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

Example 16 with OrcidBio

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

the class OrcidIndexManagerImplTest method getOrcidProfileMandatoryOnly.

/**
     * According to the validation rules on the web front end, these fields are
     * mandatory. Ultimately they may or may not make it into SOLR due to
     * visibility restrictions
     * 
     * @return OrcidProfile with only mandatory fields populated.
     */
private OrcidProfile getOrcidProfileMandatoryOnly() {
    OrcidProfile orcidProfile = new OrcidProfile();
    orcidProfile.setOrcidIdentifier("5678");
    OrcidBio orcidBio = new OrcidBio();
    orcidProfile.setOrcidBio(orcidBio);
    ContactDetails contactDetails = new ContactDetails();
    contactDetails.addOrReplacePrimaryEmail(new Email("stan@test.com"));
    orcidBio.setContactDetails(contactDetails);
    PersonalDetails personalDetails = new PersonalDetails();
    FamilyName familyName = new FamilyName("Logan");
    familyName.setVisibility(Visibility.PUBLIC);
    personalDetails.setFamilyName(familyName);
    GivenNames givenNames = new GivenNames("Donald Edward");
    givenNames.setVisibility(Visibility.PUBLIC);
    personalDetails.setGivenNames(givenNames);
    orcidBio.setPersonalDetails(personalDetails);
    OrcidActivities orcidActivities = new OrcidActivities();
    orcidProfile.setOrcidActivities(orcidActivities);
    Affiliations affiliations = new Affiliations();
    orcidActivities.setAffiliations(affiliations);
    return orcidProfile;
}

Example 17 with OrcidBio

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

the class OrcidIndexManagerImplTest method getStandardOrcid.

private OrcidProfile getStandardOrcid() {
    OrcidProfile orcidProfile = new OrcidProfile();
    orcidProfile.setOrcidIdentifier("1234");
    OrcidBio orcidBio = new OrcidBio();
    ContactDetails contactDetails = new ContactDetails();
    Email email = new Email("email");
    email.setVisibility(Visibility.PUBLIC);
    contactDetails.addOrReplacePrimaryEmail(email);
    orcidBio.setContactDetails(contactDetails);
    Keywords bioKeywords = new Keywords();
    bioKeywords.getKeyword().add(new Keyword("Pavement Studies", Visibility.PUBLIC));
    bioKeywords.getKeyword().add(new Keyword("Advanced Tea Making", Visibility.PUBLIC));
    bioKeywords.setVisibility(Visibility.PUBLIC);
    orcidBio.setKeywords(bioKeywords);
    PersonalDetails personalDetails = new PersonalDetails();
    CreditName creditName = new CreditName("credit name");
    creditName.setVisibility(Visibility.PUBLIC);
    personalDetails.setCreditName(creditName);
    FamilyName familyName = new FamilyName("familyName");
    familyName.setVisibility(Visibility.PUBLIC);
    personalDetails.setFamilyName(familyName);
    OtherNames otherNames = new OtherNames();
    otherNames.setVisibility(Visibility.PUBLIC);
    otherNames.getOtherName().add(new OtherName("Other 1", Visibility.PUBLIC));
    otherNames.getOtherName().add(new OtherName("Other 2", Visibility.PUBLIC));
    personalDetails.setOtherNames(otherNames);
    GivenNames givenNames = new GivenNames("givenNames");
    givenNames.setVisibility(Visibility.PUBLIC);
    personalDetails.setGivenNames(givenNames);
    orcidBio.setPersonalDetails(personalDetails);
    ExternalIdentifiers externalIdentifiers = new ExternalIdentifiers();
    externalIdentifiers.setVisibility(Visibility.PUBLIC);
    orcidBio.setExternalIdentifiers(externalIdentifiers);
    ExternalIdentifier externalIdentifier1 = createExternalIdentifier("45678", "defghi");
    externalIdentifiers.getExternalIdentifier().add(externalIdentifier1);
    ExternalIdentifier externalIdentifier2 = createExternalIdentifier("54321", "abc123");
    externalIdentifiers.getExternalIdentifier().add(externalIdentifier2);
    OrcidActivities orcidActivities = new OrcidActivities();
    orcidProfile.setOrcidActivities(orcidActivities);
    Affiliations affiliations = new Affiliations();
    orcidActivities.setAffiliations(affiliations);
    FundingList fundings = new FundingList();
    orcidActivities.setFundings(fundings);
    OrcidWorks orcidWorks = new OrcidWorks();
    OrcidWork orcidWork1 = new OrcidWork();
    orcidWork1.setVisibility(Visibility.PUBLIC);
    OrcidWork orcidWork2 = new OrcidWork();
    orcidWork2.setVisibility(Visibility.PUBLIC);
    OrcidWork orcidWork3 = new OrcidWork();
    orcidWork3.setVisibility(Visibility.LIMITED);
    WorkTitle workTitle1 = new WorkTitle();
    Title title1 = new Title("Work title 1");
    workTitle1.setTitle(title1);
    workTitle1.setSubtitle(null);
    orcidWork1.setWorkTitle(workTitle1);
    WorkExternalIdentifier wei = new WorkExternalIdentifier();
    wei.setWorkExternalIdentifierId(new WorkExternalIdentifierId("work1-pmid"));
    wei.setWorkExternalIdentifierType(WorkExternalIdentifierType.PMID);
    orcidWork1.setWorkExternalIdentifiers(new WorkExternalIdentifiers(Arrays.asList(wei)));
    WorkTitle workTitle2 = new WorkTitle();
    Title title2 = new Title("Work title 2");
    workTitle2.setSubtitle(null);
    workTitle2.setTitle(title2);
    orcidWork2.setWorkTitle(workTitle2);
    WorkTitle workTitle3 = new WorkTitle();
    Title title3 = new Title("Work Title 3");
    workTitle3.setSubtitle(null);
    workTitle3.setTitle(title3);
    orcidWork3.setWorkTitle(workTitle3);
    orcidWorks.setOrcidWork(new ArrayList<OrcidWork>(Arrays.asList(new OrcidWork[] { orcidWork1, orcidWork2, orcidWork3 })));
    orcidProfile.setOrcidWorks(orcidWorks);
    orcidProfile.setOrcidBio(orcidBio);
    return orcidProfile;
}

Example 18 with OrcidBio

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

the class AddDelegateForm method getOrcidProfile.

public OrcidProfile getOrcidProfile(String orcid) {
    OrcidProfile orcidProfile = new OrcidProfile();
    orcidProfile.setOrcidIdentifier(orcid);
    OrcidBio orcidBio = new OrcidBio();
    orcidProfile.setOrcidBio(orcidBio);
    Delegation delegation = new Delegation();
    orcidBio.setDelegation(delegation);
    GivenPermissionTo givenPermissionTo = new GivenPermissionTo();
    delegation.setGivenPermissionTo(givenPermissionTo);
    DelegationDetails delegationDetails = new DelegationDetails();
    givenPermissionTo.getDelegationDetails().add(delegationDetails);
    DelegateSummary delegateSummary = new DelegateSummary(new OrcidIdentifier(delegateOrcid));
    delegationDetails.setDelegateSummary(delegateSummary);
    return orcidProfile;
}

Example 19 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 20 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());
}