Examples with OrgDisambiguatedExternalIdentifierEntity org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity used on opensource projects

Example 6 with OrgDisambiguatedExternalIdentifierEntity

use of org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity in project ORCID-Source by ORCID.

the class OrgDisambiguatedManagerTest method getOrgDisambiguatedEntity.

private OrgDisambiguatedEntity getOrgDisambiguatedEntity(Boolean withExtIds) {
    OrgDisambiguatedEntity org = new OrgDisambiguatedEntity();
    org.setCity("city");
    org.setCountry(Iso3166Country.US);
    org.setName("name");
    org.setOrgType("orgType");
    org.setRegion("region");
    org.setSourceId("sourceId");
    org.setSourceType("sourceType");
    org.setUrl("url");
    if (withExtIds) {
        Set<OrgDisambiguatedExternalIdentifierEntity> orgDisambiguatedExternalIdentifiers = new HashSet<OrgDisambiguatedExternalIdentifierEntity>();
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type1", "type1_identifier1", true));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type1", "type1_identifier2", false));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type1", "type1_identifier3", false));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type2", "type2_identifier1", false));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type2", "type2_identifier2", true));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type2", "type2_identifier3", false));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type3", "type3_identifier1", false));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type3", "type3_identifier2", false));
        orgDisambiguatedExternalIdentifiers.add(getOrgDisambiguatedExternalIdentifierEntity("type3", "type3_identifier3", true));
        org.setExternalIdentifiers(orgDisambiguatedExternalIdentifiers);
    }
    return org;
}

Example 7 with OrgDisambiguatedExternalIdentifierEntity

use of org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity in project ORCID-Source by ORCID.

the class LoadFundRefData method createExternalIdentifier.

/**
     * Creates an external identifier in the
     * org_disambiguated_external_identifier table
     * */
private boolean createExternalIdentifier(OrgDisambiguatedEntity disambiguatedOrg, String identifier) {
    LOGGER.info("Creating external identifier for {}", disambiguatedOrg.getId());
    Date creationDate = new Date();
    OrgDisambiguatedExternalIdentifierEntity externalIdentifier = new OrgDisambiguatedExternalIdentifierEntity();
    externalIdentifier.setIdentifier(identifier);
    externalIdentifier.setIdentifierType(FUNDREF_SOURCE_TYPE);
    externalIdentifier.setOrgDisambiguated(disambiguatedOrg);
    externalIdentifier.setDateCreated(creationDate);
    externalIdentifier.setLastModified(creationDate);
    orgDisambiguatedExternalIdentifierDao.persist(externalIdentifier);
    return true;
}

Example 8 with OrgDisambiguatedExternalIdentifierEntity

use of org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity in project ORCID-Source by ORCID.

the class LoadGridData method processExternalIdentifiers.

private void processExternalIdentifiers(OrgDisambiguatedEntity org, JsonNode institute) {
    JsonNode externalIdsContainer = institute.get("external_ids") == null ? null : institute.get("external_ids");
    if (externalIdsContainer != null) {
        Iterator<Entry<String, JsonNode>> nodes = externalIdsContainer.fields();
        while (nodes.hasNext()) {
            Map.Entry<String, JsonNode> entry = (Map.Entry<String, JsonNode>) nodes.next();
            String identifierTypeName = entry.getKey().toUpperCase();
            String preferredId = entry.getValue().get("preferred").isNull() ? null : entry.getValue().get("preferred").asText();
            ArrayNode elements = (ArrayNode) entry.getValue().get("all");
            for (JsonNode extId : elements) {
                // If the external identifier doesn't exists yet
                OrgDisambiguatedExternalIdentifierEntity existingExternalId = orgDisambiguatedExternalIdentifierDao.findByDetails(org.getId(), extId.asText(), identifierTypeName);
                Boolean preferred = extId.asText().equals(preferredId);
                if (existingExternalId == null) {
                    if (preferred) {
                        createExternalIdentifier(org, extId.asText(), identifierTypeName, true);
                    } else {
                        createExternalIdentifier(org, extId.asText(), identifierTypeName, false);
                    }
                } else {
                    if (existingExternalId.getPreferred() != preferred) {
                        existingExternalId.setPreferred(preferred);
                        orgDisambiguatedExternalIdentifierDao.merge(existingExternalId);
                        LOGGER.info("External identifier for {} with ext id {} and type {} was updated", new Object[] { org.getId(), extId.asText(), identifierTypeName });
                        updatedExternalIdentifiers++;
                    } else {
                        LOGGER.info("External identifier for {} with ext id {} and type {} already exists", new Object[] { org.getId(), extId.asText(), identifierTypeName });
                    }
                }
            }
        }
    }
    if (!institute.get(WIKIPEDIA_URL).isNull()) {
        String url = institute.get(WIKIPEDIA_URL).asText();
        // If the external identifier doesn't exists yet
        if (orgDisambiguatedExternalIdentifierDao.findByDetails(org.getId(), url, WIKIPEDIA_URL.toUpperCase()) == null) {
            createExternalIdentifier(org, url, WIKIPEDIA_URL.toUpperCase(), true);
        } else {
            LOGGER.info("Wikipedia URL for {} already exists", org.getId());
        }
    }
}

Example 9 with OrgDisambiguatedExternalIdentifierEntity

use of org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity in project ORCID-Source by ORCID.

the class LoadRinggoldData method generateExternalIdentifiers.

private void generateExternalIdentifiers(OrgDisambiguatedEntity disambiguatedEntity, List<JsonNode> identifiers) {
    Set<OrgDisambiguatedExternalIdentifierEntity> existingExternalIdentifiers = disambiguatedEntity.getExternalIdentifiers();
    Map<Pair<String, String>, OrgDisambiguatedExternalIdentifierEntity> existingExternalIdentifiersMap = new HashMap<>();
    if (existingExternalIdentifiers != null) {
        for (OrgDisambiguatedExternalIdentifierEntity entity : existingExternalIdentifiers) {
            Pair<String, String> id = Pair.of(entity.getIdentifierType(), entity.getIdentifier());
            existingExternalIdentifiersMap.put(id, entity);
        }
    }
    if (identifiers != null && !identifiers.isEmpty()) {
        identifiers.forEach(identifierNode -> {
            String type = identifierNode.get("identifier_type").asText();
            LOGGER.info("Processing external identifier {} for {}", type, disambiguatedEntity.getId());
            String value = identifierNode.get("value").asText();
            Pair<String, String> id = Pair.of(type, value);
            OrgDisambiguatedExternalIdentifierEntity existingEntity = existingExternalIdentifiersMap.get(id);
            // If the external identifier doesn't exists or it doesn't belong to the disambiguatedEntity, lets create it
            if (existingEntity == null || !existingEntity.getOrgDisambiguated().getId().equals(disambiguatedEntity.getId())) {
                OrgDisambiguatedExternalIdentifierEntity newEntity = new OrgDisambiguatedExternalIdentifierEntity();
                Date now = new Date();
                newEntity.setDateCreated(now);
                newEntity.setLastModified(now);
                newEntity.setIdentifier(value);
                newEntity.setIdentifierType(type);
                newEntity.setOrgDisambiguated(disambiguatedEntity);
                newEntity.setPreferred(false);
                orgDisambiguatedExternalIdentifierDao.persist(newEntity);
                numAddedExtIds++;
            } else {
                existingExternalIdentifiersMap.remove(id);
            }
        });
    }
    // Then, remove all existing external identifiers that are not present in the ringgold data anymore
    for (OrgDisambiguatedExternalIdentifierEntity extIdToBeRemoved : existingExternalIdentifiersMap.values()) {
        orgDisambiguatedExternalIdentifierDao.remove(extIdToBeRemoved.getId());
    }
}

Example 10 with OrgDisambiguatedExternalIdentifierEntity

use of org.orcid.persistence.jpa.entities.OrgDisambiguatedExternalIdentifierEntity in project ORCID-Source by ORCID.

the class LoadGridDataTest method execute_UpdateExistingInstitute_Test.

@Test
public void execute_UpdateExistingInstitute_Test() throws URISyntaxException {
    when(orgDisambiguatedDao.findBySourceIdAndSourceType("grid.1", "GRID")).thenAnswer(new Answer<OrgDisambiguatedEntity>() {

        @Override
        public OrgDisambiguatedEntity answer(InvocationOnMock invocation) throws Throwable {
            OrgDisambiguatedEntity entity = new OrgDisambiguatedEntity();
            entity.setId(1L);
            entity.setName("org_1");
            entity.setSourceId("grid.1");
            entity.setCity("City One");
            entity.setCountry(Iso3166Country.US);
            entity.setOrgType("type_1");
            entity.setRegion("Alabama");
            entity.setSourceType("GRID");
            entity.setStatus("active");
            entity.setUrl("http://link1.com");
            return entity;
        }
    });
    OrgDisambiguatedExternalIdentifierEntity extId = new OrgDisambiguatedExternalIdentifierEntity();
    extId.setPreferred(Boolean.FALSE);
    OrgDisambiguatedExternalIdentifierEntity extIdPreferred = new OrgDisambiguatedExternalIdentifierEntity();
    extIdPreferred.setPreferred(Boolean.TRUE);
    when(orgDisambiguatedExternalIdentifierDao.findByDetails(1L, "ISNI1", "ISNI")).thenReturn(extId);
    when(orgDisambiguatedExternalIdentifierDao.findByDetails(1L, "FUNDREF1", "FUNDREF")).thenReturn(extIdPreferred);
    when(orgDisambiguatedExternalIdentifierDao.findByDetails(1L, "ORGREF1", "ORGREF")).thenReturn(extId);
    when(orgDisambiguatedExternalIdentifierDao.findByDetails(1L, "WIKIDATA1", "WIKIDATA")).thenReturn(extId);
    when(orgDisambiguatedExternalIdentifierDao.findByDetails(1L, "http://en.wikipedia.org/wiki/org_1", "WIKIPEDIA_URL")).thenReturn(extId);
    Path path = Paths.get(getClass().getClassLoader().getResource("grid/grid_1_org_updated_5_external_identifiers.json").toURI());
    File testFile = path.toFile();
    loadGridData.setFileToLoad(testFile);
    loadGridData.execute();
    assertEquals(0L, loadGridData.getAddedDisambiguatedOrgs());
    assertEquals(0L, loadGridData.getAddedExternalIdentifiers());
    assertEquals(1L, loadGridData.getUpdatedOrgs());
    assertEquals(0L, loadGridData.getDeprecatedOrgs());
    assertEquals(0L, loadGridData.getObsoletedOrgs());
    assertEquals(0L, loadGridData.getUpdatedExternalIdentifiers());
    ArgumentCaptor<OrgDisambiguatedEntity> captor = ArgumentCaptor.forClass(OrgDisambiguatedEntity.class);
    verify(orgDisambiguatedDao).merge(captor.capture());
    OrgDisambiguatedEntity orgToBeUpdated = captor.getValue();
    assertEquals(Iso3166Country.CR, orgToBeUpdated.getCountry());
    assertEquals(Long.valueOf(1), orgToBeUpdated.getId());
    assertEquals("City One Updated", orgToBeUpdated.getCity());
    assertEquals(IndexingStatus.PENDING, orgToBeUpdated.getIndexingStatus());
    assertEquals("org_1_updated", orgToBeUpdated.getName());
    assertEquals("type_1,type_2", orgToBeUpdated.getOrgType());
    assertEquals("San Jose", orgToBeUpdated.getRegion());
    assertEquals("grid.1", orgToBeUpdated.getSourceId());
    assertEquals("GRID", orgToBeUpdated.getSourceType());
    assertEquals("active", orgToBeUpdated.getStatus());
    assertEquals("http://link1.com/updated", orgToBeUpdated.getUrl());
}