use of org.orcid.jaxb.model.record_rc4.ExternalID in project ORCID-Source by ORCID.
the class MemberV2Test method testAddPeerReviewWithInvalidGroupingId.
@Test
public void testAddPeerReviewWithInvalidGroupingId() throws JSONException, InterruptedException, URISyntaxException {
PeerReview peerReview = (PeerReview) unmarshallFromPath("/record_2.0_rc3/samples/peer-review-2.0_rc3.xml", PeerReview.class);
peerReview.setPutCode(null);
peerReview.setGroupId("Invalid group id " + System.currentTimeMillis());
peerReview.getExternalIdentifiers().getExternalIdentifier().clear();
ExternalID pExtId = new ExternalID();
pExtId.setValue("Work Id " + System.currentTimeMillis());
pExtId.setType(WorkExternalIdentifierType.AGR.value());
pExtId.setRelationship(Relationship.SELF);
peerReview.getExternalIdentifiers().getExternalIdentifier().add(pExtId);
String accessToken = getAccessToken();
//Pattern not valid
ClientResponse postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
//Null group id
peerReview.setGroupId(null);
postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
//Empty group id
peerReview.setGroupId("");
postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
//Invalid group id
peerReview.setGroupId("orcid-generated:" + peerReview.getGroupId());
postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
}
use of org.orcid.jaxb.model.record_rc4.ExternalID in project ORCID-Source by ORCID.
the class MemberV2Test method testTokenWorksOnlyForTheScopeItWasIssued.
@SuppressWarnings({ "deprecation", "rawtypes" })
@Test
public void testTokenWorksOnlyForTheScopeItWasIssued() throws JSONException, InterruptedException, URISyntaxException {
long time = System.currentTimeMillis();
List<String> scopes = getScopes(ScopePathType.FUNDING_CREATE, ScopePathType.FUNDING_UPDATE);
String accessToken = getAccessToken(scopes);
Work work1 = (Work) unmarshallFromPath("/record_2.0_rc3/samples/work-2.0_rc3.xml", Work.class);
work1.setPutCode(null);
work1.getExternalIdentifiers().getExternalIdentifier().clear();
org.orcid.jaxb.model.record_rc3.WorkTitle title1 = new org.orcid.jaxb.model.record_rc3.WorkTitle();
title1.setTitle(new Title("Work # 1"));
work1.setWorkTitle(title1);
ExternalID wExtId1 = new ExternalID();
wExtId1.setValue("Work Id " + time);
wExtId1.setType(WorkExternalIdentifierType.AGR.value());
wExtId1.setRelationship(Relationship.SELF);
wExtId1.setUrl(new Url("http://orcid.org/work#1"));
work1.getExternalIdentifiers().getExternalIdentifier().clear();
work1.getExternalIdentifiers().getExternalIdentifier().add(wExtId1);
//Add the work
ClientResponse postResponse = memberV2ApiClient.createWorkXml(this.getUser1OrcidId(), work1, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.FORBIDDEN.getStatusCode(), postResponse.getStatus());
Funding funding = (Funding) unmarshallFromPath("/record_2.0_rc3/samples/funding-2.0_rc3.xml", Funding.class);
funding.setPutCode(null);
funding.setVisibility(Visibility.PUBLIC);
funding.getExternalIdentifiers().getExternalIdentifier().clear();
ExternalID fExtId = new ExternalID();
fExtId.setType(FundingExternalIdentifierType.GRANT_NUMBER.value());
fExtId.setValue("Funding Id " + time);
fExtId.setRelationship(Relationship.SELF);
funding.getExternalIdentifiers().getExternalIdentifier().add(fExtId);
//Add the funding
postResponse = memberV2ApiClient.createFundingXml(this.getUser1OrcidId(), funding, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.CREATED.getStatusCode(), postResponse.getStatus());
// Delete funding
Map map = postResponse.getMetadata();
assertNotNull(map);
assertTrue(map.containsKey("Location"));
List resultWithPutCode = (List) map.get("Location");
String location = resultWithPutCode.get(0).toString();
Long putCode = Long.valueOf(location.substring(location.lastIndexOf('/') + 1));
ClientResponse deleteResponse = memberV2ApiClient.deleteFundingXml(this.getUser1OrcidId(), putCode, accessToken);
assertNotNull(deleteResponse);
assertEquals(Response.Status.NO_CONTENT.getStatusCode(), deleteResponse.getStatus());
}
use of org.orcid.jaxb.model.record_rc4.ExternalID in project ORCID-Source by ORCID.
the class MemberV2Test method testAddPeerReviewWithInvalidGroupingId.
@Test
public void testAddPeerReviewWithInvalidGroupingId() throws JSONException, InterruptedException, URISyntaxException {
PeerReview peerReview = (PeerReview) unmarshallFromPath("/record_2.0_rc4/samples/peer-review-2.0_rc4.xml", PeerReview.class);
peerReview.setPutCode(null);
peerReview.setGroupId("Invalid group id " + System.currentTimeMillis());
peerReview.getExternalIdentifiers().getExternalIdentifier().clear();
ExternalID pExtId = new ExternalID();
pExtId.setValue("Work Id " + System.currentTimeMillis());
pExtId.setType(WorkExternalIdentifierType.AGR.value());
pExtId.setRelationship(Relationship.SELF);
peerReview.getExternalIdentifiers().getExternalIdentifier().add(pExtId);
String accessToken = getAccessToken();
//Pattern not valid
ClientResponse postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
//Null group id
peerReview.setGroupId(null);
postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
//Empty group id
peerReview.setGroupId("");
postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
//Invalid group id
peerReview.setGroupId("orcid-generated:" + peerReview.getGroupId());
postResponse = memberV2ApiClient.createPeerReviewXml(this.getUser1OrcidId(), peerReview, accessToken);
assertNotNull(postResponse);
assertEquals(Response.Status.BAD_REQUEST.getStatusCode(), postResponse.getStatus());
}
use of org.orcid.jaxb.model.record_rc4.ExternalID in project ORCID-Source by ORCID.
the class OrcidRecordToSolrDocument method convert.
public OrcidSolrDocument convert(Record record, List<Funding> fundings) {
OrcidSolrDocument profileIndexDocument = new OrcidSolrDocument();
profileIndexDocument.setOrcid(record.getOrcidIdentifier().getPath());
if (record.getHistory() != null) {
if (record.getHistory().getLastModifiedDate() != null) {
profileIndexDocument.setProfileLastModifiedDate(record.getHistory().getLastModifiedDate().getValue().toGregorianCalendar().getTime());
}
if (record.getHistory().getSubmissionDate() != null) {
profileIndexDocument.setProfileSubmissionDate(record.getHistory().getSubmissionDate().getValue().toGregorianCalendar().getTime());
}
}
if (record.getDeprecated() != null) {
profileIndexDocument.setPrimaryRecord(record.getDeprecated().getPrimaryRecord() != null ? record.getDeprecated().getPrimaryRecord().getOrcidIdentifier().getPath() : null);
}
if (record.getPerson() != null) {
if (record.getPerson().getName() != null) {
profileIndexDocument.setFamilyName(record.getPerson().getName().getFamilyName() != null ? record.getPerson().getName().getFamilyName().getContent() : null);
profileIndexDocument.setGivenNames(record.getPerson().getName().getGivenNames() != null ? record.getPerson().getName().getGivenNames().getContent() : null);
profileIndexDocument.setCreditName(record.getPerson().getName().getCreditName() != null ? record.getPerson().getName().getCreditName().getContent() : null);
}
if (record.getPerson().getOtherNames() != null) {
if (record.getPerson().getOtherNames().getOtherNames() != null && !record.getPerson().getOtherNames().getOtherNames().isEmpty()) {
List<String> names = new ArrayList<String>();
for (org.orcid.jaxb.model.record_v2.OtherName on : record.getPerson().getOtherNames().getOtherNames()) {
names.add(on.getContent());
}
profileIndexDocument.setOtherNames(names);
}
}
if (record.getPerson().getEmails() != null && record.getPerson().getEmails().getEmails() != null) {
for (org.orcid.jaxb.model.record_v2.Email e : record.getPerson().getEmails().getEmails()) {
profileIndexDocument.addEmailAddress(e.getEmail());
}
}
//weird, the type is not indexed...!
if (record.getPerson().getExternalIdentifiers() != null && record.getPerson().getExternalIdentifiers().getExternalIdentifiers() != null) {
List<String> extIdOrcids = new ArrayList<String>();
List<String> extIdRefs = new ArrayList<String>();
List<String> extIdOrcidsAndRefs = new ArrayList<String>();
for (PersonExternalIdentifier externalIdentifier : record.getPerson().getExternalIdentifiers().getExternalIdentifiers()) {
String sourcePath = null;
if (externalIdentifier.getSource() != null && externalIdentifier.getSource().retrieveSourcePath() != null) {
sourcePath = externalIdentifier.getSource().retrieveSourcePath();
extIdOrcids.add(sourcePath);
}
if (externalIdentifier.getValue() != null) {
//weird, the type is not indexed...!
extIdRefs.add(externalIdentifier.getValue());
}
if (NullUtils.noneNull(sourcePath, externalIdentifier.getValue())) {
extIdOrcidsAndRefs.add(sourcePath + "=" + externalIdentifier.getValue());
}
}
if (!extIdOrcids.isEmpty()) {
profileIndexDocument.setExternalIdSources(extIdOrcids);
}
if (!extIdRefs.isEmpty()) {
profileIndexDocument.setExternalIdReferences(extIdRefs);
}
if (!extIdOrcidsAndRefs.isEmpty()) {
profileIndexDocument.setExternalIdSourcesAndReferences(extIdOrcidsAndRefs);
}
}
//weird, we only index keywords if activities exist...!
if (record.getActivitiesSummary() != null) {
if (record.getPerson().getKeywords() != null && record.getPerson().getKeywords().getKeywords() != null) {
List<String> keywordValues = new ArrayList<String>();
for (org.orcid.jaxb.model.record_v2.Keyword keyword : record.getPerson().getKeywords().getKeywords()) {
keywordValues.add(keyword.getContent());
}
profileIndexDocument.setKeywords(keywordValues);
}
}
if (record.getActivitiesSummary() != null && record.getActivitiesSummary().getWorks() != null && record.getActivitiesSummary().getWorks().getWorkGroup() != null) {
//work ids
Map<String, List<String>> allExternalIdentifiers = new HashMap<String, List<String>>();
Map<String, List<String>> partOf = new HashMap<String, List<String>>();
Map<String, List<String>> self = new HashMap<String, List<String>>();
Set<String> workTitles = new HashSet<String>();
for (WorkGroup wg : record.getActivitiesSummary().getWorks().getWorkGroup()) {
if (wg.getWorkSummary() != null) {
for (WorkSummary w : wg.getWorkSummary()) {
// have to use summaries here as group does not include part-of
if (w.getExternalIdentifiers() != null && w.getExternalIdentifiers().getExternalIdentifier() != null) {
for (ExternalID id : w.getExternalIdentifiers().getExternalIdentifier()) {
//old way
if (!allExternalIdentifiers.containsKey(id.getType())) {
allExternalIdentifiers.put(id.getType(), new ArrayList<String>());
}
if (!allExternalIdentifiers.get(id.getType()).contains(id.getValue())) {
allExternalIdentifiers.get(id.getType()).add(id.getValue());
}
//new way
if (Relationship.SELF.equals(id.getRelationship())) {
if (!self.containsKey(id.getType() + SolrConstants.DYNAMIC_SELF)) {
self.put(id.getType() + SolrConstants.DYNAMIC_SELF, new ArrayList<String>());
}
if (!self.get(id.getType() + SolrConstants.DYNAMIC_SELF).contains(id.getValue())) {
self.get(id.getType() + SolrConstants.DYNAMIC_SELF).add(id.getValue());
}
}
if (Relationship.PART_OF.equals(id.getRelationship())) {
if (!partOf.containsKey(id.getType() + SolrConstants.DYNAMIC_PART_OF)) {
partOf.put(id.getType() + SolrConstants.DYNAMIC_PART_OF, new ArrayList<String>());
}
if (!partOf.get(id.getType() + SolrConstants.DYNAMIC_PART_OF).contains(id.getValue())) {
partOf.get(id.getType() + SolrConstants.DYNAMIC_PART_OF).add(id.getValue());
}
}
}
}
if (w.getTitle() != null) {
if (w.getTitle().getTitle() != null && StringUtils.isNotEmpty(w.getTitle().getTitle().getContent())) {
workTitles.add(w.getTitle().getTitle().getContent());
}
if (w.getTitle().getSubtitle() != null && StringUtils.isNotEmpty(w.getTitle().getSubtitle().getContent())) {
workTitles.add(w.getTitle().getSubtitle().getContent());
}
if (w.getTitle().getTranslatedTitle() != null && StringUtils.isNotEmpty(w.getTitle().getTranslatedTitle().getContent())) {
workTitles.add(w.getTitle().getTranslatedTitle().getContent());
}
}
}
}
}
profileIndexDocument.setSelfIds(self);
profileIndexDocument.setPartOfIds(partOf);
//now add them to the doc, the old way
addExternalIdentifiersToIndexDocument(profileIndexDocument, allExternalIdentifiers);
profileIndexDocument.setWorkTitles(new ArrayList<String>(workTitles));
}
Map<String, List<String>> organisationIds = new HashMap<String, List<String>>();
organisationIds.put(SolrConstants.FUNDREF_ORGANISATION_ID, new ArrayList<String>());
organisationIds.put(SolrConstants.RINGGOLD_ORGANISATION_ID, new ArrayList<String>());
Map<String, List<String>> organisationNames = new HashMap<String, List<String>>();
organisationNames.put(SolrConstants.AFFILIATION_ORGANISATION_NAME, new ArrayList<String>());
organisationNames.put(SolrConstants.FUNDING_ORGANISATION_NAME, new ArrayList<String>());
if (!fundings.isEmpty()) {
Set<String> fundingTitle = new HashSet<String>();
Set<String> fundingGrantNumbers = new HashSet<String>();
for (Funding f : fundings) {
if (f.getTitle() != null) {
if (f.getTitle().getTitle() != null && StringUtils.isNotEmpty(f.getTitle().getTitle().getContent())) {
fundingTitle.add(f.getTitle().getTitle().getContent());
}
if (f.getTitle().getTranslatedTitle() != null && StringUtils.isNotEmpty(f.getTitle().getTranslatedTitle().getContent())) {
fundingTitle.add(f.getTitle().getTranslatedTitle().getContent());
}
}
if (f.getExternalIdentifiers() != null && f.getExternalIdentifiers().getExternalIdentifier() != null) {
for (ExternalID id : f.getExternalIdentifiers().getExternalIdentifier()) {
if (id.getType().equals("grant_number")) {
fundingGrantNumbers.add(id.getValue());
}
}
}
if (f.getOrganization() != null) {
organisationNames.get(SolrConstants.FUNDING_ORGANISATION_NAME).add(f.getOrganization().getName());
if (f.getOrganization().getDisambiguatedOrganization() != null)
organisationIds.get(SolrConstants.FUNDREF_ORGANISATION_ID).add(f.getOrganization().getDisambiguatedOrganization().getDisambiguatedOrganizationIdentifier());
}
}
profileIndexDocument.setFundingTitles(new ArrayList<String>(fundingTitle));
profileIndexDocument.setGrantNumbers(new ArrayList<String>(fundingGrantNumbers));
}
//now do affiliations
if (record.getActivitiesSummary() != null && record.getActivitiesSummary().getEducations() != null && record.getActivitiesSummary().getEducations().getSummaries() != null) {
for (EducationSummary e : record.getActivitiesSummary().getEducations().getSummaries()) {
if (e.getOrganization() != null) {
organisationNames.get(SolrConstants.AFFILIATION_ORGANISATION_NAME).add(e.getOrganization().getName());
if (e.getOrganization().getDisambiguatedOrganization() != null)
organisationIds.get(SolrConstants.RINGGOLD_ORGANISATION_ID).add(e.getOrganization().getDisambiguatedOrganization().getDisambiguatedOrganizationIdentifier());
}
}
}
if (record.getActivitiesSummary() != null && record.getActivitiesSummary().getEmployments() != null && record.getActivitiesSummary().getEmployments().getSummaries() != null) {
for (EmploymentSummary e : record.getActivitiesSummary().getEmployments().getSummaries()) {
if (e.getOrganization() != null) {
organisationNames.get(SolrConstants.AFFILIATION_ORGANISATION_NAME).add(e.getOrganization().getName());
if (e.getOrganization().getDisambiguatedOrganization() != null)
organisationIds.get(SolrConstants.RINGGOLD_ORGANISATION_ID).add(e.getOrganization().getDisambiguatedOrganization().getDisambiguatedOrganizationIdentifier());
}
}
}
profileIndexDocument.setOrganisationIds(organisationIds);
profileIndexDocument.setOrganisationNames(organisationNames);
}
if (indexProfile) {
try {
StringWriter sw = new StringWriter();
jaxbContext_2_0_api.createMarshaller().marshal(record, sw);
profileIndexDocument.setPublicProfileMessage(sw.getBuffer().toString());
} catch (JAXBException e) {
LOG.error("problem marshalling xml", e);
}
}
LOG.debug(profileIndexDocument.toString());
return profileIndexDocument;
}
use of org.orcid.jaxb.model.record_rc4.ExternalID in project ORCID-Source by ORCID.
the class ValidateV2SamplesTest method testUnmarshallWorks.
@Test
public void testUnmarshallWorks() throws JAXBException, SAXException, URISyntaxException {
Works works = (Works) unmarshallFromPath("/record_2.0/samples/read_samples/works-2.0.xml", Works.class, "/record_2.0/activities-2.0.xsd");
assertNotNull(works);
assertNotNull(works.getLastModifiedDate());
assertNotNull(works.getLastModifiedDate().getValue());
assertEquals(3, works.getWorkGroup().size());
boolean foundWorkWithNoExtIds = false;
for (WorkGroup group : works.getWorkGroup()) {
assertNotNull(group.getLastModifiedDate().getValue());
assertNotNull(group.getIdentifiers().getExternalIdentifier());
if (group.getIdentifiers().getExternalIdentifier().isEmpty()) {
WorkSummary summary = group.getWorkSummary().get(0);
assertEquals("1", summary.getDisplayIndex());
assertEquals(1, summary.getExternalIdentifiers().getExternalIdentifier().size());
assertEquals("doi", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getType());
assertEquals("https://doi.org/123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getUrl().getValue());
assertEquals("123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getValue());
assertEquals("/8888-8888-8888-8880/work/3356", summary.getPath());
assertEquals("03", summary.getPublicationDate().getDay().getValue());
assertEquals("03", summary.getPublicationDate().getMonth().getValue());
assertEquals("2017", summary.getPublicationDate().getYear().getValue());
assertEquals("Work # 0", summary.getTitle().getTitle().getContent());
assertEquals(WorkType.CONFERENCE_PAPER, summary.getType());
assertEquals(Visibility.PUBLIC, summary.getVisibility());
foundWorkWithNoExtIds = true;
} else {
assertEquals(1, group.getIdentifiers().getExternalIdentifier().size());
ExternalID extId = group.getIdentifiers().getExternalIdentifier().get(0);
if (extId.getType().equals("arxiv")) {
assertEquals(Relationship.SELF, extId.getRelationship());
assertEquals("http://arxiv.org/abs/123456", extId.getUrl().getValue());
assertEquals("123456", extId.getValue());
} else if (extId.getType().equals("bibcode")) {
assertEquals(Relationship.SELF, extId.getRelationship());
assertEquals("http://adsabs.harvard.edu/abs/4567", extId.getUrl().getValue());
assertEquals("4567", extId.getValue());
} else {
fail("Invalid ext id type " + extId.getType());
}
assertEquals(1, group.getWorkSummary().size());
WorkSummary summary = group.getWorkSummary().get(0);
if (summary.getPutCode().equals(Long.valueOf(3357))) {
assertEquals("1", summary.getDisplayIndex());
assertEquals(1, summary.getExternalIdentifiers().getExternalIdentifier().size());
assertEquals("arxiv", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getType());
assertEquals("http://arxiv.org/abs/123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getUrl().getValue());
assertEquals("123456", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getValue());
assertEquals("/8888-8888-8888-8880/work/3357", summary.getPath());
assertEquals("02", summary.getPublicationDate().getDay().getValue());
assertEquals("02", summary.getPublicationDate().getMonth().getValue());
assertEquals("2017", summary.getPublicationDate().getYear().getValue());
assertEquals("Work # 1", summary.getTitle().getTitle().getContent());
assertEquals(WorkType.CONFERENCE_PAPER, summary.getType());
assertEquals(Visibility.PUBLIC, summary.getVisibility());
} else if (summary.getPutCode().equals(Long.valueOf(3358))) {
assertEquals("1", summary.getDisplayIndex());
assertEquals(1, summary.getExternalIdentifiers().getExternalIdentifier().size());
assertEquals("bibcode", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getType());
assertEquals("http://adsabs.harvard.edu/abs/4567", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getUrl().getValue());
assertEquals("4567", summary.getExternalIdentifiers().getExternalIdentifier().get(0).getValue());
assertEquals("/8888-8888-8888-8880/work/3358", summary.getPath());
assertEquals("03", summary.getPublicationDate().getDay().getValue());
assertEquals("03", summary.getPublicationDate().getMonth().getValue());
assertEquals("2017", summary.getPublicationDate().getYear().getValue());
assertEquals("Work # 2", summary.getTitle().getTitle().getContent());
assertEquals(WorkType.JOURNAL_ARTICLE, summary.getType());
assertEquals(Visibility.PUBLIC, summary.getVisibility());
} else {
fail("Invalid put code " + summary.getPutCode());
}
}
}
assertTrue(foundWorkWithNoExtIds);
}
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