argos/dmp-backend/dataverseRepository/src/main/java/eu/eudat/depositinterface/dataverserepository/interfaces/DataverseDeposit.java

package eu.eudat.depositinterface.dataverserepository.interfaces;

import com.fasterxml.jackson.databind.ObjectMapper;
import com.researchspace.dataverse.api.v1.DataverseAPI;
import com.researchspace.dataverse.api.v1.DataverseConfig;
import com.researchspace.dataverse.entities.DataverseContacts;
import com.researchspace.dataverse.entities.DataversePost;
import com.researchspace.dataverse.entities.DataverseResponse;
import com.researchspace.dataverse.entities.Identifier;
import com.researchspace.dataverse.entities.facade.DatasetAuthor;
import com.researchspace.dataverse.entities.facade.DatasetContact;
import com.researchspace.dataverse.entities.facade.DatasetDescription;
import com.researchspace.dataverse.entities.facade.DatasetFacade;
import com.researchspace.dataverse.http.DataverseAPIImpl;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.*;
import org.springframework.stereotype.Component;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;
import org.springframework.web.client.RestTemplate;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.Objects;
import java.util.stream.Collectors;

import static eu.eudat.depositinterface.repository.RepositoryDepositConfiguration.DepositAccountStatus.SystemDeposit;

@Component
public class DataverseDeposit implements RepositoryDeposit {
    private static final Logger logger = LoggerFactory.getLogger(DataverseDeposit.class);
    private static final ObjectMapper objectMapper = new ObjectMapper();

    private static final String API_TOKEN = "";
    private static final String SYSTEM_PARENT_DATAVERSE_ALIAS = "";
    private static final String SERVER = "";
    private static final String SYSTEM_EMAIL = "";

    private DataverseAPI api;
    private boolean isApiSet;

    private Environment environment;

    @Autowired
    public DataverseDeposit(Environment environment){
        this.environment = environment;
        this.isApiSet = false;
    }

    private void setDataverseApi() throws MalformedURLException {
        if(!this.isApiSet) {
            this.api = new DataverseAPIImpl();
            DataverseConfig config = new DataverseConfig(new URL(SERVER), API_TOKEN, SYSTEM_PARENT_DATAVERSE_ALIAS);
            api.configure(config);
            this.isApiSet = true;
        }
    }

    @Override
    public String deposit(DMPDepositModel dmpDepositModel, boolean update, String repositoryAccessToken) throws Exception {

        if(!this.isApiSet)
            this.setDataverseApi();

        DataversePost entity = new DataversePost();
        entity.setName(dmpDepositModel.getLabel());
        entity.setAlias(dmpDepositModel.getLabel().replace(" ", "_"));
        entity.setDescription(dmpDepositModel.getDescription());
        entity.setCreationDate(new Date());
        entity.setDataverseContacts(Collections.singletonList(new DataverseContacts(SYSTEM_EMAIL)));
        DataverseResponse<DataversePost> response = this.api.getDataverseOperations().createNewDataverse(SYSTEM_PARENT_DATAVERSE_ALIAS, entity);

        DatasetFacade dataset = DatasetFacade.builder()
                .title(dmpDepositModel.getLabel())
                .authors(dmpDepositModel.getUsers().stream().map(x -> DatasetAuthor.builder().authorName(x.getUser().getName()).build()).collect(Collectors.toList()))
                .contacts(dmpDepositModel.getUsers().stream().map(x -> DatasetContact.builder().datasetContactEmail(x.getUser().getEmail()).build()).collect(Collectors.toList()))
                .subject("Other")
                .description(DatasetDescription.builder().description(dmpDepositModel.getDescription()).build())
                .languages(new ArrayList<>())
                .depositor("")
                .build();
        Identifier id = this.api.getDataverseOperations().createDataset(dataset, entity.getAlias());

        String doi = this.api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);

        this.uploadFile(dmpDepositModel.getPdfFileName(), dmpDepositModel.getPdfFile(), doi);

        String contentDisposition = dmpDepositModel.getRdaJson().getHeaders().get("Content-Disposition").get(0);
        String jsonFileName = contentDisposition.substring(contentDisposition.lastIndexOf('=')  + 1);
        File rdaJson = new File(this.environment.getProperty("storage.temp") + jsonFileName);
        OutputStream output = new FileOutputStream(rdaJson);
        try {
            output.write(Objects.requireNonNull(dmpDepositModel.getRdaJson().getBody()));
            output.flush();
            output.close();
        } catch (IOException e) {
            logger.error(e.getMessage(), e);
        }
        this.uploadFile(jsonFileName, rdaJson, doi);
        Files.deleteIfExists(rdaJson.toPath());

        return doi;

    }

    private void uploadFile(String filename, File file, String doi) throws IOException {
        HttpHeaders headers = new HttpHeaders();
        headers.setContentType(MediaType.MULTIPART_FORM_DATA);
        headers.set("X-Dataverse-key", API_TOKEN);
        MultiValueMap<String, String> fileMap = new LinkedMultiValueMap<>();
        ContentDisposition contentDisposition = ContentDisposition
                .builder("form-data")
                .name("file")
                .filename(filename)
                .build();
        fileMap.add(HttpHeaders.CONTENT_DISPOSITION, contentDisposition.toString());
        HttpEntity<byte[]> fileEntity = new HttpEntity<>(Files.readAllBytes(file.toPath()), fileMap);
        MultiValueMap<String, Object> body = new LinkedMultiValueMap<>();
        body.add("file", fileEntity);
        body.add("jsonData", "{\"restrict\":\"true\", \"tabIngest\":\"false\"}");
        HttpEntity<MultiValueMap<String, Object>> requestEntity
                = new HttpEntity<>(body, headers);

        String serverUrl = SERVER + "/api/datasets/:persistentId/add?persistentId=doi:" + doi;

        RestTemplate restTemplate = new RestTemplate();
        ResponseEntity<Object> resp = restTemplate.postForEntity(serverUrl, requestEntity, Object.class);
    }

    @Override
    public RepositoryDepositConfiguration getConfiguration() {
        RepositoryDepositConfiguration conf = new RepositoryDepositConfiguration();
        conf.setRepositoryId("Dataverse");
        conf.setDepositAccountStatus(SystemDeposit.getValue());
        conf.setAccessToken(API_TOKEN);
        conf.setRepositoryUrl(SERVER + "/api/");
        conf.setRepositoryRecordUrl(SERVER + "/dataverse/");
        return conf;
    }

    @Override
    public String authenticate(String code) {
        return null;
    }
}