repository-deposit-zenodo/src/main/java/eu/eudat/depositinterface/zenodorepository/interfaces/ZenodoDeposit.java

package eu.eudat.depositinterface.zenodorepository.interfaces;

import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.models.FileEnvelope;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import eu.eudat.depositinterface.zenodorepository.config.ConfigLoader;
import eu.eudat.depositinterface.zenodorepository.config.ZenodoConfig;
import eu.eudat.depositinterface.zenodorepository.mapper.DMPToZenodoMapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
import org.springframework.http.*;
import org.springframework.stereotype.Component;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;
import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.HttpServerErrorException;
import org.springframework.web.client.RestTemplate;

import java.io.*;
import java.nio.file.Files;
import java.util.*;
import java.util.stream.Collectors;

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

    private final ConfigLoader configLoader;
    private final Environment environment;

    @Autowired
    public ZenodoDeposit(ConfigLoader configLoader, Environment environment){
        this.configLoader = configLoader;
        this.environment = environment;
    }

    @Override
    public String deposit(String repositoryId, DMPDepositModel dmpDepositModel, String zenodoToken) throws Exception {

        RepositoryDepositConfiguration conf = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);

        if(conf != null) {

            if (zenodoToken == null) {
                zenodoToken = conf.getAccessToken();
            }

            String zenodoUrl = conf.getRepositoryUrl();

            // First step, post call to Zenodo, to create the entry.
            RestTemplate restTemplate = new RestTemplate();
            HttpHeaders headers = new HttpHeaders();
            headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
            headers.setContentType(MediaType.APPLICATION_JSON);

            ZenodoConfig zenodoConfig = this.configLoader.getZenodoConfig().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
            eu.eudat.depositinterface.zenodorepository.models.ZenodoDeposit deposit = DMPToZenodoMapper.fromDMP(dmpDepositModel, zenodoConfig);

            HttpEntity<eu.eudat.depositinterface.zenodorepository.models.ZenodoDeposit> request = new HttpEntity<>(deposit, headers);
            Map createResponse;
            LinkedHashMap<String, String> links;
            String previousDOI = dmpDepositModel.getPreviousDOI();
            String unpublishedUrl = null;
            String publishUrl;
            String finalDoi;
            try {

                if (previousDOI == null) {
                    String createUrl = zenodoUrl + "deposit/depositions" + "?access_token=" + zenodoToken;
                    createResponse = restTemplate.postForEntity(createUrl, request, Map.class).getBody();
                    links = (LinkedHashMap<String, String>) createResponse.get("links");
                } else {
                    unpublishedUrl = this.getUnpublishedDOI(zenodoUrl, previousDOI, zenodoToken, dmpDepositModel.getVersion());
                    if (unpublishedUrl == null) {
                        //It requires more than one step to create a new version
                        //First, get the deposit related to the concept DOI
                        String listUrl = zenodoUrl + "deposit/depositions" + "?q=conceptdoi:\"" + previousDOI + "\"&access_token=" + zenodoToken;
                        logger.debug("listUrl = " + listUrl);
                        ResponseEntity<Map[]> listResponses = restTemplate.getForEntity(listUrl, Map[].class);
                        createResponse = listResponses.getBody()[0];
                        logger.debug("createResponse-previousDoi:");
                        logger.debug(objectMapper.writeValueAsString(createResponse));
                        links = (LinkedHashMap<String, String>) createResponse.get("links");
                        //Second, make the new version (not in the links?)
                        String newVersionUrl = links.get("latest_draft") + "/actions/newversion" + "?access_token=" + zenodoToken;
                        logger.debug("new version url: " + newVersionUrl);
                        createResponse = restTemplate.postForObject(newVersionUrl, null, Map.class);
                        logger.debug("createResponse-newVersion:");
                        logger.debug(objectMapper.writeValueAsString(createResponse));
                        links = (LinkedHashMap<String, String>) createResponse.get("links");
                        //Third, get the new deposit
                        String latestDraftUrl = links.get("latest_draft") + "?access_token=" + zenodoToken;
                        createResponse = restTemplate.getForObject(latestDraftUrl, Map.class);
                        logger.debug("createResponse-latestDraft:");
                        logger.debug(objectMapper.writeValueAsString(createResponse));
                        links = (LinkedHashMap<String, String>) createResponse.get("links");
                        //At this point it might fail to perform the next requests so enclose them with try catch
                        try {
                            //Forth, update the new deposit's metadata
                            String updateUrl = links.get("self") + "?access_token=" + zenodoToken;
                            restTemplate.put(updateUrl, request);
                            //And finally remove pre-existing files from it
                            String fileListUrl = links.get("self") + "/files" + "?access_token=" + zenodoToken;
                            ResponseEntity<Map[]> fileListResponse = restTemplate.getForEntity(fileListUrl, Map[].class);
                            for (Map file : fileListResponse.getBody()) {
                                String fileDeleteUrl = links.get("self") + "/files/" + file.get("id") + "?access_token=" + zenodoToken;
                                restTemplate.delete(fileDeleteUrl);
                            }
                        } catch (Exception e) {
                            //In case the last two steps fail delete the latest Deposit it in order to create a new one (only one at a time is allowed)
                            restTemplate.delete(latestDraftUrl);
                            throw e;
                        }
                    } else {
                        String listUrl = zenodoUrl + "deposit/depositions" + "?q=conceptdoi:\"" + previousDOI + "\"&access_token=" + zenodoToken;
                        ResponseEntity<Map[]> listResponses = restTemplate.getForEntity(listUrl, Map[].class);
                        createResponse = listResponses.getBody()[0];
                        links = (LinkedHashMap<String, String>) createResponse.get("links");
                    }
                }

                if (unpublishedUrl == null) {
                    // Second step, add the file to the entry.
                    FileEnvelope pdfEnvelope = dmpDepositModel.getPdfFile();
                    FileSystemResource fileSystemResource = new FileSystemResource(pdfEnvelope.getFile());
                    HttpHeaders fileHeaders = new HttpHeaders();
                    fileHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
                    HttpEntity<FileSystemResource> addFileMapRequest = new HttpEntity<>(fileSystemResource, fileHeaders);

                    String addFileUrl = links.get("bucket") + "/" + pdfEnvelope.getFilename() + "?access_token=" + zenodoToken;
                    restTemplate.put(addFileUrl, addFileMapRequest);

                    FileEnvelope rdaJsonEnvelope = dmpDepositModel.getRdaJsonFile();
                    HttpHeaders responseHeaders = new HttpHeaders();
                    responseHeaders.setContentLength(rdaJsonEnvelope.getFile().length());
                    responseHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM);
                    responseHeaders.set("Content-Disposition", "attachment;filename=" + rdaJsonEnvelope.getFilename());
                    responseHeaders.set("Access-Control-Expose-Headers", "Content-Disposition");
                    responseHeaders.get("Access-Control-Expose-Headers").add("Content-Type");

                    byte[] content = Files.readAllBytes(rdaJsonEnvelope.getFile().toPath());

                    ResponseEntity<byte[]> jsonFile = new ResponseEntity<>(content, responseHeaders, HttpStatus.OK);

                    UUID jsonFileUUID = UUID.randomUUID();
                    File tempJsonFile = new File(this.environment.getProperty("zenodo_plugin.storage.temp") + jsonFileUUID + ".json");
                    try (FileOutputStream jsonFos = new FileOutputStream(tempJsonFile)) {
                        jsonFos.write(jsonFile.getBody());
                        jsonFos.flush();
                    }
                    fileSystemResource = new FileSystemResource(tempJsonFile);
                    HttpHeaders jsonHeaders = new HttpHeaders();
                    jsonHeaders.add(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_OCTET_STREAM_VALUE);
                    addFileMapRequest = new HttpEntity<>(fileSystemResource, jsonHeaders);
                    String jsonFileName = jsonFile.getHeaders().get("Content-Disposition").get(0).substring(jsonFile.getHeaders().get("Content-Disposition").get(0).lastIndexOf('=') + 1);
                    addFileUrl = links.get("bucket") + "/" + jsonFileName + "?access_token=" + zenodoToken;
                    restTemplate.put(addFileUrl, addFileMapRequest);
                    Files.deleteIfExists(tempJsonFile.toPath());

                    if (dmpDepositModel.getSupportingFilesZip() != null) {
                        File supportinFilesZip = dmpDepositModel.getSupportingFilesZip();
                        String supportinFilesZipName = dmpDepositModel.getSupportingFilesZip().getName();
                        fileSystemResource = new FileSystemResource(supportinFilesZip);
                        addFileMapRequest = new HttpEntity<>(fileSystemResource, null);

                        addFileUrl = links.get("bucket") + "/" + supportinFilesZipName + "?access_token=" + zenodoToken;
                        restTemplate.put(addFileUrl, addFileMapRequest);
                    }

                    // Third post call to Zenodo to publish the entry and return the DOI.
                    publishUrl = links.get("publish") + "?access_token=" + zenodoToken;
                } else {
                    publishUrl = unpublishedUrl + "?access_token=" + zenodoToken;
                }

                return this.publish(publishUrl);

            } catch (HttpClientErrorException | HttpServerErrorException ex) {
                Map<String, String> parsedException = objectMapper.readValue(ex.getResponseBodyAsString(), HashMap.class);
                throw new IOException(parsedException.get("message"), ex);
            }

        }

        return null;

    }

    private String publish(String publishUrl){
        RestTemplate restTemplate = new RestTemplate();
        Map<String, Object> publishResponce = restTemplate.postForObject(publishUrl, "", Map.class);
        return (String) publishResponce.get("conceptdoi");
    }


    @Override
    public List<RepositoryDepositConfiguration> getConfiguration() {
        List<ZenodoConfig> zenodoConfigs = this.configLoader.getZenodoConfig();
        return (zenodoConfigs != null) ? zenodoConfigs.stream().map(ZenodoConfig::toRepoConfig).collect(Collectors.toList()) : null;
    }

    @Override
    public String authenticate(String repositoryId, String code){

        RepositoryDepositConfiguration conf = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);

        if(conf != null) {

            RestTemplate restTemplate = new RestTemplate();
            HttpHeaders headers = new HttpHeaders();
            headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
            headers.setContentType(MediaType.MULTIPART_FORM_DATA);

            MultiValueMap<String, String> map = new LinkedMultiValueMap<>();
            map.add("client_id", conf.getRepositoryClientId());
            map.add("client_secret", conf.getRepositoryClientSecret());
            map.add("grant_type", "authorization_code");
            map.add("code", code);
            map.add("redirect_uri", conf.getRedirectUri());
            HttpEntity<MultiValueMap<String, String>> request = new HttpEntity<>(map, headers);

            try {
                Map<String, Object> values = restTemplate.postForObject(conf.getRepositoryAccessTokenUrl(), request, Map.class);
                //ZenodoResponseToken zenodoResponseToken = new ZenodoResponseToken();
                Map<String, Object> user = (Map<String, Object>) values.get("user");
                //            zenodoResponseToken.setUserId((String) user.get("id"));
                //            zenodoResponseToken.setEmail((String) user.get("email"));
                //            zenodoResponseToken.setExpiresIn((Integer) values.get("expires_in"));
                //            zenodoResponseToken.setAccessToken((String) values.get("access_token"));
                //            zenodoResponseToken.setRefreshToken((String) values.get("refresh_token"));

                //return zenodoResponseToken;
                return (String) values.get("access_token");
            } catch (HttpClientErrorException ex) {
                logger.error(ex.getResponseBodyAsString(), ex);
            }

            return null;

        }

        return null;
    }

    @Override
    public String getLogo(String repositoryId) {
        RepositoryDepositConfiguration conf = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
        if(conf != null) {
            if(conf.isHasLogo()){
                byte[] logo = this.configLoader.getLogo(repositoryId);
                return (logo != null && logo.length != 0) ? Base64.getEncoder().encodeToString(logo) : null;
            }
        }
        return null;
    }

    private String getUnpublishedDOI(String zenodoUrl, String DOI, String token, Integer version) {
        try {
            RestTemplate restTemplate = new RestTemplate();
            HttpHeaders headers = new HttpHeaders();
            headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
            headers.setContentType(MediaType.APPLICATION_JSON);
            Map createResponse = null;
            LinkedHashMap<String, String> links = null;
            LinkedHashMap<String, String> metadata = null;
            String listUrl = zenodoUrl + "deposit/depositions" + "?q=conceptdoi:\"" + DOI + "\"&access_token=" + token;
            ResponseEntity<Map[]> listResponses = restTemplate.getForEntity(listUrl, Map[].class);
            createResponse = listResponses.getBody()[0];
            metadata = (LinkedHashMap<String, String>) createResponse.get("metadata");
            links = (LinkedHashMap<String, String>) createResponse.get("links");

            if (metadata.get("version").equals(version.toString())) {
                return links.get("publish");
            } else {
                return null;
            }
        }catch (Exception e) {
            logger.warn(e.getMessage(), e);
            return null;
        }
    }
}