MaDgiK-CITE
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repository-deposit-zenodo
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model changes

This commit is contained in:
Efstratios Giannopoulos 2024-03-11 13:10:39 +02:00
parent 9f02c2ad92
commit 64181d941e
14 changed files with 323 additions and 121 deletions
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2
core/pom.xml
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@ -45,7 +45,7 @@
<dependency>
<groupId>gr.cite.opendmp</groupId>
<artifactId>repositorydepositbase</artifactId>
<version>2.0.1</version>
<version>2.0.2</version>
</dependency>
<dependency>

3
core/src/main/java/eu/eudat/depositinterface/zenodorepository/configuration/GenericConfiguration.java
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@ -3,11 +3,10 @@ package eu.eudat.depositinterface.zenodorepository.configuration;
import eu.eudat.depositinterface.zenodorepository.configuration.funder.FunderProperties;
import eu.eudat.depositinterface.zenodorepository.configuration.identifier.IdentifierProperties;
import eu.eudat.depositinterface.zenodorepository.configuration.pid.PidProperties;
import eu.eudat.depositinterface.zenodorepository.configuration.zenodo.ZenodoProperties;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.context.annotation.Configuration;
@Configuration
@EnableConfigurationProperties({ZenodoProperties.class, PidProperties.class, FunderProperties.class, IdentifierProperties.class})
@EnableConfigurationProperties({PidProperties.class, FunderProperties.class, IdentifierProperties.class})
public class GenericConfiguration {
}

57
core/src/main/java/eu/eudat/depositinterface/zenodorepository/configuration/zenodo/ZenodoProperties.java
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@ -1,57 +0,0 @@
package eu.eudat.depositinterface.zenodorepository.configuration.zenodo;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import org.springframework.boot.context.properties.ConfigurationProperties;
@ConfigurationProperties(prefix = "zenodo")
public class ZenodoProperties {
private String logo;
private String community;
private String domain;
private String affiliation;
private DepositConfiguration depositConfiguration;
public void setLogo(String logo) {
this.logo = logo;
}
public String getLogo() {
return logo;
}
public String getCommunity() {
return community;
}
public void setCommunity(String community) {
this.community = community;
}
public String getDomain() {
return domain;
}
public void setDomain(String domain) {
this.domain = domain;
}
public String getAffiliation() {
return affiliation;
}
public void setAffiliation(String affiliation) {
this.affiliation = affiliation;
}
public DepositConfiguration getDepositConfiguration() {
return depositConfiguration;
}
public void setDepositConfiguration(DepositConfiguration depositConfiguration) {
this.depositConfiguration = depositConfiguration;
}
}

79
core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/builder/ZenodoBuilder.java
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@ -2,20 +2,21 @@ package eu.eudat.depositinterface.zenodorepository.model.builder;
import eu.eudat.commonmodels.enums.DmpAccessType;
import eu.eudat.commonmodels.enums.DmpUserRole;
import eu.eudat.commonmodels.models.DmpModel;
import eu.eudat.commonmodels.models.DmpUserModel;
import eu.eudat.commonmodels.models.description.*;
import eu.eudat.commonmodels.models.descriptiotemplate.DefinitionModel;
import eu.eudat.commonmodels.models.descriptiotemplate.fielddata.RadioBoxDataModel;
import eu.eudat.commonmodels.models.descriptiotemplate.fielddata.SelectDataModel;
import eu.eudat.commonmodels.models.dmp.DmpModel;
import eu.eudat.commonmodels.models.dmpreference.DmpReferenceModel;
import eu.eudat.commonmodels.models.reference.ReferenceFieldModel;
import eu.eudat.commonmodels.models.reference.ReferenceModel;
import eu.eudat.depositinterface.zenodorepository.configuration.funder.FunderProperties;
import eu.eudat.depositinterface.zenodorepository.configuration.identifier.IdentifierProperties;
import eu.eudat.depositinterface.zenodorepository.configuration.pid.PidProperties;
import eu.eudat.depositinterface.zenodorepository.configuration.zenodo.ZenodoProperties;
import eu.eudat.depositinterface.zenodorepository.enums.ZenodoAccessRight;
import eu.eudat.depositinterface.zenodorepository.model.*;
import eu.eudat.depositinterface.zenodorepository.service.zenodo.ZenodoServiceProperties;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
@ -39,35 +40,37 @@ public class ZenodoBuilder {
private final PidProperties pidProperties;
private final IdentifierProperties identifierProperties;
private final FunderProperties funderProperties;
private final ZenodoServiceProperties zenodoServiceProperties;
@Autowired
public ZenodoBuilder(PidProperties pidProperties, IdentifierProperties identifierProperties, FunderProperties funderProperties){
public ZenodoBuilder(PidProperties pidProperties, IdentifierProperties identifierProperties, FunderProperties funderProperties, ZenodoServiceProperties zenodoServiceProperties){
this.pidProperties = pidProperties;
this.identifierProperties = identifierProperties;
this.funderProperties = funderProperties;
this.zenodoServiceProperties = zenodoServiceProperties;
}
public ZenodoDeposit build(DmpModel dmp, ZenodoProperties zenodoConfig) {
public ZenodoDeposit build(DmpModel dmp) {
ZenodoDeposit deposit = new ZenodoDeposit();
this.applyZenodoRelator(dmp, deposit, zenodoConfig);
this.applyZenodoRelator(dmp, deposit);
deposit.getMetadata().setTitle(dmp.getLabel());
deposit.getMetadata().setUploadType(UPLOAD_TYPE);
deposit.getMetadata().setPublicationType(PUBLICATION_TYPE);
deposit.getMetadata().setDescription((dmp.getDescription() != null && !dmp.getDescription().isEmpty() ? dmp.getDescription() : "<p></p>"));
deposit.getMetadata().setVersion(String.valueOf(dmp.getVersion()));
String zenodoCommunity = zenodoConfig.getCommunity();
String zenodoCommunity = zenodoServiceProperties.getCommunity();
if(zenodoCommunity != null && !zenodoCommunity.isEmpty()) {
ZenodoCommunity community = new ZenodoCommunity();
community.setIdentifier(zenodoCommunity);
deposit.getMetadata().getCommunities().add(community);
}
this.applyAccessRight(dmp, deposit);
this.applyIsIdenticalTo(dmp, deposit, zenodoConfig);
this.applyLicenses(dmp, deposit, zenodoConfig);
this.applyResearchers(dmp, deposit, zenodoConfig);
this.applyGrants(dmp, deposit, zenodoConfig);
this.applyContributors(dmp, deposit, zenodoConfig);
this.applyCreators(dmp, deposit, zenodoConfig);
this.applyIsIdenticalTo(dmp, deposit);
this.applyLicenses(dmp, deposit);
this.applyResearchers(dmp, deposit);
this.applyGrants(dmp, deposit);
this.applyContributors(dmp, deposit);
this.applyCreators(dmp, deposit);
return deposit;
}
@ -92,7 +95,7 @@ public class ZenodoBuilder {
return models;
}
private Set<String> extractSchematicValues(List<eu.eudat.commonmodels.models.descriptiotemplate.FieldModel> fields, PropertyDefinitionModel propertyDefinition, List<String> acceptedPidTypes, ZenodoProperties zenodoConfig) {
private Set<String> extractSchematicValues(List<eu.eudat.commonmodels.models.descriptiotemplate.FieldModel> fields, PropertyDefinitionModel propertyDefinition, List<String> acceptedPidTypes) {
Set<String> values = new HashSet<>();
for (eu.eudat.commonmodels.models.descriptiotemplate.FieldModel field : fields) {
if (field.getData() == null) continue;
@ -141,7 +144,7 @@ public class ZenodoBuilder {
if (referenceModel == null
|| referenceModel.getType() == null || referenceModel.getType().getCode() == null || referenceModel.getType().getCode().isBlank()
|| referenceModel.getDefinition() == null || referenceModel.getDefinition().getFields() == null || referenceModel.getDefinition().getFields().isEmpty()) continue;
if (referenceModel.getType().getCode().equals(zenodoConfig.getDepositConfiguration().getOrganizationReferenceCode()) || referenceModel.getType().getCode().equals(zenodoConfig.getDepositConfiguration().getResearcherReferenceCode())) {
if (referenceModel.getType().getCode().equals(zenodoServiceProperties.getOrganizationReferenceCode()) || referenceModel.getType().getCode().equals(zenodoServiceProperties.getResearcherReferenceCode())) {
if (referenceModel.getReference() != null && !referenceModel.getReference().isBlank()) {
values.add(referenceModel.getReference());
}
@ -164,11 +167,17 @@ public class ZenodoBuilder {
}
private List<ReferenceModel> getReferenceModelOfType(DmpModel dmp, String code){
if (dmp.getReferences() == null) return new ArrayList<>();
return dmp.getReferences().stream().filter(x -> x.getType() != null && x.getType().getCode().equals(code)).toList();
List<ReferenceModel> response = new ArrayList<>();
if (dmp.getReferences() == null) return response;
for (DmpReferenceModel dmpReferenceModel : dmp.getReferences()){
if (dmpReferenceModel.getReference() != null && dmpReferenceModel.getReference().getType() != null && dmpReferenceModel.getReference().getType().getCode() != null && dmpReferenceModel.getReference().getType().getCode().equals(code)){
response.add(dmpReferenceModel.getReference());
}
}
return response;
}
private void applyZenodoRelator(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig) {
private void applyZenodoRelator(DmpModel dmp, ZenodoDeposit deposit) {
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<String> acceptedPidTypes = this.pidProperties.getAcceptedTypes();
@ -176,7 +185,7 @@ public class ZenodoBuilder {
for(DescriptionModel descriptionModel: dmp.getDescriptions()){
for(String relatedId: this.identifierProperties.getRelated()){
List<eu.eudat.commonmodels.models.descriptiotemplate.FieldModel> fields = this.findSchematicValues(relatedId, descriptionModel.getDescriptionTemplate().getDefinition());
Set<String> values = extractSchematicValues(fields, descriptionModel.getProperties(), acceptedPidTypes, zenodoConfig);
Set<String> values = extractSchematicValues(fields, descriptionModel.getProperties(), acceptedPidTypes);
for(String value: values){
ZenodoRelator relator = new ZenodoRelator();
relator.setRelation(relatedId.substring(relatedId.lastIndexOf(".") + 1));
@ -212,22 +221,22 @@ public class ZenodoBuilder {
}
}
private void applyIsIdenticalTo(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig){
private void applyIsIdenticalTo(DmpModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
if (dmp.getAccessType().equals(DmpAccessType.Public)) {
ZenodoRelator relator = new ZenodoRelator();
relator.setIdentifier(zenodoConfig.getDomain() + "/external/zenodo/" + dmp.getId().toString());
relator.setIdentifier(zenodoServiceProperties.getDomain() + "/external/zenodo/" + dmp.getId().toString());
relator.setRelation(IS_IDENTICAL_TO);
if (deposit.getMetadata().getRelatedIdentifiers() == null)deposit.getMetadata().setRelatedIdentifiers(new ArrayList<>());
deposit.getMetadata().getRelatedIdentifiers().add(relator);
}
}
private void applyLicenses(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig){
private void applyLicenses(DmpModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceModel> dmpLicenses = this.getReferenceModelOfType(dmp, zenodoConfig.getDepositConfiguration().getResearcherReferenceCode());
List<ReferenceModel> dmpLicenses = this.getReferenceModelOfType(dmp, zenodoServiceProperties.getResearcherReferenceCode());
if (dmpLicenses != null && !dmpLicenses.isEmpty()) {
for (ReferenceModel dmpLicense : dmpLicenses) {
if (dmpLicense != null && dmpLicense.getReference() != null && !dmpLicense.getReference().isBlank()) {
@ -238,18 +247,18 @@ public class ZenodoBuilder {
}
}
private void applyResearchers(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig){
private void applyResearchers(DmpModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ZenodoContributor> researchers = new ArrayList<>();
List<ReferenceModel> dmpResearchers = this.getReferenceModelOfType(dmp, zenodoConfig.getDepositConfiguration().getResearcherReferenceCode());
List<ReferenceModel> dmpResearchers = this.getReferenceModelOfType(dmp, zenodoServiceProperties.getResearcherReferenceCode());
if (dmpResearchers != null && !dmpResearchers.isEmpty()) {
for (ReferenceModel researcher : dmpResearchers) {
ZenodoContributor contributor = new ZenodoContributor();
contributor.setName(researcher.getLabel());
contributor.setType(CONTRIBUTOR_TYPE_RESEARCHER);
contributor.setAffiliation(researcher.getSource());
if (researcher.getSource().equalsIgnoreCase(zenodoConfig.getDepositConfiguration().getOrcidResearcherSourceCode())) {
if (researcher.getSource().equalsIgnoreCase(zenodoServiceProperties.getOrcidResearcherSourceCode())) {
contributor.setOrcid(researcher.getReference());
}
researchers.add(contributor);
@ -261,13 +270,13 @@ public class ZenodoBuilder {
deposit.getMetadata().getContributors().addAll(researchers);
}
private void applyGrants(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig){
private void applyGrants(DmpModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceModel> dmpGrants = this.getReferenceModelOfType(dmp, zenodoConfig.getDepositConfiguration().getGrantReferenceCode());
List<ReferenceModel> dmpFunders = this.getReferenceModelOfType(dmp, zenodoConfig.getDepositConfiguration().getFunderReferenceCode());
List<ReferenceModel> dmpGrants = this.getReferenceModelOfType(dmp, zenodoServiceProperties.getGrantReferenceCode());
List<ReferenceModel> dmpFunders = this.getReferenceModelOfType(dmp, zenodoServiceProperties.getFunderReferenceCode());
if (dmpGrants != null && !dmpGrants.isEmpty()) {
ReferenceModel depositGrant = dmpGrants.stream().filter(x-> x.getSource().equalsIgnoreCase(zenodoConfig.getDepositConfiguration().getOpenaireGrantSourceCode())).findFirst().orElse(null);
ReferenceModel depositGrant = dmpGrants.stream().filter(x-> x.getSource().equalsIgnoreCase(zenodoServiceProperties.getOpenaireGrantSourceCode())).findFirst().orElse(null);
if (depositGrant != null) {
String grantReferenceTail = depositGrant.getReference().split(":")[2];
@ -289,13 +298,13 @@ public class ZenodoBuilder {
}
}
private void applyContributors(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig){
private void applyContributors(DmpModel dmp, ZenodoDeposit deposit){
if (dmp.getUsers() == null) return;
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceModel> dmpOrganizations = this.getReferenceModelOfType(dmp, zenodoConfig.getDepositConfiguration().getOrganizationReferenceCode());
String zenodoAffiliation = zenodoConfig.getAffiliation();
List<ReferenceModel> dmpOrganizations = this.getReferenceModelOfType(dmp, zenodoServiceProperties.getOrganizationReferenceCode());
String zenodoAffiliation = zenodoServiceProperties.getAffiliation();
List<ZenodoContributor> contributors = new ArrayList<>();
for (DmpUserModel userDMP: dmp.getUsers()) {
@ -317,13 +326,13 @@ public class ZenodoBuilder {
}
private void applyCreators(DmpModel dmp, ZenodoDeposit deposit, ZenodoProperties zenodoConfig){
private void applyCreators(DmpModel dmp, ZenodoDeposit deposit){
if (dmp.getUsers() == null) return;
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceModel> dmpOrganizations = this.getReferenceModelOfType(dmp, zenodoConfig.getDepositConfiguration().getOrganizationReferenceCode());
String zenodoAffiliation = zenodoConfig.getAffiliation();
List<ReferenceModel> dmpOrganizations = this.getReferenceModelOfType(dmp, zenodoServiceProperties.getOrganizationReferenceCode());
String zenodoAffiliation = zenodoServiceProperties.getAffiliation();
ZenodoCreator creator = new ZenodoCreator();
DmpUserModel dmpModel = dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(DmpUserRole.Owner)).findFirst().orElse(null);

7
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/storage/FileStorageService.java Normal file
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@ -0,0 +1,7 @@
package eu.eudat.depositinterface.zenodorepository.service.storage;
public interface FileStorageService {
String storeFile(byte[] data);
byte[] readFile(String fileRef);
}

9
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/storage/FileStorageServiceConfiguration.java Normal file
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@ -0,0 +1,9 @@
package eu.eudat.depositinterface.zenodorepository.service.storage;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.context.annotation.Configuration;
@Configuration
@EnableConfigurationProperties({FileStorageServiceProperties.class})
public class FileStorageServiceConfiguration {
}

50
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/storage/FileStorageServiceImpl.java Normal file
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@ -0,0 +1,50 @@
package eu.eudat.depositinterface.zenodorepository.service.storage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardOpenOption;
import java.util.Locale;
import java.util.UUID;
@Service
public class FileStorageServiceImpl implements FileStorageService {
private final static Logger logger = LoggerFactory.getLogger(FileStorageServiceImpl.class);
private final FileStorageServiceProperties properties;
@Autowired
public FileStorageServiceImpl(FileStorageServiceProperties properties) {
this.properties = properties;
}
@Override
public String storeFile(byte[] data) {
try {
String fileName = UUID.randomUUID().toString().replace("-", "").toLowerCase(Locale.ROOT);
Path storagePath = Paths.get(properties.getTransientPath() + "/" + fileName);
Files.write(storagePath, data, StandardOpenOption.CREATE_NEW);
return fileName;
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
return null;
}
@Override
public byte[] readFile(String fileRef) {
try (FileInputStream inputStream = new FileInputStream(properties.getTransientPath() + "/" + fileRef)) {
return inputStream.readAllBytes();
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
return new byte[0];
}
}

24
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/storage/FileStorageServiceProperties.java Normal file
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@ -0,0 +1,24 @@
package eu.eudat.depositinterface.zenodorepository.service.storage;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.boot.context.properties.bind.ConstructorBinding;
@ConfigurationProperties(prefix = "file.storage")
public class FileStorageServiceProperties {
private final String temp;
private final String transientPath;
@ConstructorBinding
public FileStorageServiceProperties(String temp, String transientPath) {
this.temp = temp;
this.transientPath = transientPath;
}
public String getTemp() {
return temp;
}
public String getTransientPath() {
return transientPath;
}
}

4
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/ZenodoDepositService.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/zenodo/ZenodoDepositService.java
View File

@ -1,6 +1,6 @@
package eu.eudat.depositinterface.zenodorepository.service;
package eu.eudat.depositinterface.zenodorepository.service.zenodo;
import eu.eudat.commonmodels.models.DmpModel;
import eu.eudat.commonmodels.models.dmp.DmpModel;
import eu.eudat.depositinterface.repository.DepositConfiguration;
public interface ZenodoDepositService {

59
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/ZenodoDepositServiceImpl.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/zenodo/ZenodoDepositServiceImpl.java
View File

@ -1,18 +1,19 @@
package eu.eudat.depositinterface.zenodorepository.service;
package eu.eudat.depositinterface.zenodorepository.service.zenodo;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.commonmodels.models.DmpModel;
import eu.eudat.commonmodels.models.FileEnvelopeModel;
import eu.eudat.commonmodels.models.dmp.DmpModel;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import eu.eudat.depositinterface.zenodorepository.configuration.zenodo.ZenodoProperties;
import eu.eudat.depositinterface.zenodorepository.model.ZenodoDeposit;
import eu.eudat.depositinterface.zenodorepository.model.builder.ZenodoBuilder;
import eu.eudat.depositinterface.zenodorepository.service.storage.FileStorageService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.ParameterizedTypeReference;
import org.springframework.core.io.ByteArrayResource;
import org.springframework.http.*;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Component;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;
@ -22,7 +23,9 @@ import org.springframework.web.client.HttpServerErrorException;
import org.springframework.web.reactive.function.BodyInserters;
import org.springframework.web.reactive.function.client.WebClient;
import java.io.*;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.*;
@Component
@ -47,16 +50,18 @@ public class ZenodoDepositServiceImpl implements ZenodoDepositService {
private static final Logger logger = LoggerFactory.getLogger(ZenodoDepositServiceImpl.class);
private static final ObjectMapper objectMapper = new ObjectMapper();
private final ZenodoProperties zenodoProperties;
private final ZenodoBuilder mapper;
private final ZenodoServiceProperties zenodoServiceProperties;
private final ZenodoBuilder zenodoBuilder;
private final FileStorageService storageService;
private byte[] logo;
@Autowired
public ZenodoDepositServiceImpl(ZenodoProperties zenodoProperties, ZenodoBuilder mapper){
this.zenodoProperties = zenodoProperties;
this.mapper = mapper;
this.logo = null;
public ZenodoDepositServiceImpl(ZenodoServiceProperties zenodoServiceProperties, ZenodoBuilder mapper, FileStorageService storageService){
this.zenodoServiceProperties = zenodoServiceProperties;
this.zenodoBuilder = mapper;
this.storageService = storageService;
this.logo = null;
}
@Override
@ -75,9 +80,9 @@ public class ZenodoDepositServiceImpl implements ZenodoDepositService {
// First step, post call to Zenodo, to create the entry.
WebClient zenodoClient = WebClient.builder().build();
DepositConfiguration zenodoConfig = this.zenodoProperties.getDepositConfiguration();
DepositConfiguration zenodoConfig = this.zenodoServiceProperties.getDepositConfiguration();
if (zenodoConfig == null) return null;
eu.eudat.depositinterface.zenodorepository.model.ZenodoDeposit deposit = mapper.build(dmpModel, this.zenodoProperties);
eu.eudat.depositinterface.zenodorepository.model.ZenodoDeposit deposit = zenodoBuilder.build(dmpModel);
LinkedHashMap<String, String> links;
String previousDOI = dmpModel.getPreviousDOI();
@ -105,15 +110,31 @@ public class ZenodoDepositServiceImpl implements ZenodoDepositService {
if (links == null || !links.containsKey(ZENODO_LINKS_BUCKET)) throw new Exception("bucket not found");
String addFileUrl = links.get(ZENODO_LINKS_BUCKET) + "/" + pdfEnvelope.getFilename() + "?access_token=" + zenodoToken;
byte[] pdfFileBytes = null;
if (this.getConfiguration().isUseSharedStorage() && pdfEnvelope.getFileRef() != null && !pdfEnvelope.getFileRef().isBlank()) {
pdfFileBytes = this.storageService.readFile(pdfEnvelope.getFileRef());
}
if (pdfFileBytes == null || pdfFileBytes.length == 0){
pdfFileBytes = pdfEnvelope.getFile();
}
zenodoClient.put().uri(addFileUrl)
.body(BodyInserters
.fromResource(new ByteArrayResource(pdfEnvelope.getFile())))
.fromResource(new ByteArrayResource(pdfFileBytes)))
.retrieve().toEntity(Map.class).block();
FileEnvelopeModel rdaJsonEnvelope = dmpModel.getRdaJsonFile();
String jsonFileName = rdaJsonEnvelope.getFilename();
addFileUrl = links.get(ZENODO_LINKS_BUCKET) + "/" + jsonFileName + "?access_token=" + zenodoToken;
zenodoClient.put().uri(addFileUrl).headers(httpHeaders -> httpHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM)).body(BodyInserters.fromResource(new ByteArrayResource(rdaJsonEnvelope.getFile()))).retrieve().toEntity(Map.class).block();
byte[] rdaJsonBytes = null;
if (this.getConfiguration().isUseSharedStorage() && rdaJsonEnvelope.getFileRef() != null && !rdaJsonEnvelope.getFileRef().isBlank()) {
rdaJsonBytes = this.storageService.readFile(rdaJsonEnvelope.getFileRef());
}
if (rdaJsonBytes == null || rdaJsonBytes.length == 0){
rdaJsonBytes = rdaJsonEnvelope.getFile();
}
zenodoClient.put().uri(addFileUrl).headers(httpHeaders -> httpHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM)).body(BodyInserters.fromResource(new ByteArrayResource(rdaJsonBytes))).retrieve().toEntity(Map.class).block();
if (dmpModel.getSupportingFilesZip() != null) {
String supportingFilesZipName = dmpModel.getSupportingFilesZip().getFilename();
@ -237,7 +258,7 @@ public class ZenodoDepositServiceImpl implements ZenodoDepositService {
@Override
public DepositConfiguration getConfiguration() {
return this.zenodoProperties.getDepositConfiguration();
return this.zenodoServiceProperties.getDepositConfiguration();
}
@Override
@ -281,11 +302,11 @@ public class ZenodoDepositServiceImpl implements ZenodoDepositService {
@Override
public String getLogo() {
DepositConfiguration zenodoConfig = this.zenodoProperties.getDepositConfiguration();
if(zenodoConfig != null && zenodoConfig.isHasLogo() && this.zenodoProperties.getLogo() != null && !this.zenodoProperties.getLogo().isBlank()) {
DepositConfiguration zenodoConfig = this.zenodoServiceProperties.getDepositConfiguration();
if(zenodoConfig != null && zenodoConfig.isHasLogo() && this.zenodoServiceProperties.getLogo() != null && !this.zenodoServiceProperties.getLogo().isBlank()) {
if (this.logo == null) {
try {
java.io.File logoFile = ResourceUtils.getFile(this.zenodoProperties.getLogo());
java.io.File logoFile = ResourceUtils.getFile(this.zenodoServiceProperties.getLogo());
if (!logoFile.exists()) return null;
try(InputStream inputStream = new FileInputStream(logoFile)){
this.logo = inputStream.readAllBytes();

9
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/zenodo/ZenodoServiceConfiguration.java Normal file
View File

@ -0,0 +1,9 @@
package eu.eudat.depositinterface.zenodorepository.service.zenodo;
import org.springframework.boot.context.properties.EnableConfigurationProperties;
import org.springframework.context.annotation.Configuration;
@Configuration
@EnableConfigurationProperties({ZenodoServiceProperties.class})
public class ZenodoServiceConfiguration {
}

122
core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/zenodo/ZenodoServiceProperties.java Normal file
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@ -0,0 +1,122 @@
package eu.eudat.depositinterface.zenodorepository.service.zenodo;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.boot.context.properties.bind.ConstructorBinding;
@ConfigurationProperties(prefix = "zenodo")
public class ZenodoServiceProperties {
private String logo;
private String community;
private String domain;
private String affiliation;
private DepositConfiguration depositConfiguration;
private String organizationReferenceCode;
private String grantReferenceCode;
private String funderReferenceCode;
private String researcherReferenceCode;
private String licensesReferenceCode;
private String openaireGrantSourceCode;
private String orcidResearcherSourceCode;
public String getLogo() {
return logo;
}
public void setLogo(String logo) {
this.logo = logo;
}
public String getCommunity() {
return community;
}
public void setCommunity(String community) {
this.community = community;
}
public String getDomain() {
return domain;
}
public void setDomain(String domain) {
this.domain = domain;
}
public String getAffiliation() {
return affiliation;
}
public void setAffiliation(String affiliation) {
this.affiliation = affiliation;
}
public DepositConfiguration getDepositConfiguration() {
return depositConfiguration;
}
public void setDepositConfiguration(DepositConfiguration depositConfiguration) {
this.depositConfiguration = depositConfiguration;
}
public String getOrganizationReferenceCode() {
return organizationReferenceCode;
}
public void setOrganizationReferenceCode(String organizationReferenceCode) {
this.organizationReferenceCode = organizationReferenceCode;
}
public String getGrantReferenceCode() {
return grantReferenceCode;
}
public void setGrantReferenceCode(String grantReferenceCode) {
this.grantReferenceCode = grantReferenceCode;
}
public String getFunderReferenceCode() {
return funderReferenceCode;
}
public void setFunderReferenceCode(String funderReferenceCode) {
this.funderReferenceCode = funderReferenceCode;
}
public String getResearcherReferenceCode() {
return researcherReferenceCode;
}
public void setResearcherReferenceCode(String researcherReferenceCode) {
this.researcherReferenceCode = researcherReferenceCode;
}
public String getLicensesReferenceCode() {
return licensesReferenceCode;
}
public void setLicensesReferenceCode(String licensesReferenceCode) {
this.licensesReferenceCode = licensesReferenceCode;
}
public String getOpenaireGrantSourceCode() {
return openaireGrantSourceCode;
}
public void setOpenaireGrantSourceCode(String openaireGrantSourceCode) {
this.openaireGrantSourceCode = openaireGrantSourceCode;
}
public String getOrcidResearcherSourceCode() {
return orcidResearcherSourceCode;
}
public void setOrcidResearcherSourceCode(String orcidResearcherSourceCode) {
this.orcidResearcherSourceCode = orcidResearcherSourceCode;
}
}

6
web/src/main/java/eu/eudat/deposit/controller/DepositController.java
View File

@ -1,13 +1,11 @@
package eu.eudat.deposit.controller;
import eu.eudat.commonmodels.models.DmpModel;
import eu.eudat.commonmodels.models.dmp.DmpModel;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import eu.eudat.depositinterface.zenodorepository.service.ZenodoDepositService;
import eu.eudat.depositinterface.zenodorepository.service.zenodo.ZenodoDepositService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.*;
import java.util.List;
@RestController
@RequestMapping("/api/deposit")
public class DepositController implements eu.eudat.depositinterface.repository.DepositController {

13
web/src/main/resources/config/zenodo-dev.yml
View File

@ -3,6 +3,16 @@ zenodo:
affiliation: ARGOS
domain: https://argos.openaire.eu/
logo: classpath:zenodo.jpg
organizationReferenceCode: "organisations"
grantReferenceCode: "grants"
funderReferenceCode: "funders"
researcherReferenceCode: "researchers"
licenceReferenceCode: "licenses"
projectReferenceCode: "projects"
datasetReferenceCode: "datasets"
publicationReferenceCode: "publications"
openaireGrantSourceCode: "openaire"
orcidResearcherSourceCode: "ORCID"
depositConfiguration:
deposit-type: 2
repository-id: Zenodo
@ -14,4 +24,5 @@ zenodo:
repository-client-id:
repository-client-secret:
redirect-uri: http://localhost:4200/login/external/zenodo
has-logo: true
has-logo: true
useSharedStorage: true