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Merge branch 'dmp-refactoring' of code-repo.d4science.org:MaDgiK-CITE/argos into dmp-refactoring 

# Conflicts:
#	dmp-backend/web/src/main/java/eu/eudat/controllers/Admin.java
This commit is contained in:
Efstratios Giannopoulos 2023-11-06 17:17:34 +02:00
parent 87e22040c5 e42bdcfc0a
commit 20873ca13e
6 changed files with 103 additions and 75 deletions
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8
dmp-backend/core/src/main/java/eu/eudat/configurations/deposit/DepositProperties.java
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@ -22,14 +22,16 @@ public class DepositProperties {
public static class DepositSource {
private final String url;
private final List<String> codes;
private final String issuerUrl;
private final String clientId;
private final String clientSecret;
private final String scope;
@ConstructorBinding
public DepositSource(String url, String issuerUrl, String clientId, String clientSecret, String scope) {
public DepositSource(String url, List<String> codes, String issuerUrl, String clientId, String clientSecret, String scope) {
this.url = url;
this.codes = codes;
this.issuerUrl = issuerUrl;
this.clientId = clientId;
this.clientSecret = clientSecret;
@ -55,5 +57,9 @@ public class DepositProperties {
public String getScope() {
return scope;
}
public List<String> getCodes() {
return codes;
}
}
}

17
dmp-backend/core/src/main/java/eu/eudat/query/EntityDoiQuery.java
View File

@ -34,6 +34,8 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
private Collection<String> dois;
private Collection<UUID> entityIds;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
public EntityDoiQuery ids(UUID value) {
@ -111,6 +113,21 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
return this;
}
public EntityDoiQuery entityIds(Collection<UUID> values) {
this.entityIds = values;
return this;
}
public EntityDoiQuery entityIds(UUID value) {
this.entityIds = List.of(value);
return this;
}
public EntityDoiQuery entityIds(UUID... value) {
this.entityIds = Arrays.asList(value);
return this;
}
public EntityDoiQuery authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;

6
dmp-backend/core/src/main/java/eu/eudat/repository/DepositRepository.java
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@ -12,11 +12,9 @@ import java.util.List;
public class DepositRepository implements RepositoryDeposit {
private final WebClient depositClient;
private final List<String> configurationIds;
public DepositRepository(WebClient depositClient) {
this.depositClient = depositClient;
this.configurationIds = new ArrayList<>();
}
@ -39,8 +37,4 @@ public class DepositRepository implements RepositoryDeposit {
public String getLogo(String repositoryId) {
return depositClient.get().uri("/logo/" + repositoryId).exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
public List<String> getConfigurationIds() {
return configurationIds;
}
}

126
dmp-backend/core/src/main/java/eu/eudat/service/deposit/RepositoryDepositService.java
View File

@ -2,76 +2,94 @@ package eu.eudat.service.deposit;
import eu.eudat.authorization.Permission;
import eu.eudat.cache.deposit.RepositoryDepositConfigurationCache;
import eu.eudat.commons.enums.EntityType;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.configurations.deposit.DepositProperties;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.DmpEntity;
import eu.eudat.data.EntityDoiEntity;
import eu.eudat.data.old.DMP;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.models.FileEnvelope;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.doi.DepositRequest;
import eu.eudat.model.doi.Doi;
import eu.eudat.model.doi.RepositoryConfig;
import eu.eudat.model.doi.RepositoryConfigs;
import eu.eudat.model.mapper.deposit.DmpEntityDepositMapper;
import eu.eudat.model.persist.EntityDoiPersist;
import eu.eudat.query.DmpQuery;
import eu.eudat.query.EntityDoiQuery;
import eu.eudat.repository.DepositRepository;
import eu.eudat.service.entitydoi.EntityDoiService;
import eu.eudat.utilities.pdf.PDFUtils;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.commons.web.oidc.apikey.ApiKeyCacheService;
import gr.cite.commons.web.oidc.apikey.webflux.ApiKeyExchangeFilterFunction;
import gr.cite.commons.web.oidc.apikey.webflux.ApiKeyWebfluxModel;
import gr.cite.tools.data.query.Ordering;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.fieldset.FieldSet;
import jakarta.persistence.EntityManager;
import jakarta.persistence.NoResultException;
import jakarta.persistence.criteria.CriteriaBuilder;
import jakarta.persistence.criteria.CriteriaQuery;
import jakarta.persistence.criteria.Join;
import jakarta.persistence.criteria.Root;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.ApplicationContext;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
import org.springframework.util.ResourceUtils;
import org.springframework.web.reactive.function.client.WebClient;
import javax.management.InvalidApplicationException;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.time.Instant;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import java.util.*;
@Service
public class RepositoryDepositService {
private static final Logger logger = LoggerFactory.getLogger(RepositoryDepositService.class);
private final DepositProperties depositProperties;
private final List<DepositRepository> clients;
private final Map<String, DepositRepository> clients;
private final ApiKeyCacheService apiKeyCacheService;
private final RepositoryDepositConfigurationCache repositoryDepositConfigurationCache;
private final EntityManager entityManager;
private final AuthorizationService authorizationService;
private final ConventionService conventionService;
private final Environment environment;
private final DmpEntityDepositMapper depositMapper;
private final WebClient.Builder webClientBuilder;
private final EntityDoiService doiService;
private final ApplicationContext applicationContext;
@Autowired
public RepositoryDepositService(DepositProperties depositProperties, ApiKeyCacheService apiKeyCacheService, RepositoryDepositConfigurationCache repositoryDepositConfigurationCache, WebClient.Builder builder, EntityManager entityManager, AuthorizationService authorizationService, ConventionService conventionService, Environment environment, DmpEntityDepositMapper depositMapper) {
public RepositoryDepositService(DepositProperties depositProperties, ApiKeyCacheService apiKeyCacheService, RepositoryDepositConfigurationCache repositoryDepositConfigurationCache, WebClient.Builder builder, EntityManager entityManager, AuthorizationService authorizationService, ConventionService conventionService, Environment environment, DmpEntityDepositMapper depositMapper, DmpQuery dmpQuery, EntityDoiQuery doiQuery, EntityDoiService doiService, ApplicationContext applicationContext) {
this.depositProperties = depositProperties;
this.apiKeyCacheService = apiKeyCacheService;
this.repositoryDepositConfigurationCache = repositoryDepositConfigurationCache;
this.clients = depositRepositories(builder);
this.entityManager = entityManager;
this.authorizationService = authorizationService;
this.conventionService = conventionService;
this.environment = environment;
this.depositMapper = depositMapper;
//GK: I don't like this but that way you can both cache the available configurations and set Configuration Ids for each client
getAvailableConfigurations();
this.webClientBuilder = builder;
this.doiService = doiService;
this.applicationContext = applicationContext;
this.clients = new HashMap<>();
}
private DepositRepository getRepository(String repoId) {
if (this.clients.containsKey(repoId)) return this.clients.get(repoId);
//GK: It's register time
DepositProperties.DepositSource source = depositProperties.getSources().stream().filter(depositSource -> depositSource.getCodes().contains(repoId)).findFirst().orElse(null);
if (source != null) {
String host = URI.create(source.getUrl()).getHost();
ApiKeyWebfluxModel apiKeyWebfluxModel = new ApiKeyWebfluxModel(host + "_" + source.getClientId(), source.getIssuerUrl(), source.getClientId(), source.getClientSecret(), source.getScope());
ApiKeyExchangeFilterFunction apiKeyExchangeFilterFunction = new ApiKeyExchangeFilterFunction(this.apiKeyCacheService, apiKeyWebfluxModel);
DepositRepository repository = new DepositRepository(webClientBuilder.baseUrl(source.getUrl() + "/api/deposit").filters(exchangeFilterFunctions -> exchangeFilterFunctions.add(apiKeyExchangeFilterFunction)).build());
source.getCodes().forEach(code -> this.clients.put(code, repository));
return repository;
}
return null;
}
@ -79,11 +97,12 @@ public class RepositoryDepositService {
RepositoryConfigs configs = repositoryDepositConfigurationCache.lookup("base");
if (configs == null) {
List<RepositoryConfig> configurations = new ArrayList<>();
//GK: So much for lazy loading
List<DepositRepository> repositories = depositProperties.getSources().stream().map(depositSource -> getRepository(depositSource.getCodes().get(0))).toList();
clients.forEach((client) -> {
repositories.forEach((client) -> {
List<RepositoryDepositConfiguration> repositoryConfigs = client.getConfiguration();
if (repositoryConfigs != null && !repositoryConfigs.isEmpty()) {
client.getConfigurationIds().addAll(repositoryConfigs.stream().map(RepositoryDepositConfiguration::getRepositoryId).toList());
configurations.addAll(repositoryConfigs.stream().map(RepositoryConfig::toModel).toList());
}
});
@ -95,14 +114,15 @@ public class RepositoryDepositService {
return configs.getRepositoryConfigs();
}
public Doi deposit(DepositRequest dmpDepositModel) {
public EntityDoi deposit(DepositRequest dmpDepositModel) throws InvalidApplicationException {
this.authorizationService.authorize(Permission.EditDmp);
//GK: Why it is in that service, and why it's not static?
this.conventionService.isValidGuid(UUID.fromString(dmpDepositModel.getDmpId()));
//GK: First get the right client
DepositRepository repository = clients.stream().filter(client -> client.getConfigurationIds().contains(dmpDepositModel.getRepositoryId())).findFirst().orElseThrow();
DepositRepository repository = getRepository(dmpDepositModel.getRepositoryId());
//GK: Second get the Target Data Management Plan
DmpEntity dmpEntity = this.entityManager.find(DmpEntity.class, UUID.fromString(dmpDepositModel.getDmpId()));
DmpQuery dmpQuery = applicationContext.getBean(DmpQuery.class);
DmpEntity dmpEntity = dmpQuery.ids(UUID.fromString(dmpDepositModel.getDmpId())).first();
//GK: Third get the DOI from the previous Data Management Plan (if it exists)
String previousDOI = null;
@ -117,7 +137,7 @@ public class RepositoryDepositService {
FileEnvelope jsonEnvelope = new FileEnvelope();
File zip = new File(environment.getProperty("temp.temp") + UUID.randomUUID() + ".zip");
try {
File documentFile = ResourceUtils.getFile(this.environment.getProperty("coniguration.h2020template"));
File documentFile = ResourceUtils.getFile(this.environment.getProperty("configuration.h2020template"));
docEnvelope.setFilename("test.docx");
docEnvelope.setFile(documentFile);
File pdfFile = PDFUtils.convertToPDF(docEnvelope, environment);
@ -145,52 +165,38 @@ public class RepositoryDepositService {
if (doi.isEmpty())
return null;
//GK: doi is fine store it in database
EntityDoiEntity doiEntity = new EntityDoiEntity();
doiEntity.setId(UUID.randomUUID());
doiEntity.setDoi(doi);
doiEntity.setEntityType(EntityType.DMP);
DMP dmp = new DMP();
dmp.setId(dmpEntity.getId());
doiEntity.setEntityId(dmp);
doiEntity.setCreatedAt(Instant.now());
doiEntity.setIsActive(IsActive.Active);
entityManager.persist(doiEntity);
return Doi.fromDataModel(doiEntity);
EntityDoiPersist doiPersist = new EntityDoiPersist();
doiPersist.setRepositoryId(dmpDepositModel.getRepositoryId());
doiPersist.setDoi(doi);
doiPersist.setEntityId(dmpEntity.getId());
FieldSet fieldSet = new BaseFieldSet();
return doiService.persist(doiPersist, fieldSet);
}
private List<DepositRepository> depositRepositories(WebClient.Builder builder) {
List<DepositRepository> tclients = new ArrayList<>();
for (DepositProperties.DepositSource source: depositProperties.getSources()) {
String host = URI.create(source.getUrl()).getHost();
ApiKeyWebfluxModel apiKeyWebfluxModel = new ApiKeyWebfluxModel(host + "_" + source.getClientId(), source.getIssuerUrl(), source.getClientId(), source.getClientSecret(), source.getScope());
ApiKeyExchangeFilterFunction apiKeyExchangeFilterFunction = new ApiKeyExchangeFilterFunction(this.apiKeyCacheService, apiKeyWebfluxModel);
tclients.add(new DepositRepository(builder.baseUrl(source.getUrl() + "/api/deposit").filters(exchangeFilterFunctions -> exchangeFilterFunctions.add(apiKeyExchangeFilterFunction)).build()));
public String getLogo(String repoId) {
//GK: First get the right client
DepositRepository repository = getRepository(repoId);
if (repository != null) {
return repository.getLogo(repoId);
}
return tclients;
return null;
}
private String getPreviousDOI(UUID groupId, UUID currentId, String repoId) {
CriteriaBuilder builder = this.entityManager.getCriteriaBuilder();
EntityDoiEntity doiEntity = null;
//GK: Step one get the previous version of the Data management plan
CriteriaQuery<DmpEntity> query = builder.createQuery(DmpEntity.class);
Root<DmpEntity> root = query.from(DmpEntity.class);
query = query.select(root.get("id"));
query = query.where(builder.and(builder.equal(root.get("groupId"), groupId), builder.equal(root.get("isActive"), IsActive.Active)));
query = query.orderBy(builder.desc(root.get("version")));
List<UUID> dmpIds = this.entityManager.createQuery(query).getResultList().stream().map(DmpEntity::getId).toList();
DmpQuery dmpQuery = this.applicationContext.getBean(DmpQuery.class);
Ordering ordering = new Ordering();
ordering.setItems(List.of("-version"));
dmpQuery.setOrder(ordering);
FieldSet fieldSet = new BaseFieldSet();
fieldSet.ensure("id");
List<UUID> dmpIds = dmpQuery.groupIds(groupId).isActive(IsActive.Active).collectAs(fieldSet).stream().map(DmpEntity::getId).toList();
//GK: Step two get it's doiEntity
CriteriaQuery<EntityDoiEntity> doiQuery = builder.createQuery(EntityDoiEntity.class);
Root<EntityDoiEntity> doiRoot = doiQuery.from(EntityDoiEntity.class);
doiQuery = doiQuery.multiselect(doiRoot.get("entityId").get("id"), doiRoot.get("doi"));
doiQuery = doiQuery.where(builder.and(doiRoot.get("entityId").get("id").in(dmpIds), builder.equal(doiRoot.get("isActive"), IsActive.Active), builder.equal(doiRoot.get("repositoryId"), repoId)));
List<EntityDoiEntity> dois = this.entityManager.createQuery(doiQuery).getResultList();
EntityDoiQuery doiQuery = this.applicationContext.getBean(EntityDoiQuery.class);
List<EntityDoiEntity> dois = doiQuery.entityIds(dmpIds).isActive(IsActive.Active).collect();
for(UUID uuid: dmpIds)
{

20
dmp-backend/web/src/main/java/eu/eudat/controllers/DepositController.java
View File

@ -3,11 +3,13 @@ package eu.eudat.controllers;
import eu.eudat.authorization.Permission;
import eu.eudat.logic.managers.DepositManager;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.doi.DepositCode;
import eu.eudat.model.doi.DepositRequest;
import eu.eudat.model.doi.Doi;
import eu.eudat.model.doi.RepositoryConfig;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.service.deposit.RepositoryDepositService;
import eu.eudat.types.ApiMessageCode;
import gr.cite.commons.web.authz.service.AuthorizationService;
import org.slf4j.Logger;
@ -27,12 +29,14 @@ public class DepositController extends BaseController {
private final DepositManager depositManager;
private final AuthorizationService authorizationService;
private final RepositoryDepositService repositoryDepositService;
@Autowired
public DepositController(ApiContext apiContext, DepositManager depositManager, AuthorizationService authorizationService){
public DepositController(ApiContext apiContext, DepositManager depositManager, AuthorizationService authorizationService, RepositoryDepositService repositoryDepositService){
super(apiContext);
this.depositManager = depositManager;
this.authorizationService = authorizationService;
this.repositoryDepositService = repositoryDepositService;
}
@RequestMapping(method = RequestMethod.GET, value = {"/repos"})
@ -40,7 +44,7 @@ public class DepositController extends BaseController {
ResponseEntity<ResponseItem<List<RepositoryConfig>>> getAvailableRepos() {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
List<RepositoryConfig> ids = this.depositManager.getAvailableRepos();
List<RepositoryConfig> ids = this.repositoryDepositService.getAvailableConfigurations();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<RepositoryConfig>>().status(ApiMessageCode.NO_MESSAGE).payload(ids));
}
@ -55,19 +59,19 @@ public class DepositController extends BaseController {
@RequestMapping(method = RequestMethod.POST, value = {"/createDoi"})
public @ResponseBody
ResponseEntity<ResponseItem<Doi>> createDoi(@RequestBody DepositRequest depositRequest) {
ResponseEntity<ResponseItem<EntityDoi>> createDoi(@RequestBody DepositRequest depositRequest) {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
try {
Doi doi = this.depositManager.deposit(depositRequest);
EntityDoi doi = this.repositoryDepositService.deposit(depositRequest);
if(doi != null){
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Doi>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Successfully created DOI for Data Datamanagement Plan in question.").payload(doi));
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<EntityDoi>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Successfully created DOI for Data Datamanagement Plan in question.").payload(doi));
}
else{
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<Doi>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan"));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<EntityDoi>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan"));
}
} catch (Exception e) {
logger.error(e.getMessage(), e);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<Doi>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan: " + e.getMessage()));
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<EntityDoi>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan: " + e.getMessage()));
}
}
@ -76,7 +80,7 @@ public class DepositController extends BaseController {
ResponseEntity<ResponseItem<String>> getLogo(@PathVariable("repositoryId") String repositoryId) {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
try {
String encodedLogo = this.depositManager.getRepositoryLogo(repositoryId);
String encodedLogo = this.repositoryDepositService.getLogo(repositoryId);
if(encodedLogo != null){
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Successfully loaded " + repositoryId + "'s logo.").payload(encodedLogo));
}

1
dmp-backend/web/src/main/resources/config/deposit.yml
View File

@ -1,6 +1,7 @@
deposit:
sources:
- url: http://localhost:8082
codes: [ zenodo ]
issuer-url: ${ZENODO_ISSUER_URI:IDP_APIKEY_ISSUER_URI}
client-id: ${ZENODO_DEPOSIT_CLIENT_ID:}
client-secret: ${ZENODO_DEPOSIT_CLIENT_SECRET:}