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

Example 16 with ExternalIdentifier

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

the class OrcidIndexManagerImplTest method createExternalIdentifier.

private ExternalIdentifier createExternalIdentifier(String orcid, String reference) {
    ExternalIdentifier externalIdentifier1 = new ExternalIdentifier();
    Source source = new Source();
    source.setSourceOrcid(new SourceOrcid(orcid));
    externalIdentifier1.setSource(source);
    externalIdentifier1.setExternalIdReference(new ExternalIdReference(reference));
    //you have to set this as visibility will filter out null visibilities.
    externalIdentifier1.setVisibility(Visibility.PUBLIC);
    return externalIdentifier1;
}

Example 17 with ExternalIdentifier

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

the class OrcidProfileToSolrDocument method convert.

@Deprecated
public OrcidSolrDocument convert(OrcidProfile profile) {
    // Check if the profile is locked
    if (profile.isLocked()) {
        profile.downgradeToOrcidIdentifierOnly();
    }
    OrcidSolrDocument profileIndexDocument = new OrcidSolrDocument();
    profileIndexDocument.setOrcid(profile.getOrcidIdentifier().getPath());
    OrcidDeprecated orcidDeprecated = profile.getOrcidDeprecated();
    if (orcidDeprecated != null) {
        profileIndexDocument.setPrimaryRecord(orcidDeprecated.getPrimaryRecord() != null ? orcidDeprecated.getPrimaryRecord().getOrcidIdentifier().getPath() : null);
    }
    OrcidBio orcidBio = profile.getOrcidBio();
    if (orcidBio != null) {
        PersonalDetails personalDetails = orcidBio.getPersonalDetails();
        boolean persistPersonalDetails = personalDetails != null;
        if (persistPersonalDetails) {
            profileIndexDocument.setFamilyName(personalDetails.getFamilyName() != null ? personalDetails.getFamilyName().getContent() : null);
            profileIndexDocument.setGivenNames(personalDetails.getGivenNames() != null ? personalDetails.getGivenNames().getContent() : null);
            profileIndexDocument.setCreditName(personalDetails.getCreditName() != null ? personalDetails.getCreditName().getContent() : null);
            List<OtherName> otherNames = personalDetails.getOtherNames() != null ? personalDetails.getOtherNames().getOtherName() : null;
            if (otherNames != null && !otherNames.isEmpty()) {
                List<String> names = new ArrayList<String>();
                for (OtherName otherName : otherNames) {
                    names.add(otherName.getContent());
                }
                profileIndexDocument.setOtherNames(names);
            }
        }
        ContactDetails contactDetails = orcidBio.getContactDetails();
        if (contactDetails != null) {
            for (Email email : contactDetails.getEmail()) {
                profileIndexDocument.addEmailAddress(email.getValue());
            }
        }
        ExternalIdentifiers externalIdentifiers = orcidBio.getExternalIdentifiers();
        if (externalIdentifiers != null) {
            List<String> extIdOrcids = new ArrayList<String>();
            List<String> extIdRefs = new ArrayList<String>();
            List<String> extIdOrcidsAndRefs = new ArrayList<String>();
            for (ExternalIdentifier externalIdentifier : externalIdentifiers.getExternalIdentifier()) {
                Source source = externalIdentifier.getSource();
                String sourcePath = null;
                if (source != null) {
                    sourcePath = source.retrieveSourcePath();
                    if (sourcePath != null) {
                        extIdOrcids.add(sourcePath);
                    }
                }
                ExternalIdReference externalIdReference = externalIdentifier.getExternalIdReference();
                if (externalIdReference != null) {
                    extIdRefs.add(externalIdReference.getContent());
                }
                if (NullUtils.noneNull(sourcePath, externalIdReference)) {
                    extIdOrcidsAndRefs.add(sourcePath + "=" + externalIdReference.getContent());
                }
            }
            if (!extIdOrcids.isEmpty()) {
                profileIndexDocument.setExternalIdSources(extIdOrcids);
            }
            if (!extIdRefs.isEmpty()) {
                profileIndexDocument.setExternalIdReferences(extIdRefs);
            }
            if (!extIdOrcidsAndRefs.isEmpty()) {
                profileIndexDocument.setExternalIdSourcesAndReferences(extIdOrcidsAndRefs);
            }
        }
        OrcidActivities orcidActivities = profile.getOrcidActivities();
        if (orcidActivities != null) {
            if (orcidBio != null && orcidBio.getKeywords() != null) {
                List<Keyword> keyWords = orcidBio.getKeywords().getKeyword();
                if (keyWords != null && keyWords.size() > 0) {
                    List<String> keywordValues = new ArrayList<String>();
                    for (Keyword keyword : keyWords) {
                        keywordValues.add(keyword.getContent());
                    }
                    profileIndexDocument.setKeywords(keywordValues);
                }
            }
        }
        List<OrcidWork> orcidWorks = profile.retrieveOrcidWorks() != null ? profile.retrieveOrcidWorks().getOrcidWork() : null;
        if (orcidWorks != null) {
            List<String> workTitles = new ArrayList<String>();
            Map<WorkExternalIdentifierType, List<String>> allExternalIdentifiers = new HashMap<WorkExternalIdentifierType, List<String>>();
            for (OrcidWork orcidWork : orcidWorks) {
                if (orcidWork.getWorkExternalIdentifiers() != null) {
                    for (WorkExternalIdentifier workExternalIdentifier : orcidWork.getWorkExternalIdentifiers().getWorkExternalIdentifier()) {
                        /**
                             * Creates a map that contains all different
                             * external identifiers for the current work
                             */
                        boolean nullSafeCheckForWorkExternalIdentifier = workExternalIdentifier.getWorkExternalIdentifierId() != null && !StringUtils.isBlank(workExternalIdentifier.getWorkExternalIdentifierId().getContent());
                        if (nullSafeCheckForWorkExternalIdentifier) {
                            WorkExternalIdentifierType type = workExternalIdentifier.getWorkExternalIdentifierType();
                            if (!allExternalIdentifiers.containsKey(type)) {
                                List<String> content = new ArrayList<String>();
                                content.add(workExternalIdentifier.getWorkExternalIdentifierId().getContent());
                                allExternalIdentifiers.put(type, content);
                            } else {
                                allExternalIdentifiers.get(type).add(workExternalIdentifier.getWorkExternalIdentifierId().getContent());
                            }
                        }
                    }
                }
                if (orcidWork.getWorkTitle() != null) {
                    Title workMainTitle = orcidWork.getWorkTitle().getTitle();
                    Subtitle worksubTitle = orcidWork.getWorkTitle().getSubtitle();
                    TranslatedTitle translatedTitle = orcidWork.getWorkTitle().getTranslatedTitle();
                    if (workMainTitle != null && !StringUtils.isBlank(workMainTitle.getContent())) {
                        workTitles.add(workMainTitle.getContent());
                    }
                    if (worksubTitle != null && !StringUtils.isBlank(worksubTitle.getContent())) {
                        workTitles.add(worksubTitle.getContent());
                    }
                    if (translatedTitle != null && !StringUtils.isBlank(translatedTitle.getContent())) {
                        workTitles.add(translatedTitle.getContent());
                    }
                }
            }
            profileIndexDocument.setWorkTitles(workTitles);
            // Set the list of external identifiers to the document list
            addExternalIdentifiersToIndexDocument(profileIndexDocument, allExternalIdentifiers);
        }
        List<Funding> orcidFundings = profile.retrieveFundings() != null ? profile.retrieveFundings().getFundings() : null;
        if (orcidFundings != null) {
            List<String> fundingTitle = new ArrayList<String>();
            for (Funding orcidFunding : orcidFundings) {
                FundingTitle title = orcidFunding.getTitle();
                if (title != null) {
                    if (title.getTitle() != null && !StringUtils.isBlank(title.getTitle().getContent())) {
                        fundingTitle.add(title.getTitle().getContent());
                    }
                    if (title.getTranslatedTitle() != null && StringUtils.isBlank(title.getTranslatedTitle().getContent())) {
                        fundingTitle.add(title.getTranslatedTitle().getContent());
                    }
                }
            }
            profileIndexDocument.setFundingTitles(fundingTitle);
        }
    }
    OrcidMessage orcidMessage = new OrcidMessage();
    orcidMessage.setMessageVersion(OrcidMessage.DEFAULT_VERSION);
    orcidMessage.setOrcidProfile(profile);
    OrcidHistory orcidHistory = profile.getOrcidHistory();
    if (orcidHistory != null) {
        LastModifiedDate lastModifiedDate = orcidHistory.getLastModifiedDate();
        if (lastModifiedDate != null) {
            profileIndexDocument.setProfileLastModifiedDate(lastModifiedDate.getValue().toGregorianCalendar().getTime());
        }
        SubmissionDate submissionDate = orcidHistory.getSubmissionDate();
        if (submissionDate != null) {
            profileIndexDocument.setProfileSubmissionDate(submissionDate.getValue().toGregorianCalendar().getTime());
        }
    }
    return profileIndexDocument;
}

Example 18 with ExternalIdentifier

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

the class OrcidIndexManagerImpl method persistProfileInformationForIndexing.

@Override
@Deprecated
public void persistProfileInformationForIndexing(OrcidProfile orcidProfile) {
    // Check if the profile is locked
    if (orcidProfile.isLocked()) {
        orcidProfile.downgradeToOrcidIdentifierOnly();
    }
    OrcidMessage messageToFilter = new OrcidMessage();
    messageToFilter.setOrcidProfile(orcidProfile);
    OrcidMessage filteredMessage = visibilityFilter.filter(messageToFilter, Visibility.PUBLIC);
    OrcidProfile filteredProfile = filteredMessage.getOrcidProfile();
    OrcidSolrDocument profileIndexDocument = new OrcidSolrDocument();
    profileIndexDocument.setOrcid(filteredProfile.getOrcidIdentifier().getPath());
    OrcidDeprecated orcidDeprecated = filteredProfile.getOrcidDeprecated();
    if (orcidDeprecated != null) {
        profileIndexDocument.setPrimaryRecord(orcidDeprecated.getPrimaryRecord() != null ? orcidDeprecated.getPrimaryRecord().getOrcidIdentifier().getPath() : null);
    }
    OrcidBio orcidBio = filteredProfile.getOrcidBio();
    if (orcidBio != null) {
        PersonalDetails personalDetails = orcidBio.getPersonalDetails();
        boolean persistPersonalDetails = personalDetails != null;
        if (persistPersonalDetails) {
            profileIndexDocument.setFamilyName(personalDetails.getFamilyName() != null ? personalDetails.getFamilyName().getContent() : null);
            profileIndexDocument.setGivenNames(personalDetails.getGivenNames() != null ? personalDetails.getGivenNames().getContent() : null);
            profileIndexDocument.setCreditName(personalDetails.getCreditName() != null ? personalDetails.getCreditName().getContent() : null);
            List<OtherName> otherNames = personalDetails.getOtherNames() != null ? personalDetails.getOtherNames().getOtherName() : null;
            if (otherNames != null && !otherNames.isEmpty()) {
                List<String> names = new ArrayList<String>();
                for (OtherName otherName : otherNames) {
                    names.add(otherName.getContent());
                }
                profileIndexDocument.setOtherNames(names);
            }
        }
        ContactDetails contactDetails = orcidBio.getContactDetails();
        if (contactDetails != null) {
            for (Email email : contactDetails.getEmail()) {
                profileIndexDocument.addEmailAddress(email.getValue());
            }
        }
        ExternalIdentifiers externalIdentifiers = orcidBio.getExternalIdentifiers();
        if (externalIdentifiers != null) {
            List<String> extIdOrcids = new ArrayList<String>();
            List<String> extIdRefs = new ArrayList<String>();
            List<String> extIdOrcidsAndRefs = new ArrayList<String>();
            for (ExternalIdentifier externalIdentifier : externalIdentifiers.getExternalIdentifier()) {
                Source source = externalIdentifier.getSource();
                String sourcePath = null;
                if (source != null) {
                    sourcePath = source.retrieveSourcePath();
                    if (sourcePath != null) {
                        extIdOrcids.add(sourcePath);
                    }
                }
                ExternalIdReference externalIdReference = externalIdentifier.getExternalIdReference();
                if (externalIdReference != null) {
                    extIdRefs.add(externalIdReference.getContent());
                }
                if (NullUtils.noneNull(sourcePath, externalIdReference)) {
                    extIdOrcidsAndRefs.add(sourcePath + "=" + externalIdReference.getContent());
                }
            }
            if (!extIdOrcids.isEmpty()) {
                profileIndexDocument.setExternalIdSources(extIdOrcids);
            }
            if (!extIdRefs.isEmpty()) {
                profileIndexDocument.setExternalIdReferences(extIdRefs);
            }
            if (!extIdOrcidsAndRefs.isEmpty()) {
                profileIndexDocument.setExternalIdSourcesAndReferences(extIdOrcidsAndRefs);
            }
        }
        OrcidActivities orcidActivities = filteredProfile.getOrcidActivities();
        if (orcidActivities != null) {
            // Affiliations affiliations =
            // orcidActivities.getAffiliations();
            // if (affiliations != null) {
            // List<Affiliation> pastInsts = affiliations
            // .getAffiliationsByType(AffiliationType.PAST_INSTITUTION);
            // if (pastInsts != null && !pastInsts.isEmpty()) {
            // List<String> pastInstNames = new ArrayList<String>();
            // for (Affiliation pastAffiliation : pastInsts) {
            // pastInstNames.add(pastAffiliation
            // .getAffiliationName());
            // }
            //
            // profileIndexDocument
            // .setAffiliatePastInstitutionNames(pastInstNames);
            // }
            //
            // List<Affiliation> primaryInsts = affiliations
            // .getAffiliationsByType(AffiliationType.CURRENT_PRIMARY_INSTITUTION);
            // if (primaryInsts != null && !primaryInsts.isEmpty()) {
            // List<String> primaryInstNames = new ArrayList<String>();
            // for (Affiliation primaryAffiliation : primaryInsts) {
            // primaryInstNames.add(primaryAffiliation
            // .getAffiliationName());
            // }
            //
            // profileIndexDocument
            // .setAffiliatePrimaryInstitutionNames(primaryInstNames);
            // }
            //
            // List<Affiliation> currentNonPrimaryInsts = affiliations
            // .getAffiliationsByType(AffiliationType.CURRENT_INSTITUTION);
            // if (currentNonPrimaryInsts != null
            // && !currentNonPrimaryInsts.isEmpty()) {
            // List<String> affiliateInstNames = new ArrayList<String>();
            // for (Affiliation currentAffiliation : currentNonPrimaryInsts)
            // {
            // affiliateInstNames.add(currentAffiliation
            // .getAffiliationName());
            // }
            //
            // profileIndexDocument
            // .setAffiliateInstitutionNames(affiliateInstNames);
            // }
            // }
            List<String> keywords = extractKeywordsAsStringFromBio(orcidBio);
            if (keywords != null) {
                profileIndexDocument.setKeywords(keywords);
            }
        }
        List<OrcidWork> orcidWorks = filteredProfile.retrieveOrcidWorks() != null ? filteredProfile.retrieveOrcidWorks().getOrcidWork() : null;
        if (orcidWorks != null) {
            List<String> workTitles = new ArrayList<String>();
            Map<WorkExternalIdentifierType, List<String>> allExternalIdentifiers = new HashMap<WorkExternalIdentifierType, List<String>>();
            for (OrcidWork orcidWork : orcidWorks) {
                if (orcidWork.getWorkExternalIdentifiers() != null) {
                    for (WorkExternalIdentifier workExternalIdentifier : orcidWork.getWorkExternalIdentifiers().getWorkExternalIdentifier()) {
                        /**
                             * Creates a map that contains all different
                             * external identifiers for the current work
                             * */
                        if (nullSafeCheckForWorkExternalIdentifier(workExternalIdentifier)) {
                            WorkExternalIdentifierType type = workExternalIdentifier.getWorkExternalIdentifierType();
                            if (!allExternalIdentifiers.containsKey(type)) {
                                List<String> content = new ArrayList<String>();
                                content.add(workExternalIdentifier.getWorkExternalIdentifierId().getContent());
                                allExternalIdentifiers.put(type, content);
                            } else {
                                allExternalIdentifiers.get(type).add(workExternalIdentifier.getWorkExternalIdentifierId().getContent());
                            }
                        }
                    }
                }
                if (orcidWork.getWorkTitle() != null) {
                    Title workMainTitle = orcidWork.getWorkTitle().getTitle();
                    Subtitle worksubTitle = orcidWork.getWorkTitle().getSubtitle();
                    TranslatedTitle translatedTitle = orcidWork.getWorkTitle().getTranslatedTitle();
                    if (workMainTitle != null && !StringUtils.isBlank(workMainTitle.getContent())) {
                        workTitles.add(workMainTitle.getContent());
                    }
                    if (worksubTitle != null && !StringUtils.isBlank(worksubTitle.getContent())) {
                        workTitles.add(worksubTitle.getContent());
                    }
                    if (translatedTitle != null && !StringUtils.isBlank(translatedTitle.getContent())) {
                        workTitles.add(translatedTitle.getContent());
                    }
                }
            }
            profileIndexDocument.setWorkTitles(workTitles);
            // Set the list of external identifiers to the document list
            addExternalIdentifiersToIndexDocument(profileIndexDocument, allExternalIdentifiers);
        }
        List<Funding> orcidFundings = filteredProfile.retrieveFundings() != null ? filteredProfile.retrieveFundings().getFundings() : null;
        if (orcidFundings != null) {
            List<String> fundingTitle = new ArrayList<String>();
            for (Funding orcidFunding : orcidFundings) {
                FundingTitle title = orcidFunding.getTitle();
                if (title != null) {
                    if (title.getTitle() != null && !StringUtils.isBlank(title.getTitle().getContent())) {
                        fundingTitle.add(title.getTitle().getContent());
                    }
                    if (title.getTranslatedTitle() != null && StringUtils.isBlank(title.getTranslatedTitle().getContent())) {
                        fundingTitle.add(title.getTranslatedTitle().getContent());
                    }
                }
            }
            profileIndexDocument.setFundingTitles(fundingTitle);
        }
    }
    OrcidMessage orcidMessage = new OrcidMessage();
    orcidMessage.setMessageVersion(OrcidMessage.DEFAULT_VERSION);
    orcidMessage.setOrcidProfile(filteredProfile);
    OrcidHistory orcidHistory = filteredProfile.getOrcidHistory();
    if (orcidHistory != null) {
        LastModifiedDate lastModifiedDate = orcidHistory.getLastModifiedDate();
        if (lastModifiedDate != null) {
            profileIndexDocument.setProfileLastModifiedDate(lastModifiedDate.getValue().toGregorianCalendar().getTime());
        }
        SubmissionDate submissionDate = orcidHistory.getSubmissionDate();
        if (submissionDate != null) {
            profileIndexDocument.setProfileSubmissionDate(submissionDate.getValue().toGregorianCalendar().getTime());
        }
    }
    if (indexPublicProfile) {
        profileIndexDocument.setPublicProfileMessage(orcidMessage.toXmlString());
    }
    solrDao.persist(profileIndexDocument);
}

Example 19 with ExternalIdentifier

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

the class Jpa2JaxbAdapterTest method checkSourceOnAllElements.

@Test
@Transactional
public void checkSourceOnAllElements() {
    ProfileEntity profileEntity = profileDao.find(userOrcid);
    assertNotNull(profileEntity);
    assertEquals(userOrcid, profileEntity.getId());
    OrcidProfile orcidProfile = adapter.toOrcidProfile(profileEntity);
    assertNotNull(orcidProfile);
    testOrcidIdentifier(orcidProfile.getOrcidIdentifier());
    assertNotNull(orcidProfile.getOrcidActivities());
    // Check works
    OrcidWorks orcidWorks = orcidProfile.getOrcidActivities().getOrcidWorks();
    if (orcidWorks != null && orcidWorks.getOrcidWork() != null && !orcidWorks.getOrcidWork().isEmpty()) {
        for (OrcidWork work : orcidWorks.getOrcidWork()) {
            checkSource(work.getSource(), null);
        }
    }
    // Check affiliations
    Affiliations affiliations = orcidProfile.getOrcidActivities().getAffiliations();
    if (affiliations != null && affiliations.getAffiliation() != null && !affiliations.getAffiliation().isEmpty()) {
        for (Affiliation affiliation : affiliations.getAffiliation()) {
            checkSource(affiliation.getSource(), null);
        }
    }
    // Check fundings
    FundingList fundings = orcidProfile.getOrcidActivities().getFundings();
    if (fundings != null && fundings.getFundings() != null && !fundings.getFundings().isEmpty()) {
        for (Funding funding : fundings.getFundings()) {
            checkSource(funding.getSource(), null);
        }
    }
    assertNotNull(orcidProfile.getOrcidBio());
    // Check external identifiers
    ExternalIdentifiers extIds = orcidProfile.getOrcidBio().getExternalIdentifiers();
    if (extIds != null && extIds.getExternalIdentifier() != null && !extIds.getExternalIdentifier().isEmpty()) {
        for (ExternalIdentifier extId : extIds.getExternalIdentifier()) {
            checkSource(extId.getSource(), null);
        }
    }
}

Example 20 with ExternalIdentifier

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

the class OrcidProfileManagerImplTest method testDeactivateProfile.

@Test
@Transactional
@Rollback(true)
public void testDeactivateProfile() {
    OrcidProfile profile1 = createBasicProfile();
    profile1.getOrcidBio().getPersonalDetails().setCreditName(new CreditName("My Credit Name"));
    ExternalIdentifiers extIds = new ExternalIdentifiers();
    ExternalIdentifier extId = new ExternalIdentifier();
    extId.setExternalIdCommonName(new ExternalIdCommonName("External body"));
    extId.setExternalIdReference(new ExternalIdReference("abc123"));
    extIds.getExternalIdentifier().add(extId);
    profile1.getOrcidBio().setExternalIdentifiers(extIds);
    OtherNames otherNames = new OtherNames();
    otherNames.addOtherName("OtherName 1", null);
    otherNames.addOtherName("OtherName 2", null);
    profile1.getOrcidBio().getPersonalDetails().setOtherNames(otherNames);
    profile1 = orcidProfileManager.createOrcidProfile(profile1, false, false);
    assertEquals(1, profile1.getOrcidBio().getExternalIdentifiers().getExternalIdentifier().size());
    assertEquals(2, profile1.getOrcidBio().getPersonalDetails().getOtherNames().getOtherName().size());
    assertEquals("My Credit Name", profile1.getOrcidBio().getPersonalDetails().getCreditName().getContent());
    assertEquals(Visibility.PRIVATE, profile1.getOrcidBio().getExternalIdentifiers().getExternalIdentifier().iterator().next().getVisibility());
    orcidProfileManager.deactivateOrcidProfile(profile1);
    OrcidProfile retrievedProfile = orcidProfileManager.retrieveOrcidProfile(profile1.getOrcidIdentifier().getPath());
    assertTrue(retrievedProfile.getOrcidBio().getExternalIdentifiers().getExternalIdentifier().isEmpty());
    assertNull(retrievedProfile.getOrcidBio().getPersonalDetails().getCreditName());
    assertEquals(0, retrievedProfile.getOrcidBio().getPersonalDetails().getOtherNames().getOtherName().size());
    assertEquals("Given Names Deactivated", retrievedProfile.getOrcidBio().getPersonalDetails().getGivenNames().getContent());
    assertEquals("Family Name Deactivated", retrievedProfile.getOrcidBio().getPersonalDetails().getFamilyName().getContent());
    assertNull(retrievedProfile.getOrcidBio().getBiography().getContent());
}