisibility() {
    OrcidProfile profile = createBasicProfile();
    String orcidIdentifier = null;
    profile.setOrcidIdentifier(orcidIdentifier);
    setBio(profile, Visibility.LIMITED);
    OrcidHistory orcidHistory = new OrcidHistory();
    orcidHistory.setClaimed(new Claimed(true));
    orcidHistory.setCreationMethod(CreationMethod.DIRECT);
    orcidHistory.setSubmissionDate(new SubmissionDate(DateUtils.convertToXMLGregorianCalendar(new Date())));
    profile.setOrcidHistory(orcidHistory);
    Preferences preferences = new Preferences();
    preferences.setSendChangeNotifications(new SendChangeNotifications(true));
    preferences.setSendOrcidNews(new SendOrcidNews(true));
    //Default visibility for user will be LIMITED
    preferences.setActivitiesVisibilityDefault(new ActivitiesVisibilityDefault(Visibility.LIMITED));
    preferences.setNotificationsEnabled(DefaultPreferences.NOTIFICATIONS_ENABLED);
    preferences.setSendEmailFrequencyDays(DefaultPreferences.SEND_EMAIL_FREQUENCY_DAYS);
    preferences.setSendMemberUpdateRequests(DefaultPreferences.SEND_MEMBER_UPDATE_REQUESTS);
    OrcidInternal internal = new OrcidInternal();
    internal.setPreferences(preferences);
    profile.setOrcidInternal(internal);
    profile = orcidProfileManager.createOrcidProfile(profile, true, false);
    //Update it setting it to PUBLIC and check
    profile = orcidProfileManager.retrieveOrcidProfile(profile.getOrcidIdentifier().getPath());
    assertNotNull(profile);
    assertNotNull(profile.getOrcidBio());
    OrcidBio bioToUpdate = profile.getOrcidBio();
    assertEquals(Visibility.LIMITED, bioToUpdate.getBiography().getVisibility());
    assertEquals("This is my biography", bioToUpdate.getBiography().getContent());
    assertEquals(Visibility.LIMITED, bioToUpdate.getContactDetails().getAddress().getCountry().getVisibility());
    assertEquals(Iso3166Country.US, bioToUpdate.getContactDetails().getAddress().getCountry().getValue());
    assertEquals(Visibility.LIMITED, bioToUpdate.getExternalIdentifiers().getVisibility());
    assertEquals(1, bioToUpdate.getExternalIdentifiers().getExternalIdentifier().size());
    assertEquals(Visibility.LIMITED, bioToUpdate.getKeywords().getVisibility());
    assertEquals(1, bioToUpdate.getKeywords().getKeyword().size());
    assertEquals(Visibility.LIMITED, bioToUpdate.getPersonalDetails().getOtherNames().getVisibility());
    assertEquals(1, bioToUpdate.getPersonalDetails().getOtherNames().getOtherName().size());
    assertEquals(Visibility.LIMITED, bioToUpdate.getResearcherUrls().getVisibility());
    assertEquals(1, bioToUpdate.getResearcherUrls().getResearcherUrl().size());
    //Update bio
    bioToUpdate.getBiography().setContent("Updated biography");
    bioToUpdate.getBiography().setVisibility(Visibility.PRIVATE);
    //Update address
    bioToUpdate.getContactDetails().getAddress().getCountry().setValue(Iso3166Country.CR);
    bioToUpdate.getContactDetails().getAddress().getCountry().setVisibility(Visibility.PRIVATE);
    //Update external identifiers
    ExternalIdentifier extId = new ExternalIdentifier();
    extId.setExternalIdCommonName(new ExternalIdCommonName("common-name-2"));
    extId.setExternalIdReference(new ExternalIdReference("ext-id-reference-2"));
    extId.setExternalIdUrl(new ExternalIdUrl("http://orcid.org/ext-id/2"));
    extId.setVisibility(Visibility.PRIVATE);
    bioToUpdate.getExternalIdentifiers().setVisibility(Visibility.PRIVATE);
    bioToUpdate.getExternalIdentifiers().getExternalIdentifier().add(extId);
    //Update keywords
    Keyword k = new Keyword();
    k.setContent("keyword-2");
    k.setVisibility(Visibility.PRIVATE);
    bioToUpdate.getKeywords().getKeyword().add(k);
    bioToUpdate.getKeywords().setVisibility(Visibility.PRIVATE);
    //Update researcher urls
    ResearcherUrl rUrl = new ResearcherUrl();
    rUrl.setUrl(new Url("http://orcid.org/researcher-url-2"));
    rUrl.setUrlName(new UrlName("url-name-2"));
    rUrl.setVisibility(Visibility.PRIVATE);
    bioToUpdate.getResearcherUrls().getResearcherUrl().add(rUrl);
    bioToUpdate.getResearcherUrls().setVisibility(Visibility.PRIVATE);
    //Update other names
    OtherName o = new OtherName();
    o.setContent("other-name-2");
    o.setVisibility(Visibility.PRIVATE);
    bioToUpdate.getPersonalDetails().getOtherNames().getOtherName().add(o);
    bioToUpdate.getPersonalDetails().getOtherNames().setVisibility(Visibility.PRIVATE);
    //Update the biography
    orcidProfileManager.updateOrcidBio(profile);
    //Get the record again and check that visibilities where not updated 
    OrcidProfile updatedProfile = orcidProfileManager.retrieveOrcidProfile(profile.getOrcidIdentifier().getPath());
    assertNotNull(updatedProfile);
    assertNotNull(updatedProfile.getOrcidBio());
    OrcidBio updatedBio = updatedProfile.getOrcidBio();
    assertEquals(Visibility.LIMITED, updatedBio.getBiography().getVisibility());
    assertEquals("Updated biography", updatedBio.getBiography().getContent());
    assertEquals(Visibility.LIMITED, updatedBio.getContactDetails().getAddress().getCountry().getVisibility());
    assertEquals(Iso3166Country.US, updatedBio.getContactDetails().getAddress().getCountry().getValue());
    assertEquals(Visibility.LIMITED, updatedBio.getExternalIdentifiers().getVisibility());
    assertEquals(2, updatedBio.getExternalIdentifiers().getExternalIdentifier().size());
    assertEquals(Visibility.LIMITED, updatedBio.getKeywords().getVisibility());
    assertEquals(2, updatedBio.getKeywords().getKeyword().size());
    assertEquals(Visibility.LIMITED, updatedBio.getPersonalDetails().getOtherNames().getVisibility());
    assertEquals(2, updatedBio.getPersonalDetails().getOtherNames().getOtherName().size());
    assertEquals(Visibility.LIMITED, updatedBio.getResearcherUrls().getVisibility());
    assertEquals(2, updatedBio.getResearcherUrls().getResearcherUrl().size());
}

Example 14 with OrcidBio

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

the class OrcidSearchManagerImplTest method getOrcidProfileAllIndexFieldsPopulated.

private OrcidProfile getOrcidProfileAllIndexFieldsPopulated() {
    OrcidProfile orcidProfile = new OrcidProfile();
    orcidProfile.setOrcidIdentifier("5678");
    OrcidBio orcidBio = new OrcidBio();
    PersonalDetails personalDetails = new PersonalDetails();
    personalDetails.setFamilyName(new FamilyName("Logan"));
    personalDetails.setGivenNames(new GivenNames("Donald Edward"));
    personalDetails.setCreditName(new CreditName("Stanley Higgins"));
    OtherNames otherNames = new OtherNames();
    otherNames.getOtherName().add(new OtherName("Edward Bass", null));
    otherNames.getOtherName().add(new OtherName("Gareth Dove", null));
    personalDetails.setOtherNames(otherNames);
    orcidBio.setPersonalDetails(personalDetails);
    orcidProfile.setOrcidBio(orcidBio);
    OrcidActivities orcidActivities = new OrcidActivities();
    orcidProfile.setOrcidActivities(orcidActivities);
    Affiliations affiliations = new Affiliations();
    orcidActivities.setAffiliations(affiliations);
    OrcidWorks orcidWorks = new OrcidWorks();
    orcidProfile.setOrcidWorks(orcidWorks);
    OrcidWork orcidWork1 = new OrcidWork();
    OrcidWork orcidWork2 = new OrcidWork();
    assignWorkIdentifers(orcidWork1, orcidWork2);
    orcidWorks.getOrcidWork().add(orcidWork1);
    orcidWorks.getOrcidWork().add(orcidWork2);
    orcidProfile.setOrcidWorks(orcidWorks);
    FundingList orcidFundings = new FundingList();
    orcidProfile.setFundings(orcidFundings);
    Funding funding1 = new Funding();
    funding1.setVisibility(Visibility.PUBLIC);
    FundingTitle title = new FundingTitle();
    title.setTitle(new Title("grant1"));
    funding1.setTitle(title);
    funding1.setDescription("Grant 1 - a short description");
    funding1.setPutCode("grant 1 - put-code");
    Funding funding2 = new Funding();
    funding2.setVisibility(Visibility.PUBLIC);
    FundingTitle title2 = new FundingTitle();
    title2.setTitle(new Title("grant2"));
    funding2.setTitle(title2);
    funding2.setDescription("Grant 2 - a short description");
    funding2.setPutCode("grant 2 - put-code");
    orcidFundings.getFundings().add(funding1);
    orcidFundings.getFundings().add(funding2);
    return orcidProfile;
}

Example 15 with OrcidBio

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

the class OrcidSearchManagerImplTest method getOrcidProfile6789MandatoryOnly.

private OrcidProfile getOrcidProfile6789MandatoryOnly() {
    OrcidProfile orcidProfile = new OrcidProfile();
    orcidProfile.setOrcidIdentifier("6789");
    OrcidBio orcidBio = new OrcidBio();
    orcidProfile.setOrcidBio(orcidBio);
    ContactDetails contactDetails = new ContactDetails();
    contactDetails.addOrReplacePrimaryEmail(new Email("don@semantico.com"));
    orcidBio.setContactDetails(contactDetails);
    PersonalDetails personalDetails = new PersonalDetails();
    orcidBio.setPersonalDetails(personalDetails);
    personalDetails.setFamilyName(new FamilyName("Thomson"));
    personalDetails.setGivenNames(new GivenNames("Homer J"));
    OrcidActivities orcidActivities = new OrcidActivities();
    orcidProfile.setOrcidActivities(orcidActivities);
    Affiliations affiliations = new Affiliations();
    orcidActivities.setAffiliations(affiliations);
    return orcidProfile;
}