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

Example 16 with Funding

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

the class OrcidSearchManagerImplTest method orcidRetrievalAllDataPresentInDb.

@Test
@Rollback
public void orcidRetrievalAllDataPresentInDb() throws Exception {
    when(solrDao.findByOrcid("1434")).thenReturn(getSolrRes5678());
    when(orcidProfileCacheManager.retrievePublicBio("5678")).thenReturn(getOrcidProfileAllIndexFieldsPopulated());
    String orcid = "1434";
    // demonstrate that the mapping from solr (profile 1234) and dao (5678)
    // are truly seperate - the search results only return a subset of the
    // full orcid
    // because we want to keep the payload down.
    OrcidMessage retrievedOrcidMessage = orcidSearchManager.findOrcidSearchResultsById(orcid);
    assertNotNull(retrievedOrcidMessage);
    assertTrue(retrievedOrcidMessage.getOrcidSearchResults().getOrcidSearchResult().size() == 1);
    OrcidSearchResult result = retrievedOrcidMessage.getOrcidSearchResults().getOrcidSearchResult().get(0);
    assertTrue(new Float(37.2).compareTo(result.getRelevancyScore().getValue()) == 0);
    OrcidProfile retrievedProfile = result.getOrcidProfile();
    assertEquals("5678", retrievedProfile.getOrcidIdentifier().getPath());
    OrcidBio orcidBio = retrievedProfile.getOrcidBio();
    assertEquals("Logan", orcidBio.getPersonalDetails().getFamilyName().getContent());
    assertEquals("Donald Edward", orcidBio.getPersonalDetails().getGivenNames().getContent());
    assertEquals("Stanley Higgins", orcidBio.getPersonalDetails().getCreditName().getContent());
    List<String> otherNames = orcidBio.getPersonalDetails().getOtherNames().getOtherNamesAsStrings();
    assertTrue(otherNames.contains("Edward Bass"));
    assertTrue(otherNames.contains("Gareth Dove"));
    OrcidWorks orcidWorks = retrievedProfile.retrieveOrcidWorks();
    OrcidWork orcidWork1 = orcidWorks.getOrcidWork().get(0);
    OrcidWork orcidWork2 = orcidWorks.getOrcidWork().get(1);
    assertTrue(orcidWork1.getWorkExternalIdentifiers().getWorkExternalIdentifier().size() == 1);
    assertEquals("work1-doi1", orcidWork1.getWorkExternalIdentifiers().getWorkExternalIdentifier().get(0).getWorkExternalIdentifierId().getContent());
    assertTrue(orcidWork2.getWorkExternalIdentifiers().getWorkExternalIdentifier().size() == 2);
    assertEquals("work2-doi1", orcidWork2.getWorkExternalIdentifiers().getWorkExternalIdentifier().get(0).getWorkExternalIdentifierId().getContent());
    assertEquals("work2-doi2", orcidWork2.getWorkExternalIdentifiers().getWorkExternalIdentifier().get(1).getWorkExternalIdentifierId().getContent());
    List<Funding> fundings = retrievedProfile.retrieveFundings().getFundings();
    Funding funding1 = fundings.get(0);
    Funding funding2 = fundings.get(1);
    // check returns a reduced payload
    assertNotNull(funding1.getTitle());
    assertNotNull(funding1.getTitle().getTitle());
    assertEquals("grant1", funding1.getTitle().getTitle().getContent());
    assertEquals("Grant 1 - a short description", funding1.getDescription());
    assertNull(funding1.getPutCode());
    assertNotNull(funding2.getTitle());
    assertNotNull(funding2.getTitle().getTitle());
    assertEquals("grant2", funding2.getTitle().getTitle().getContent());
    assertEquals("Grant 2 - a short description", funding2.getDescription());
    assertNull(funding2.getPutCode());
}

Example 17 with Funding

use of org.orcid.jaxb.model.message.Funding 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 18 with Funding

use of org.orcid.jaxb.model.message.Funding 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 19 with Funding

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

the class Jaxb2JpaAdapterImpl method setFundings.

private void setFundings(ProfileEntity profileEntity, FundingList orcidFundings) {
    SortedSet<ProfileFundingEntity> existingProfileFundingEntities = profileEntity.getProfileFunding();
    if (existingProfileFundingEntities == null) {
        existingProfileFundingEntities = new TreeSet<>();
    }
    // Create a map containing the existing profile funding entities
    Map<String, ProfileFundingEntity> existingProfileFundingEntitiesMap = createProfileFundingEntitiesMap(existingProfileFundingEntities);
    // A set that will contain the updated profile funding entities that
    // comes from the orcidGrant object
    SortedSet<ProfileFundingEntity> updatedProfileFundingEntities = new TreeSet<>();
    // from the fundingList object
    if (orcidFundings != null && orcidFundings.getFundings() != null && !orcidFundings.getFundings().isEmpty()) {
        for (Funding orcidFunding : orcidFundings.getFundings()) {
            ProfileFundingEntity newProfileGrantEntity = getProfileFundingEntity(orcidFunding, existingProfileFundingEntitiesMap.get(orcidFunding.getPutCode()));
            newProfileGrantEntity.setProfile(profileEntity);
            updatedProfileFundingEntities.add(newProfileGrantEntity);
        }
    }
    // Create a map containing the profile funding that comes in the
    // orcidGrant object and that will be persisted
    Map<String, ProfileFundingEntity> updatedProfileGrantEntitiesMap = createProfileFundingEntitiesMap(updatedProfileFundingEntities);
    // Remove orphans
    for (Iterator<ProfileFundingEntity> iterator = existingProfileFundingEntities.iterator(); iterator.hasNext(); ) {
        ProfileFundingEntity existingEntity = iterator.next();
        if (!updatedProfileGrantEntitiesMap.containsKey(String.valueOf(existingEntity.getId()))) {
            iterator.remove();
        }
    }
    // Add new
    for (ProfileFundingEntity updatedEntity : updatedProfileFundingEntities) {
        if (updatedEntity.getId() == null) {
            existingProfileFundingEntities.add(updatedEntity);
        }
    }
    profileEntity.setProfileFunding(existingProfileFundingEntities);
}

Example 20 with Funding

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

the class OrcidMessageVersionConverterImplV1_2_rc3ToV1_2_rc4 method downgradeProfile.

private void downgradeProfile(OrcidProfile orcidProfile) {
    if (orcidProfile != null) {
        if (orcidProfile.getOrcidHistory() != null) {
            if (orcidProfile.getOrcidHistory().getVerifiedEmail() != null) {
                orcidProfile.getOrcidHistory().setVerifiedEmail(null);
            }
            if (orcidProfile.getOrcidHistory().getVerifiedPrimaryEmail() != null) {
                orcidProfile.getOrcidHistory().setVerifiedPrimaryEmail(null);
            }
        }
        if (orcidProfile.getOrcidInternal() != null) {
            // earlier versions of the XSD don't have GroupOrcidIdentifier 
            if (orcidProfile.getOrcidInternal().getReferredBy() != null) {
                orcidProfile.getOrcidInternal().setReferredBy(null);
            }
            // earlier versions of the XSD don't have 
            if (orcidProfile.getOrcidInternal().getPreferences() != null && orcidProfile.getOrcidInternal().getPreferences().getDeveloperToolsEnabled() != null) {
                orcidProfile.getOrcidInternal().getPreferences().setDeveloperToolsEnabled(null);
            }
        }
        if (orcidProfile.getOrcidInternal() != null) {
            if (orcidProfile.getOrcidInternal().getPreferences() != null) {
                Preferences prefs = orcidProfile.getOrcidInternal().getPreferences();
                if (prefs.getActivitiesVisibilityDefault() != null && prefs.getActivitiesVisibilityDefault().getValue() != null) {
                    prefs.setWorkVisibilityDefault(new WorkVisibilityDefault(prefs.getActivitiesVisibilityDefault().getValue()));
                    prefs.setActivitiesVisibilityDefault(null);
                }
            }
        }
        //Previews versions doesnt have organization defined funding type
        if (orcidProfile.getOrcidActivities() != null) {
            OrcidActivities activities = orcidProfile.getOrcidActivities();
            if (activities.getFundings() != null) {
                FundingList fundingList = activities.getFundings();
                for (Funding funding : fundingList.getFundings()) {
                    funding.setOrganizationDefinedFundingType(null);
                }
            }
        }
    }
}