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

Example 26 with OrcidWork

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

the class Api12MembersTest method addUpdateWorkTest.

@Test
public void addUpdateWorkTest() throws Exception {
    String clientId = getClient1ClientId();
    String clientRedirectUri = getClient1RedirectUri();
    String clientSecret = getClient1ClientSecret();
    String userId = getUser1OrcidId();
    String password = getUser1Password();
    String accessToken = getAccessToken(userId, password, Arrays.asList("/orcid-works/read-limited", "/activities/update"), clientId, clientSecret, clientRedirectUri, true);
    String title = "Work " + System.currentTimeMillis();
    Long putCode = null;
    Api12Helper.addWork(userId, accessToken, title, t2OAuthClient_1_2);
    ClientResponse response = t2OAuthClient_1_2.viewWorksDetailsXml(userId, accessToken);
    assertNotNull(response);
    assertEquals(200, response.getStatus());
    assertEquals("application/vnd.orcid+xml; charset=UTF-8; qs=5", response.getType().toString());
    OrcidMessage orcidMessageWithNewWork = response.getEntity(OrcidMessage.class);
    assertNotNull(orcidMessageWithNewWork);
    assertNotNull(orcidMessageWithNewWork.getOrcidProfile());
    assertNotNull(orcidMessageWithNewWork.getOrcidProfile().getOrcidActivities());
    assertNotNull(orcidMessageWithNewWork.getOrcidProfile().getOrcidActivities().getOrcidWorks());
    assertNotNull(orcidMessageWithNewWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork());
    int initialSize = orcidMessageWithNewWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork().size();
    boolean found = false;
    for (OrcidWork work : orcidMessageWithNewWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork()) {
        if (title.equals(work.getWorkTitle().getTitle().getContent())) {
            assertNotNull(work.getPutCode());
            putCode = Long.valueOf(work.getPutCode());
            found = true;
        }
    }
    assertTrue(found);
    // Update it
    String newTitle = "Updated - " + title;
    WorkType newType = WorkType.BOOK;
    String newExtId = String.valueOf(System.currentTimeMillis());
    Iterator<OrcidWork> it = orcidMessageWithNewWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork().iterator();
    while (it.hasNext()) {
        OrcidWork work = it.next();
        if (clientId.equals(work.getSource().retrieveSourcePath())) {
            if (title.equals(work.getWorkTitle().getTitle().getContent())) {
                assertNotNull(work.getPutCode());
                // Update title
                work.getWorkTitle().getTitle().setContent(newTitle);
                // Update ext ids
                work.getWorkExternalIdentifiers().getWorkExternalIdentifier().get(0).getWorkExternalIdentifierId().setContent(newExtId);
                // Update type
                work.setWorkType(newType);
            }
        } else {
            it.remove();
        }
    }
    ClientResponse updateResponse = t2OAuthClient_1_2.updateWorksXml(userId, orcidMessageWithNewWork, accessToken);
    assertEquals(ClientResponse.Status.OK.getStatusCode(), updateResponse.getStatus());
    // Fetch them again and verify the values has been updated
    response = t2OAuthClient_1_2.viewWorksDetailsXml(userId, accessToken);
    assertNotNull(response);
    assertEquals(200, response.getStatus());
    assertEquals("application/vnd.orcid+xml; charset=UTF-8; qs=5", response.getType().toString());
    OrcidMessage orcidMessageWithUpdatedWork = response.getEntity(OrcidMessage.class);
    assertNotNull(orcidMessageWithUpdatedWork);
    assertNotNull(orcidMessageWithUpdatedWork.getOrcidProfile());
    assertNotNull(orcidMessageWithUpdatedWork.getOrcidProfile().getOrcidActivities());
    assertNotNull(orcidMessageWithUpdatedWork.getOrcidProfile().getOrcidActivities().getOrcidWorks());
    assertNotNull(orcidMessageWithUpdatedWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork());
    int size = orcidMessageWithUpdatedWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork().size();
    assertEquals(initialSize, size);
    found = false;
    for (OrcidWork work : orcidMessageWithUpdatedWork.getOrcidProfile().getOrcidActivities().getOrcidWorks().getOrcidWork()) {
        assertNotNull(work.getPutCode());
        if (putCode.equals(Long.valueOf(work.getPutCode()))) {
            assertEquals(newTitle, work.getWorkTitle().getTitle().getContent());
            assertEquals(newType, work.getWorkType());
            assertEquals(1, work.getWorkExternalIdentifiers().getWorkExternalIdentifier().size());
            assertEquals(newExtId, work.getWorkExternalIdentifiers().getWorkExternalIdentifier().get(0).getWorkExternalIdentifierId().getContent());
            found = true;
        }
    }
    assertTrue(found);
    // Delete it
    ClientResponse deleteResponse = memberV2ApiClient.deleteWorkXml(this.getUser1OrcidId(), putCode, accessToken);
    assertEquals(Response.Status.NO_CONTENT.getStatusCode(), deleteResponse.getStatus());
}

Example 27 with OrcidWork

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

the class FindOrcidWorkDuplicates method dedupeWorksForOrcid.

private List<OrcidWorkDeduped> dedupeWorksForOrcid(OrcidWorks orcidWorks) {
    Map<OrcidWorkMatcher, List<OrcidWork>> worksSplitByDuplicates = splitWorksIntoDuplicateSets(orcidWorks);
    List<OrcidWorkDeduped> orcidWorkDupes = new ArrayList<FindOrcidWorkDuplicates.OrcidWorkDeduped>();
    for (Map.Entry<OrcidWorkMatcher, List<OrcidWork>> entry : worksSplitByDuplicates.entrySet()) {
        List<OrcidWork> allOrcidWorks = entry.getValue();
        // there may have been more than one work on a profile, but may not be duplicates
        if (allOrcidWorks.size() < 2) {
            continue;
        }
        // sort by desc put code in case we cant rely on visibility
        Collections.sort(allOrcidWorks, new Comparator<OrcidWork>() {

            public int compare(OrcidWork work1, OrcidWork work2) {
                return Integer.valueOf(work2.getPutCode()).compareTo(Integer.valueOf(work1.getPutCode()));
            }
        });
        // yes
        // add to string
        // determine which is the dupe and which the definitive XML
        OrcidWork definitiveWork = null;
        OrcidWork definitivePublicWork = null;
        OrcidWork definitiveLimitedWork = null;
        // if there are varying visibilities then the definitive is the must public level of visibility
        for (OrcidWork orcidWork : allOrcidWorks) {
            if (Visibility.PUBLIC.equals(orcidWork.getVisibility())) {
                definitivePublicWork = orcidWork;
                break;
            } else // once set
            if (Visibility.LIMITED.equals(orcidWork.getVisibility()) && definitiveLimitedWork == null) {
                definitiveLimitedWork = orcidWork;
            }
        }
        // fallback onto limited work and if nothing else the max put code
        definitiveWork = definitivePublicWork != null ? definitivePublicWork : definitiveLimitedWork;
        // if they all match the definitive is the most recent date
        definitiveWork = definitiveWork != null ? definitiveWork : allOrcidWorks.get(0);
        allOrcidWorks.remove(definitiveWork);
        orcidWorkDupes.add(new OrcidWorkDeduped(definitiveWork, allOrcidWorks));
    }
    return orcidWorkDupes;
}

Example 28 with OrcidWork

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

the class OrcidSearchManagerImplTest method orcidRetrievalAllDataPresentInDb.

@Test
@Rollback
public void orcidRetrievalAllDataPresentInDb() throws Exception {
    when(mockSolrDao.findByOrcid("1434")).thenReturn(getOrcidSolrResult("5678", new Float(37.2)));
    when(mockOrcidProfileCacheManager.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 29 with OrcidWork

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

the class OrcidSearchManagerImpl method buildSearchResultsFromPublicProfile.

private List<OrcidSearchResult> buildSearchResultsFromPublicProfile(List<OrcidSolrResult> solrResults) {
    List<OrcidSearchResult> orcidSearchResults = new ArrayList<OrcidSearchResult>();
    for (OrcidSolrResult solrResult : solrResults) {
        OrcidMessage orcidMessage = null;
        String orcid = solrResult.getOrcid();
        try {
            orcidSecurityManager.checkProfile(orcid);
        } catch (DeactivatedException | LockedException | OrcidDeprecatedException x) {
            OrcidSearchResult orcidSearchResult = new OrcidSearchResult();
            RelevancyScore relevancyScore = new RelevancyScore();
            relevancyScore.setValue(solrResult.getRelevancyScore());
            orcidSearchResult.setRelevancyScore(relevancyScore);
            OrcidProfile orcidProfile = new OrcidProfile();
            orcidProfile.setOrcidIdentifier(new OrcidIdentifier(jpaJaxbAdapter.getOrcidIdBase(orcid)));
            OrcidHistory history = new OrcidHistory();
            Date recordLastModified = profileDaoReadOnly.retrieveLastModifiedDate(orcid);
            history.setLastModifiedDate(new LastModifiedDate(DateUtils.convertToXMLGregorianCalendar(recordLastModified)));
            orcidProfile.setOrcidHistory(history);
            orcidSearchResult.setOrcidProfile(orcidProfile);
            orcidSearchResults.add(orcidSearchResult);
            continue;
        }
        if (cachingSource.equals(SOLR)) {
            try (Reader reader = solrDao.findByOrcidAsReader(orcid)) {
                if (reader != null) {
                    BufferedReader br = new BufferedReader(reader);
                    orcidMessage = OrcidMessage.unmarshall(br);
                }
            } catch (IOException e) {
                throw new OrcidSearchException("Error closing record stream from solr search results for orcid: " + orcid, e);
            }
        }
        OrcidProfile orcidProfile = null;
        if (orcidMessage == null) {
            // Fall back to DB
            orcidProfile = orcidProfileCacheManager.retrievePublicBio(orcid);
        } else {
            orcidProfile = orcidMessage.getOrcidProfile();
        }
        if (orcidProfile != null) {
            OrcidSearchResult orcidSearchResult = new OrcidSearchResult();
            RelevancyScore relevancyScore = new RelevancyScore();
            relevancyScore.setValue(solrResult.getRelevancyScore());
            orcidSearchResult.setRelevancyScore(relevancyScore);
            OrcidWorks orcidWorksTitlesOnly = new OrcidWorks();
            OrcidWorks fullOrcidWorks = orcidProfile.retrieveOrcidWorks();
            if (fullOrcidWorks != null && !fullOrcidWorks.getOrcidWork().isEmpty()) {
                for (OrcidWork fullOrcidWork : fullOrcidWorks.getOrcidWork()) {
                    OrcidWork orcidWorkSubset = new OrcidWork();
                    orcidWorkSubset.setVisibility(fullOrcidWork.getVisibility());
                    orcidWorkSubset.setWorkTitle(fullOrcidWork.getWorkTitle());
                    orcidWorkSubset.setWorkExternalIdentifiers(fullOrcidWork.getWorkExternalIdentifiers());
                    orcidWorksTitlesOnly.getOrcidWork().add(orcidWorkSubset);
                }
            }
            FundingList reducedFundings = new FundingList();
            FundingList fullOrcidFundings = orcidProfile.retrieveFundings();
            if (fullOrcidFundings != null && !fullOrcidFundings.getFundings().isEmpty()) {
                for (Funding fullOrcidFunding : fullOrcidFundings.getFundings()) {
                    Funding reducedFunding = new Funding();
                    reducedFunding.setVisibility(fullOrcidFunding.getVisibility());
                    reducedFunding.setDescription(fullOrcidFunding.getDescription());
                    reducedFunding.setTitle(fullOrcidFunding.getTitle());
                    reducedFundings.getFundings().add(reducedFunding);
                }
            }
            orcidProfile.setOrcidWorks(orcidWorksTitlesOnly);
            orcidProfile.setFundings(reducedFundings);
            orcidSearchResult.setOrcidProfile(orcidProfile);
            orcidSearchResults.add(orcidSearchResult);
        }
    }
    return orcidSearchResults;
}

Example 30 with OrcidWork

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

the class OrcidProfileManagerImpl method addOrcidWorks.

@Override
@Transactional
public void addOrcidWorks(OrcidProfile updatedOrcidProfile) {
    String orcid = updatedOrcidProfile.getOrcidIdentifier().getPath();
    OrcidProfile existingProfile = null;
    List<OrcidWork> updatedOrcidWorksList = null;
    try {
        synchronized (getLock(orcid)) {
            existingProfile = retrieveOrcidProfile(orcid);
            if (existingProfile == null) {
                throw new IllegalArgumentException("No record found for " + orcid);
            }
            OrcidWorks existingOrcidWorks = existingProfile.retrieveOrcidWorks();
            OrcidWorks updatedOrcidWorks = updatedOrcidProfile.retrieveOrcidWorks();
            Visibility workVisibilityDefault = existingProfile.getOrcidInternal().getPreferences().getActivitiesVisibilityDefault().getValue();
            Boolean claimed = existingProfile.getOrcidHistory().isClaimed();
            setWorkPrivacy(updatedOrcidWorks, workVisibilityDefault, claimed == null ? false : claimed);
            if (updatedOrcidWorks != null) {
                addSourceToWorks(updatedOrcidWorks, getSource());
            }
            updatedOrcidWorks = dedupeWorks(updatedOrcidWorks);
            updatedOrcidWorksList = updatedOrcidWorks.getOrcidWork();
            checkUserCanHoldMoreElement(existingProfile.retrieveOrcidWorks(), updatedOrcidProfile.retrieveOrcidWorks());
            if (compareWorksUsingScopusWay) {
                checkForAlreadyExistingWorks(orcid, existingOrcidWorks, updatedOrcidWorksList);
                if (existingOrcidWorks != null)
                    checkWorkExternalIdentifiersAreNotDuplicated(updatedOrcidWorksList, existingOrcidWorks.getOrcidWork());
                else
                    checkWorkExternalIdentifiersAreNotDuplicated(updatedOrcidWorksList, null);
            } else {
                checkForAlreadyExistingWorksLegacyMode(existingOrcidWorks, updatedOrcidWorksList);
            }
            persistAddedWorks(orcid, updatedOrcidWorksList);
            profileDao.flush();
        }
    } finally {
        releaseLock(orcid);
    }
    boolean notificationsEnabled = existingProfile.getOrcidInternal().getPreferences().getNotificationsEnabled();
    if (notificationsEnabled && updatedOrcidWorksList != null) {
        List<Item> activities = new ArrayList<>();
        for (OrcidWork updatedWork : updatedOrcidWorksList) {
            Item activity = new Item();
            activity.setItemName(updatedWork.getWorkTitle().getTitle().getContent());
            activity.setItemType(ItemType.WORK);
            activity.setPutCode(updatedWork.getPutCode());
            activities.add(activity);
        }
        notificationManager.sendAmendEmail(orcid, AmendedSection.WORK, activities);
    }
}