201 lines
9.4 KiB
Java
201 lines
9.4 KiB
Java
package eu.eudat.depositinterface.dataverserepository.interfaces;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.researchspace.dataverse.api.v1.DataverseAPI;
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import com.researchspace.dataverse.api.v1.DataverseConfig;
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import com.researchspace.dataverse.entities.*;
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import com.researchspace.dataverse.entities.facade.DatasetAuthor;
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import com.researchspace.dataverse.entities.facade.DatasetContact;
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import com.researchspace.dataverse.entities.facade.DatasetDescription;
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import com.researchspace.dataverse.entities.facade.DatasetFacade;
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import com.researchspace.dataverse.http.DataverseAPIImpl;
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import eu.eudat.depositinterface.dataverserepository.config.ConfigLoader;
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import eu.eudat.depositinterface.models.DMPDepositModel;
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import eu.eudat.depositinterface.repository.RepositoryDeposit;
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import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
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import org.json.JSONObject;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.core.env.Environment;
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import org.springframework.http.*;
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import org.springframework.stereotype.Component;
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import org.springframework.util.LinkedMultiValueMap;
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import org.springframework.util.MultiValueMap;
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import org.springframework.web.client.RestTemplate;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.OutputStream;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.nio.charset.StandardCharsets;
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import java.nio.file.Files;
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import java.util.*;
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import java.util.stream.Collectors;
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import static com.researchspace.dataverse.entities.Version.MAJOR;
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import static com.researchspace.dataverse.entities.Version.MINOR;
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@Component
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public class DataverseDeposit implements RepositoryDeposit {
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private static final Logger logger = LoggerFactory.getLogger(DataverseDeposit.class);
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private static final ObjectMapper objectMapper = new ObjectMapper();
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private DataverseAPI api;
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private boolean isApiSet;
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private ConfigLoader configLoader;
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private Environment environment;
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@Autowired
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public DataverseDeposit(ConfigLoader configLoader, Environment environment){
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this.configLoader = configLoader;
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this.environment = environment;
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this.isApiSet = false;
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}
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private void setDataverseApi() throws MalformedURLException {
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if(!this.isApiSet) {
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this.api = new DataverseAPIImpl();
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eu.eudat.depositinterface.dataverserepository.config.DataverseConfig jsonConfig = this.configLoader.getDataverseConfig();
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DataverseConfig config = new DataverseConfig(new URL(jsonConfig.getServer()), jsonConfig.getApiToken(), jsonConfig.getParentDataverseAlias());
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api.configure(config);
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this.isApiSet = true;
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}
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}
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@Override
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public String deposit(DMPDepositModel dmpDepositModel, String repositoryAccessToken) throws Exception {
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if(!this.isApiSet)
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this.setDataverseApi();
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String doi;
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DatasetFacade dataset = DatasetFacade.builder()
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.title(dmpDepositModel.getLabel())
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.authors(dmpDepositModel.getUsers().stream().map(x -> DatasetAuthor.builder().authorName(x.getUser().getName()).build()).collect(Collectors.toList()))
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.contacts(dmpDepositModel.getUsers().stream().map(x -> DatasetContact.builder().datasetContactEmail(x.getUser().getEmail()).build()).collect(Collectors.toList()))
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.subject("Other")
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.description(DatasetDescription.builder().description(dmpDepositModel.getDescription()).build())
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.languages(new ArrayList<>())
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.depositor("")
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.build();
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if(dmpDepositModel.getPreviousDOI() == null || dmpDepositModel.getPreviousDOI().isEmpty()){
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Identifier id = this.api.getDataverseOperations().createDataset(dataset, this.configLoader.getDataverseConfig().getParentDataverseAlias());
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doi = this.api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);
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this.uploadFiles(dmpDepositModel, doi);
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this.api.getDatasetOperations().publishDataset(id, MAJOR);
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}
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else{
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Map<String, Object> datasetJson = this.getDatasetIdentifier(dmpDepositModel.getPreviousDOI());
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Identifier id = new Identifier();
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id.setId(((Integer) datasetJson.get("id")).longValue());
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JsonNode jsonNode = this.objectMapper.readTree(new JSONObject(datasetJson).toString());
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List<JsonNode> files = jsonNode.findValues("dataFile");
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for(JsonNode file: files){
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int fileId = file.get("id").asInt();
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this.deleteFile(fileId);
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}
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this.uploadFiles(dmpDepositModel, dmpDepositModel.getPreviousDOI());
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this.api.getDatasetOperations().updateDataset(dataset, id);
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DataverseResponse<PublishedDataset> publishedDataset = this.api.getDatasetOperations().publishDataset(id, MAJOR);
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doi = publishedDataset.getData().getAuthority() + "/" + publishedDataset.getData().getIdentifier();
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}
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return doi;
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}
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private void deleteFile(int fileId){
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HttpHeaders headers = this.createBasicAuthHeaders(this.configLoader.getDataverseConfig().getApiToken(), "");
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String serverUrl = this.configLoader.getDataverseConfig().getServer() + "/dvn/api/data-deposit/v1.1/swordv2/edit-media/file/" + fileId;
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RestTemplate restTemplate = new RestTemplate();
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restTemplate.exchange(serverUrl, HttpMethod.DELETE, new HttpEntity<>(headers), Object.class);
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}
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private HttpHeaders createBasicAuthHeaders(String username, String password) {
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return new HttpHeaders() {{
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String auth = username + ":" + password;
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byte[] encodedAuth = Base64.getEncoder().encode(
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auth.getBytes(StandardCharsets.UTF_8));
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String authHeader = "Basic " + new String(encodedAuth);
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set("Authorization", authHeader);
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}};
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}
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private void uploadFiles(DMPDepositModel dmpDepositModel, String doi) throws IOException {
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this.uploadFile(dmpDepositModel.getPdfFileName(), dmpDepositModel.getPdfFile(), doi);
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String contentDisposition = dmpDepositModel.getRdaJson().getHeaders().get("Content-Disposition").get(0);
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String jsonFileName = contentDisposition.substring(contentDisposition.lastIndexOf('=') + 1);
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File rdaJson = new File(this.environment.getProperty("storage.temp") + jsonFileName);
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OutputStream output = new FileOutputStream(rdaJson);
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try {
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output.write(Objects.requireNonNull(dmpDepositModel.getRdaJson().getBody()));
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output.flush();
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output.close();
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} catch (IOException e) {
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logger.error(e.getMessage(), e);
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}
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this.uploadFile(jsonFileName, rdaJson, doi);
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Files.deleteIfExists(rdaJson.toPath());
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if(dmpDepositModel.getSupportingFilesZip() != null) {
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this.uploadFile(dmpDepositModel.getSupportingFilesZip().getName(), dmpDepositModel.getSupportingFilesZip(), doi);
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}
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}
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private Map<String, Object> getDatasetIdentifier(String previousDOI) {
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HttpHeaders headers = new HttpHeaders();
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headers.set("X-Dataverse-key", this.configLoader.getDataverseConfig().getApiToken());
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String serverUrl = this.configLoader.getDataverseConfig().getServer() + "/api/datasets/:persistentId?persistentId=doi:" + previousDOI;
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RestTemplate restTemplate = new RestTemplate();
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return (Map<String, Object>) restTemplate.exchange(serverUrl, HttpMethod.GET, new HttpEntity<>(headers), Map.class).getBody().get("data");
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}
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private void uploadFile(String filename, File file, String doi) throws IOException {
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HttpHeaders headers = new HttpHeaders();
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headers.setContentType(MediaType.MULTIPART_FORM_DATA);
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headers.set("X-Dataverse-key", this.configLoader.getDataverseConfig().getApiToken());
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MultiValueMap<String, String> fileMap = new LinkedMultiValueMap<>();
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ContentDisposition contentDisposition = ContentDisposition
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.builder("form-data")
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.name("file")
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.filename(filename)
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.build();
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fileMap.add(HttpHeaders.CONTENT_DISPOSITION, contentDisposition.toString());
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HttpEntity<byte[]> fileEntity = new HttpEntity<>(Files.readAllBytes(file.toPath()), fileMap);
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MultiValueMap<String, Object> body = new LinkedMultiValueMap<>();
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body.add("file", fileEntity);
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body.add("jsonData", "{\"restrict\":\"false\", \"tabIngest\":\"false\"}");
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HttpEntity<MultiValueMap<String, Object>> requestEntity
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= new HttpEntity<>(body, headers);
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String serverUrl = this.configLoader.getDataverseConfig().getServer() + "/api/datasets/:persistentId/add?persistentId=doi:" + doi;
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RestTemplate restTemplate = new RestTemplate();
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ResponseEntity<Object> resp = restTemplate.postForEntity(serverUrl, requestEntity, Object.class);
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}
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@Override
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public RepositoryDepositConfiguration getConfiguration() {
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eu.eudat.depositinterface.dataverserepository.config.DataverseConfig dataverseConfig = this.configLoader.getDataverseConfig();
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return dataverseConfig.toRepoConfig();
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}
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@Override
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public String authenticate(String code) {
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return null;
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}
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}
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