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dmps are deposited in dataverse as datasets under a parent predefined dataverse collenction 

when a new dmp version is created and deposited, the corresponding dataset in dataverse/collection in zenodo create a new version too
deposit dmps as published not drafts
This commit is contained in:
Bernaldo Mihasi 2022-11-22 09:40:05 +02:00
parent 6c13d3b68f
commit 5e2639848b
22 changed files with 593 additions and 128 deletions
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28
dmp-backend/dataverseRepository/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.7.4</version>
<version>2.5.2</version>
<relativePath/>
</parent>
<groupId>eu.eudat.depositinterface</groupId>
@ -43,4 +43,30 @@
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<mainClass>eu.eudat.EuDatApplication</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>
</plugins>
</build>
</project>

5
dmp-backend/dataverseRepository/src/main/java/eu/eudat/depositinterface/dataverserepository/config/ConfigLoader.java Normal file
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@ -0,0 +1,5 @@
package eu.eudat.depositinterface.dataverserepository.config;
public interface ConfigLoader {
DataverseConfig getDataverseConfig();
}

45
dmp-backend/dataverseRepository/src/main/java/eu/eudat/depositinterface/dataverserepository/config/ConfigLoaderImpl.java Normal file
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@ -0,0 +1,45 @@
package eu.eudat.depositinterface.dataverserepository.config;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@Service("dataverseConfigLoader")
public class ConfigLoaderImpl implements ConfigLoader{
private static final Logger logger = LoggerFactory.getLogger(ConfigLoaderImpl.class);
private static final ObjectMapper mapper = new ObjectMapper();
private DataverseConfig dataverseConfig;
@Autowired
private Environment environment;
@Override
public DataverseConfig getDataverseConfig() {
if(dataverseConfig == null){
try{
dataverseConfig = mapper.readValue(getStreamFromPath(environment.getProperty("configuration.dataverse")), DataverseConfig.class);
} catch (IOException e) {
logger.error(e.getLocalizedMessage(), e);
}
}
return dataverseConfig;
}
private InputStream getStreamFromPath(String filePath) {
try {
return new FileInputStream(filePath);
} catch (FileNotFoundException e) {
logger.info("loading from classpath");
return getClass().getClassLoader().getResourceAsStream(filePath);
}
}
}

88
dmp-backend/dataverseRepository/src/main/java/eu/eudat/depositinterface/dataverserepository/config/DataverseConfig.java Normal file
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@ -0,0 +1,88 @@
package eu.eudat.depositinterface.dataverserepository.config;
import com.fasterxml.jackson.annotation.JsonProperty;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
public class DataverseConfig {
private enum DepositType {
SystemDeposit(0), UserDeposit(1), BothWaysDeposit(2);
private final int value;
DepositType(int value) {
this.value = value;
}
public int getValue() {
return value;
}
public static DepositType fromInteger(int value) {
switch (value) {
case 0:
return SystemDeposit;
case 1:
return UserDeposit;
case 2:
return BothWaysDeposit;
default:
throw new RuntimeException("Unsupported Deposit Type");
}
}
}
@JsonProperty("depositType")
private int depositType;
@JsonProperty("repositoryId")
private String repositoryId;
@JsonProperty("apiToken")
private String apiToken;
@JsonProperty("repositoryUrl")
private String repositoryUrl;
@JsonProperty("repositoryRecordUrl")
private String repositoryRecordUrl;
public int getDepositType() {
return depositType;
}
public void setDepositType(int depositType) {
this.depositType = depositType;
}
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public String getApiToken() {
return apiToken;
}
public void setApiToken(String apiToken) {
this.apiToken = apiToken;
}
public String getRepositoryUrl() {
return repositoryUrl;
}
public void setRepositoryUrl(String repositoryUrl) {
this.repositoryUrl = repositoryUrl;
}
public String getRepositoryRecordUrl() {
return repositoryRecordUrl;
}
public void setRepositoryRecordUrl(String repositoryRecordUrl) {
this.repositoryRecordUrl = repositoryRecordUrl;
}
public RepositoryDepositConfiguration toRepoConfig() {
RepositoryDepositConfiguration config = new RepositoryDepositConfiguration();
config.setDepositType(this.depositType);
config.setRepositoryId(this.repositoryId);
config.setRepositoryUrl(this.repositoryUrl);
config.setRepositoryRecordUrl(this.repositoryRecordUrl);
return config;
}
}

74
dmp-backend/dataverseRepository/src/main/java/eu/eudat/depositinterface/dataverserepository/interfaces/DataverseDeposit.java
View File

@ -9,6 +9,7 @@ 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.dataverserepository.config.ConfigLoader;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
@ -29,13 +30,11 @@ 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.*;
import java.util.stream.Collectors;
import static eu.eudat.depositinterface.repository.RepositoryDepositConfiguration.DepositAccountStatus.SystemDeposit;
import static com.researchspace.dataverse.entities.Version.MAJOR;
import static com.researchspace.dataverse.entities.Version.MINOR;
@Component
public class DataverseDeposit implements RepositoryDeposit {
@ -50,10 +49,12 @@ public class DataverseDeposit implements RepositoryDeposit {
private DataverseAPI api;
private boolean isApiSet;
private ConfigLoader configLoader;
private Environment environment;
@Autowired
public DataverseDeposit(Environment environment){
public DataverseDeposit(ConfigLoader configLoader, Environment environment){
this.configLoader = configLoader;
this.environment = environment;
this.isApiSet = false;
}
@ -73,18 +74,7 @@ public class DataverseDeposit implements RepositoryDeposit {
if(!this.isApiSet)
this.setDataverseApi();
String alias = dmpDepositModel.getLabel().replace(" ", "_");
DataverseGet dataverse = this.api.getDataverseOperations().getDataverseById(alias);
if(dataverse == null) {
DataversePost entity = new DataversePost();
entity.setName(dmpDepositModel.getLabel());
entity.setAlias(alias);
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);
}
String doi;
DatasetFacade dataset = DatasetFacade.builder()
.title(dmpDepositModel.getLabel())
.authors(dmpDepositModel.getUsers().stream().map(x -> DatasetAuthor.builder().authorName(x.getUser().getName()).build()).collect(Collectors.toList()))
@ -94,10 +84,34 @@ public class DataverseDeposit implements RepositoryDeposit {
.languages(new ArrayList<>())
.depositor("")
.build();
Identifier id = this.api.getDataverseOperations().createDataset(dataset, alias);
String doi = this.api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);
if(dmpDepositModel.getPreviousDOI() == null || dmpDepositModel.getPreviousDOI().isEmpty()){
Identifier id = this.api.getDataverseOperations().createDataset(dataset, SYSTEM_PARENT_DATAVERSE_ALIAS);
doi = this.api.getDatasetOperations().getDataset(id).getDoiId().orElse(null);
this.uploadFiles(dmpDepositModel, doi);
this.api.getDatasetOperations().publishDataset(id, MAJOR);
}
else{
Map<String, Object> datasetJson = this.getDatasetIdentifier(dmpDepositModel.getPreviousDOI());
Identifier id = new Identifier();
id.setId(((Integer) datasetJson.get("id")).longValue());
this.uploadFiles(dmpDepositModel, dmpDepositModel.getPreviousDOI());
this.api.getDatasetOperations().updateDataset(dataset, id);
DataverseResponse<PublishedDataset> publishedDataset = this.api.getDatasetOperations().publishDataset(id, MAJOR);
doi = publishedDataset.getData().getAuthority() + "/" + publishedDataset.getData().getIdentifier();
}
return doi;
}
private void uploadFiles(DMPDepositModel dmpDepositModel, String doi) throws IOException {
this.uploadFile(dmpDepositModel.getPdfFileName(), dmpDepositModel.getPdfFile(), doi);
String contentDisposition = dmpDepositModel.getRdaJson().getHeaders().get("Content-Disposition").get(0);
@ -113,9 +127,14 @@ public class DataverseDeposit implements RepositoryDeposit {
}
this.uploadFile(jsonFileName, rdaJson, doi);
Files.deleteIfExists(rdaJson.toPath());
}
return doi;
private Map<String, Object> getDatasetIdentifier(String previousDOI) {
HttpHeaders headers = new HttpHeaders();
headers.set("X-Dataverse-key", API_TOKEN);
String serverUrl = SERVER + "/api/datasets/:persistentId?persistentId=doi:" + previousDOI;
RestTemplate restTemplate = new RestTemplate();
return (Map<String, Object>) restTemplate.exchange(serverUrl, HttpMethod.GET, new HttpEntity<>(headers), Map.class).getBody().get("data");
}
private void uploadFile(String filename, File file, String doi) throws IOException {
@ -132,7 +151,7 @@ public class DataverseDeposit implements RepositoryDeposit {
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\"}");
body.add("jsonData", "{\"restrict\":\"false\", \"tabIngest\":\"false\"}");
HttpEntity<MultiValueMap<String, Object>> requestEntity
= new HttpEntity<>(body, headers);
@ -144,13 +163,8 @@ public class DataverseDeposit implements RepositoryDeposit {
@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 + "/dataset.xhtml?persistentId=doi:");
return conf;
eu.eudat.depositinterface.dataverserepository.config.DataverseConfig dataverseConfig = this.configLoader.getDataverseConfig();
return dataverseConfig.toRepoConfig();
}
@Override

1
dmp-backend/dataverseRepository/src/main/resources/application.properties
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@ -1 +1,2 @@
storage.temp=
configuration.dataverse=dataverse.json

7
dmp-backend/dataverseRepository/src/main/resources/dataverse.json Normal file
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@ -0,0 +1,7 @@
{
"depositType": 0,
"repositoryId": "Dataverse",
"apiToken": "",
"repositoryUrl": "",
"repositoryRecordUrl": ""
}

58
dmp-backend/depositinterface/src/main/java/eu/eudat/depositinterface/repository/RepositoryDepositConfiguration.java
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@ -2,12 +2,12 @@ package eu.eudat.depositinterface.repository;
public class RepositoryDepositConfiguration {
public enum DepositAccountStatus {
public enum DepositType {
SystemDeposit(0), UserDeposit(1), BothWaysDeposit(2);
private int value;
DepositAccountStatus(int value) {
DepositType(int value) {
this.value = value;
}
@ -15,7 +15,7 @@ public class RepositoryDepositConfiguration {
return value;
}
public static DepositAccountStatus fromInteger(int value) {
public static DepositType fromInteger(int value) {
switch (value) {
case 0:
return SystemDeposit;
@ -24,27 +24,27 @@ public class RepositoryDepositConfiguration {
case 2:
return BothWaysDeposit;
default:
throw new RuntimeException("Unsupported Deposit Account Status");
throw new RuntimeException("Unsupported Deposit Account Type");
}
}
}
private int depositAccountStatus;
private int depositType;
private String repositoryId;
private String accessToken;
private String repositoryUrl;
private String repositoryAuthorizationUrl;
private String repositoryRecordUrl;
private String repositoryLoginAccessTokenUrl;
private String repositoryLoginClientId;
private String repositoryLoginClientSecret;
private String repositoryLoginRedirectUri;
private String repositoryAccessTokenUrl;
private String repositoryClientId;
private String repositoryClientSecret;
private String redirectUri;
public int getDepositAccountStatus() {
return depositAccountStatus;
public int getDepositType() {
return depositType;
}
public void setDepositAccountStatus(int depositAccountStatus) {
this.depositAccountStatus = depositAccountStatus;
public void setDepositType(int depositType) {
this.depositType = depositType;
}
public String getRepositoryId() {
@ -82,31 +82,31 @@ public class RepositoryDepositConfiguration {
this.repositoryRecordUrl = repositoryRecordUrl;
}
public String getRepositoryLoginAccessTokenUrl() {
return repositoryLoginAccessTokenUrl;
public String getRepositoryAccessTokenUrl() {
return repositoryAccessTokenUrl;
}
public void setRepositoryLoginAccessTokenUrl(String repositoryLoginAccessTokenUrl) {
this.repositoryLoginAccessTokenUrl = repositoryLoginAccessTokenUrl;
public void setRepositoryAccessTokenUrl(String repositoryAccessTokenUrl) {
this.repositoryAccessTokenUrl = repositoryAccessTokenUrl;
}
public String getRepositoryLoginClientId() {
return repositoryLoginClientId;
public String getRepositoryClientId() {
return repositoryClientId;
}
public void setRepositoryLoginClientId(String repositoryLoginClientId) {
this.repositoryLoginClientId = repositoryLoginClientId;
public void setRepositoryClientId(String repositoryClientId) {
this.repositoryClientId = repositoryClientId;
}
public String getRepositoryLoginClientSecret() {
return repositoryLoginClientSecret;
public String getRepositoryClientSecret() {
return repositoryClientSecret;
}
public void setRepositoryLoginClientSecret(String repositoryLoginClientSecret) {
this.repositoryLoginClientSecret = repositoryLoginClientSecret;
public void setRepositoryClientSecret(String repositoryClientSecret) {
this.repositoryClientSecret = repositoryClientSecret;
}
public String getRepositoryLoginRedirectUri() {
return repositoryLoginRedirectUri;
public String getRedirectUri() {
return redirectUri;
}
public void setRepositoryLoginRedirectUri(String repositoryLoginRedirectUri) {
this.repositoryLoginRedirectUri = repositoryLoginRedirectUri;
public void setRedirectUri(String redirectUri) {
this.redirectUri = redirectUri;
}
}

27
dmp-backend/web/pom.xml
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@ -222,14 +222,37 @@
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<layout>ZIP</layout>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>eu.eudat.EuDatApplication</mainClass>
<classpathPrefix>dependency-jars/</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.5.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>repackage</goal>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>
${project.build.directory}/dependency-jars/
</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>

8
dmp-backend/web/src/main/java/eu/eudat/controllers/DepositController.java
View File

@ -1,12 +1,12 @@
package eu.eudat.controllers;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import eu.eudat.logic.managers.DepositManager;
import eu.eudat.logic.security.claims.ClaimedAuthorities;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.doi.DepositCode;
import eu.eudat.models.data.doi.DepositRequest;
import eu.eudat.models.data.doi.Doi;
import eu.eudat.models.data.doi.RepositoryConfig;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
@ -36,9 +36,9 @@ public class DepositController extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"/repos"})
public @ResponseBody
ResponseEntity<ResponseItem<List<RepositoryDepositConfiguration>>> getAvailableRepos(@ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) {
List<RepositoryDepositConfiguration> ids = this.depositManager.getAvailableRepos();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<RepositoryDepositConfiguration>>().status(ApiMessageCode.NO_MESSAGE).payload(ids));
ResponseEntity<ResponseItem<List<RepositoryConfig>>> getAvailableRepos(@ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) {
List<RepositoryConfig> ids = this.depositManager.getAvailableRepos();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<RepositoryConfig>>().status(ApiMessageCode.NO_MESSAGE).payload(ids));
}
@RequestMapping(method = RequestMethod.POST, value = {"/getAccessToken"})

46
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java
View File

@ -1062,9 +1062,9 @@ public class DataManagementPlanManager {
});
UserInfo user = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
sendNotification(dmp, user, NotificationType.DMP_PUBLISH);
if (dmp.getDoi() != null && !dmp.getDoi().isEmpty()) {
this.createZenodoDoi(dmp.getId(), principal, true);
}
// if (dmp.getDois() != null && !dmp.getDois().isEmpty()) {
// this.createZenodoDoi(dmp.getId(), principal, true);
// }
}
@Transactional
@ -2011,23 +2011,28 @@ public class DataManagementPlanManager {
* DOI Generation
* */
private String getPreviousDOI(UUID groupId, UUID selfId) {
private String getPreviousDOI(UUID groupId, UUID selfId, String repositoryId) {
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
List<UUID> groupIds = new ArrayList<>();
groupIds.add(groupId);
criteria.setGroupIds(groupIds);
criteria.setAllVersions(true);
List<DMP> dmps = this.databaseRepository.getDmpDao().getWithCriteria(criteria).toList();
String doi = null;
dmps.sort((DMP d1, DMP d2) -> d2.getVersion() - d1.getVersion());
for (DMP dmp: dmps) {
if (!dmp.getId().equals(selfId)) {
if (dmp.getDoi() != null && !dmp.getDoi().isEmpty()) {
doi = dmp.getDoi();
if (dmp.getDois() != null && !dmp.getDois().isEmpty()) {
for (Iterator<EntityDoi> it = dmp.getDois().iterator(); it.hasNext(); ) {
EntityDoi entityDoi = it.next();
if(entityDoi.getRepositoryId().equals(repositoryId)){
return entityDoi.getDoi();
}
}
}
}
}
return doi;
return null;
}
private String getUnpublishedDOI(String DOI, String token, Integer version) {
@ -2079,7 +2084,7 @@ public class DataManagementPlanManager {
} catch (Exception e) {
throw e;
}
String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId());
String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId(), "Zenodo");
DMPDepositModel dmpDepositModel = DMPToDepositMapper.fromDMP(dmp, pdfFile, fileName, jsonFile, previousDOI);
@ -2094,10 +2099,23 @@ public class DataManagementPlanManager {
String finalDoi = null;
for(RepositoryDeposit repo: this.repositoriesDeposit) { //temp
finalDoi = repo.deposit(dmpDepositModel, update, zenodoToken);
if (finalDoi != null) {
dmp.setDoi(finalDoi);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
if(repo.getConfiguration().getRepositoryId().equals("Zenodo")) {
finalDoi = repo.deposit(dmpDepositModel, update, zenodoToken);
if (finalDoi != null) {
EntityDoi doiEntity = new EntityDoi();
doiEntity.setId(UUID.randomUUID());
doiEntity.setEntityType(EntityDoi.EntityType.DMP);
doiEntity.setDoi(finalDoi);
doiEntity.setRepositoryId("Zenodo");
Date now = new Date();
doiEntity.setCreatedAt(now);
doiEntity.setUpdatedAt(now);
doiEntity.setEntityId(dmp);
apiContext.getOperationsContext().getDatabaseRepository().getEntityDoiDao().createOrUpdate(doiEntity);
dmp.getDois().add(doiEntity);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
}
}
}
Files.deleteIfExists(file.getFile().toPath());
@ -2124,7 +2142,7 @@ public class DataManagementPlanManager {
} catch (Exception e) {
throw e;
}
String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId());
String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId(), depositRequest.getRepositoryId());
DMPDepositModel dmpDepositModel = DMPToDepositMapper.fromDMP(dmp, pdfFile, fileName, jsonFile, previousDOI);

10
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DepositManager.java
View File

@ -10,6 +10,7 @@ import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
import eu.eudat.logic.utilities.documents.pdf.PDFUtils;
import eu.eudat.models.data.doi.DepositRequest;
import eu.eudat.models.data.doi.Doi;
import eu.eudat.models.data.doi.RepositoryConfig;
import eu.eudat.models.data.security.Principal;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -36,12 +37,13 @@ public class DepositManager {
this.dataManagementPlanManager = dataManagementPlanManager;
}
public List<RepositoryDepositConfiguration> getAvailableRepos() {
List<RepositoryDepositConfiguration> repos = new ArrayList<>();
public List<RepositoryConfig> getAvailableRepos() {
List<RepositoryConfig> reposConfigModel = new ArrayList<>();
for (RepositoryDeposit r: this.repositories) {
repos.add(r.getConfiguration());
RepositoryConfig repoModel = new RepositoryConfig();
reposConfigModel.add(repoModel.toModel(r.getConfiguration()));
}
return repos;
return reposConfigModel;
}
public String authenticate(String id, String code) {

65
dmp-backend/web/src/main/java/eu/eudat/models/data/doi/RepositoryConfig.java Normal file
View File

@ -0,0 +1,65 @@
package eu.eudat.models.data.doi;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
public class RepositoryConfig {
private int depositType;
private String repositoryId;
private String repositoryAuthorizationUrl;
private String repositoryRecordUrl;
private String repositoryClientId;
private String redirectUri;
public int getDepositType() {
return depositType;
}
public void setDepositType(int depositType) {
this.depositType = depositType;
}
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public String getRepositoryAuthorizationUrl() {
return repositoryAuthorizationUrl;
}
public void setRepositoryAuthorizationUrl(String repositoryAuthorizationUrl) {
this.repositoryAuthorizationUrl = repositoryAuthorizationUrl;
}
public String getRepositoryRecordUrl() {
return repositoryRecordUrl;
}
public void setRepositoryRecordUrl(String repositoryRecordUrl) {
this.repositoryRecordUrl = repositoryRecordUrl;
}
public String getRepositoryClientId() {
return repositoryClientId;
}
public void setRepositoryClientId(String repositoryClientId) {
this.repositoryClientId = repositoryClientId;
}
public String getRedirectUri() {
return redirectUri;
}
public void setRedirectUri(String redirectUri) {
this.redirectUri = redirectUri;
}
public RepositoryConfig toModel(RepositoryDepositConfiguration r){
this.setDepositType(r.getDepositType());
this.setRepositoryId(r.getRepositoryId());
this.setRepositoryAuthorizationUrl(r.getRepositoryAuthorizationUrl());
this.setRepositoryRecordUrl(r.getRepositoryRecordUrl());
this.setRepositoryClientId(r.getRepositoryClientId());
this.setRedirectUri(r.getRedirectUri());
return this;
}
}

2
dmp-backend/zenodoRepository/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>2.7.4</version>
<version>2.5.2</version>
<relativePath/>
</parent>
<groupId>eu.eudat.depositinterface</groupId>

1
dmp-backend/zenodoRepository/src/main/java/eu/eudat/depositinterface/zenodorepository/config/ConfigLoader.java
View File

@ -4,4 +4,5 @@ import java.util.List;
public interface ConfigLoader {
List<DOIFunder> getDOIFunders();
ZenodoConfig getZenodoConfig();
}

18
dmp-backend/zenodoRepository/src/main/java/eu/eudat/depositinterface/zenodorepository/config/ConfigLoaderImpl.java
View File

@ -7,10 +7,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@ -22,6 +19,7 @@ public class ConfigLoaderImpl implements ConfigLoader{
private static final ObjectMapper mapper = new ObjectMapper();
private List<DOIFunder> doiFunders = new ArrayList<>();
private ZenodoConfig zenodoConfig;
@Autowired
private Environment environment;
@ -39,6 +37,18 @@ public class ConfigLoaderImpl implements ConfigLoader{
return doiFunders;
}
@Override
public ZenodoConfig getZenodoConfig() {
if (zenodoConfig == null) {
try {
zenodoConfig = mapper.readValue(getStreamFromPath("zenodo.json"), ZenodoConfig.class);
} catch (IOException e) {
logger.error(e.getLocalizedMessage(), e);
}
}
return zenodoConfig;
}
private InputStream getStreamFromPath(String filePath) {
try {
return new FileInputStream(filePath);

140
dmp-backend/zenodoRepository/src/main/java/eu/eudat/depositinterface/zenodorepository/config/ZenodoConfig.java Normal file
View File

@ -0,0 +1,140 @@
package eu.eudat.depositinterface.zenodorepository.config;
import com.fasterxml.jackson.annotation.JsonProperty;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
public class ZenodoConfig {
private enum DepositType {
SystemDeposit(0), UserDeposit(1), BothWaysDeposit(2);
private final int value;
DepositType(int value) {
this.value = value;
}
public int getValue() {
return value;
}
public static DepositType fromInteger(int value) {
switch (value) {
case 0:
return SystemDeposit;
case 1:
return UserDeposit;
case 2:
return BothWaysDeposit;
default:
throw new RuntimeException("Unsupported Deposit Type");
}
}
}
@JsonProperty("depositType")
private int depositType;
@JsonProperty("repositoryId")
private String repositoryId;
@JsonProperty("accessToken")
private String accessToken;
@JsonProperty("repositoryUrl")
private String repositoryUrl;
@JsonProperty("repositoryAuthorizationUrl")
private String repositoryAuthorizationUrl;
@JsonProperty("repositoryRecordUrl")
private String repositoryRecordUrl;
@JsonProperty("repositoryAccessTokenUrl")
private String repositoryAccessTokenUrl;
@JsonProperty("repositoryClientId")
private String repositoryClientId;
@JsonProperty("repositoryClientSecret")
private String repositoryClientSecret;
@JsonProperty("redirectUri")
private String redirectUri;
public int getDepositType() {
return depositType;
}
public void setDepositType(int depositType) {
this.depositType = depositType;
}
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public String getAccessToken() {
return accessToken;
}
public void setAccessToken(String accessToken) {
this.accessToken = accessToken;
}
public String getRepositoryUrl() {
return repositoryUrl;
}
public void setRepositoryUrl(String repositoryUrl) {
this.repositoryUrl = repositoryUrl;
}
public String getRepositoryAuthorizationUrl() {
return repositoryAuthorizationUrl;
}
public void setRepositoryAuthorizationUrl(String repositoryAuthorizationUrl) {
this.repositoryAuthorizationUrl = repositoryAuthorizationUrl;
}
public String getRepositoryRecordUrl() {
return repositoryRecordUrl;
}
public void setRepositoryRecordUrl(String repositoryRecordUrl) {
this.repositoryRecordUrl = repositoryRecordUrl;
}
public String getRepositoryAccessTokenUrl() {
return repositoryAccessTokenUrl;
}
public void setRepositoryAccessTokenUrl(String repositoryAccessTokenUrl) {
this.repositoryAccessTokenUrl = repositoryAccessTokenUrl;
}
public String getRepositoryClientId() {
return repositoryClientId;
}
public void setRepositoryClientId(String repositoryClientId) {
this.repositoryClientId = repositoryClientId;
}
public String getRepositoryClientSecret() {
return repositoryClientSecret;
}
public void setRepositoryClientSecret(String repositoryClientSecret) {
this.repositoryClientSecret = repositoryClientSecret;
}
public String getRedirectUri() {
return redirectUri;
}
public void setRedirectUri(String redirectUri) {
this.redirectUri = redirectUri;
}
public RepositoryDepositConfiguration toRepoConfig() {
RepositoryDepositConfiguration config = new RepositoryDepositConfiguration();
config.setDepositType(this.depositType);
config.setRepositoryId(this.repositoryId);
config.setAccessToken(this.accessToken);
config.setRepositoryUrl(this.repositoryUrl);
config.setRepositoryAuthorizationUrl(this.repositoryAuthorizationUrl);
config.setRepositoryRecordUrl(this.repositoryRecordUrl);
config.setRepositoryAccessTokenUrl(this.repositoryAccessTokenUrl);
config.setRepositoryClientId(this.repositoryClientId);
config.setRepositoryClientSecret(this.repositoryClientSecret);
config.setRedirectUri(this.redirectUri);
return config;
}
}

67
dmp-backend/zenodoRepository/src/main/java/eu/eudat/depositinterface/zenodorepository/interfaces/ZenodoDeposit.java
View File

@ -5,6 +5,7 @@ import eu.eudat.depositinterface.models.DMPDepositModel;
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;
@ -27,8 +28,6 @@ import java.io.IOException;
import java.nio.file.Files;
import java.util.*;
import static eu.eudat.depositinterface.repository.RepositoryDepositConfiguration.DepositAccountStatus.*;
@Component
public class ZenodoDeposit implements RepositoryDeposit {
private static final Logger logger = LoggerFactory.getLogger(ZenodoDeposit.class);
@ -73,7 +72,8 @@ public class ZenodoDeposit implements RepositoryDeposit {
createResponse = restTemplate.postForEntity(createUrl, request, Map.class).getBody();
links = (LinkedHashMap<String, String>) createResponse.get("links");
finalDoi = (String) createResponse.get("conceptdoi");
} else {
}
else {
unpublishedUrl = this.getUnpublishedDOI(zenodoUrl, previousDOI, zenodoToken, dmpDepositModel.getVersion());
if (unpublishedUrl == null) {
//It requires more than one step to create a new version
@ -121,8 +121,7 @@ public class ZenodoDeposit implements RepositoryDeposit {
if (unpublishedUrl == null) {
// Second step, add the file to the entry.
File pdfFile = dmpDepositModel.getPdfFile();
String name = dmpDepositModel.getPdfFileName();
String fileName = name + ".pdf";
String fileName = dmpDepositModel.getPdfFileName();
FileSystemResource fileSystemResource = new FileSystemResource(pdfFile);
HttpEntity<FileSystemResource> addFileMapRequest = new HttpEntity<>(fileSystemResource, null);
@ -148,18 +147,15 @@ public class ZenodoDeposit implements RepositoryDeposit {
// Third post call to Zenodo to publish the entry and return the DOI.
publishUrl = links.get("publish") + "?access_token=" + zenodoToken;
} else {
}
else {
publishUrl = unpublishedUrl + "?access_token=" + zenodoToken;
}
// if (dmp.isPublic()) {
Map<String, Object> publishResponce = restTemplate.postForObject(publishUrl, "", Map.class);
finalDoi = (String) publishResponce.get("conceptdoi");
// }
finalDoi = this.publish(publishUrl);
} else {
Map<String, Object> editResponce = restTemplate.postForObject(links.get("edit") + "?access_token=" + zenodoToken, "", Map.class);
restTemplate.put(links.get("self") + "?access_token=" + zenodoToken, request);
Map<String, Object> publishResponce = restTemplate.postForObject(links.get("publish") + "?access_token=" + zenodoToken, "", Map.class);
finalDoi = (String) publishResponce.get("conceptdoi");
finalDoi = this.publish(links.get("publish") + "?access_token=" + zenodoToken);
}
return finalDoi;
@ -170,20 +166,35 @@ public class ZenodoDeposit implements RepositoryDeposit {
}
private String publish(String publishUrl){
RestTemplate restTemplate = new RestTemplate();
Map<String, Object> publishResponce = restTemplate.postForObject(publishUrl, "", Map.class);
return (String) publishResponce.get("conceptdoi");
}
private void publishIfNot(String zenodoUrl, String doi, String zenodoToken, DMPDepositModel dmpDepositModel){
RestTemplate restTemplate = new RestTemplate();
HttpHeaders headers = new HttpHeaders();
headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
headers.setContentType(MediaType.APPLICATION_JSON);
eu.eudat.depositinterface.zenodorepository.models.ZenodoDeposit deposit = DMPToZenodoMapper.fromDMP(dmpDepositModel, "argos", "ARGOS", "https://argos.openaire.eu/", this.configLoader.getDOIFunders());
HttpEntity<eu.eudat.depositinterface.zenodorepository.models.ZenodoDeposit> request = new HttpEntity<>(deposit, headers);
String listUrl = zenodoUrl + "deposit/depositions" + "?q=conceptdoi:\"" + doi + "\"&access_token=" + zenodoToken;
ResponseEntity<Map[]> listResponses = restTemplate.getForEntity(listUrl, Map[].class);
Map createResponse = listResponses.getBody()[0];
LinkedHashMap<String, String> links = (LinkedHashMap<String, String>) createResponse.get("links");
Map<String, Object> editResponce = restTemplate.postForObject(links.get("edit") + "?access_token=" + zenodoToken, "", Map.class);
restTemplate.put(links.get("self") + "?access_token=" + zenodoToken, request);
this.publish(links.get("publish") + "?access_token=" + zenodoToken);
}
@Override
public RepositoryDepositConfiguration getConfiguration() {
RepositoryDepositConfiguration conf = new RepositoryDepositConfiguration();
conf.setDepositAccountStatus(BothWaysDeposit.getValue());
conf.setRepositoryId("Zenodo");
conf.setAccessToken("pcqw4LGLrhp17FF5GoXNCXakkEi82ThchZw7Tk4qh74VrDE3EmliG3UlhYtd");
conf.setRepositoryUrl("https://sandbox.zenodo.org/api/");
conf.setRepositoryAuthorizationUrl("https://sandbox.zenodo.org/oauth/authorize");
conf.setRepositoryRecordUrl("https://sandbox.zenodo.org/record/");
conf.setRepositoryLoginAccessTokenUrl("https://sandbox.zenodo.org/oauth/token");
conf.setRepositoryLoginClientId("hEmVRNc1OzRmWyi2GDR3XVKbhG3OtfJXLXkkOGXx");
conf.setRepositoryLoginClientSecret("7VSU0NjiAg0P3mv14wemMYy2XhvlmV6F7xoszxPH4ZDx98v8FdMpBbxlncqr");
conf.setRepositoryLoginRedirectUri("http://localhost:4200/login/external/zenodo");
return conf;
ZenodoConfig zenodoConfig = this.configLoader.getZenodoConfig();
return zenodoConfig.toRepoConfig();
}
@Override
@ -197,15 +208,15 @@ public class ZenodoDeposit implements RepositoryDeposit {
headers.setContentType(MediaType.MULTIPART_FORM_DATA);
MultiValueMap<String, String> map = new LinkedMultiValueMap<>();
map.add("client_id", conf.getRepositoryLoginClientId());
map.add("client_secret", conf.getRepositoryLoginClientSecret());
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.getRepositoryLoginRedirectUri());
map.add("redirect_uri", conf.getRedirectUri());
HttpEntity<MultiValueMap<String, String>> request = new HttpEntity<>(map, headers);
try {
Map<String, Object> values = restTemplate.postForObject(conf.getRepositoryLoginAccessTokenUrl(), request, Map.class);
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"));

1
dmp-backend/zenodoRepository/src/main/resources/application.properties
View File

@ -1 +1,2 @@
configuration.doi_funder=DOI_Funder.json
configuration.zenodo=zenodo.json

12
dmp-backend/zenodoRepository/src/main/resources/zenodo.json Normal file
View File

@ -0,0 +1,12 @@
{
"depositType": 2,
"repositoryId": "Zenodo",
"accessToken": "",
"repositoryUrl": "https://sandbox.zenodo.org/api/",
"repositoryAuthorizationUrl": "https://sandbox.zenodo.org/oauth/authorize",
"repositoryRecordUrl": "https://sandbox.zenodo.org/record/",
"repositoryAccessTokenUrl": "https://sandbox.zenodo.org/oauth/token",
"repositoryClientId": "",
"repositoryClientSecret": "",
"redirectUri": "http://localhost:4200/login/external/zenodo"
}

10
dmp-frontend/src/app/core/model/deposit/deposit-configuration.ts
View File

@ -1,14 +1,10 @@
import { DepositConfigurationStatus } from "@app/core/common/enum/deposit-configuration-status";
export class DepositConfigurationModel {
depositAccountStatus: DepositConfigurationStatus;
depositType: DepositConfigurationStatus;
repositoryId: string;
accessToken: string;
repositoryUrl: string;
repositoryAuthorizationUrl: string;
repositoryRecordUrl: string;
repositoryLoginAccessTokenUrl: string;
repositoryLoginClientId: string;
repositoryLoginClientSecret: string;
repositoryLoginRedirectUri: string;
repositoryClientId: string;
redirectUri: string;
}

8
dmp-frontend/src/app/ui/dmp/editor/dmp-deposit-dialog/dmp-deposit-dialog.component.ts
View File

@ -60,7 +60,7 @@ export class DmpDepositDialogComponent extends BaseComponent implements OnInit {
deposit(repo: DepositConfigurationModel) {
if(repo.depositAccountStatus == DepositConfigurationStatus.BothSystemAndUser){
if(repo.depositType == DepositConfigurationStatus.BothSystemAndUser){
const dialogRef = this.dialog.open(MultipleChoiceDialogComponent, {
maxWidth: '600px',
@ -73,9 +73,9 @@ export class DmpDepositDialogComponent extends BaseComponent implements OnInit {
dialogRef.afterClosed().pipe(takeUntil(this._destroyed)).subscribe(result => {
switch (result) {
case 0:
this.showOauth2Dialog(repo.repositoryAuthorizationUrl + '?client_id=' + repo.repositoryLoginClientId
this.showOauth2Dialog(repo.repositoryAuthorizationUrl + '?client_id=' + repo.repositoryClientId
+ '&response_type=code&scope=deposit:write+deposit:actions+user:email&state=astate&redirect_uri='
+ repo.repositoryLoginRedirectUri, repo, this.dmp);
+ repo.redirectUri, repo, this.dmp);
break;
case 1:
this.depositRepositoriesService.createDoi(repo.repositoryId, this.dmp.id, null)
@ -93,7 +93,7 @@ export class DmpDepositDialogComponent extends BaseComponent implements OnInit {
});
}
else if(repo.depositAccountStatus == DepositConfigurationStatus.System){
else if(repo.depositType == DepositConfigurationStatus.System){
this.depositRepositoriesService.createDoi(repo.repositoryId, this.dmp.id, null)
.pipe(takeUntil(this._destroyed))
.subscribe(doi =>{