Examples with Funding org.orcid.jaxb.model.record_rc4.Funding used on opensource projects

Example 46 with Funding

use of org.orcid.jaxb.model.record_rc4.Funding in project ORCID-Source by ORCID.

the class JSONFundingExternalIdentifiersConverterV2Test method getFunding.

private Funding getFunding() throws JAXBException {
    JAXBContext context = JAXBContext.newInstance(new Class[] { Funding.class });
    Unmarshaller unmarshaller = context.createUnmarshaller();
    String name = "/record_2.0/samples/read_samples/funding-full-2.0.xml";
    InputStream inputStream = getClass().getResourceAsStream(name);
    return (Funding) unmarshaller.unmarshal(inputStream);
}

Example 47 with Funding

use of org.orcid.jaxb.model.record_rc4.Funding in project ORCID-Source by ORCID.

the class SourceInActivitiesTest method sourceDoesntChange_Funding_Test.

@Test
@Transactional
public void sourceDoesntChange_Funding_Test() {
    when(mockSourceManager.retrieveSourceEntity()).thenReturn(new SourceEntity(new ProfileEntity(userOrcid)));
    Funding funding1 = getFunding(userOrcid);
    assertNotNull(funding1);
    assertNotNull(funding1.getTitle());
    assertNotNull(funding1.getTitle().getTitle());
    assertFalse(PojoUtil.isEmpty(funding1.getTitle().getTitle().getContent()));
    assertEquals(userOrcid, funding1.getSource().retrieveSourcePath());
    when(mockSourceManager.retrieveSourceEntity()).thenReturn(new SourceEntity(new ClientDetailsEntity(CLIENT_1_ID)));
    Funding funding2 = getFunding(userOrcid);
    assertNotNull(funding2.getTitle());
    assertNotNull(funding2.getTitle().getTitle());
    assertFalse(PojoUtil.isEmpty(funding2.getTitle().getTitle().getContent()));
    assertEquals(CLIENT_1_ID, funding2.getSource().retrieveSourcePath());
    when(mockSourceManager.retrieveSourceEntity()).thenReturn(new SourceEntity(new ClientDetailsEntity(CLIENT_2_ID)));
    Funding funding3 = getFunding(userOrcid);
    assertNotNull(funding3.getTitle());
    assertNotNull(funding3.getTitle().getTitle());
    assertFalse(PojoUtil.isEmpty(funding3.getTitle().getTitle().getContent()));
    assertEquals(CLIENT_2_ID, funding3.getSource().retrieveSourcePath());
    when(mockSourceManager.retrieveSourceEntity()).thenReturn(new SourceEntity(new ProfileEntity(userOrcid)));
    Funding funding4 = getFunding(userOrcid);
    assertNotNull(funding4.getTitle());
    assertNotNull(funding4.getTitle().getTitle());
    assertFalse(PojoUtil.isEmpty(funding4.getTitle().getTitle().getContent()));
    assertEquals(userOrcid, funding4.getSource().retrieveSourcePath());
    Funding fromDb1 = profileFundingManager.getFunding(userOrcid, funding1.getPutCode());
    assertNotNull(fromDb1);
    assertEquals(userOrcid, fromDb1.getSource().retrieveSourcePath());
    Funding fromDb2 = profileFundingManager.getFunding(userOrcid, funding2.getPutCode());
    assertNotNull(fromDb2);
    assertEquals(CLIENT_1_ID, fromDb2.getSource().retrieveSourcePath());
    Funding fromDb3 = profileFundingManager.getFunding(userOrcid, funding3.getPutCode());
    assertNotNull(fromDb3);
    assertEquals(CLIENT_2_ID, fromDb3.getSource().retrieveSourcePath());
    Funding fromDb4 = profileFundingManager.getFunding(userOrcid, funding4.getPutCode());
    assertNotNull(fromDb4);
    assertEquals(userOrcid, fromDb4.getSource().retrieveSourcePath());
}

Example 48 with Funding

use of org.orcid.jaxb.model.record_rc4.Funding in project ORCID-Source by ORCID.

the class SolrMessageProcessor method updateSolrIndex.

private void updateSolrIndex(BaseMessage message) {
    String orcid = message.getOrcid();
    LOG.info("Updating using Record " + orcid + " in SOLR index");
    if (!isSolrIndexingEnabled) {
        LOG.info("Solr indexing is disabled");
        return;
    }
    try {
        org.orcid.jaxb.model.record_v2.Record record = orcid20ApiClient.fetchPublicRecord(message);
        // Remove deactivated records from SOLR index
        if (record.getHistory() != null && record.getHistory().getDeactivationDate() != null && record.getHistory().getDeactivationDate().getValue() != null) {
            solrUpdater.processInvalidRecord(orcid);
            recordStatusManager.markAsSent(orcid, AvailableBroker.SOLR);
            return;
        }
        // get detailed funding so we can discover org name and id
        List<Funding> fundings = new ArrayList<Funding>();
        if (record.getActivitiesSummary() != null && record.getActivitiesSummary().getFundings() != null && record.getActivitiesSummary().getFundings().getFundingGroup() != null) {
            for (FundingGroup group : record.getActivitiesSummary().getFundings().getFundingGroup()) {
                if (group.getFundingSummary() != null) {
                    for (FundingSummary f : group.getFundingSummary()) {
                        fundings.add(orcid20ApiClient.fetchFunding(record.getOrcidIdentifier().getPath(), f.getPutCode()));
                    }
                }
            }
        }
        solrUpdater.persist(recordConv.convert(record, fundings));
        recordStatusManager.markAsSent(orcid, AvailableBroker.SOLR);
    } catch (LockedRecordException lre) {
        LOG.error("Record " + orcid + " is locked");
        solrUpdater.processInvalidRecord(orcid);
        recordStatusManager.markAsSent(orcid, AvailableBroker.SOLR);
    } catch (DeprecatedRecordException dre) {
        LOG.error("Record " + orcid + " is deprecated");
        solrUpdater.processInvalidRecord(orcid);
        recordStatusManager.markAsSent(orcid, AvailableBroker.SOLR);
    } catch (Exception e) {
        LOG.error("Unable to fetch record " + orcid + " for SOLR");
        LOG.error(e.getMessage(), e);
        recordStatusManager.markAsFailed(orcid, AvailableBroker.SOLR);
    }
}

Example 49 with Funding

use of org.orcid.jaxb.model.record_rc4.Funding in project ORCID-Source by ORCID.

the class OrcidRecordToSolrDocumentTest method testNonSchemaExternalID.

@Test
public void testNonSchemaExternalID() throws JAXBException {
    // as above, but with PDB identifier
    Record record = getRecord("/v20recordWithPDB.xml");
    OrcidRecordToSolrDocument v20 = new OrcidRecordToSolrDocument(false);
    OrcidSolrDocument v20Doc = v20.convert(record, new ArrayList<Funding>());
    Assert.assertEquals("cite-self", v20Doc.getSelfIds().get("cit-self").get(0));
    Assert.assertEquals("pdb-value-self", v20Doc.getSelfIds().get("pdb-self").get(0));
    Assert.assertEquals("cit-part-of", v20Doc.getPartOfIds().get("cit-part-of").get(0));
    Assert.assertEquals("pdb-value-part-of", v20Doc.getPartOfIds().get("pdb-part-of").get(0));
    Assert.assertTrue(v20Doc.getDigitalObjectIds().containsAll(v20Doc.getSelfIds().get("doi-self")));
    Assert.assertTrue(v20Doc.getSelfIds().get("doi-self").containsAll(v20Doc.getDigitalObjectIds()));
    Assert.assertTrue(v20Doc.getOtherIdentifierType().contains("pdb-value-self"));
    Assert.assertTrue(v20Doc.getOtherIdentifierType().contains("pdb-value-part-of"));
}

Example 50 with Funding

use of org.orcid.jaxb.model.record_rc4.Funding 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>());
        organisationIds.put(SolrConstants.GRID_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) {
                        String sourceType = e.getOrganization().getDisambiguatedOrganization().getDisambiguationSource();
                        if (SolrConstants.RINGGOLD_ORG_TYPE.equals(sourceType)) {
                            organisationIds.get(SolrConstants.RINGGOLD_ORGANISATION_ID).add(e.getOrganization().getDisambiguatedOrganization().getDisambiguatedOrganizationIdentifier());
                        } else if (SolrConstants.GRID_ORG_TYPE.equals(sourceType)) {
                            organisationIds.get(SolrConstants.GRID_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) {
                        String sourceType = e.getOrganization().getDisambiguatedOrganization().getDisambiguationSource();
                        if (SolrConstants.RINGGOLD_ORG_TYPE.equals(sourceType)) {
                            organisationIds.get(SolrConstants.RINGGOLD_ORGANISATION_ID).add(e.getOrganization().getDisambiguatedOrganization().getDisambiguatedOrganizationIdentifier());
                        } else if (SolrConstants.GRID_ORG_TYPE.equals(sourceType)) {
                            organisationIds.get(SolrConstants.GRID_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;
}