1038 lines
45 KiB
Java
1038 lines
45 KiB
Java
package eu.dnetlib.repo.manager.service;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.JsonArray;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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import eu.dnetlib.api.functionality.ValidatorServiceException;
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import eu.dnetlib.domain.data.Repository;
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import eu.dnetlib.domain.data.RepositoryInterface;
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import eu.dnetlib.domain.enabling.Vocabulary;
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import eu.dnetlib.domain.functionality.validator.JobForValidation;
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import eu.dnetlib.repo.manager.domain.*;
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import eu.dnetlib.repo.manager.domain.dto.Role;
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import eu.dnetlib.repo.manager.exception.ResourceNotFoundException;
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import eu.dnetlib.repo.manager.service.aai.registry.AaiRegistryService;
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import eu.dnetlib.repo.manager.service.security.AuthoritiesUpdater;
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import eu.dnetlib.repo.manager.service.security.AuthorizationService;
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import eu.dnetlib.repo.manager.service.security.RoleMappingService;
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import eu.dnetlib.repo.manager.utils.Converter;
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import gr.uoa.di.driver.enabling.vocabulary.VocabularyLoader;
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import org.apache.commons.codec.digest.DigestUtils;
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import org.apache.http.entity.ContentType;
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import org.apache.log4j.Logger;
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import org.json.JSONArray;
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import org.json.JSONException;
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import org.json.JSONObject;
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import org.mitre.openid.connect.model.OIDCAuthenticationToken;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.context.annotation.Lazy;
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import org.springframework.core.ParameterizedTypeReference;
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import org.springframework.http.*;
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import org.springframework.http.converter.json.MappingJackson2HttpMessageConverter;
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import org.springframework.security.core.Authentication;
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import org.springframework.security.core.context.SecurityContextHolder;
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import org.springframework.stereotype.Service;
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import org.springframework.util.MimeType;
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import org.springframework.web.client.HttpClientErrorException;
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import org.springframework.web.client.RestTemplate;
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import org.springframework.web.util.UriComponents;
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import org.springframework.web.util.UriComponentsBuilder;
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import javax.annotation.PostConstruct;
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import java.io.IOException;
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import java.sql.Timestamp;
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import java.util.*;
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import java.util.concurrent.ConcurrentHashMap;
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import java.util.stream.Collectors;
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@Service("repositoryService")
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public class RepositoryServiceImpl implements RepositoryService {
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private static final Logger LOGGER = Logger.getLogger(RepositoryServiceImpl.class);
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private final AuthorizationService authorizationService;
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private final RoleMappingService roleMappingService;
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private final AaiRegistryService registryCalls;
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private final AuthoritiesUpdater authoritiesUpdater;
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private final RestTemplate restTemplate;
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private final VocabularyLoader vocabularyLoader;
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private final PiWikService piWikService;
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private final EmailUtils emailUtils;
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private final ValidatorService validatorService;
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@Value("${api.baseAddress}")
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private String baseAddress;
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@Value("${services.repo-manager.adminEmail}")
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private String adminEmail;
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@Value("${services.repomanager.usageStatisticsDiagramsBaseURL}")
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private String usageStatisticsDiagramsBaseURL;
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@Value("${services.repomanager.usageStatisticsNumbersBaseURL}")
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private String usageStatisticsNumbersBaseURL;
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private static final Map<String, List<String>> dataSourceClass = new HashMap<>();
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private static final Map<String, String> invertedDataSourceClass = new HashMap<>();
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private final String[] vocabularyNames = {"dnet:countries", "dnet:datasource_typologies", "dnet:compatibilityLevel"};
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private final Map<String, Vocabulary> vocabularyMap = new ConcurrentHashMap<>();
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private final Map<String, String> countriesMap = new HashMap<>();
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private final Map<String, String> inverseCountriesMap = new HashMap<>();
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private HttpHeaders httpHeaders;
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@Autowired
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public RepositoryServiceImpl(AuthorizationService authorizationService,
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RoleMappingService roleMappingService,
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AaiRegistryService registryCalls,
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AuthoritiesUpdater authoritiesUpdater,
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VocabularyLoader vocabularyLoader,
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RestTemplate restTemplate,
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@Lazy EmailUtils emailUtils,
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@Lazy ValidatorService validatorService,
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@Lazy PiWikService piWikService) {
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this.authorizationService = authorizationService;
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this.roleMappingService = roleMappingService;
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this.registryCalls = registryCalls;
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this.authoritiesUpdater = authoritiesUpdater;
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this.vocabularyLoader = vocabularyLoader;
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this.piWikService = piWikService;
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this.emailUtils = emailUtils;
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this.validatorService = validatorService;
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this.restTemplate = restTemplate;
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}
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private String getAuthenticatedUserEmail() {
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OIDCAuthenticationToken authenticationToken = (OIDCAuthenticationToken) SecurityContextHolder.getContext().getAuthentication();
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return authenticationToken.getUserInfo().getEmail();
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}
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@PostConstruct
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private void init() {
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LOGGER.debug("Initialization method of repository api!");
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LOGGER.debug("Updated version!");
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dataSourceClass.put("opendoar", Arrays.asList("pubsrepository::institutional", "pubsrepository::thematic", "pubsrepository::unknown", "pubsrepository::mock"));
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dataSourceClass.put("re3data", Collections.singletonList("datarepository::unknown"));
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dataSourceClass.put("journal", Collections.singletonList("pubsrepository::journal"));
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dataSourceClass.put("aggregator", Arrays.asList("aggregator::pubsrepository::institutional", "aggregator::pubsrepository::journals", "aggregator::datarepository", "aggregator::pubsrepository::unknown"));
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invertedDataSourceClass.put("pubsrepository::institutional", "opendoar");
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invertedDataSourceClass.put("pubsrepository::thematic", "opendoar");
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invertedDataSourceClass.put("pubsrepository::unknown", "opendoar");
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invertedDataSourceClass.put("pubsrepository::mock", "opendoar");
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invertedDataSourceClass.put("datarepository::unknown", "re3data");
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invertedDataSourceClass.put("pubsrepository::journal", "journal");
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invertedDataSourceClass.put("aggregator::pubsrepository::institutional", "aggregator");
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invertedDataSourceClass.put("aggregator::pubsrepository::journals", "aggregator");
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invertedDataSourceClass.put("aggregator::datarepository", "aggregator");
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invertedDataSourceClass.put("aggregator::pubsrepository::unknown", "aggregator");
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httpHeaders = new HttpHeaders();
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httpHeaders.setContentType(MediaType.APPLICATION_JSON_UTF8);
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for (String vocName : vocabularyNames) {
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vocabularyMap.put(vocName, vocabularyLoader.getVocabulary(vocName, Locale.ENGLISH, Locale.ROOT));
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}
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Country[] countries = getCountries();
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for (Country c : countries) {
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countriesMap.put(c.getName(), c.getCode());
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inverseCountriesMap.put(c.getCode(), c.getName());
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}
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}
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@Override
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public Country[] getCountries() {
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UriComponents uriComponents = UriComponentsBuilder
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.fromHttpUrl(baseAddress + "/ds/countries")
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.build().encode();
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return restTemplate.getForObject(uriComponents.toUri(), Country[].class);
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}
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// FIXME: with the new roles of the users the "requestFilter.setRegisteredby(userEmail)" can no longer be used
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// and the "requestFilter.setId(repoId)" should return only one result at a time, thus,
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// another way for paging must be implemented.
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@Override
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public List<Repository> getRepositories(List<String> ids) throws JSONException {
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return getRepositories(ids, 0, 10);
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}
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// FIXME: with the new roles of the users the "requestFilter.setRegisteredby(userEmail)" can no longer be used
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// and the "requestFilter.setId(repoId)" should return only one result at a time, thus,
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// another way for paging must be implemented.
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@Override
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public List<Repository> getRepositories(List<String> ids, int page, int size) throws JSONException {
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List<Repository> repos = new ArrayList<>();
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LOGGER.debug("Retreiving repositories with ids : " + String.join(", ", ids));
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UriComponents uriComponents = searchDatasource(Integer.toString(Math.abs(page)), Integer.toString(Math.abs(size)));
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RequestFilter requestFilter = new RequestFilter();
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for (String repoId : ids) {
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requestFilter.setId(repoId);
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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repos.addAll(Converter.jsonToRepositoryList(new JSONObject(rs)));
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}
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for (Repository r : repos)
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r.setPiwikInfo(piWikService.getPiwikSiteForRepo(r.getId()));
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return repos;
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}
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// FIXME: with the new roles of the users the "requestFilter.setRegisteredby(userEmail)" can no longer be used
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// and the "requestFilter.setId(repoId)" should return only one result at a time, thus,
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// another way for paging must be implemented.
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@Override
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public List<RepositorySnippet> getRepositoriesSnippets(List<String> ids) throws Exception {
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return getRepositoriesSnippets(ids, 0, 10);
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}
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// FIXME: with the new roles of the users the "requestFilter.setRegisteredby(userEmail)" can no longer be used
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// and the "requestFilter.setId(repoId)" should return only one result at a time, thus,
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// another way for paging must be implemented.
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@Override
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public List<RepositorySnippet> getRepositoriesSnippets(List<String> ids, int page, int size) throws Exception {
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List<RepositorySnippet> resultSet = new ArrayList<>();
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ObjectMapper mapper = new ObjectMapper();
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// here page should be 0
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UriComponents uriComponents = searchSnipperDatasource(Integer.toString(Math.abs(page)), Integer.toString(Math.abs(size)));
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RequestFilter requestFilter = new RequestFilter();
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try {
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for (String repoId : ids) {
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requestFilter.setId(repoId);
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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JSONArray jsonArray = (JSONArray) new JSONObject(rs).get("datasourceInfo");
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resultSet.addAll(mapper.readValue(String.valueOf(jsonArray),
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mapper.getTypeFactory().constructCollectionType(List.class, RepositorySnippet.class)));
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}
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} catch (Exception e) {
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LOGGER.debug("Exception on getRepositoriesSnippetOfUser", e);
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throw e;
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}
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LOGGER.debug("resultSet:" + resultSet);
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resultSet.parallelStream().forEach(repositorySnippet -> {
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repositorySnippet.setPiwikInfo(piWikService.getPiwikSiteForRepo(repositorySnippet.getId()));
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});
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return resultSet;
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}
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@Override
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public List<RepositorySnippet> getRepositoriesByCountry(String country,
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String mode,
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Boolean managed) throws JSONException, IOException {
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LOGGER.debug("Getting repositories by country!");
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int page = 0;
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int size = 100;
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List<RepositorySnippet> resultSet = new ArrayList<>();
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ObjectMapper mapper = new ObjectMapper();
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String filterKey = "UNKNOWN";
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if (mode.equalsIgnoreCase("opendoar"))
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filterKey = "openaire____::opendoar";
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else if (mode.equalsIgnoreCase("re3data"))
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filterKey = "openaire____::re3data";
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LOGGER.debug("Country code equals : " + country);
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LOGGER.debug("Filter mode equals : " + filterKey);
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UriComponents uriComponents = searchSnipperDatasource(String.valueOf(page), String.valueOf(size));
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RequestFilter requestFilter = new RequestFilter();
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requestFilter.setCountry(country);
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requestFilter.setCollectedfrom(filterKey);
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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JSONArray jsonArray = (JSONArray) new JSONObject(rs).get("datasourceInfo");
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while (jsonArray.length() > 0) {
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LOGGER.debug("json: " + jsonArray);
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resultSet.addAll(mapper.readValue(String.valueOf(jsonArray),
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mapper.getTypeFactory().constructCollectionType(List.class, RepositorySnippet.class)));
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page += 1;
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uriComponents = searchSnipperDatasource(String.valueOf(page), String.valueOf(size));
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rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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jsonArray = (JSONArray) new JSONObject(rs).get("datasourceInfo");
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}
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return resultSet;
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}
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public List<RepositorySnippet> searchRegisteredRepositories(String country, String typology, String englishName,
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String officialName, String requestSortBy, String order, int page, int pageSize) throws Exception {
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LOGGER.debug("Searching registered repositories");
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List<RepositorySnippet> resultSet = new ArrayList<>();
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ObjectMapper mapper = new ObjectMapper();
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UriComponents uriComponents = searchRegisteredDatasource(requestSortBy, order, Integer.toString(page), Integer.toString(pageSize));
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RequestFilter requestFilter = new RequestFilter();
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requestFilter.setCountry(country);
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requestFilter.setTypology(typology);
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requestFilter.setOfficialname(officialName);
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requestFilter.setEnglishname(englishName);
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try {
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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JSONArray jsonArray = (JSONArray) new JSONObject(rs).get("datasourceInfo");
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resultSet.addAll(mapper.readValue(String.valueOf(jsonArray), mapper.getTypeFactory().constructCollectionType(List.class, RepositorySnippet.class)));
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return resultSet;
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} catch (Exception e) {
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LOGGER.error("Error searching registered datasources", e);
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throw e;
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}
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}
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@Override
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public int getTotalRegisteredRepositories() {
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UriComponents uriComponents = UriComponentsBuilder
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.fromHttpUrl(baseAddress + "/ds/countregistered")
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.queryParam("fromDate", "1900-01-01")
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.build().encode();
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return restTemplate.getForObject(uriComponents.toUri(), Integer.class);
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}
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private Repository updateRepositoryInfo(Repository r) throws JSONException {
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/*
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* from datasource class
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* we get the datasource type form the inverted map
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* */
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r.setDatasourceType(getRepositoryType(r.getDatasourceClass()));
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r.setInterfaces(this.getRepositoryInterface(r.getId()));
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r.setPiwikInfo(piWikService.getPiwikSiteForRepo(r.getId()));
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r.setCountryName(getCountryName(r.getCountryCode()));
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return r;
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}
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private Collection<Repository> getRepositoriesByMode(String mode, List<Repository> rs) {
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List<Repository> reps = new ArrayList<>();
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for (Repository r : rs) {
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if (r.getCollectedFrom() != null && r.getCollectedFrom().equals(mode))
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reps.add(r);
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}
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return reps;
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}
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@Override
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public List<Repository> getRepositoriesOfUser(String page, String size) throws JSONException {
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String userEmail = ((OIDCAuthenticationToken) SecurityContextHolder.getContext().getAuthentication()).getUserInfo().getEmail();
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LOGGER.debug("Retreiving repositories of authenticated user : " + userEmail);
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Collection<String> repoIds = roleMappingService.getRepoIdsByRoleIds(authorizationService.getUserRoles());
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return getRepositories(new ArrayList<>(repoIds));
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}
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@Override
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public List<Repository> getRepositoriesOfUser(String userEmail, String page, String size) throws JSONException {
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LOGGER.debug("Retreiving repositories of authenticated user : " + userEmail);
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Collection<String> repoIds = roleMappingService.getRepoIdsByRoleIds(authorizationService.getUserRoles(userEmail));
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return getRepositories(new ArrayList<>(repoIds));
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}
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@Override
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public List<RepositorySnippet> getRepositoriesSnippetsOfUser(String page, String size) throws Exception {
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Collection<String> repoIds = roleMappingService.getRepoIdsByRoleIds(authorizationService.getUserRoles());
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return getRepositoriesSnippets(new ArrayList<>(repoIds));
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}
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@Override
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public List<RepositorySnippet> getRepositoriesSnippetsOfUser(String userEmail, String page, String size) throws Exception {
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Collection<String> repoIds = roleMappingService.getRepoIdsByRoleIds(authorizationService.getUserRoles(userEmail));
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return getRepositoriesSnippets(new ArrayList<>(repoIds));
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}
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@Override
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public RepositorySnippet getRepositorySnippetById(String id) throws JSONException, ResourceNotFoundException {
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LOGGER.debug("Retreiving repositories with id : " + id);
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RepositorySnippet repo = null;
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UriComponents uriComponents = searchSnipperDatasource("0", "100");
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RequestFilter requestFilter = new RequestFilter();
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requestFilter.setId(id);
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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JSONArray jsonArray = (JSONArray) new JSONObject(rs).get("datasourceInfo");
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if (jsonArray.length() == 0)
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throw new ResourceNotFoundException();
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repo = Converter.jsonToRepositorySnippetObject(jsonArray.getJSONObject(0));
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return repo;
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}
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@Override
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public Repository getRepositoryById(String id) throws JSONException, ResourceNotFoundException {
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LOGGER.debug("Retreiving repositories with id : " + id);
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Repository repo = null;
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UriComponents uriComponents = searchDatasource("0", "100");
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RequestFilter requestFilter = new RequestFilter();
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requestFilter.setId(id);
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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JSONArray jsonArray = (JSONArray) new JSONObject(rs).get("datasourceInfo");
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if (jsonArray.length() == 0)
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throw new ResourceNotFoundException();
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repo = Converter.jsonToRepositoryObject(jsonArray.getJSONObject(0));
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return updateRepositoryInfo(repo);
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}
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@Override
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public List<AggregationDetails> getRepositoryAggregations(String id, int from, int size) throws JSONException {
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LOGGER.debug("Retreiving aggregations for repository with id : " + id);
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UriComponents uriComponents = searchDatasource(from + "", size + "");
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RequestFilter requestFilter = new RequestFilter();
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requestFilter.setId(id);
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List<AggregationDetails> aggregationHistory = new ArrayList<>();
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long start = System.currentTimeMillis();
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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long end = System.currentTimeMillis();
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System.out.println("Aggregations request through rest template took " + (end - start) + "ms");
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JSONObject repository = new JSONObject(rs);
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if (repository.getJSONArray("datasourceInfo").length() == 0)
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return aggregationHistory;
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start = System.currentTimeMillis();
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aggregationHistory.addAll(Converter.getAggregationHistoryFromJson(repository.getJSONArray("datasourceInfo").getJSONObject(0)));
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end = System.currentTimeMillis();
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System.out.println("Getting aggregations history from json " + (end - start) + "ms");
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return aggregationHistory.size() == 0 ? aggregationHistory : aggregationHistory.stream()
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.sorted(Comparator.comparing(AggregationDetails::getDate).reversed())
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.limit(size)
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.collect(Collectors.toList());
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}
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@Override
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public Map<String, List<AggregationDetails>> getRepositoryAggregationsByYear(String id) throws JSONException {
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LOGGER.debug("Retreiving aggregations (by year) for repository with id : " + id);
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UriComponents uriComponents = searchDatasource("0", "100");
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RequestFilter requestFilter = new RequestFilter();
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requestFilter.setId(id);
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List<AggregationDetails> aggregationHistory = new ArrayList<>();
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Map<String, List<AggregationDetails>> aggregationByYear = new HashMap<>();
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String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
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JSONObject repository = new JSONObject(rs);
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if (repository.getJSONArray("datasourceInfo").length() == 0)
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return aggregationByYear;
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aggregationHistory.addAll(Converter.getAggregationHistoryFromJson(repository.getJSONArray("datasourceInfo").getJSONObject(0)));
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return aggregationHistory.size() == 0 ? aggregationByYear : createYearMap(aggregationHistory);
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}
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private Map<String, List<AggregationDetails>> createYearMap(List<AggregationDetails> aggregationHistory) {
|
|
Map<String, List<AggregationDetails>> aggregationByYear;
|
|
aggregationHistory = aggregationHistory.stream()
|
|
.sorted(Comparator.comparing(AggregationDetails::getDate).reversed())
|
|
.collect(Collectors.toList());
|
|
|
|
return aggregationHistory.stream()
|
|
.collect(Collectors.groupingBy(AggregationDetails::getYear));
|
|
}
|
|
|
|
|
|
@Override
|
|
public List<Repository> getRepositoriesByName(String name,
|
|
String page,
|
|
String size) throws JSONException {
|
|
|
|
LOGGER.debug("Retreiving repositories with official name : " + name);
|
|
UriComponents uriComponents = searchDatasource("0", "100");
|
|
RequestFilter requestFilter = new RequestFilter();
|
|
requestFilter.setOfficialname(name);
|
|
|
|
String rs = restTemplate.postForObject(uriComponents.toUri(), requestFilter, String.class);
|
|
List<Repository> repos = Converter.jsonToRepositoryList(new JSONObject(rs));
|
|
for (Repository r : repos)
|
|
updateRepositoryInfo(r);
|
|
return repos;
|
|
|
|
}
|
|
|
|
@Override
|
|
public List<RepositoryInterface> getRepositoryInterface(String id) throws JSONException {
|
|
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/api/")
|
|
.path("/{id}")
|
|
.build().expand(id).encode();
|
|
|
|
String rs = restTemplate.getForObject(uriComponents.toUri(), String.class);
|
|
return Converter.jsonToRepositoryInterfaceList(new JSONObject(rs));
|
|
|
|
}
|
|
|
|
@Override
|
|
public Repository addRepository(String datatype, Repository repository) throws Exception {
|
|
|
|
LOGGER.debug("storing " + datatype + " repository with id: " + repository.getId());
|
|
|
|
repository.setCountryCode(countriesMap.get(repository.getCountryName()));
|
|
repository.setActivationId(UUID.randomUUID().toString());
|
|
repository.setCollectedFrom("infrastruct_::openaire");
|
|
|
|
if (datatype.equals("journal")) {
|
|
repository.setId("openaire____::issn" + repository.getIssn());
|
|
repository.setNamespacePrefix("issn" + repository.getIssn());
|
|
this.storeRepository(repository, SecurityContextHolder.getContext().getAuthentication());
|
|
} else if (datatype.equals("aggregator")) {
|
|
repository.setId("openaire____::" + DigestUtils.md5Hex(repository.getOfficialName()));
|
|
repository.setNamespacePrefix(DigestUtils.md5Hex(repository.getOfficialName()).substring(0, 12));
|
|
this.storeRepository(repository, SecurityContextHolder.getContext().getAuthentication());
|
|
} else {
|
|
this.latentUpdate(repository, SecurityContextHolder.getContext().getAuthentication());
|
|
}
|
|
|
|
// TODO: move the following code elsewhere (creation and assignment of role to user) ??
|
|
// Create new role
|
|
String newRoleName = roleMappingService.getRoleIdByRepoId(repository.getId());
|
|
Role newRole = new Role(newRoleName, repository.getOfficialName());
|
|
Integer couId = null;
|
|
try {
|
|
couId = registryCalls.createRole(newRole);
|
|
} catch (HttpClientErrorException e) {
|
|
couId = registryCalls.getCouId(newRoleName);
|
|
if (couId == null) {
|
|
LOGGER.error(String.format("Could not create role '%s'", newRoleName), e);
|
|
}
|
|
} catch (Exception e) {
|
|
LOGGER.error(String.format("Could not create role '%s'", newRoleName), e);
|
|
throw e;
|
|
}
|
|
|
|
// Assign new role to the user that created it
|
|
Integer coPersonId = registryCalls.getCoPersonIdByIdentifier();
|
|
if (couId != null) {
|
|
Integer role = registryCalls.getRoleId(coPersonId, couId);
|
|
try {
|
|
registryCalls.assignMemberRole(coPersonId, couId, role);
|
|
|
|
// Add role to current user authorities
|
|
authoritiesUpdater.addRole(roleMappingService.convertRepoIdToAuthority(repository.getId()));
|
|
} catch (Exception e) {
|
|
LOGGER.debug("Exception on assign role to user during add repository", e);
|
|
throw e;
|
|
}
|
|
|
|
}
|
|
|
|
|
|
return repository;
|
|
}
|
|
|
|
/* update method acting as add -> send email with registration topic/body*/
|
|
private Repository latentUpdate(Repository repository, Authentication authentication) throws Exception {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/update/")
|
|
.build()
|
|
.encode();
|
|
|
|
String json_repository = Converter.repositoryObjectToJson(repository);
|
|
LOGGER.debug("JSON to add(update) -> " + json_repository);
|
|
|
|
HttpEntity<String> httpEntity = new HttpEntity<String>(json_repository, httpHeaders);
|
|
ResponseEntity responseEntity = restTemplate.exchange(uriComponents.toUri(), HttpMethod.POST, httpEntity, ResponseEntity.class);
|
|
|
|
if (responseEntity.getStatusCode().equals(HttpStatus.OK)) {
|
|
try {
|
|
emailUtils.sendUserRegistrationEmail(repository, authentication);
|
|
emailUtils.sendAdminRegistrationEmail(repository, authentication);
|
|
} catch (Exception e) {
|
|
LOGGER.error("Error sending email", e);
|
|
}
|
|
} else
|
|
LOGGER.error("Error storing repository: " + responseEntity.getBody().toString());
|
|
|
|
return repository;
|
|
}
|
|
|
|
@Override
|
|
public Repository updateRepository(Repository repository, Authentication authentication) throws Exception {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/update/")
|
|
.build()
|
|
.encode();
|
|
|
|
String json_repository = Converter.repositoryObjectToJson(repository);
|
|
|
|
LOGGER.debug("JSON to update -> " + json_repository);
|
|
|
|
HttpEntity<String> httpEntity = new HttpEntity<String>(json_repository, httpHeaders);
|
|
ResponseEntity responseEntity = restTemplate.exchange(uriComponents.toUri(), HttpMethod.POST, httpEntity
|
|
, ResponseEntity.class);
|
|
|
|
if (responseEntity.getStatusCode().equals(HttpStatus.OK)) {
|
|
try {
|
|
emailUtils.sendUserUpdateRepositoryInfoEmail(repository, authentication);
|
|
emailUtils.sendAdminUpdateRepositoryInfoEmail(repository, authentication);
|
|
} catch (Exception e) {
|
|
LOGGER.error("Error sending emails: " + e);
|
|
}
|
|
} else
|
|
LOGGER.debug(responseEntity.getBody().toString());
|
|
|
|
return repository;
|
|
}
|
|
|
|
private void storeRepository(Repository repository, Authentication authentication) throws Exception {
|
|
|
|
Date utilDate = new Date();
|
|
Timestamp date = new Timestamp(utilDate.getTime());
|
|
repository.setDateOfCollection(date);
|
|
repository.setAggregator("OPENAIRE");
|
|
repository.setCountryCode(countriesMap.get(repository.getCountryName()));
|
|
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/add/")
|
|
.build()
|
|
.encode();
|
|
String json_repository = Converter.repositoryObjectToJson(repository);
|
|
HttpEntity<String> httpEntity = new HttpEntity<String>(json_repository, httpHeaders);
|
|
ResponseEntity responseEntity = restTemplate.exchange(uriComponents.toUri(), HttpMethod.POST, httpEntity, ResponseEntity.class);
|
|
|
|
if (responseEntity.getStatusCode().equals(HttpStatus.OK)) {
|
|
try {
|
|
emailUtils.sendUserRegistrationEmail(repository, authentication);
|
|
emailUtils.sendAdminRegistrationEmail(repository, authentication);
|
|
} catch (Exception e) {
|
|
LOGGER.error("Error sending emails: " + e);
|
|
}
|
|
} else {
|
|
LOGGER.debug(responseEntity.getBody().toString());
|
|
}
|
|
}
|
|
|
|
@Override
|
|
public void deleteRepositoryInterface(String id,
|
|
String registeredBy) {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/api/")
|
|
.path("/{id}")
|
|
.build().expand(id).encode();
|
|
LOGGER.debug(uriComponents.toUri());
|
|
restTemplate.delete(uriComponents.toUri());
|
|
}
|
|
|
|
@Override
|
|
public RepositoryInterface addRepositoryInterface(String datatype,
|
|
String repoId,
|
|
String registeredBy,
|
|
String comment, RepositoryInterface repositoryInterface) throws Exception {
|
|
Repository e = this.getRepositoryById(repoId);
|
|
repositoryInterface = createRepositoryInterface(e, repositoryInterface, datatype);
|
|
String json_interface = Converter.repositoryInterfaceObjectToJson(e, repositoryInterface);
|
|
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/api/add/")
|
|
.build()
|
|
.encode();
|
|
|
|
HttpEntity<String> httpEntity = new HttpEntity<>(json_interface, httpHeaders);
|
|
|
|
restTemplate.postForObject(uriComponents.toUri(), httpEntity, String.class);
|
|
|
|
try {
|
|
emailUtils.sendAdminRegisterInterfaceEmail(e, comment, repositoryInterface, SecurityContextHolder.getContext().getAuthentication());
|
|
emailUtils.sendUserRegisterInterfaceEmail(e, comment, repositoryInterface, SecurityContextHolder.getContext().getAuthentication());
|
|
} catch (Exception ex) {
|
|
LOGGER.error("Error sending emails: " + ex);
|
|
}
|
|
|
|
submitInterfaceValidation(e, registeredBy, repositoryInterface, false);
|
|
|
|
return repositoryInterface;
|
|
}
|
|
|
|
@Override
|
|
public RepositoryInterface updateRepositoryInterface(String repoId,
|
|
String registeredBy,
|
|
String comment, RepositoryInterface repositoryInterface) throws Exception {
|
|
|
|
this.updateBaseUrl(repoId, repositoryInterface.getId(), repositoryInterface.getBaseUrl());
|
|
this.updateCompliance(repoId, repositoryInterface.getId(), repositoryInterface.getCompliance());
|
|
this.updateValidationSet(repoId, repositoryInterface.getId(), repositoryInterface.getAccessSet());
|
|
|
|
Repository repository = this.getRepositoryById(repoId);
|
|
try {
|
|
try {
|
|
emailUtils.sendAdminUpdateInterfaceEmail(repository, comment, repositoryInterface, SecurityContextHolder.getContext().getAuthentication());
|
|
emailUtils.sendUserUpdateInterfaceEmail(repository, comment, repositoryInterface, SecurityContextHolder.getContext().getAuthentication());
|
|
} catch (Exception e) {
|
|
LOGGER.error("Error sending emails: " + e);
|
|
}
|
|
} catch (Exception e) {
|
|
LOGGER.warn("Could not send emails", e);
|
|
}
|
|
|
|
submitInterfaceValidation(getRepositoryById(repoId), registeredBy, repositoryInterface, true);
|
|
|
|
return repositoryInterface;
|
|
}
|
|
|
|
private void submitInterfaceValidation(Repository repo, String userEmail, RepositoryInterface iFace, boolean updateExisting) throws ValidatorServiceException {
|
|
JobForValidation job = new JobForValidation();
|
|
|
|
job.setActivationId(UUID.randomUUID().toString());
|
|
job.setAdminEmails(Collections.singletonList(this.adminEmail));
|
|
job.setBaseUrl(iFace.getBaseUrl());
|
|
job.setDatasourceId(repo.getId());
|
|
job.setDesiredCompatibilityLevel(iFace.getDesiredCompatibilityLevel());
|
|
job.setInterfaceId(iFace.getId());
|
|
job.setOfficialName(repo.getOfficialName());
|
|
job.setRepoType(repo.getDatasourceType());
|
|
job.setUserEmail(userEmail);
|
|
job.setValidationSet((iFace.getAccessSet().isEmpty() ? "none" : iFace.getAccessSet()));
|
|
job.setRecords(-1);
|
|
job.setRegistration(!updateExisting);
|
|
job.setUpdateExisting(updateExisting);
|
|
|
|
this.validatorService.submitJobForValidation(job);
|
|
}
|
|
|
|
private RepositoryInterface createRepositoryInterface(Repository repo, RepositoryInterface iFace, String datatype) {
|
|
|
|
iFace.setContentDescription("metadata");
|
|
iFace.setCompliance("UNKNOWN");
|
|
|
|
if (datatype.equals("re3data"))
|
|
iFace.setAccessFormat("oai_datacite");
|
|
else
|
|
iFace.setAccessFormat("oai_dc");
|
|
|
|
|
|
if (repo.getDatasourceClass() != null && !repo.getDatasourceClass().isEmpty())
|
|
iFace.setTypology(repo.getDatasourceClass());
|
|
else if (datatype.equalsIgnoreCase("journal"))
|
|
iFace.setTypology("pubsrepository::journal");
|
|
else if (datatype.equalsIgnoreCase("aggregator"))
|
|
iFace.setTypology("aggregator::pubsrepository::unknown");
|
|
else if (datatype.equalsIgnoreCase("opendoar"))
|
|
iFace.setTypology("pubsrepository::unknown");
|
|
else if (datatype.equalsIgnoreCase("re3data"))
|
|
iFace.setTypology("datarepository::unknown");
|
|
|
|
iFace.setRemovable(true);
|
|
iFace.setAccessProtocol("oai");
|
|
iFace.setMetadataIdentifierPath("//*[local-name()='header']/*[local-name()='identifier']");
|
|
iFace.setId("api_________::" + repo.getId() + "::" + UUID.randomUUID().toString().substring(0, 8));
|
|
if (iFace.getAccessSet() == null || iFace.getAccessSet().isEmpty()) {
|
|
LOGGER.debug("set is empty: " + iFace.getAccessSet());
|
|
iFace.removeAccessSet();
|
|
iFace.setAccessSet("none");
|
|
}
|
|
return iFace;
|
|
}
|
|
|
|
@Override
|
|
public List<String> getDnetCountries() {
|
|
LOGGER.debug("Getting dnet-countries!");
|
|
return Converter.readFile("countries.txt");
|
|
}
|
|
|
|
@Override
|
|
public List<String> getTypologies() {
|
|
return Converter.readFile("typologies.txt");
|
|
}
|
|
|
|
@Override
|
|
public List<Timezone> getTimezones() {
|
|
List<String> timezones = Converter.readFile("timezones.txt");
|
|
return Converter.toTimezones(timezones);
|
|
}
|
|
|
|
@Override
|
|
public List<String> getUrlsOfUserRepos(String userEmail,
|
|
String page,
|
|
String size) {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/api/baseurl/")
|
|
.path("/{page}/{size}")
|
|
.build().expand(page, size).encode();
|
|
|
|
RequestFilter requestFilter = new RequestFilter();
|
|
requestFilter.setRegisteredby(userEmail);
|
|
return Arrays.asList(restTemplate.postForObject(uriComponents.toUri(), requestFilter, String[].class));
|
|
}
|
|
|
|
@Override
|
|
public List<String> getDatasourceVocabularies(String mode) {
|
|
|
|
List<String> resultSet = new ArrayList<>();
|
|
for (Map.Entry<String, String> entry : this.getVocabulary("dnet:datasource_typologies").getAsMap().entrySet()) {
|
|
if (mode.equalsIgnoreCase("aggregator")) {
|
|
if (entry.getKey().contains("aggregator"))
|
|
resultSet.add(entry.getValue());
|
|
} else if (mode.equalsIgnoreCase("journal")) {
|
|
if (entry.getKey().contains("journal"))
|
|
resultSet.add(entry.getValue());
|
|
} else if (mode.equalsIgnoreCase("opendoar")) {
|
|
if (entry.getKey().contains("pubsrepository"))
|
|
resultSet.add(entry.getValue());
|
|
} else if (mode.equalsIgnoreCase("re3data")) {
|
|
if (entry.getKey().contains("datarepository"))
|
|
resultSet.add(entry.getValue());
|
|
}
|
|
}
|
|
|
|
|
|
return resultSet;
|
|
}
|
|
|
|
private Vocabulary getVocabulary(String vocName) {
|
|
|
|
if (!vocabularyMap.containsKey(vocName)) {
|
|
vocabularyMap.put(vocName, vocabularyLoader.getVocabulary(vocName, Locale.ENGLISH, Locale.ROOT));
|
|
}
|
|
return vocabularyMap.get(vocName);
|
|
}
|
|
|
|
|
|
@Override
|
|
public Map<String, String> getCompatibilityClasses(String mode) {
|
|
|
|
LOGGER.debug("Getting compatibility classes for mode: " + mode);
|
|
Map<String, String> retMap = new HashMap<String, String>();
|
|
|
|
Map<String, String> compatibilityClasses = this.getVocabulary("dnet:compatibilityLevel").getAsMap();
|
|
boolean foundData = false;
|
|
for (Map.Entry<String, String> entry : compatibilityClasses.entrySet()) {
|
|
if (mode.equalsIgnoreCase(Constants.REPOSITORY_MODE_ALL))
|
|
return compatibilityClasses;
|
|
else if (mode.equalsIgnoreCase(Constants.REPOSITORY_MODE_RE3DATA)) {
|
|
if (entry.getKey().matches("^openaire[1-9].0_data$")) {
|
|
retMap.put(entry.getKey(), entry.getValue());
|
|
foundData = true;
|
|
}
|
|
} else {
|
|
if (entry.getKey().matches("^openaire[1-9].0$") || entry.getKey().equals("driver"))
|
|
retMap.put(entry.getKey(), entry.getValue());
|
|
}
|
|
}
|
|
|
|
//TODO TO BE REMOVED WHEN VOCABULARIES ARE UPDATED
|
|
if (mode.equalsIgnoreCase(Constants.REPOSITORY_MODE_RE3DATA) && !foundData)
|
|
retMap.put("openaire2.0_data", "OpenAIRE Data (funded, referenced datasets)");
|
|
|
|
return retMap;
|
|
}
|
|
|
|
@Override
|
|
public Map<String, String> getDatasourceClasses(String mode) {
|
|
|
|
LOGGER.debug("Getting datasource classes for mode: " + mode);
|
|
|
|
Map<String, String> retMap = new HashMap<String, String>();
|
|
|
|
for (Map.Entry<String, String> entry : this.getVocabulary("dnet:datasource_typologies").getAsMap().entrySet()) {
|
|
if (mode.equalsIgnoreCase("aggregator")) {
|
|
if (entry.getKey().contains("aggregator"))
|
|
retMap.put(entry.getKey(), entry.getValue());
|
|
} else if (mode.equalsIgnoreCase("journal")) {
|
|
if (entry.getKey().contains("journal"))
|
|
retMap.put(entry.getKey(), entry.getValue());
|
|
} else if (mode.equalsIgnoreCase("opendoar")) {
|
|
if (entry.getKey().contains("pubsrepository"))
|
|
retMap.put(entry.getKey(), entry.getValue());
|
|
} else if (mode.equalsIgnoreCase("re3data")) {
|
|
if (entry.getKey().contains("datarepository"))
|
|
retMap.put(entry.getKey(), entry.getValue());
|
|
}
|
|
}
|
|
return filterResults(retMap, mode);
|
|
|
|
}
|
|
|
|
private Map<String, String> filterResults(Map<String, String> map, String mode) {
|
|
|
|
HashMap<String, String> filteredMap = new HashMap<>();
|
|
for (String key : map.keySet())
|
|
if (dataSourceClass.get(mode).contains(key))
|
|
filteredMap.put(key, map.get(key));
|
|
|
|
return filteredMap;
|
|
}
|
|
|
|
@Override
|
|
public String getCountryName(String countryCode) {
|
|
return inverseCountriesMap.get(countryCode);
|
|
}
|
|
|
|
@Override
|
|
public MetricsInfo getMetricsInfoForRepository(String repoId) throws RepositoryServiceException {
|
|
try {
|
|
|
|
MetricsInfo metricsInfo = new MetricsInfo();
|
|
metricsInfo.setDiagramsBaseURL(this.usageStatisticsDiagramsBaseURL);
|
|
metricsInfo.setMetricsNumbers(getMetricsNumbers(getOpenAIREId(repoId)));
|
|
return metricsInfo;
|
|
|
|
} catch (Exception e) {
|
|
LOGGER.error("Error while getting metrics info for repository: ", e);
|
|
throw new RepositoryServiceException("General error", RepositoryServiceException.ErrorCode.GENERAL_ERROR);
|
|
}
|
|
}
|
|
|
|
@Override
|
|
public Map<String, String> getListLatestUpdate(String mode) throws JSONException {
|
|
if (mode.equals("opendoar"))
|
|
return Collections.singletonMap("lastCollectionDate", getRepositoryInterface("openaire____::" + mode).get(0).getLastCollectionDate());
|
|
else
|
|
/*
|
|
* first api of re3data has null value on collection date
|
|
* */
|
|
return Collections.singletonMap("lastCollectionDate", getRepositoryInterface("openaire____::" + mode).get(1).getLastCollectionDate());
|
|
}
|
|
|
|
private void updateValidationSet(String repositoryId, String repositoryInterfaceId, String validationSet) throws Exception {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/api/oaiset")
|
|
.queryParam("dsId", repositoryId)
|
|
.queryParam("apiId", repositoryInterfaceId)
|
|
.queryParam("oaiSet", validationSet)
|
|
.build().encode();
|
|
restTemplate.exchange(uriComponents.toUri(), HttpMethod.POST, null, ResponseEntity.class);
|
|
|
|
}
|
|
|
|
|
|
private void updateBaseUrl(String repositoryId, String repositoryInterfaceId, String baseUrl) {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/api/baseurl")
|
|
.queryParam("dsId", repositoryId)
|
|
.queryParam("apiId", repositoryInterfaceId)
|
|
.queryParam("baseUrl", baseUrl)
|
|
.build().encode();
|
|
restTemplate.postForObject(uriComponents.toUri(), null, String.class);
|
|
}
|
|
|
|
private void updateCompliance(String repositoryId, String repositoryInterfaceId, String compliance) {
|
|
UriComponents uriComponents = UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/api/compliance")
|
|
.queryParam("dsId", repositoryId)
|
|
.queryParam("apiId", repositoryInterfaceId)
|
|
.queryParam("compliance", compliance)
|
|
.build().encode();
|
|
restTemplate.postForObject(uriComponents.toUri(), null, String.class);
|
|
}
|
|
|
|
private MetricsNumbers getMetricsNumbers(String openAIREID) throws BrokerException {
|
|
|
|
//build the uri params
|
|
UriComponentsBuilder builder = UriComponentsBuilder.fromHttpUrl(this.usageStatisticsNumbersBaseURL + openAIREID + "/clicks");
|
|
|
|
//create new template engine
|
|
RestTemplate template = new RestTemplate();
|
|
template.getMessageConverters().add(new MappingJackson2HttpMessageConverter());
|
|
ResponseEntity<MetricsNumbers> resp;
|
|
|
|
//communicate with endpoint
|
|
resp = template.exchange(
|
|
builder.build().encode().toUri(),
|
|
HttpMethod.GET,
|
|
null,
|
|
new ParameterizedTypeReference<MetricsNumbers>() {
|
|
});
|
|
|
|
return resp.getBody();
|
|
}
|
|
|
|
private String getOpenAIREId(String repoId) {
|
|
|
|
if (repoId != null && repoId.contains("::")) {
|
|
return repoId.split("::")[0] + "::" + DigestUtils.md5Hex(repoId.split("::")[1]);
|
|
}
|
|
|
|
return null;
|
|
}
|
|
|
|
private UriComponents searchDatasource(String page, String size) {
|
|
|
|
return UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/search/")
|
|
.path("/{page}/{size}/")
|
|
.queryParam("requestSortBy", "officialname")
|
|
.queryParam("order", "ASCENDING")
|
|
.build().expand(page, size).encode();
|
|
}
|
|
|
|
private UriComponents searchSnipperDatasource(String page, String size) {
|
|
|
|
return UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/searchsnippet/")
|
|
.path("/{page}/{size}/")
|
|
.queryParam("requestSortBy", "officialname")
|
|
.queryParam("order", "ASCENDING")
|
|
.build().expand(page, size).encode();
|
|
}
|
|
|
|
private UriComponents searchRegisteredDatasource(String requestSortBy, String order, String page, String size) {
|
|
|
|
return UriComponentsBuilder
|
|
.fromHttpUrl(baseAddress + "/ds/searchregistered/")
|
|
.path("/{page}/{size}/")
|
|
.queryParam("requestSortBy", requestSortBy)
|
|
.queryParam("order", order)
|
|
.build().expand(page, size).encode();
|
|
}
|
|
|
|
private String getRepositoryType(String typology) {
|
|
return invertedDataSourceClass.get(typology);
|
|
}
|
|
|
|
private List<String> getRoleIdsFromUserRoles(String userEmail) {
|
|
Integer coPersonId = registryCalls.getCoPersonIdByEmail(userEmail);
|
|
JsonArray roles;
|
|
ArrayList<String> roleIds = new ArrayList<>();
|
|
ArrayList<Integer> couIds = new ArrayList<>();
|
|
if (coPersonId != null) {
|
|
roles = registryCalls.getRolesWithStatus(coPersonId, AaiRegistryService.RoleStatus.ACTIVE);
|
|
for (JsonElement role : roles) {
|
|
JsonObject object = role.getAsJsonObject();
|
|
if (object.get("CouId") == null) {
|
|
continue;
|
|
}
|
|
couIds.add(object.get("CouId").getAsInt());
|
|
}
|
|
|
|
roleIds.addAll(registryCalls.getCouNames(couIds).values());
|
|
|
|
}
|
|
return roleIds;
|
|
}
|
|
}
|