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repository-deposit-zenodo
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sync with new models

This commit is contained in:
Efstratios Giannopoulos 2023-12-07 18:13:13 +02:00
parent 36892093bd
commit c5570d15b7
13 changed files with 248 additions and 178 deletions
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7
core/src/main/java/eu/eudat/depositinterface/zenodorepository/configuration/zenodo/ZenodoProperties.java
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@ -1,5 +1,6 @@
package eu.eudat.depositinterface.zenodorepository.configuration.zenodo;
import eu.eudat.depositinterface.enums.DepositType;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.boot.context.properties.ConstructorBinding;
@ -29,7 +30,7 @@ public class ZenodoProperties {
}
public static class ZenodoConfig extends RepositoryDepositConfiguration {
private final int depositType;
private final DepositType depositType;
private final String repositoryId;
private final String accessToken;
private final String repositoryUrl;
@ -47,7 +48,7 @@ public class ZenodoProperties {
private final String domain;
@ConstructorBinding
public ZenodoConfig(int depositType, String repositoryId, String accessToken, String repositoryUrl, String repositoryAuthorizationUrl, String repositoryRecordUrl, String repositoryAccessTokenUrl, String repositoryClientId, String repositoryClientSecret, String redirectUri, boolean hasLogo, String logo, String doiFunder, String community, String affiliation, String domain) {
public ZenodoConfig(DepositType depositType, String repositoryId, String accessToken, String repositoryUrl, String repositoryAuthorizationUrl, String repositoryRecordUrl, String repositoryAccessTokenUrl, String repositoryClientId, String repositoryClientSecret, String redirectUri, boolean hasLogo, String logo, String doiFunder, String community, String affiliation, String domain) {
this.depositType = depositType;
this.repositoryId = repositoryId;
this.accessToken = accessToken;
@ -66,7 +67,7 @@ public class ZenodoProperties {
this.domain = domain;
}
public int getDepositType() {
public DepositType getDepositType() {
return depositType;
}

36
core/src/main/java/eu/eudat/depositinterface/zenodorepository/enums/ZenodoAccessRight.java Normal file
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@ -0,0 +1,36 @@
package eu.eudat.depositinterface.zenodorepository.enums;
import com.fasterxml.jackson.annotation.JsonValue;
import eu.eudat.depositinterface.enums.EnumUtils;
import eu.eudat.depositinterface.enums.EnumValueProvider;
import eu.eudat.depositinterface.enums.FieldType;
import java.util.Map;
public enum ZenodoAccessRight implements EnumValueProvider<String> {
RESTRICTED(Names.Restricted), EMBARGOED(Names.Embargoed), OPEN(Names.Open);
private final String value;
public static class Names {
public static final String Restricted = "restricted";
public static final String Embargoed = "embargoed";
public static final String Open = "open";
}
ZenodoAccessRight(String value) {
this.value = value;
}
@Override
@JsonValue
public String getValue() {
return value;
}
private static final Map<String, ZenodoAccessRight> map = EnumUtils.getEnumValueMap(ZenodoAccessRight.class);
public static ZenodoAccessRight of(String i) {
return map.get(i);
}
}

275
core/src/main/java/eu/eudat/depositinterface/zenodorepository/mapper/DMPToZenodoMapper.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/mapper/ZenodoBuilderMapper.java
View File

@ -2,18 +2,21 @@ package eu.eudat.depositinterface.zenodorepository.mapper;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.depositinterface.enums.FieldType;
import eu.eudat.depositinterface.enums.DmpAccessType;
import eu.eudat.depositinterface.enums.DmpUserRole;
import eu.eudat.depositinterface.enums.ReferenceType;
import eu.eudat.depositinterface.models.*;
import eu.eudat.depositinterface.models.reference.FieldDepositModel;
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.models.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.eudat.depositinterface.zenodorepository.enums.ZenodoAccessRight;
import eu.eudat.depositinterface.zenodorepository.model.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;
import java.time.Instant;
@ -21,32 +24,58 @@ import java.util.*;
import java.util.stream.Collectors;
@Component
public class DMPToZenodoMapper {
private static final Logger logger = LoggerFactory.getLogger(DMPToZenodoMapper.class);
private static final ObjectMapper objectMapper = new ObjectMapper();
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class ZenodoBuilderMapper {
private final PidProperties pidProperties;
private final IdentifierProperties identifierProperties;
private final FunderProperties funderProperties;
@Autowired
public DMPToZenodoMapper(PidProperties pidProperties, IdentifierProperties identifierProperties, FunderProperties funderProperties){
public ZenodoBuilderMapper(PidProperties pidProperties, IdentifierProperties identifierProperties, FunderProperties funderProperties){
this.pidProperties = pidProperties;
this.identifierProperties = identifierProperties;
this.funderProperties = funderProperties;
}
public ZenodoDeposit build(DmpDepositModel dmp, ZenodoProperties.ZenodoConfig zenodoConfig) throws JsonProcessingException {
ZenodoDeposit deposit = new ZenodoDeposit();
this.applyZenodoRelator(dmp, deposit);
deposit.getMetadata().setTitle(dmp.getLabel());
deposit.getMetadata().setUploadType("publication");
deposit.getMetadata().setPublicationType("datamanagementplan");
deposit.getMetadata().setDescription((dmp.getDescription() != null && !dmp.getDescription().isEmpty() ? dmp.getDescription() : "<p></p>"));
deposit.getMetadata().setVersion(String.valueOf(dmp.getVersion()));
String zenodoCommunity = zenodoConfig.getCommunity();
if(zenodoCommunity != null && !zenodoCommunity.isEmpty()) {
ZenodoComunity community = new ZenodoComunity();
community.setIdentifier(zenodoCommunity);
deposit.getMetadata().getCommunities().add(community);
}
this.applyAccessRight(dmp, deposit);
this.applyIsIdenticalTo(dmp, deposit, zenodoConfig);
this.applyLicenses(dmp, deposit);
this.applyResearchers(dmp, deposit);
this.applyGrants(dmp, deposit);
this.applyContributors(dmp, deposit, zenodoConfig);
this.applyCreators(dmp, deposit, zenodoConfig);
return deposit;
}
private List<DatasetFieldsDepositModel> findSchemanticValues(String relatedId, List<DatasetFieldsDepositModel> fields){
return fields.stream().filter(f -> f.getSchematics().contains(relatedId)).collect(Collectors.toList());
}
private Set<String> extractSchemanticValues(List<DatasetFieldsDepositModel> fields, List<String> acceptedPidTypes) throws JsonProcessingException{
private Set<String> extractSchematicValues(List<DatasetFieldsDepositModel> fields, List<String> acceptedPidTypes) throws JsonProcessingException{
ObjectMapper objectMapper = new ObjectMapper();
Set<String> values = new HashSet<>();
for(DatasetFieldsDepositModel field: fields){
String value = (String) field.getValue();
if(value != null && !value.isEmpty()) {
switch (FieldType.fromName(field.getRenderStyleType())) {
switch (field.getFieldType()) {
case FREE_TEXT:
case TEXT_AREA:
case RICH_TEXT_AREA:
@ -54,7 +83,8 @@ public class DMPToZenodoMapper {
case DATE_PICKER:
values.add(value);
break;
case COMBO_BOX:
case AUTO_COMPLETE:
case WORD_LIST:
if (field.isMultiple()) {
List<String> selected = objectMapper.readValue(value, new TypeReference<List<String>>() {});
values.addAll(selected);
@ -63,7 +93,6 @@ public class DMPToZenodoMapper {
values.add(value);
}
break;
case REGISTRIES:
case SERVICES:
case EXTERNAL_DATASETS:
case DATA_REPOSITORIES:
@ -120,155 +149,185 @@ public class DMPToZenodoMapper {
}
return values;
}
public ZenodoDeposit fromDMP(DMPDepositModel dmp, ZenodoProperties.ZenodoConfig zenodoConfig) throws JsonProcessingException {
Map<String, Object> extraProperties = dmp.getExtraProperties() != null ? new org.json.JSONObject(dmp.getExtraProperties()).toMap() : new HashMap<>();
ZenodoDeposit deposit = new ZenodoDeposit();
Map<String, Object> schematicsMap = new HashMap<>();
List<ZenodoRelator> relatedIdentifiers = new ArrayList<>();
List<ZenodoComunity> communities = new ArrayList<>();
List<ZenodoContributor> contributors = new ArrayList<>();
List<ZenodoCreator> creators = new ArrayList<>();
List<ZenodoGrant> grants = new ArrayList<>();
List<String> keywords = new ArrayList<>();
List<String> references = new ArrayList<>();
private List<ReferenceDepositModel> getReferenceDepositModelOfType(DmpDepositModel dmp, ReferenceType referenceType){
if (dmp.getReferences() == null) return new ArrayList<>();
return dmp.getReferences().stream().filter(x -> x.getType().equals(referenceType)).toList();
}
private void applyZenodoRelator(DmpDepositModel dmp, ZenodoDeposit deposit) throws JsonProcessingException {
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<String> acceptedPidTypes = this.pidProperties.getAcceptedTypes();
for(DatasetDepositModel dataset: dmp.getDatasets()){
List<ZenodoRelator> relatedIdentifiers = new ArrayList<>();
for(DescriptionDepositModel descriptionDepositModel: dmp.getDescriptions()){
for(String relatedId: this.identifierProperties.getRelated()){
List<DatasetFieldsDepositModel> fields = findSchemanticValues(relatedId, dataset.getFields());
Set<String> values = extractSchemanticValues(fields, acceptedPidTypes);
List<DatasetFieldsDepositModel> fields = findSchemanticValues(relatedId, descriptionDepositModel.getFields());
Set<String> values = extractSchematicValues(fields, acceptedPidTypes);
for(String value: values){
ZenodoRelator relator = new ZenodoRelator();
relator.setRelation(relatedId.substring(relatedId.lastIndexOf(".") + 1));
relator.setIdentifier(value);
relatedIdentifiers.add(relator);
}
}
}
schematicsMap.put("related_identifiers", relatedIdentifiers);
schematicsMap.put("communities", communities);
schematicsMap.put("contributors", contributors);
schematicsMap.put("creators", creators);
schematicsMap.put("grants", grants);
schematicsMap.put("keywords", keywords);
schematicsMap.put("references", references);
String schematicsString = objectMapper.writeValueAsString(schematicsMap);
objectMapper.enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY);
ZenodoDepositMetadata metadata = objectMapper.readValue(schematicsString, new TypeReference<ZenodoDepositMetadata>(){});
deposit.setMetadata(metadata);
deposit.getMetadata().setTitle(dmp.getLabel());
deposit.getMetadata().setUploadType("publication");
deposit.getMetadata().setPublicationType("datamanagementplan");
deposit.getMetadata().setDescription((dmp.getDescription() != null && !dmp.getDescription().isEmpty() ? dmp.getDescription() : "<p></p>"));
deposit.getMetadata().setVersion(String.valueOf(dmp.getVersion()));
String zenodoCommunity = zenodoConfig.getCommunity();
if(zenodoCommunity != null && !zenodoCommunity.isEmpty()) {
ZenodoComunity community = new ZenodoComunity();
community.setIdentifier(zenodoCommunity);
deposit.getMetadata().getCommunities().add(community);
}
if (extraProperties.get("visible") == null) {
deposit.getMetadata().setRelatedIdentifiers(relatedIdentifiers);
}
private void applyAccessRight(DmpDepositModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
if (dmp.getAccessType() == null) {
deposit.getMetadata().setAccessRight(ZenodoAccessRight.RESTRICTED);
deposit.getMetadata().setAccessConditions("");
} else {
if (((Boolean) extraProperties.get("visible"))) {
Instant publicationDate = Instant.parse(extraProperties.get("publicDate").toString());
if (dmp.getAccessType().equals(DmpAccessType.Public)) {
Instant publicationDate = dmp.getFinalizedAt();
if (publicationDate == null) publicationDate = Instant.now().minusSeconds(1);
if (publicationDate.isBefore(Instant.now())) {
deposit.getMetadata().setAccessRight(ZenodoAccessRight.OPEN);
} else {
deposit.getMetadata().setAccessRight(ZenodoAccessRight.EMBARGOED);
deposit.getMetadata().setEmbargoDate(publicationDate.toString());
}
if (extraProperties.get("license") != null) {
deposit.getMetadata().setLicense(((Map<?, ?>) extraProperties.get("license")).get("pid").toString());
}
} else {
deposit.getMetadata().setAccessRight(ZenodoAccessRight.RESTRICTED);
deposit.getMetadata().setAccessConditions("");
}
}
if (dmp.isPublic()) {
}
private void applyIsIdenticalTo(DmpDepositModel dmp, ZenodoDeposit deposit, ZenodoProperties.ZenodoConfig zenodoConfig){
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.setRelation("isIdenticalTo");
if (deposit.getMetadata().getRelatedIdentifiers() == null)deposit.getMetadata().setRelatedIdentifiers(new ArrayList<>());
deposit.getMetadata().getRelatedIdentifiers().add(relator);
}
String zenodoAffiliation = zenodoConfig.getAffiliation();
List<ZenodoContributor> contributors1 = dmp.getUsers().stream().map(userDMP -> {
ZenodoContributor contributor = new ZenodoContributor();
contributor.setName(userDMP.getUser().getName());
contributor.setType("ProjectMember");
if (dmp.getOrganisations() != null && !dmp.getOrganisations().isEmpty()) {
contributor.setAffiliation(dmp.getOrganisations()
.stream().map(OrganisationDepositModel::getLabel).collect(Collectors.joining(", ")));
} else {
if(zenodoAffiliation != null && !zenodoAffiliation.isEmpty()) {
contributor.setAffiliation(zenodoAffiliation);
}
private void applyLicenses(DmpDepositModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceDepositModel> dmpLicenses = this.getReferenceDepositModelOfType(dmp, ReferenceType.Licenses);
if (dmpLicenses != null && !dmpLicenses.isEmpty()) {
for (ReferenceDepositModel dmpLicense : dmpLicenses) {
String pid = dmpLicense.getDefinition().getFields().stream().filter(x-> "pid".equalsIgnoreCase(x.getCode())).map(FieldDepositModel::getValue).findFirst().orElse(null);
if (pid != null && !pid.isBlank()) {
deposit.getMetadata().setLicense(pid);
break;
}
}
return contributor;
}).collect(Collectors.toList());
}
}
List<ZenodoContributor> researchers = dmp.getResearchers().stream().map(researcher -> {
ZenodoContributor contributor = new ZenodoContributor();
contributor.setName(researcher.getLabel());
contributor.setType("Researcher");
String referenceHead = researcher.getReference().split(":")[0];
String referenceTail = researcher.getReference().replace(referenceHead + ":", "");
contributor.setAffiliation(referenceHead);
if (referenceHead.equalsIgnoreCase("ORCID")) {
contributor.setOrcid(referenceTail);
private void applyResearchers(DmpDepositModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ZenodoContributor> researchers = new ArrayList<>();
List<ReferenceDepositModel> dmpResearchers = this.getReferenceDepositModelOfType(dmp, ReferenceType.Researcher);
if (dmpResearchers != null && !dmpResearchers.isEmpty()) {
for (ReferenceDepositModel researcher : dmpResearchers) {
ZenodoContributor contributor = new ZenodoContributor();
contributor.setName(researcher.getLabel());
contributor.setType("Researcher");
contributor.setAffiliation(researcher.getSource());
if (researcher.getSource().equalsIgnoreCase("ORCID")) {
contributor.setOrcid(researcher.getReference());
}
researchers.add(contributor);
}
return contributor;
}).collect(Collectors.toList());
}
if (deposit.getMetadata().getContributors() == null)deposit.getMetadata().setContributors(new ArrayList<>());
deposit.getMetadata().getContributors().addAll(contributors1);
deposit.getMetadata().getContributors().addAll(researchers);
}
if (dmp.getGrant() != null) {
if (dmp.getGrant().getReference() == null) {
dmp.getGrant().setReference("dmp:" + dmp.getGrant().getId());
}
String grantReferenceHead = dmp.getGrant().getReference().split(":")[0];
if (grantReferenceHead.equals("openaire")) {
String grantReferenceTail = dmp.getGrant().getReference().split(":")[3];
private void applyGrants(DmpDepositModel dmp, ZenodoDeposit deposit){
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceDepositModel> dmpGrants = this.getReferenceDepositModelOfType(dmp, ReferenceType.Grants);
List<ReferenceDepositModel> dmpFunders = this.getReferenceDepositModelOfType(dmp, ReferenceType.Funder);
if (dmpGrants != null && !dmpGrants.isEmpty()) {
ReferenceDepositModel depositGrant = dmpGrants.stream().filter(x-> x.getSource().equals("openaire")).findFirst().orElse(null);
if (depositGrant != null) {
String grantReferenceTail = depositGrant.getReference().split(":")[2];
List<FunderProperties.DOIFunder> doiFunders = this.funderProperties.getAvailable();
if (dmp.getGrant().getFunder() != null && dmp.getGrant().getFunder().getLabel() != null) {
if (dmpFunders != null && !dmpFunders.isEmpty()) {
ReferenceDepositModel depositFunder = dmpFunders.get(0);
FunderProperties.DOIFunder doiFunder = doiFunders.stream()
.filter(doiFunder1 -> dmp.getGrant().getFunder().getLabel().contains(doiFunder1.getFunder()) || doiFunder1.getFunder().contains(dmp.getGrant().getFunder().getLabel()))
.filter(doiFunder1 -> depositFunder.getLabel().contains(doiFunder1.getFunder()) || doiFunder1.getFunder().contains(depositFunder.getLabel()))
.findFirst().orElse(null);
if (doiFunder != null) {
String finalId = doiFunder.getDoi() + "::" + grantReferenceTail;
ZenodoGrant grant = new ZenodoGrant();
grant.setId(finalId);
if (deposit.getMetadata().getGrants() == null)deposit.getMetadata().setGrants(new ArrayList<>());
deposit.getMetadata().getGrants().add(grant);
}
}
}
}
}
private void applyContributors(DmpDepositModel dmp, ZenodoDeposit deposit, ZenodoProperties.ZenodoConfig zenodoConfig){
if (dmp.getUsers() == null) return;
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceDepositModel> dmpOrganizations = this.getReferenceDepositModelOfType(dmp, ReferenceType.Organizations);
String zenodoAffiliation = zenodoConfig.getAffiliation();
List<ZenodoContributor> contributors = new ArrayList<>();
for (UserDmpDepositModel userDMP: dmp.getUsers()) {
ZenodoContributor contributor = new ZenodoContributor();
contributor.setName(userDMP.getUser().getName());
contributor.setType("ProjectMember");
if (dmpOrganizations != null && !dmpOrganizations.isEmpty()) {
contributor.setAffiliation(dmpOrganizations.stream().map(ReferenceDepositModel::getLabel).collect(Collectors.joining(", ")));
} else {
if(zenodoAffiliation != null && !zenodoAffiliation.isEmpty()) {
contributor.setAffiliation(zenodoAffiliation);
}
}
contributors.add(contributor);
}
if (deposit.getMetadata().getContributors() == null)deposit.getMetadata().setContributors(new ArrayList<>());
deposit.getMetadata().getContributors().addAll(contributors);
}
private void applyCreators(DmpDepositModel dmp, ZenodoDeposit deposit, ZenodoProperties.ZenodoConfig zenodoConfig){
if (dmp.getUsers() == null) return;
if (deposit.getMetadata() == null) deposit.setMetadata(new ZenodoDepositMetadata());
List<ReferenceDepositModel> dmpOrganizations = this.getReferenceDepositModelOfType(dmp, ReferenceType.Organizations);
String zenodoAffiliation = zenodoConfig.getAffiliation();
ZenodoCreator creator = new ZenodoCreator();
creator.setName(dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMPDepositModel.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getName());
if (dmp.getOrganisations() != null && !dmp.getOrganisations().isEmpty()) {
creator.setAffiliation(dmp.getOrganisations()
.stream().map(OrganisationDepositModel::getLabel).collect(Collectors.joining(", ")));
UserDmpDepositModel dmpDepositModel = dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(DmpUserRole.Owner)).findFirst().orElse(null);
if (dmpDepositModel == null || dmpDepositModel.getUser() == null) return;
creator.setName(dmpDepositModel.getUser().getName());
if (dmpOrganizations != null && !dmpOrganizations.isEmpty()) {
creator.setAffiliation(dmpOrganizations.stream().map(ReferenceDepositModel::getLabel).collect(Collectors.joining(", ")));
} else {
if(zenodoAffiliation != null && !zenodoAffiliation.isEmpty()) {
creator.setAffiliation(zenodoAffiliation);
}
}
if (deposit.getMetadata().getCreators() == null)deposit.getMetadata().setCreators(new ArrayList<>());
deposit.getMetadata().getCreators().add(creator);
return deposit;
}
}

2
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoComunity.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoComunity.java
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@ -1,4 +1,4 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;

2
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoContributor.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoContributor.java
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@ -1,4 +1,4 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;

2
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoCreator.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoCreator.java
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@ -1,4 +1,4 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;

2
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoDeposit.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoDeposit.java
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@ -1,4 +1,4 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;

3
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoDepositMetadata.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoDepositMetadata.java
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@ -1,8 +1,9 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
import eu.eudat.depositinterface.zenodorepository.enums.ZenodoAccessRight;
import java.util.List;

2
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoGrant.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoGrant.java
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@ -1,4 +1,4 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;

2
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoRelator.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/model/ZenodoRelator.java
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@ -1,4 +1,4 @@
package eu.eudat.depositinterface.zenodorepository.models;
package eu.eudat.depositinterface.zenodorepository.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonInclude;

18
core/src/main/java/eu/eudat/depositinterface/zenodorepository/models/ZenodoAccessRight.java
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@ -1,18 +0,0 @@
package eu.eudat.depositinterface.zenodorepository.models;
import com.fasterxml.jackson.annotation.JsonValue;
public enum ZenodoAccessRight {
RESTRICTED("restricted"), EMBARGOED("embargoed"), OPEN("open");
private final String value;
ZenodoAccessRight(String value) {
this.value = value;
}
@JsonValue
public String getValue() {
return value;
}
}

71
core/src/main/java/eu/eudat/depositinterface/zenodorepository/interfaces/ZenodoDeposit.java → core/src/main/java/eu/eudat/depositinterface/zenodorepository/service/zenodo/ZenodoDepositService.java
View File

@ -1,12 +1,12 @@
package eu.eudat.depositinterface.zenodorepository.interfaces;
package eu.eudat.depositinterface.zenodorepository.service.zenodo;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.models.DmpDepositModel;
import eu.eudat.depositinterface.models.FileEnvelope;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import eu.eudat.depositinterface.zenodorepository.configuration.zenodo.ZenodoProperties;
import eu.eudat.depositinterface.zenodorepository.mapper.DMPToZenodoMapper;
import eu.eudat.depositinterface.zenodorepository.mapper.ZenodoBuilderMapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -23,36 +23,35 @@ import org.springframework.web.reactive.function.BodyInserters;
import org.springframework.web.reactive.function.client.WebClient;
import java.io.*;
import java.nio.file.Files;
import java.util.*;
import java.util.stream.Collectors;
@Component
public class ZenodoDeposit implements RepositoryDeposit {
private static final Logger logger = LoggerFactory.getLogger(ZenodoDeposit.class);
public class ZenodoDepositService implements RepositoryDeposit {
private static final Logger logger = LoggerFactory.getLogger(ZenodoDepositService.class);
private static final ObjectMapper objectMapper = new ObjectMapper();
private final ZenodoProperties zenodoProperties;
private final DMPToZenodoMapper mapper;
private final ZenodoBuilderMapper mapper;
@Autowired
public ZenodoDeposit(ZenodoProperties zenodoProperties, DMPToZenodoMapper mapper){
public ZenodoDepositService(ZenodoProperties zenodoProperties, ZenodoBuilderMapper mapper){
this.zenodoProperties = zenodoProperties;
this.mapper = mapper;
}
@Override
public String deposit(String repositoryId, DMPDepositModel dmpDepositModel, String zenodoToken) throws Exception {
public String deposit(String repositoryId, DmpDepositModel dmpDepositModel, String zenodoToken) throws Exception {
RepositoryDepositConfiguration conf = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
RepositoryDepositConfiguration repositoryDepositConfiguration = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
if(conf != null) {
if(repositoryDepositConfiguration != null) {
if (zenodoToken == null || zenodoToken.isEmpty()) {
zenodoToken = conf.getAccessToken();
zenodoToken = repositoryDepositConfiguration.getAccessToken();
}
String zenodoUrl = conf.getRepositoryUrl();
String zenodoUrl = repositoryDepositConfiguration.getRepositoryUrl();
// First step, post call to Zenodo, to create the entry.
WebClient zenodoClient = WebClient.builder().build();
@ -61,7 +60,7 @@ public class ZenodoDeposit implements RepositoryDeposit {
headers.setContentType(MediaType.APPLICATION_JSON);
ZenodoProperties.ZenodoConfig zenodoConfig = this.zenodoProperties.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
eu.eudat.depositinterface.zenodorepository.models.ZenodoDeposit deposit = mapper.fromDMP(dmpDepositModel, zenodoConfig);
eu.eudat.depositinterface.zenodorepository.model.ZenodoDeposit deposit = mapper.build(dmpDepositModel, zenodoConfig);
Map createResponse;
LinkedHashMap<String, String> links;
@ -143,20 +142,19 @@ public class ZenodoDeposit implements RepositoryDeposit {
String addFileUrl = links.get("bucket") + "/" + pdfEnvelope.getFilename() + "?access_token=" + zenodoToken;
zenodoClient.put().uri(addFileUrl)
.body(BodyInserters
.fromResource(new ByteArrayResource(Files.readAllBytes(pdfEnvelope.getFile().toPath()))))
.fromResource(new ByteArrayResource(pdfEnvelope.getFile())))
.retrieve().toEntity(Map.class).block();
FileEnvelope rdaJsonEnvelope = dmpDepositModel.getRdaJsonFile();
String jsonFileName = rdaJsonEnvelope.getFilename();
addFileUrl = links.get("bucket") + "/" + jsonFileName + "?access_token=" + zenodoToken;
zenodoClient.put().uri(addFileUrl).headers(httpHeaders -> httpHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM)).body(BodyInserters.fromResource(new ByteArrayResource(Files.readAllBytes(rdaJsonEnvelope.getFile().toPath())))).retrieve().toEntity(Map.class).block();
zenodoClient.put().uri(addFileUrl).headers(httpHeaders -> httpHeaders.setContentType(MediaType.APPLICATION_OCTET_STREAM)).body(BodyInserters.fromResource(new ByteArrayResource(rdaJsonEnvelope.getFile()))).retrieve().toEntity(Map.class).block();
if (dmpDepositModel.getSupportingFilesZip() != null) {
File supportinFilesZip = dmpDepositModel.getSupportingFilesZip();
String supportinFilesZipName = dmpDepositModel.getSupportingFilesZip().getName();
String supportinFilesZipName = dmpDepositModel.getSupportingFilesZip().getFilename();
addFileUrl = links.get("bucket") + "/" + supportinFilesZipName + "?access_token=" + zenodoToken;
zenodoClient.put().uri(addFileUrl).body(BodyInserters.fromResource(new ByteArrayResource(Files.readAllBytes(supportinFilesZip.toPath())))).retrieve().toEntity(Map.class).block();
zenodoClient.put().uri(addFileUrl).body(BodyInserters.fromResource(new ByteArrayResource(supportinFilesZipName.getBytes()))).retrieve().toEntity(Map.class).block();
}
// Third post call to Zenodo to publish the entry and return the DOI.
@ -179,7 +177,6 @@ public class ZenodoDeposit implements RepositoryDeposit {
}
private String publish(String publishUrl){
//RestTemplate restTemplate = new RestTemplate();
WebClient webClient = WebClient.builder().build();
Map<String, Object> publishResponce = webClient.post().uri(publishUrl).bodyValue("").exchangeToMono(mono -> {
if (!mono.statusCode().is2xxSuccessful()) {
@ -202,30 +199,25 @@ public class ZenodoDeposit implements RepositoryDeposit {
@Override
public String authenticate(String repositoryId, String code){
RepositoryDepositConfiguration conf = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
RepositoryDepositConfiguration repositoryDepositConfiguration = this.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
if(conf != null) {
if(repositoryDepositConfiguration != null) {
WebClient client = WebClient.builder().defaultHeaders(httpHeaders -> {
httpHeaders.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
httpHeaders.setContentType(MediaType.MULTIPART_FORM_DATA);
}).build();
HttpHeaders headers = new HttpHeaders();
headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
headers.setContentType(MediaType.MULTIPART_FORM_DATA);
MultiValueMap<String, String> map = new LinkedMultiValueMap<>();
map.add("client_id", conf.getRepositoryClientId());
map.add("client_secret", conf.getRepositoryClientSecret());
map.add("client_id", repositoryDepositConfiguration.getRepositoryClientId());
map.add("client_secret", repositoryDepositConfiguration.getRepositoryClientSecret());
map.add("grant_type", "authorization_code");
map.add("code", code);
map.add("redirect_uri", conf.getRedirectUri());
HttpEntity<MultiValueMap<String, String>> request = new HttpEntity<>(map, headers);
map.add("redirect_uri", repositoryDepositConfiguration.getRedirectUri());
try {
Map<String, Object> values = client.post().uri(conf.getRepositoryAccessTokenUrl()).bodyValue(map).retrieve().bodyToMono(Map.class).block();
Map<String, Object> user = (Map<String, Object>) values.get("user");
return (String) values.get("access_token");
Map<String, Object> values = client.post().uri(repositoryDepositConfiguration.getRepositoryAccessTokenUrl()).bodyValue(map).retrieve().bodyToMono(Map.class).block();
return values != null ? (String) values.get("access_token") : null;
} catch (HttpClientErrorException ex) {
logger.error(ex.getResponseBodyAsString(), ex);
}
@ -244,9 +236,11 @@ public class ZenodoDeposit implements RepositoryDeposit {
if(conf.isHasLogo()){
byte[] logo;
try {
File logoFile = ResourceUtils.getFile(conf.getLogo());
InputStream logoStream = new FileInputStream(logoFile);
logo = logoStream.readAllBytes();
java.io.File logoFile = ResourceUtils.getFile(conf.getLogo());
if (!logoFile.exists()) return null;
try(InputStream inputStream = new FileInputStream(logoFile)){
logo = inputStream.readAllBytes();
};
} catch (IOException e) {
throw new RuntimeException(e);
}
@ -256,16 +250,13 @@ public class ZenodoDeposit implements RepositoryDeposit {
return null;
}
private String getUnpublishedDOI(String zenodoUrl, String DOI, String token, Integer version) {
private String getUnpublishedDOI(String zenodoUrl, String doi, String token, Short version) {
try {
WebClient client = WebClient.builder().build();
HttpHeaders headers = new HttpHeaders();
headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
headers.setContentType(MediaType.APPLICATION_JSON);
Map createResponse = null;
LinkedHashMap<String, String> links;
LinkedHashMap<String, String> metadata;
String listUrl = zenodoUrl + "deposit/depositions" + "?q=conceptdoi:\"" + DOI + "\"&access_token=" + token;
String listUrl = zenodoUrl + "deposit/depositions" + "?q=conceptdoi:\"" + doi + "\"&access_token=" + token;
ResponseEntity<List<Map>> listResponses = client.get().uri(listUrl).retrieve().toEntityList(Map.class).block();
createResponse = listResponses.getBody().get(0);
metadata = (LinkedHashMap<String, String>) createResponse.get("metadata");

4
web/src/main/java/eu/eudat/deposit/controller/DepositController.java
View File

@ -1,6 +1,6 @@
package eu.eudat.deposit.controller;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.models.DmpDepositModel;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import org.springframework.beans.factory.annotation.Autowired;
@ -20,7 +20,7 @@ public class DepositController {
}
@PostMapping("/{id}")
public String deposit(@PathVariable("id") String repositoryId, @RequestBody DMPDepositModel dmpDepositModel, @RequestParam("authToken")String authToken) throws Exception {
public String deposit(@PathVariable("id") String repositoryId, @RequestBody DmpDepositModel dmpDepositModel, @RequestParam("authToken")String authToken) throws Exception {
return repositoryDeposit.deposit(repositoryId, dmpDepositModel, authToken);
}