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zenodo model changes

This commit is contained in:
Efstratios Giannopoulos 2023-12-13 11:42:59 +02:00
parent aa8c73b6ed
commit 048980ac39
79 changed files with 1779 additions and 1082 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
dmp-backend/core/pom.xml
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@ -37,7 +37,7 @@
<dependency>
<groupId>gr.cite.opendmp</groupId>
<artifactId>repositorydepositbase</artifactId>
<version>1.0.4</version>
<version>2.0.0</version>
</dependency>
<dependency>
<groupId>gr.cite</groupId>

4
dmp-backend/core/src/main/java/eu/eudat/audit/AuditableAction.java
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@ -104,4 +104,8 @@ public class AuditableAction {
public static final EventId Lock_Persist = new EventId(17002, "Lock_Persist");
public static final EventId Lock_Delete = new EventId(17003, "Lock_Delete");
public static final EventId Deposit_GetAvailableRepositories = new EventId(18000, "Deposit_GetAvailableRepositories");
public static final EventId Deposit_GetAccessToken = new EventId(18001, "Deposit_GetAccessToken");
public static final EventId Deposit_Deposit = new EventId(18002, "Deposit_Deposit");
public static final EventId Deposit_GetLogo = new EventId(18003, "Deposit_GetLogo");
}

3
dmp-backend/core/src/main/java/eu/eudat/authorization/Permission.java
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@ -26,6 +26,9 @@ public final class Permission {
//Elastic
public static String ManageElastic = "ManageElastic";
//Deposit
public static String BrowseDeposit = "BrowseDeposit";
public static String EditDeposit = "BrowseDeposit";
//Language

21
dmp-backend/core/src/main/java/eu/eudat/cache/deposit/RepositoryDepositConfigurationCache.java vendored
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@ -1,21 +0,0 @@
package eu.eudat.cache.deposit;
import eu.eudat.configurations.deposit.DepositCacheOptions;
import eu.eudat.model.doi.RepositoryConfigs;
import gr.cite.tools.cache.CacheService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@Component
public class RepositoryDepositConfigurationCache extends CacheService<RepositoryConfigs> {
@Autowired
public RepositoryDepositConfigurationCache(DepositCacheOptions options) {
super(options);
}
@Override
protected Class<RepositoryConfigs> valueClass() {
return RepositoryConfigs.class;
}
}

57
dmp-backend/core/src/main/java/eu/eudat/configurations/deposit/DepositProperties.java
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@ -8,58 +8,71 @@ import java.util.List;
@ConfigurationProperties(prefix = "deposit")
public class DepositProperties {
private final List<DepositSource> sources;
@ConstructorBinding
public DepositProperties(List<DepositSource> sources) {
this.sources = sources;
}
private List<DepositSource> sources;
public List<DepositSource> getSources() {
return sources;
}
public void setSources(List<DepositSource> sources) {
this.sources = sources;
}
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;
private String repositoryId;
private String url;
private String issuerUrl;
private String clientId;
private String clientSecret;
private String scope;
@ConstructorBinding
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;
this.scope = scope;
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public String getIssuerUrl() {
return issuerUrl;
}
public void setIssuerUrl(String issuerUrl) {
this.issuerUrl = issuerUrl;
}
public String getClientId() {
return clientId;
}
public void setClientId(String clientId) {
this.clientId = clientId;
}
public String getClientSecret() {
return clientSecret;
}
public void setClientSecret(String clientSecret) {
this.clientSecret = clientSecret;
}
public String getScope() {
return scope;
}
public List<String> getCodes() {
return codes;
public void setScope(String scope) {
this.scope = scope;
}
}
}

78
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/BaseDepositBuilder.java Normal file
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@ -0,0 +1,78 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.convention.ConventionService;
import gr.cite.tools.data.builder.Builder;
import gr.cite.tools.data.query.QueryBase;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.LoggerService;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
public abstract class BaseDepositBuilder<M, D> implements Builder {
protected final LoggerService logger;
protected final ConventionService conventionService;
public BaseDepositBuilder(
ConventionService conventionService,
LoggerService logger
) {
this.conventionService = conventionService;
this.logger = logger;
}
public M build(D data) throws MyApplicationException {
if (data == null) {
//this.logger.Debug(new MapLogEntry("requested build for null item requesting fields").And("fields", directives));
// return default(M);
M model = null;
return null; //TODO
}
List<DepositBuilderItemResponse<M, D>> models = this.buildInternal(List.of(data));
return models.stream().map(DepositBuilderItemResponse::getModel).findFirst().orElse(null); //TODO
}
public List<M> build(List<D> data) throws MyApplicationException{
List<DepositBuilderItemResponse<M, D>> models = this.buildInternal(data);
return models == null ? null : models.stream().map(DepositBuilderItemResponse::getModel).collect(Collectors.toList());
}
protected abstract List<DepositBuilderItemResponse<M, D>> buildInternal(List<D> data) throws MyApplicationException;
public <K> Map<K, M> asForeignKey(QueryBase<D> query, Function<D, K> keySelector) throws MyApplicationException {
this.logger.trace("Building references from query");
List<D> data = query.collect();
this.logger.debug("collected {} items to build", Optional.ofNullable(data).map(List::size).orElse(0));
return this.asForeignKey(data, keySelector);
}
public <K> Map<K, M> asForeignKey(List<D> data, Function<D, K> keySelector) throws MyApplicationException {
this.logger.trace("building references");
List<DepositBuilderItemResponse<M, D>> models = this.buildInternal(data);
this.logger.debug("mapping {} build items from {} requested", Optional.ofNullable(models).map(List::size).orElse(0), Optional.ofNullable(data).map(List::size).orElse(0));
return models == null ? new HashMap<>() : models.stream().collect(Collectors.toMap(x-> keySelector.apply(x.getData()), DepositBuilderItemResponse::getModel));
}
public <K> Map<K, List<M>> asMasterKey(QueryBase<D> query,Function<D, K> keySelector) throws MyApplicationException {
this.logger.trace("Building details from query");
List<D> data = query.collect();
this.logger.debug("collected {} items to build", Optional.ofNullable(data).map(List::size).orElse(0));
return this.asMasterKey(data, keySelector);
}
public <K> Map<K, List<M>> asMasterKey(List<D> data, Function<D, K> keySelector) throws MyApplicationException {
this.logger.trace("building details");
List<DepositBuilderItemResponse<M, D>> models = this.buildInternal(data);
this.logger.debug("mapping {} build items from {} requested", Optional.ofNullable(models).map(List::size).orElse(0), Optional.ofNullable(data).map(List::size).orElse(0));
Map<K, List<M>> map = new HashMap<>();
if (models == null) return map;
for (DepositBuilderItemResponse<M, D> model : models) {
K key = keySelector.apply(model.getData());
if (!map.containsKey(key)) map.put(key, new ArrayList<M>());
map.get(key).add(model.getModel());
}
return map;
}
}

19
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/DepositBuilderItemResponse.java Normal file
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@ -0,0 +1,19 @@
package eu.eudat.model.builder.deposit;
public class DepositBuilderItemResponse<M, D>{
private final M model;
private final D data;
public DepositBuilderItemResponse(M model, D data) {
this.model = model;
this.data = data;
}
public D getData() {
return data;
}
public M getModel() {
return model;
}
}

67
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/DepositConfigurationBuilder.java Normal file
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@ -0,0 +1,67 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.TagEntity;
import eu.eudat.model.Tag;
import eu.eudat.model.User;
import eu.eudat.model.builder.BaseBuilder;
import eu.eudat.model.builder.UserBuilder;
import eu.eudat.model.deposit.DepositConfiguration;
import eu.eudat.query.UserQuery;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.DataLogEntry;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.*;
import java.util.stream.Collectors;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DepositConfigurationBuilder extends BaseBuilder<DepositConfiguration, eu.eudat.depositinterface.repository.DepositConfiguration> {
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public DepositConfigurationBuilder(
ConventionService conventionService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DepositConfigurationBuilder.class)));
}
public DepositConfigurationBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
public List<DepositConfiguration> build(FieldSet fields, List<eu.eudat.depositinterface.repository.DepositConfiguration> data) throws MyApplicationException {
this.logger.debug("building for {} items requesting {} fields", Optional.ofNullable(data).map(List::size).orElse(0), Optional.ofNullable(fields).map(FieldSet::getFields).map(Set::size).orElse(0));
this.logger.trace(new DataLogEntry("requested fields", fields));
if (fields == null || data == null || fields.isEmpty())
return new ArrayList<>();
List<DepositConfiguration> models = new ArrayList<>();
for (eu.eudat.depositinterface.repository.DepositConfiguration d : data) {
DepositConfiguration m = new DepositConfiguration();
if (fields.hasField(this.asIndexer(DepositConfiguration._depositType))) m.setDepositType(d.getDepositType());
if (fields.hasField(this.asIndexer(DepositConfiguration._redirectUri))) m.setRedirectUri(d.getRedirectUri());
if (fields.hasField(this.asIndexer(DepositConfiguration._repositoryId))) m.setRepositoryId(d.getRepositoryId());
if (fields.hasField(this.asIndexer(DepositConfiguration._repositoryAuthorizationUrl))) m.setRepositoryAuthorizationUrl(d.getRepositoryAuthorizationUrl());
if (fields.hasField(this.asIndexer(DepositConfiguration._repositoryRecordUrl))) m.setRepositoryRecordUrl(d.getRepositoryRecordUrl());
if (fields.hasField(this.asIndexer(DepositConfiguration._repositoryClientId))) m.setRepositoryClientId(d.getRepositoryClientId());
if (fields.hasField(this.asIndexer(DepositConfiguration._hasLogo))) m.setHasLogo(d.isHasLogo());
models.add(m);
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

100
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/DescriptionDepositBuilder.java Normal file
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@ -0,0 +1,100 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.types.description.PropertyDefinitionEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.DescriptionEntity;
import eu.eudat.data.DescriptionTemplateEntity;
import eu.eudat.depositinterface.models.DescriptionDepositModel;
import eu.eudat.model.*;
import eu.eudat.model.builder.*;
import eu.eudat.model.builder.descriptionpropertiesdefinition.PropertyDefinitionBuilder;
import eu.eudat.query.*;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.DataLogEntry;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.*;
import java.util.stream.Collectors;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DescriptionDepositBuilder extends BaseDepositBuilder<DescriptionDepositModel, DescriptionEntity> {
private final QueryFactory queryFactory;
private final BuilderFactory builderFactory;
private final JsonHandlingService jsonHandlingService;
private final XmlHandlingService xmlHandlingService;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public DescriptionDepositBuilder(
ConventionService conventionService,
QueryFactory queryFactory,
BuilderFactory builderFactory, JsonHandlingService jsonHandlingService, XmlHandlingService xmlHandlingService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DescriptionDepositBuilder.class)));
this.queryFactory = queryFactory;
this.builderFactory = builderFactory;
this.jsonHandlingService = jsonHandlingService;
this.xmlHandlingService = xmlHandlingService;
}
public DescriptionDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
protected List<DepositBuilderItemResponse<DescriptionDepositModel, DescriptionEntity>> buildInternal(List<DescriptionEntity> data) throws MyApplicationException {
this.logger.debug("building for {}", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null || data.isEmpty()) return new ArrayList<>();
Map<UUID, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity> definitionMap = this.collectDescriptionTemplates(data);
List<DepositBuilderItemResponse<DescriptionDepositModel, DescriptionEntity>> models = new ArrayList<>();
for (DescriptionEntity d : data) {
DescriptionDepositModel m = new DescriptionDepositModel();
m.setLabel(d.getLabel());
m.setDescription(d.getDescription());
if (d.getProperties() != null){
PropertyDefinitionEntity propertyDefinition = this.jsonHandlingService.fromJsonSafe(PropertyDefinitionEntity.class, d.getProperties());
if (definitionMap != null && definitionMap.containsKey(d.getDescriptionTemplateId()) && propertyDefinition != null && !this.conventionService.isListNullOrEmpty(propertyDefinition.getFields())) m.setFields(this.builderFactory.builder(DescriptionFieldDepositBuilder.class).authorize(this.authorize).setDefinition(definitionMap.get(d.getDescriptionTemplateId())).build(propertyDefinition.getFields()));
}
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
private Map<UUID, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity> collectDescriptionTemplates(List<DescriptionEntity> data) throws MyApplicationException {
if (data.isEmpty())
return null;
this.logger.debug("checking related - {}", DescriptionTemplate.class.getSimpleName());
List<DescriptionTemplateEntity> descriptionTemplateEntities = this.queryFactory.query(DescriptionTemplateQuery.class).isActive(IsActive.Active).authorize(this.authorize).ids(data.stream().map(DescriptionEntity::getDescriptionTemplateId).distinct().collect(Collectors.toList())).collectAs(new BaseFieldSet().ensure(DescriptionTemplate._id).ensure(DescriptionTemplate._definition));
Map<UUID, eu.eudat.commons.types.descriptiontemplate.DefinitionEntity>itemMap = new HashMap<>();
for (DescriptionTemplateEntity descriptionTemplateEntity : descriptionTemplateEntities){
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity definition = this.xmlHandlingService.fromXmlSafe(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition());
itemMap.put(descriptionTemplateEntity.getId(), definition);
}
return itemMap;
}
}

121
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/DescriptionFieldDepositBuilder.java Normal file
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@ -0,0 +1,121 @@
package eu.eudat.model.builder.deposit;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.types.description.FieldEntity;
import eu.eudat.commons.types.descriptiontemplate.DefinitionEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.depositinterface.enums.FieldType;
import eu.eudat.depositinterface.models.DescriptionFieldDepositModel;
import eu.eudat.service.fielddatahelper.FieldDataHelperServiceProvider;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.ArrayList;
import java.util.EnumSet;
import java.util.List;
import java.util.Optional;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DescriptionFieldDepositBuilder extends BaseDepositBuilder<DescriptionFieldDepositModel, FieldEntity> {
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
private eu.eudat.commons.types.descriptiontemplate.DefinitionEntity definition;
private final FieldDataHelperServiceProvider fieldDataHelperServiceProvider;
@Autowired
public DescriptionFieldDepositBuilder(
ConventionService conventionService, FieldDataHelperServiceProvider fieldDataHelperServiceProvider
) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DescriptionFieldDepositBuilder.class)));
this.fieldDataHelperServiceProvider = fieldDataHelperServiceProvider;
}
public DescriptionFieldDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
public DescriptionFieldDepositBuilder setDefinition(DefinitionEntity definition) {
this.definition = definition;
return this;
}
@Override
protected List<DepositBuilderItemResponse<DescriptionFieldDepositModel, FieldEntity>> buildInternal(List<FieldEntity> data) throws MyApplicationException {
this.logger.debug("building for {}", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null || data.isEmpty()) return new ArrayList<>();
List<DepositBuilderItemResponse<DescriptionFieldDepositModel, FieldEntity>> models = new ArrayList<>();
ObjectMapper objectMapper = new ObjectMapper();
for (FieldEntity d : data) {
DescriptionFieldDepositModel m = new DescriptionFieldDepositModel();
if (definition != null){
List<eu.eudat.commons.types.descriptiontemplate.FieldEntity> fieldEntities = definition.getFieldById(d.getKey());
if (!this.conventionService.isListNullOrEmpty(fieldEntities)){
eu.eudat.commons.types.descriptiontemplate.FieldEntity field = fieldEntities.getFirst();
m.setSchematics(field.getSchematics());
if (field.getData() != null) {
boolean isMultiValue = fieldDataHelperServiceProvider.get(field.getData().getFieldType()).isMultiValue(field.getData());
if (!isMultiValue) m.setValues(List.of(d.getValue()));
else {
try {
//TODO: Find better Solution
List<Object> values = objectMapper.readValue(d.getValue(), new TypeReference<List<Object>>() {});
m.setValues(values);
} catch (JsonProcessingException e) {
throw new RuntimeException(e);
}
}
switch (field.getData().getFieldType()) {
case AUTO_COMPLETE -> m.setFieldType(FieldType.AUTO_COMPLETE);
case WORD_LIST -> m.setFieldType(FieldType.WORD_LIST);
case BOOLEAN_DECISION -> m.setFieldType(FieldType.BOOLEAN_DECISION);
case RADIO_BOX -> m.setFieldType(FieldType.RADIO_BOX);
case INTERNAL_DMP_ENTRIES_RESEARCHERS -> m.setFieldType(FieldType.INTERNAL_DMP_ENTRIES_RESEARCHERS);
case INTERNAL_DMP_ENTRIES_DMPS -> m.setFieldType(FieldType.INTERNAL_DMP_ENTRIES_DMPS);
case INTERNAL_DMP_ENTRIES_DATASETS -> m.setFieldType(FieldType.INTERNAL_DMP_ENTRIES_DATASETS);
case CHECK_BOX -> m.setFieldType(FieldType.CHECK_BOX);
case FREE_TEXT -> m.setFieldType(FieldType.FREE_TEXT);
case TEXT_AREA -> m.setFieldType(FieldType.TEXT_AREA);
case RICH_TEXT_AREA -> m.setFieldType(FieldType.RICH_TEXT_AREA);
case UPLOAD -> m.setFieldType(FieldType.UPLOAD);
case DATE_PICKER -> m.setFieldType(FieldType.DATE_PICKER);
case EXTERNAL_DATASETS -> m.setFieldType(FieldType.EXTERNAL_DATASETS);
case DATA_REPOSITORIES -> m.setFieldType(FieldType.DATA_REPOSITORIES);
case JOURNAL_REPOSITORIES -> m.setFieldType(FieldType.JOURNAL_REPOSITORIES);
case PUB_REPOSITORIES -> m.setFieldType(FieldType.PUB_REPOSITORIES);
case LICENSES -> m.setFieldType(FieldType.LICENSES);
case PUBLICATIONS -> m.setFieldType(FieldType.PUBLICATIONS);
case REGISTRIES -> m.setFieldType(FieldType.REGISTRIES);
case SERVICES -> m.setFieldType(FieldType.SERVICES);
case TAGS -> m.setFieldType(FieldType.TAGS);
case RESEARCHERS -> m.setFieldType(FieldType.RESEARCHERS);
case ORGANIZATIONS -> m.setFieldType(FieldType.ORGANIZATIONS);
case DATASET_IDENTIFIER -> m.setFieldType(FieldType.DATASET_IDENTIFIER);
case CURRENCY -> m.setFieldType(FieldType.CURRENCY);
case VALIDATION -> m.setFieldType(FieldType.VALIDATION);
case TAXONOMIES -> m.setFieldType(FieldType.TAXONOMIES);
default -> throw new MyApplicationException("unrecognized type " + field.getData().getFieldType());
}
}
}
}
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

173
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/DmpDepositBuilder.java Normal file
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@ -0,0 +1,173 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.*;
import eu.eudat.depositinterface.enums.DmpAccessType;
import eu.eudat.depositinterface.models.*;
import eu.eudat.model.*;
import eu.eudat.query.*;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.query.Ordering;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.BaseFieldSet;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.*;
import java.util.stream.Collectors;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DmpDepositBuilder extends BaseDepositBuilder<DmpDepositModel, DmpEntity> {
private final QueryFactory queryFactory;
private final BuilderFactory builderFactory;
private FileEnvelope pdfFile;
private FileEnvelope rdaJsonFile;
private FileEnvelope supportingFilesZip;
private String repositoryId;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public DmpDepositBuilder(ConventionService conventionService,
QueryFactory queryFactory,
BuilderFactory builderFactory) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpDepositBuilder.class)));
this.queryFactory = queryFactory;
this.builderFactory = builderFactory;
}
public DmpDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
public DmpDepositBuilder setPdfFile(FileEnvelope pdfFile) {
this.pdfFile = pdfFile;
return this;
}
public DmpDepositBuilder setRdaJsonFile(FileEnvelope rdaJsonFile) {
this.rdaJsonFile = rdaJsonFile;
return this;
}
public DmpDepositBuilder setSupportingFilesZip(FileEnvelope supportingFilesZip) {
this.supportingFilesZip = supportingFilesZip;
return this;
}
public DmpDepositBuilder setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
return this;
}
@Override
protected List<DepositBuilderItemResponse<DmpDepositModel, DmpEntity>> buildInternal(List<DmpEntity> data) throws MyApplicationException {
this.logger.debug("building for {}", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null || data.isEmpty()) return new ArrayList<>();
List<DepositBuilderItemResponse<DmpDepositModel, DmpEntity>> models = new ArrayList<>();
Map<UUID, List<ReferenceDepositModel>> dmpReferencesMap = this.collectReferences(data);
Map<UUID, List<DmpUserDepositModel>> dmpUsersMap = this.collectDmpUsers(data);
Map<UUID, List<DescriptionDepositModel>> descriptionsMap = this.collectDmpDescriptions(data);
for (DmpEntity d : data) {
DmpDepositModel m = new DmpDepositModel();
m.setId(d.getId());
m.setLabel(d.getLabel());
m.setVersion(d.getVersion());
m.setDescription(d.getDescription());
m.setFinalizedAt(d.getFinalizedAt());
m.setPdfFile(this.pdfFile);
m.setRdaJsonFile(this.rdaJsonFile);
m.setSupportingFilesZip(this.supportingFilesZip);
if (d.getVersion() > (short)1) m.setPreviousDOI(this.getPreviousDOI(d.getGroupId(), d.getId()));
switch (d.getAccessType()){
case Public -> m.setAccessType(DmpAccessType.Public);
case Restricted -> m.setAccessType(DmpAccessType.Restricted);
case null -> m.setAccessType(null);
default -> throw new MyApplicationException("unrecognized type " + d.getAccessType().getValue());
}
if (dmpReferencesMap != null && !dmpReferencesMap.isEmpty() && dmpReferencesMap.containsKey(d.getId())) m.setReferences(dmpReferencesMap.get(d.getId()));
if (dmpUsersMap != null && !dmpUsersMap.isEmpty() && dmpUsersMap.containsKey(d.getId())) m.setUsers(dmpUsersMap.get(d.getId()));
if (descriptionsMap != null && !descriptionsMap.isEmpty() && descriptionsMap.containsKey(d.getId())) m.setDescriptions(descriptionsMap.get(d.getId()));
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
private String getPreviousDOI(UUID dmpGroup, UUID currentDmpId) {
if (repositoryId == null || repositoryId.isEmpty()) throw new MyApplicationException("repositoryId required");
//GK: Step one get the previous version of the Data management plan
DmpQuery dmpQuery = this.queryFactory.query(DmpQuery.class);
dmpQuery.setOrder(new Ordering().addDescending(Dmp._version));
List<UUID> dmpIds = dmpQuery.groupIds(dmpGroup).excludedIds(currentDmpId).isActive(IsActive.Active).collectAs(new BaseFieldSet().ensure(Dmp._id)).stream().map(DmpEntity::getId).toList();
//GK: Step two get it's doiEntity
List<EntityDoiEntity> dois = this.queryFactory.query(EntityDoiQuery.class).repositoryIds(repositoryId).entityIds(dmpIds).isActive(IsActive.Active).collectAs(new BaseFieldSet().ensure(EntityDoi._entityId, EntityDoi._doi));
for(UUID uuid: dmpIds) {
EntityDoiEntity doiEntity = dois.stream().filter(x -> x.getEntityId().equals(uuid)).findFirst().orElse(null);
if (doiEntity != null) return doiEntity.getDoi();
}
return null;
}
private Map<UUID, List<ReferenceDepositModel>> collectReferences(List<DmpEntity> data) throws MyApplicationException {
if (data.isEmpty()) return null;
this.logger.debug("checking related - {}", DmpReference.class.getSimpleName());
List<DmpReferenceEntity> dmpReferences = this.queryFactory.query(DmpReferenceQuery.class).isActives(IsActive.Active).authorize(this.authorize).dmpIds(data.stream().map(DmpEntity::getId).distinct().collect(Collectors.toList())).collectAs(new BaseFieldSet().ensure(DmpReference._dmp).ensure(DmpReference._reference));
Map<UUID, List<ReferenceDepositModel>> itemMap = new HashMap<>();
ReferenceQuery query = this.queryFactory.query(ReferenceQuery.class).authorize(this.authorize).isActive(IsActive.Active).ids(dmpReferences.stream().map(DmpReferenceEntity::getReferenceId).distinct().collect(Collectors.toList()));
Map<UUID, ReferenceDepositModel> referenceDepositModelMap = this.builderFactory.builder(ReferenceDepositBuilder.class).authorize(this.authorize).asForeignKey(query, ReferenceEntity::getId);
if (referenceDepositModelMap == null) return null;
for (DmpReferenceEntity dmpReference : dmpReferences) {
ReferenceDepositModel model =referenceDepositModelMap.getOrDefault(dmpReference.getReferenceId(), null);
if (model == null) continue;;
UUID key = dmpReference.getDmpId();
if (!itemMap.containsKey(key)) itemMap.put(key, new ArrayList<>());
itemMap.get(key).add(model);
}
return itemMap;
}
private Map<UUID, List<DmpUserDepositModel>> collectDmpUsers(List<DmpEntity> data) throws MyApplicationException {
this.logger.debug("checking related - {}", DmpUser.class.getSimpleName());
Map<UUID, List<DmpUserDepositModel>> itemMap;
DmpUserQuery query = this.queryFactory.query(DmpUserQuery.class).isActives(IsActive.Active).authorize(this.authorize).dmpIds(data.stream().map(DmpEntity::getId).distinct().collect(Collectors.toList()));
itemMap = this.builderFactory.builder(DmpUserDepositBuilder.class).authorize(this.authorize).asMasterKey(query, DmpUserEntity::getDmpId);
return itemMap;
}
private Map<UUID, List<DescriptionDepositModel>> collectDmpDescriptions(List<DmpEntity> data) throws MyApplicationException {
if (data.isEmpty()) return null;
this.logger.debug("checking related - {}", Description.class.getSimpleName());
Map<UUID, List<DescriptionDepositModel>> itemMap;
DescriptionQuery query = this.queryFactory.query(DescriptionQuery.class).isActive(IsActive.Active).authorize(this.authorize).dmpIds(data.stream().map(DmpEntity::getId).distinct().collect(Collectors.toList()));
itemMap = this.builderFactory.builder(DescriptionDepositBuilder.class).authorize(this.authorize).asMasterKey(query, DescriptionEntity::getDmpId);
return itemMap;
}
}

84
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/DmpUserDepositBuilder.java Normal file
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@ -0,0 +1,84 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.DmpUserEntity;
import eu.eudat.data.UserEntity;
import eu.eudat.depositinterface.enums.DmpUserRole;
import eu.eudat.depositinterface.models.DmpUserDepositModel;
import eu.eudat.depositinterface.models.UserDepositModel;
import eu.eudat.query.UserQuery;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.*;
import java.util.stream.Collectors;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DmpUserDepositBuilder extends BaseDepositBuilder<DmpUserDepositModel, DmpUserEntity> {
private final BuilderFactory builderFactory;
private final QueryFactory queryFactory;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public DmpUserDepositBuilder(
ConventionService conventionService,
BuilderFactory builderFactory, QueryFactory queryFactory) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpUserDepositBuilder.class)));
this.builderFactory = builderFactory;
this.queryFactory = queryFactory;
}
public DmpUserDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
protected List<DepositBuilderItemResponse<DmpUserDepositModel, DmpUserEntity>> buildInternal(List<DmpUserEntity> data) throws MyApplicationException {
this.logger.debug("building for {} items ", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null)
return new ArrayList<>();
Map<UUID, UserDepositModel> userItemsMap = this.collectUsers(data);
List<DepositBuilderItemResponse<DmpUserDepositModel, DmpUserEntity>> models = new ArrayList<>();
for (DmpUserEntity d : data) {
DmpUserDepositModel m = new DmpUserDepositModel();
switch (d.getRole()){
case User -> m.setRole(DmpUserRole.User);
case Owner -> m.setRole(DmpUserRole.Owner);
default -> throw new MyApplicationException("unrecognized type " + d.getRole().getValue());
}
if (userItemsMap != null && userItemsMap.containsKey(d.getUserId())) m.setUser(userItemsMap.get(d.getUserId()));
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
private Map<UUID, UserDepositModel> collectUsers(List<DmpUserEntity> data) throws MyApplicationException {
if (data.isEmpty())
return null;
this.logger.debug("checking related - {}", UserDepositModel.class.getSimpleName());
Map<UUID, UserDepositModel> itemMap;
UserQuery q = this.queryFactory.query(UserQuery.class).isActive(IsActive.Active).authorize(this.authorize).ids(data.stream().map(DmpUserEntity::getUserId).distinct().collect(Collectors.toList()));
itemMap = this.builderFactory.builder(UserDepositBuilder.class).authorize(this.authorize).asForeignKey(q, UserEntity::getId);
return itemMap;
}
}

49
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/ReferenceDefinitionDepositBuilder.java Normal file
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@ -0,0 +1,49 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.depositinterface.models.reference.DefinitionDepositModel;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
import java.util.*;
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class ReferenceDefinitionDepositBuilder extends BaseDepositBuilder<DefinitionDepositModel, DefinitionEntity> {
private final BuilderFactory builderFactory;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public ReferenceDefinitionDepositBuilder(
ConventionService conventionService, BuilderFactory builderFactory) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(ReferenceDefinitionDepositBuilder.class)));
this.builderFactory = builderFactory;
}
public ReferenceDefinitionDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
protected List<DepositBuilderItemResponse<DefinitionDepositModel, DefinitionEntity>> buildInternal(List<DefinitionEntity> data) throws MyApplicationException {
this.logger.debug("building for {}", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null || data.isEmpty()) return new ArrayList<>();
List<DepositBuilderItemResponse<DefinitionDepositModel, DefinitionEntity>> models = new ArrayList<>();
for (DefinitionEntity d : data) {
DefinitionDepositModel m = new DefinitionDepositModel();
if (d.getFields() != null) m.setFields(this.builderFactory.builder(ReferenceFieldDepositBuilder.class).authorize(this.authorize).build(d.getFields()));
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

92
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/ReferenceDepositBuilder.java Normal file
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@ -0,0 +1,92 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.eudat.depositinterface.enums.ReferenceSourceType;
import eu.eudat.depositinterface.enums.ReferenceType;
import eu.eudat.depositinterface.models.ReferenceDepositModel;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.ArrayList;
import java.util.EnumSet;
import java.util.List;
import java.util.Optional;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class ReferenceDepositBuilder extends BaseDepositBuilder<ReferenceDepositModel, ReferenceEntity> {
private final BuilderFactory builderFactory;
private final XmlHandlingService xmlHandlingService;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public ReferenceDepositBuilder(
ConventionService conventionService,
BuilderFactory builderFactory, XmlHandlingService xmlHandlingService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(ReferenceDepositBuilder.class)));
this.builderFactory = builderFactory;
this.xmlHandlingService = xmlHandlingService;
}
public ReferenceDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
protected List<DepositBuilderItemResponse<ReferenceDepositModel, ReferenceEntity>> buildInternal(List<ReferenceEntity> data) throws MyApplicationException {
this.logger.debug("building for {}", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null || data.isEmpty()) return new ArrayList<>();
List<DepositBuilderItemResponse<ReferenceDepositModel, ReferenceEntity>> models = new ArrayList<>();
for (ReferenceEntity d : data) {
ReferenceDepositModel m = new ReferenceDepositModel();
m.setId(d.getId());
m.setLabel(d.getLabel());
if (d.getDefinition() != null){
DefinitionEntity definition = this.xmlHandlingService.fromXmlSafe(DefinitionEntity.class, d.getDefinition());
m.setDefinition(this.builderFactory.builder(ReferenceDefinitionDepositBuilder.class).authorize(this.authorize).build(definition));
}
m.setReference(d.getReference());
m.setAbbreviation(d.getAbbreviation());
m.setDescription(d.getDescription());
m.setSource(d.getSource());
switch (d.getSourceType()){
case Internal -> m.setSourceType(ReferenceSourceType.Internal);
case External -> m.setSourceType(ReferenceSourceType.External);
default -> throw new MyApplicationException("unrecognized type " + d.getSourceType().getValue());
}
switch (d.getType()){
case Taxonomies -> m.setType(ReferenceType.Taxonomies);
case Licenses -> m.setType(ReferenceType.Licenses);
case Publications -> m.setType(ReferenceType.Publications);
case Journals -> m.setType(ReferenceType.Journals);
case PubRepositories -> m.setType(ReferenceType.PubRepositories);
case DataRepositories -> m.setType(ReferenceType.DataRepositories);
case Registries -> m.setType(ReferenceType.Registries);
case Services -> m.setType(ReferenceType.Services);
case Project -> m.setType(ReferenceType.Project);
case Funder -> m.setType(ReferenceType.Funder);
case Datasets -> m.setType(ReferenceType.Datasets);
case Organizations -> m.setType(ReferenceType.Organizations);
case Grants -> m.setType(ReferenceType.Grants);
case Researcher -> m.setType(ReferenceType.Researcher);
default -> throw new MyApplicationException("unrecognized type " + d.getType().getValue());
}
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

51
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/ReferenceFieldDepositBuilder.java Normal file
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@ -0,0 +1,51 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.depositinterface.models.reference.FieldDepositModel;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
import java.util.ArrayList;
import java.util.EnumSet;
import java.util.List;
import java.util.Optional;
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class ReferenceFieldDepositBuilder extends BaseDepositBuilder<FieldDepositModel, FieldEntity> {
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public ReferenceFieldDepositBuilder(
ConventionService conventionService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(ReferenceFieldDepositBuilder.class)));
}
public ReferenceFieldDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
protected List<DepositBuilderItemResponse<FieldDepositModel, FieldEntity>> buildInternal(List<FieldEntity> data) throws MyApplicationException {
this.logger.debug("building for {}", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null || data.isEmpty()) return new ArrayList<>();
List<DepositBuilderItemResponse<FieldDepositModel, FieldEntity>> models = new ArrayList<>();
for (FieldEntity d : data) {
FieldDepositModel m = new FieldDepositModel();
m.setCode(d.getCode());
m.setValue(d.getValue());
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

54
dmp-backend/core/src/main/java/eu/eudat/model/builder/deposit/UserDepositBuilder.java Normal file
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@ -0,0 +1,54 @@
package eu.eudat.model.builder.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.UserEntity;
import eu.eudat.depositinterface.models.UserDepositModel;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
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.util.ArrayList;
import java.util.EnumSet;
import java.util.List;
import java.util.Optional;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class UserDepositBuilder extends BaseDepositBuilder<UserDepositModel, UserEntity> {
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public UserDepositBuilder(ConventionService conventionService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(UserDepositBuilder.class)));
}
public UserDepositBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
protected List<DepositBuilderItemResponse<UserDepositModel, UserEntity>> buildInternal(List<UserEntity> data) throws MyApplicationException {
this.logger.debug("building for {} items ", Optional.ofNullable(data).map(List::size).orElse(0));
if (data == null)
return new ArrayList<>();
List<DepositBuilderItemResponse<UserDepositModel, UserEntity>> models = new ArrayList<>();
for (UserEntity d : data) {
UserDepositModel m = new UserDepositModel();
m.setName(d.getName());
models.add(new DepositBuilderItemResponse<>(m, d));
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

43
dmp-backend/core/src/main/java/eu/eudat/model/censorship/deposit/DepositConfigurationCensor.java Normal file
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@ -0,0 +1,43 @@
package eu.eudat.model.censorship.deposit;
import eu.eudat.authorization.Permission;
import eu.eudat.convention.ConventionService;
import eu.eudat.model.Description;
import eu.eudat.model.censorship.*;
import eu.eudat.model.censorship.descriptionproperties.PropertyDefinitionCensor;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.censor.CensorFactory;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.DataLogEntry;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;
import java.util.UUID;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DepositConfigurationCensor extends BaseCensor {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DepositConfigurationCensor.class));
protected final AuthorizationService authService;
public DepositConfigurationCensor(ConventionService conventionService, AuthorizationService authService) {
super(conventionService);
this.authService = authService;
}
public void censor(FieldSet fields, UUID userId) {
logger.debug(new DataLogEntry("censoring fields", fields));
if (fields == null || fields.isEmpty())
return;
this.authService.authorizeForce(Permission.BrowseDeposit);
}
}

33
dmp-backend/core/src/main/java/eu/eudat/model/doi/RepositoryConfig.java → dmp-backend/core/src/main/java/eu/eudat/model/deposit/DepositConfiguration.java
View File

@ -1,23 +1,28 @@
package eu.eudat.model.doi;
package eu.eudat.model.deposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import eu.eudat.depositinterface.enums.DepositType;
import java.util.List;
public class DepositConfiguration {
public class RepositoryConfig {
private int depositType;
private DepositType depositType;
public static final String _depositType = "depositType";
private String repositoryId;
public static final String _repositoryId = "repositoryId";
private String repositoryAuthorizationUrl;
public static final String _repositoryAuthorizationUrl = "repositoryAuthorizationUrl";
private String repositoryRecordUrl;
public static final String _repositoryRecordUrl = "repositoryRecordUrl";
private String repositoryClientId;
public static final String _repositoryClientId = "repositoryClientId";
private String redirectUri;
public static final String _redirectUri = "redirectUri";
private boolean hasLogo;
public static final String _hasLogo = "hasLogo";
public int getDepositType() {
public DepositType getDepositType() {
return depositType;
}
public void setDepositType(int depositType) {
public void setDepositType(DepositType depositType) {
this.depositType = depositType;
}
@ -62,17 +67,5 @@ public class RepositoryConfig {
public void setHasLogo(boolean hasLogo) {
this.hasLogo = hasLogo;
}
public static RepositoryConfig toModel(RepositoryDepositConfiguration r){
RepositoryConfig repositoryConfig = new RepositoryConfig();
repositoryConfig.setDepositType(r.getDepositType());
repositoryConfig.setRepositoryId(r.getRepositoryId());
repositoryConfig.setRepositoryAuthorizationUrl(r.getRepositoryAuthorizationUrl());
repositoryConfig.setRepositoryRecordUrl(r.getRepositoryRecordUrl());
repositoryConfig.setRepositoryClientId(r.getRepositoryClientId());
repositoryConfig.setRedirectUri(r.getRedirectUri());
repositoryConfig.setHasLogo(r.isHasLogo());
return repositoryConfig;
}
}

29
dmp-backend/core/src/main/java/eu/eudat/model/doi/DepositRequest.java
View File

@ -1,29 +0,0 @@
package eu.eudat.model.doi;
public class DepositRequest {
private String repositoryId;
private String dmpId;
private String accessToken;
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public String getDmpId() {
return dmpId;
}
public void setDmpId(String dmpId) {
this.dmpId = dmpId;
}
public String getAccessToken() {
return accessToken;
}
public void setAccessToken(String accessToken) {
this.accessToken = accessToken;
}
}

82
dmp-backend/core/src/main/java/eu/eudat/model/doi/Doi.java
View File

@ -1,82 +0,0 @@
package eu.eudat.model.doi;
import eu.eudat.data.EntityDoiEntity;
import eu.eudat.model.Dmp;
import java.util.Date;
import java.util.UUID;
public class Doi {
private UUID id;
private String repositoryId;
private String doi;
private Date createdAt;
private Date updatedAt;
private Dmp dmp;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public Date getCreatedAt() {
return createdAt;
}
public void setCreatedAt(Date createdAt) {
this.createdAt = createdAt;
}
public Date getUpdatedAt() {
return updatedAt;
}
public void setUpdatedAt(Date updatedAt) {
this.updatedAt = updatedAt;
}
public Dmp getDmp() {
return dmp;
}
public void setDmp(Dmp dmp) {
this.dmp = dmp;
}
public static Doi fromDataModel(EntityDoiEntity entity) {
Doi doi1 = new Doi();
doi1.id = entity.getId();
doi1.repositoryId = entity.getRepositoryId();
doi1.doi = entity.getDoi();
doi1.createdAt = Date.from(entity.getCreatedAt());
doi1.updatedAt = Date.from(entity.getUpdatedAt());
return doi1;
}
public EntityDoiEntity toDataModel() throws Exception {
EntityDoiEntity entityDoi = new EntityDoiEntity();
entityDoi.setId(this.id);
entityDoi.setRepositoryId(this.repositoryId);
entityDoi.setDoi(this.doi);
entityDoi.setCreatedAt(this.createdAt.toInstant());
entityDoi.setUpdatedAt(this.updatedAt.toInstant());
return entityDoi;
}
public String getHint() {
return null;
}
}

22
dmp-backend/core/src/main/java/eu/eudat/model/doi/RepositoryConfigs.java
View File

@ -1,22 +0,0 @@
package eu.eudat.model.doi;
import java.util.List;
public class RepositoryConfigs {
private List<RepositoryConfig> repositoryConfigs;
public RepositoryConfigs() {
}
public RepositoryConfigs(List<RepositoryConfig> repositoryConfigs) {
this.repositoryConfigs = repositoryConfigs;
}
public List<RepositoryConfig> getRepositoryConfigs() {
return repositoryConfigs;
}
public void setRepositoryConfigs(List<RepositoryConfig> repositoryConfigs) {
this.repositoryConfigs = repositoryConfigs;
}
}

162
dmp-backend/core/src/main/java/eu/eudat/model/mapper/deposit/DMPToDepositMapper.java
View File

@ -1,162 +0,0 @@
package eu.eudat.model.mapper.deposit;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.DescriptionEntity;
import eu.eudat.data.DmpEntity;
import eu.eudat.data.UserEntity;
import eu.eudat.data.old.*;
import eu.eudat.depositinterface.models.*;
import eu.eudat.commons.types.xml.XmlBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.transaction.annotation.Transactional;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import javax.xml.xpath.*;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class DMPToDepositMapper {
private static final Logger logger = LoggerFactory.getLogger(DMPToDepositMapper.class);
private static final ObjectMapper mapper = new ObjectMapper();
@Transactional
public static DMPDepositModel fromDMP(DmpEntity entity, FileEnvelope pdfFile, FileEnvelope jsonFile, File supportingFilesZip, String previousDOI) {
DMPDepositModel deposit = new DMPDepositModel();
// deposit.setId(entity.getId());
// deposit.setVersion(entity.getVersion());
// deposit.setLabel(entity.getLabel());
// deposit.setDescription(entity.getDescription());
// deposit.setPublic(entity.isPublic());
// deposit.setDatasets(entity.getDataset().stream().map(DMPToDepositMapper::fromDataset).collect(Collectors.toList()));
// deposit.setUsers(entity.getUsers().stream().map(DMPToDepositMapper::fromUserDMP).collect(Collectors.toSet()));
// deposit.setOrganisations(entity.getOrganisations().stream().map(DMPToDepositMapper::fromOrganisation).collect(Collectors.toSet()));
// deposit.setResearchers(entity.getResearchers().stream().map(DMPToDepositMapper::fromResearcher).collect(Collectors.toSet()));
// if (entity.getGrant() != null) {
// deposit.setGrant(fromGrant(entity.getGrant()));
// }
//
// deposit.setPdfFile(pdfFile);
// deposit.setRdaJsonFile(jsonFile);
// deposit.setSupportingFilesZip(supportingFilesZip);
// deposit.setPreviousDOI(previousDOI);
//
// deposit.setExtraProperties(entity.getExtraProperties());
return deposit;
}
@Transactional
private static DatasetDepositModel fromDataset(DescriptionEntity entity){
DatasetDepositModel deposit = new DatasetDepositModel();
deposit.setLabel(entity.getLabel());
deposit.setDescription(entity.getDescription());
//TODO
//deposit.setProfileDefinition(entity.getProfile().getDefinition());
deposit.setProperties(entity.getProperties());
deposit.setFields(fromDefinitionAndProperties(deposit.getProfileDefinition(), deposit.getProperties()));
return deposit;
}
private static List<DatasetFieldsDepositModel> fromDefinitionAndProperties(String definition, String properties){
List<DatasetFieldsDepositModel> deposit = new ArrayList<>();
try {
Map<String, Object> datasetAnswers = mapper.readValue(properties, HashMap.class);
Document document = XmlBuilder.fromXml(definition);
XPathFactory xpathFactory = XPathFactory.newInstance();
XPath xpath = xpathFactory.newXPath();
XPathExpression expr = xpath.compile("//schematics");
NodeList schematics = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
for (int i = 0; i < schematics.getLength(); i++) {
Node schematicsNode = schematics.item(i);
NodeList schematicsList = schematicsNode.getChildNodes();
DatasetFieldsDepositModel fieldDeposit = new DatasetFieldsDepositModel();
List<String> schematicsDeposit = new ArrayList<>();
if(schematicsList != null){
for(int j = 0; j < schematicsList.getLength(); j++){
Node schematic = schematicsList.item(j);
if(schematic.getTextContent().matches(".*\\w+.*")) {
schematicsDeposit.add(schematic.getTextContent());
}
}
}
fieldDeposit.setSchematics(schematicsDeposit);
String fieldId = schematicsNode.getParentNode().getAttributes().getNamedItem("id").getNodeValue();
Object value = datasetAnswers.get(fieldId);
fieldDeposit.setValue(value);
Element field = (Element) schematicsNode.getParentNode();
Element viewStyle = (Element) field.getElementsByTagName("viewStyle").item(0);
String renderStyle = viewStyle.getAttribute("renderstyle");
fieldDeposit.setRenderStyleType(renderStyle);
Element data = (Element) field.getElementsByTagName("data").item(0);
String multipleSelection = data.getAttribute("multiList");
String multipleAutoComplete = data.getAttribute("multiAutoComplete");
if(!multipleSelection.isEmpty()){
fieldDeposit.setMultiple(Boolean.parseBoolean(multipleSelection));
}
else if(!multipleAutoComplete.isEmpty()){
fieldDeposit.setMultiple(Boolean.parseBoolean(multipleAutoComplete));
}
else{
fieldDeposit.setMultiple(false);
}
deposit.add(fieldDeposit);
}
}
catch (XPathExpressionException | JsonProcessingException ex){
logger.error(ex.getMessage(), ex);
return null;
}
return deposit;
}
// private static UserDMPDepositModel fromUserDMP(DmpUserEntity entity){
// UserDMPDepositModel deposit = new UserDMPDepositModel();
// deposit.setUser(fromUserInfo(entity.getUser()));
// deposit.setRole(entity.getRole().getValue().intValue());
// return deposit;
// }
private static UserInfoDepositModel fromUserInfo(UserEntity entity){
UserInfoDepositModel deposit = new UserInfoDepositModel();
deposit.setName(entity.getName());
//deposit.setEmail(entity.getEmail());//TODO: GetEmail
return deposit;
}
private static OrganisationDepositModel fromOrganisation(Organisation entity){
OrganisationDepositModel deposit = new OrganisationDepositModel();
deposit.setLabel(entity.getLabel());
return deposit;
}
private static ResearcherDepositModel fromResearcher(Researcher entity){
ResearcherDepositModel deposit = new ResearcherDepositModel();
deposit.setLabel(entity.getLabel());
deposit.setReference(entity.getReference());
return deposit;
}
private static GrantDepositModel fromGrant(Grant entity){
GrantDepositModel deposit = new GrantDepositModel();
deposit.setId(entity.getId());
deposit.setReference(entity.getReference());
deposit.setFunder(fromFunder(entity.getFunder()));
return deposit;
}
private static FunderDepositModel fromFunder(Funder entity){
FunderDepositModel deposit = new FunderDepositModel();
deposit.setLabel(entity.getLabel());
return deposit;
}
}

158
dmp-backend/core/src/main/java/eu/eudat/model/mapper/deposit/DmpEntityDepositMapper.java
View File

@ -1,158 +0,0 @@
package eu.eudat.model.mapper.deposit;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.types.xml.XmlBuilder;
import eu.eudat.data.*;
import eu.eudat.data.UserEntity;
import eu.eudat.depositinterface.models.*;
import eu.eudat.model.UserContactInfo;
import eu.eudat.query.*;
import gr.cite.tools.data.query.Ordering;
import gr.cite.tools.data.query.QueryFactory;
import jakarta.persistence.EntityManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.ApplicationContext;
import org.springframework.stereotype.Component;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import javax.xml.xpath.*;
import java.io.File;
import java.util.*;
import java.util.stream.Collectors;
@Component
public class DmpEntityDepositMapper {
private static final Logger logger = LoggerFactory.getLogger(DmpEntityDepositMapper.class);
private final ObjectMapper mapper;
private final ApplicationContext applicationContext;
private final EntityManager entityManager;
private final QueryFactory queryFactory;
public DmpEntityDepositMapper(ApplicationContext applicationContext, EntityManager entityManager, QueryFactory queryFactory) {
this.applicationContext = applicationContext;
this.entityManager = entityManager;
this.queryFactory = queryFactory;
this.mapper = new ObjectMapper();
}
//TODO: WIP, missing some things like researchers, organizations etc. Must check Blueprint properties and check if those have some standard way to be identified
public DMPDepositModel toDeposit(DmpEntity dmpEntity, File zip, FileEnvelope pdf, FileEnvelope json, String previousDOI) {
DMPDepositModel model = new DMPDepositModel();
List<DescriptionEntity> desciptions = this.getDescriptions(dmpEntity.getId());
List<DmpUserEntity> users = getUsers(dmpEntity.getId());
model.setId(dmpEntity.getId());
model.setLabel(dmpEntity.getLabel());
model.setDescription(dmpEntity.getDescription());
model.setVersion(dmpEntity.getVersion());
model.setPdfFile(pdf);
model.setRdaJsonFile(json);
model.setSupportingFilesZip(zip);
model.setDatasets(desciptions.stream().map(this::toDatasetDeposit).toList());
model.setExtraProperties(dmpEntity.getProperties());
model.setUsers(users.stream().map(this::toUserDeposit).collect(Collectors.toSet()));
model.setPreviousDOI(previousDOI);
return model;
}
private List<DescriptionEntity> getDescriptions(UUID dmpId) {
DescriptionQuery descriptionQuery = this.queryFactory.query(DescriptionQuery.class);
return descriptionQuery.dmpDescriptionTemplateSubQuery(this.queryFactory.query(DmpDescriptionTemplateQuery.class).dmpIds(dmpId).isActive(IsActive.Active)).isActive(IsActive.Active).collect();
}
private DatasetDepositModel toDatasetDeposit(DescriptionEntity entity) {
DatasetDepositModel model = new DatasetDepositModel();
model.setLabel(entity.getLabel());
model.setDescription(entity.getDescription());
model.setProperties(entity.getProperties());
DescriptionTemplateEntity descriptionTemplateEntity = getDescriptionTemplate(entity.getDescriptionTemplateId());
model.setProfileDefinition(descriptionTemplateEntity.getDefinition());
model.setFields(fromDefinitionAndProperties(descriptionTemplateEntity.getDefinition(), entity.getProperties()));
return model;
}
private DescriptionTemplateEntity getDescriptionTemplate(UUID descriptionTemplateId) {
DescriptionTemplateQuery descriptionTemplateQuery = this.queryFactory.query(DescriptionTemplateQuery.class);
return descriptionTemplateQuery.ids(descriptionTemplateId).isActive(IsActive.Active).first();
}
private List<DatasetFieldsDepositModel> fromDefinitionAndProperties(String definition, String properties){
List<DatasetFieldsDepositModel> deposit = new ArrayList<>();
try {
Map<String, Object> datasetAnswers = mapper.readValue(properties, HashMap.class);
Document document = XmlBuilder.fromXml(definition);
XPathFactory xpathFactory = XPathFactory.newInstance();
XPath xpath = xpathFactory.newXPath();
XPathExpression expr = xpath.compile("//schematics");
NodeList schematics = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
for (int i = 0; i < schematics.getLength(); i++) {
Node schematicsNode = schematics.item(i);
NodeList schematicsList = schematicsNode.getChildNodes();
DatasetFieldsDepositModel fieldDeposit = new DatasetFieldsDepositModel();
List<String> schematicsDeposit = new ArrayList<>();
if(schematicsList != null){
for(int j = 0; j < schematicsList.getLength(); j++){
Node schematic = schematicsList.item(j);
if(schematic.getTextContent().matches(".*\\w+.*")) {
schematicsDeposit.add(schematic.getTextContent());
}
}
}
fieldDeposit.setSchematics(schematicsDeposit);
String fieldId = schematicsNode.getParentNode().getAttributes().getNamedItem("id").getNodeValue();
Object value = datasetAnswers.get(fieldId);
fieldDeposit.setValue(value);
Element field = (Element) schematicsNode.getParentNode();
Element viewStyle = (Element) field.getElementsByTagName("viewStyle").item(0);
String renderStyle = viewStyle.getAttribute("renderstyle");
fieldDeposit.setRenderStyleType(renderStyle);
Element data = (Element) field.getElementsByTagName("data").item(0);
String multipleSelection = data.getAttribute("multiList");
String multipleAutoComplete = data.getAttribute("multiAutoComplete");
if(!multipleSelection.isEmpty()){
fieldDeposit.setMultiple(Boolean.parseBoolean(multipleSelection));
}
else if(!multipleAutoComplete.isEmpty()){
fieldDeposit.setMultiple(Boolean.parseBoolean(multipleAutoComplete));
}
else{
fieldDeposit.setMultiple(false);
}
deposit.add(fieldDeposit);
}
}
catch (XPathExpressionException | JsonProcessingException ex){
logger.error(ex.getMessage(), ex);
return null;
}
return deposit;
}
private List<DmpUserEntity> getUsers(UUID dmpId) {
return this.queryFactory.query(DmpUserQuery.class).userIds(dmpId).collect();
}
private UserDMPDepositModel toUserDeposit(DmpUserEntity user) {
UserDMPDepositModel userDMPDepositModel = new UserDMPDepositModel();
userDMPDepositModel.setUser(new UserInfoDepositModel());
UserEntity userInfo = this.entityManager.find(UserEntity.class, user.getUserId());
userDMPDepositModel.getUser().setName(userInfo.getName());
UserContactInfoQuery query = this.queryFactory.query(UserContactInfoQuery.class).userIds(userInfo.getId());
query.setOrder(new Ordering().addAscending(UserContactInfo._ordinal));
userDMPDepositModel.getUser().setEmail(query.first().getValue());
userDMPDepositModel.setRole(user.getRole().getValue().intValue());
return userDMPDepositModel;
}
}

12
dmp-backend/core/src/main/java/eu/eudat/model/doi/DepositCode.java → dmp-backend/core/src/main/java/eu/eudat/model/persist/deposit/DepositAuthenticateRequest.java
View File

@ -1,8 +1,16 @@
package eu.eudat.model.doi;
package eu.eudat.model.persist.deposit;
public class DepositCode {
import jakarta.validation.constraints.NotEmpty;
import jakarta.validation.constraints.NotNull;
public class DepositAuthenticateRequest {
@NotNull(message = "{validation.empty}")
@NotEmpty(message = "{validation.empty}")
private String repositoryId;
@NotNull(message = "{validation.empty}")
@NotEmpty(message = "{validation.empty}")
private String code;
public String getRepositoryId() {

49
dmp-backend/core/src/main/java/eu/eudat/model/persist/deposit/DepositRequest.java Normal file
View File

@ -0,0 +1,49 @@
package eu.eudat.model.persist.deposit;
import eu.eudat.commons.validation.ValidId;
import gr.cite.tools.fieldset.BaseFieldSet;
import jakarta.validation.constraints.NotEmpty;
import jakarta.validation.constraints.NotNull;
import java.util.UUID;
public class DepositRequest {
@NotNull(message = "{validation.empty}")
@NotEmpty(message = "{validation.empty}")
private String repositoryId;
@NotNull(message = "{validation.empty}")
@ValidId(message = "{validation.invalidid}")
private UUID dmpId;
private String accessToken;
private BaseFieldSet project;
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
public UUID getDmpId() {
return dmpId;
}
public void setDmpId(UUID dmpId) {
this.dmpId = dmpId;
}
public String getAccessToken() {
return accessToken;
}
public void setAccessToken(String accessToken) {
this.accessToken = accessToken;
}
public BaseFieldSet getProject() {
return project;
}
public void setProject(BaseFieldSet project) {
this.project = project;
}
}

2
dmp-backend/core/src/main/java/eu/eudat/query/DmpReferenceQuery.java
View File

@ -222,6 +222,8 @@ public class DmpReferenceQuery extends QueryBase<DmpReferenceEntity> {
if (item.match(DmpReference._id) || item.match(PublicDmpReference._id)) return DmpReferenceEntity._id;
else if (item.prefix(DmpReference._dmp) || item.prefix(PublicDmpReference._dmp)) return DmpReferenceEntity._dmpId;
else if (item.prefix(DmpReference._reference) || item.prefix(PublicDmpReference._reference)) return DmpReferenceEntity._referenceId;
else if (item.match(DmpReference._dmp) || item.match(PublicDmpReference._dmp)) return DmpReferenceEntity._dmpId;
else if (item.match(DmpReference._reference) || item.match(PublicDmpReference._reference)) return DmpReferenceEntity._referenceId;
else if (item.match(DmpReference._data)) return DmpReferenceEntity._data;
else if (item.match(DmpReference._createdAt)) return DmpReferenceEntity._createdAt;
else if (item.match(DmpReference._updatedAt)) return DmpReferenceEntity._updatedAt;

30
dmp-backend/core/src/main/java/eu/eudat/query/EntityDoiQuery.java
View File

@ -33,6 +33,7 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
private Collection<EntityType> types;
private Collection<UUID> excludedIds;
private Collection<String> repositoryIds;
private Collection<String> dois;
@ -115,6 +116,21 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
return this;
}
public EntityDoiQuery repositoryIds(Collection<String> values) {
this.repositoryIds = values;
return this;
}
public EntityDoiQuery repositoryIds(String value) {
this.repositoryIds = List.of(value);
return this;
}
public EntityDoiQuery repositoryIds(String... value) {
this.repositoryIds = Arrays.asList(value);
return this;
}
public EntityDoiQuery entityIds(Collection<UUID> values) {
this.entityIds = values;
return this;
@ -135,16 +151,10 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
return this;
}
private final UserScope userScope;
private final AuthorizationService authService;
public EntityDoiQuery(
UserScope userScope,
AuthorizationService authService
) {
this.userScope = userScope;
this.authService = authService;
}
@Override
@ -154,7 +164,7 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
@Override
protected Boolean isFalseQuery() {
return this.isEmpty(this.ids) || this.isEmpty(this.isActives) || this.isEmpty(this.excludedIds) || this.isEmpty(this.types);
return this.isEmpty(this.ids) || this.isEmpty(this.isActives)|| this.isEmpty(this.repositoryIds) || this.isEmpty(this.excludedIds) || this.isEmpty(this.types);
}
@Override
@ -191,6 +201,12 @@ public class EntityDoiQuery extends QueryBase<EntityDoiEntity> {
inClause.value(item);
predicates.add(inClause);
}
if (this.repositoryIds != null) {
CriteriaBuilder.In<String> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(EntityDoiEntity._repositoryId));
for (String item : this.repositoryIds)
inClause.value(item);
predicates.add(inClause);
}
if (this.entityIds != null) {
CriteriaBuilder.In<UUID> inClause = queryContext.CriteriaBuilder.in(queryContext.Root.get(EntityDoiEntity._entityId));

40
dmp-backend/core/src/main/java/eu/eudat/repository/DepositRepository.java
View File

@ -1,40 +0,0 @@
package eu.eudat.repository;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import org.springframework.core.ParameterizedTypeReference;
import org.springframework.web.reactive.function.client.WebClient;
import java.util.ArrayList;
import java.util.List;
public class DepositRepository implements RepositoryDeposit {
private final WebClient depositClient;
public DepositRepository(WebClient depositClient) {
this.depositClient = depositClient;
}
@Override
public String deposit(String repositoryId, DMPDepositModel dmpDepositModel, String repositoryAccessToken) throws Exception {
return depositClient.post().uri("/" + repositoryId, uriBuilder -> uriBuilder.queryParam("authToken", repositoryAccessToken).build()).bodyValue(dmpDepositModel).exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
@Override
public String authenticate(String repositoryId, String code) {
return depositClient.get().uri("/authenticate/" + repositoryId, uriBuilder -> uriBuilder.queryParam("authToken", code).build()).exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
@Override
public List<RepositoryDepositConfiguration> getConfiguration() {
return depositClient.get().uri("/configuration").exchangeToMono(mono -> mono.bodyToMono(new ParameterizedTypeReference<List<RepositoryDepositConfiguration>>() {})).block();
}
@Override
public String getLogo(String repositoryId) {
return depositClient.get().uri("/logo/" + repositoryId).exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
}

37
dmp-backend/core/src/main/java/eu/eudat/service/deposit/DepositClientImpl.java Normal file
View File

@ -0,0 +1,37 @@
package eu.eudat.service.deposit;
import eu.eudat.depositinterface.models.DmpDepositModel;
import eu.eudat.depositinterface.repository.DepositClient;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import org.springframework.core.ParameterizedTypeReference;
import org.springframework.web.reactive.function.client.WebClient;
public class DepositClientImpl implements DepositClient {
private final WebClient depositClient;
public DepositClientImpl(WebClient depositClient) {
this.depositClient = depositClient;
}
@Override
public String deposit(DmpDepositModel dmpDepositModel, String repositoryAccessToken) throws Exception {
return depositClient.post().uri("/", uriBuilder -> uriBuilder.queryParam("authToken", repositoryAccessToken).build()).bodyValue(dmpDepositModel).exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
@Override
public String authenticate(String code) {
return depositClient.get().uri("/authenticate/", uriBuilder -> uriBuilder.queryParam("authToken", code).build()).exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
@Override
public DepositConfiguration getConfiguration() {
return depositClient.get().uri("/configuration").exchangeToMono(mono -> mono.bodyToMono(new ParameterizedTypeReference<DepositConfiguration>() {})).block();
}
@Override
public String getLogo() {
return depositClient.get().uri("/logo/").exchangeToMono(mono -> mono.bodyToMono(String.class)).block();
}
}

10
dmp-backend/core/src/main/java/eu/eudat/service/deposit/DepositConfigurationCacheOptions.java Normal file
View File

@ -0,0 +1,10 @@
package eu.eudat.service.deposit;
import gr.cite.tools.cache.CacheOptions;
import org.springframework.boot.context.properties.ConfigurationProperties;
import org.springframework.context.annotation.Configuration;
@Configuration
@ConfigurationProperties(prefix = "cache.deposit-config-by-id")
public class DepositConfigurationCacheOptions extends CacheOptions {
}

66
dmp-backend/core/src/main/java/eu/eudat/service/deposit/DepositConfigurationCacheService.java Normal file
View File

@ -0,0 +1,66 @@
package eu.eudat.service.deposit;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import gr.cite.tools.cache.CacheService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.HashMap;
@Service
public class DepositConfigurationCacheService extends CacheService<DepositConfigurationCacheService.DepositConfigurationCacheValue> {
public static class DepositConfigurationCacheValue {
public DepositConfigurationCacheValue() {
}
public DepositConfigurationCacheValue(String repositoryId, DepositConfiguration configuration) {
this.repositoryId = repositoryId;
this.configuration = configuration;
}
private String repositoryId;
public String getRepositoryId() {
return repositoryId;
}
public void setRepositoryId(String repositoryId) {
this.repositoryId = repositoryId;
}
private DepositConfiguration configuration;
public DepositConfiguration getConfiguration() {
return configuration;
}
public void setConfiguration(DepositConfiguration configuration) {
this.configuration = configuration;
}
}
@Autowired
public DepositConfigurationCacheService(DepositConfigurationCacheOptions options) {
super(options);
}
@Override
protected Class<DepositConfigurationCacheValue> valueClass() {
return DepositConfigurationCacheValue.class;
}
@Override
public String keyOf(DepositConfigurationCacheValue value) {
return this.buildKey(value.getRepositoryId());
}
public String buildKey(String subject) {
HashMap<String, String> keyParts = new HashMap<>();
keyParts.put("$repositoryId$", subject);
return this.generateKey(keyParts);
}
}

19
dmp-backend/core/src/main/java/eu/eudat/service/deposit/DepositService.java Normal file
View File

@ -0,0 +1,19 @@
package eu.eudat.service.deposit;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.persist.deposit.DepositAuthenticateRequest;
import eu.eudat.model.persist.deposit.DepositRequest;
import eu.eudat.model.deposit.DepositConfiguration;
import gr.cite.tools.fieldset.FieldSet;
import java.util.List;
public interface DepositService {
List<eu.eudat.model.deposit.DepositConfiguration> getAvailableConfigurations(FieldSet fieldSet);
EntityDoi deposit(DepositRequest dmpDepositModel) throws Exception;
String getLogo(String repositoryId);
String authenticate(DepositAuthenticateRequest model);
}

187
dmp-backend/core/src/main/java/eu/eudat/service/deposit/DepositServiceImpl.java Normal file
View File

@ -0,0 +1,187 @@
package eu.eudat.service.deposit;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.authorization.Permission;
import eu.eudat.configurations.deposit.DepositProperties;
import eu.eudat.data.DmpEntity;
import eu.eudat.depositinterface.models.DmpDepositModel;
import eu.eudat.depositinterface.models.FileEnvelope;
import eu.eudat.depositinterface.repository.DepositClient;
import eu.eudat.depositinterface.repository.DepositConfiguration;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.builder.deposit.DepositConfigurationBuilder;
import eu.eudat.model.builder.deposit.DmpDepositBuilder;
import eu.eudat.model.persist.deposit.DepositAuthenticateRequest;
import eu.eudat.model.persist.deposit.DepositRequest;
import eu.eudat.model.persist.EntityDoiPersist;
import eu.eudat.query.DmpQuery;
import eu.eudat.service.entitydoi.EntityDoiService;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.commons.web.oidc.filter.webflux.TokenExchangeCacheService;
import gr.cite.commons.web.oidc.filter.webflux.TokenExchangeFilterFunction;
import gr.cite.commons.web.oidc.filter.webflux.TokenExchangeModel;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyNotFoundException;
import gr.cite.tools.fieldset.FieldSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.MessageSource;
import org.springframework.context.i18n.LocaleContextHolder;
import org.springframework.stereotype.Service;
import org.springframework.web.reactive.function.client.WebClient;
import java.net.URI;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@Service
public class DepositServiceImpl implements DepositService {
private static final Logger logger = LoggerFactory.getLogger(DepositServiceImpl.class);
private final DepositProperties depositProperties;
private final Map<String, DepositClient> clients;
private final TokenExchangeCacheService tokenExchangeCacheService;
private final AuthorizationService authorizationService;
private final WebClient.Builder webClientBuilder;
private final EntityDoiService doiService;
private final QueryFactory queryFactory;
private final MessageSource messageSource;
private final BuilderFactory builderFactory;
private final DepositConfigurationCacheService depositConfigurationCacheService;
@Autowired
public DepositServiceImpl(DepositProperties depositProperties,
TokenExchangeCacheService tokenExchangeCacheService,
WebClient.Builder builder,
AuthorizationService authorizationService,
EntityDoiService doiService,
QueryFactory queryFactory,
MessageSource messageSource,
BuilderFactory builderFactory, DepositConfigurationCacheService depositConfigurationCacheService) {
this.depositProperties = depositProperties;
this.tokenExchangeCacheService = tokenExchangeCacheService;
this.authorizationService = authorizationService;
this.webClientBuilder = builder;
this.doiService = doiService;
this.queryFactory = queryFactory;
this.messageSource = messageSource;
this.builderFactory = builderFactory;
this.depositConfigurationCacheService = depositConfigurationCacheService;
this.clients = new HashMap<>();
}
private DepositClient getDepositClient(String repositoryId) {
if (this.clients.containsKey(repositoryId)) return this.clients.get(repositoryId);
//GK: It's register time
DepositProperties.DepositSource source = depositProperties.getSources().stream().filter(depositSource -> depositSource.getRepositoryId().equals(repositoryId)).findFirst().orElse(null);
if (source != null) {
String host = URI.create(source.getUrl()).getHost();
TokenExchangeModel tokenExchangeModel = new TokenExchangeModel("deposit:" + source.getRepositoryId(), source.getIssuerUrl(), source.getClientId(), source.getClientSecret(), source.getScope());
TokenExchangeFilterFunction apiKeyExchangeFilterFunction = new TokenExchangeFilterFunction(this.tokenExchangeCacheService, tokenExchangeModel);
WebClient webClient = webClientBuilder.baseUrl(source.getUrl() + "/api/deposit").filters(exchangeFilterFunctions -> exchangeFilterFunctions.add(apiKeyExchangeFilterFunction)).build();
DepositClientImpl repository = new DepositClientImpl(webClient);
this.clients.put(source.getRepositoryId(), repository);
return repository;
}
return null;
}
@Override
public List<eu.eudat.model.deposit.DepositConfiguration> getAvailableConfigurations(FieldSet fieldSet) {
this.authorizationService.authorizeForce(Permission.BrowseDeposit);
List<eu.eudat.model.deposit.DepositConfiguration> configurations = new ArrayList<>();
for (DepositProperties.DepositSource depositSource : depositProperties.getSources()) {
DepositConfigurationCacheService.DepositConfigurationCacheValue cacheValue = this.depositConfigurationCacheService.lookup(this.depositConfigurationCacheService.buildKey(depositSource.getRepositoryId()));
if (cacheValue == null){
DepositClient depositClient = getDepositClient(depositSource.getRepositoryId());
if (depositClient == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{depositSource.getRepositoryId(), DepositClient.class.getSimpleName()}, LocaleContextHolder.getLocale()));
DepositConfiguration configuration = depositClient.getConfiguration();
cacheValue = new DepositConfigurationCacheService.DepositConfigurationCacheValue(depositSource.getRepositoryId(), configuration);
this.depositConfigurationCacheService.put(cacheValue);
}
eu.eudat.model.deposit.DepositConfiguration depositConfiguration = this.builderFactory.builder(DepositConfigurationBuilder.class).build(fieldSet, cacheValue.getConfiguration());
configurations.add(depositConfiguration);
}
return configurations;
}
@Override
public EntityDoi deposit(DepositRequest dmpDepositModel) throws Exception {
this.authorizationService.authorizeForce(Permission.EditDeposit);
this.authorizationService.authorize(Permission.EditDmp);
//GK: First get the right client
DepositClient depositClient = getDepositClient(dmpDepositModel.getRepositoryId());
if (depositClient == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{dmpDepositModel.getRepositoryId(), DepositClient.class.getSimpleName()}, LocaleContextHolder.getLocale()));
//GK: Second get the Target Data Management Plan
DmpEntity dmpEntity = this.queryFactory.query(DmpQuery.class).ids(dmpDepositModel.getDmpId()).first();
if (dmpEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{dmpDepositModel.getDmpId(), DmpEntity.class.getSimpleName()}, LocaleContextHolder.getLocale()));
//GK: Forth make the required files to be uploaded with the deposit
//TODO: Properly create required files
FileEnvelope docEnvelope = new FileEnvelope();
FileEnvelope pdfEnvelope = new FileEnvelope();
FileEnvelope jsonEnvelope = new FileEnvelope();
FileEnvelope zip = new FileEnvelope();
//TODO: Create Files
// File zip = new File(environment.getProperty("temp.temp") + UUID.randomUUID() + ".zip");
// try {
// docEnvelope.setFilename("test.docx");
// docEnvelope.setFile(this.storageFileService.getH2020TemplateFile());
// File pdfFile = PDFUtils.convertToPDF(docEnvelope, environment);
// pdfEnvelope.setFilename("test.pdf");
// pdfEnvelope.setFile(pdfFile);
// File jsonFile = new File(this.environment.getProperty("temp.temp") + UUID.randomUUID() + ".json");
// jsonEnvelope.setFilename("test.json");
// jsonEnvelope.setFile(jsonFile);
//
// } catch (IOException e) {
// logger.error(e.getMessage(), e);
// }
//GK: Fifth Transform them to the DepositModel
DmpDepositModel depositModel = this.builderFactory.builder(DmpDepositBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic)
.setRepositoryId(dmpDepositModel.getRepositoryId()).setPdfFile(pdfEnvelope).setRdaJsonFile(jsonEnvelope).setSupportingFilesZip(zip).build(dmpEntity);
//GK: Sixth Perform the deposit
String doi = depositClient.deposit(depositModel, dmpDepositModel.getAccessToken());
//GK: Something has gone wrong return null
if (doi.isEmpty()) return null;
//GK: doi is fine store it in database
EntityDoiPersist doiPersist = new EntityDoiPersist();
doiPersist.setRepositoryId(dmpDepositModel.getRepositoryId());
doiPersist.setDoi(doi);
doiPersist.setEntityId(dmpEntity.getId());
return doiService.persist(doiPersist, dmpDepositModel.getProject());
}
@Override
public String getLogo(String repositoryId) {
this.authorizationService.authorizeForce(Permission.BrowseDeposit);
DepositClient depositClient = getDepositClient(repositoryId);
if (depositClient == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{repositoryId, DepositClient.class.getSimpleName()}, LocaleContextHolder.getLocale()));
return depositClient.getLogo();
}
@Override
public String authenticate(DepositAuthenticateRequest model) {
this.authorizationService.authorizeForce(Permission.BrowseDeposit);
DepositClient depositClient = getDepositClient(model.getRepositoryId());
if (depositClient == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{model.getRepositoryId(), DepositClient.class.getSimpleName()}, LocaleContextHolder.getLocale()));
return depositClient.authenticate(model.getCode());
}
}

213
dmp-backend/core/src/main/java/eu/eudat/service/deposit/RepositoryDepositService.java
View File

@ -1,213 +0,0 @@
package eu.eudat.service.deposit;
import eu.eudat.authorization.Permission;
import eu.eudat.cache.deposit.RepositoryDepositConfigurationCache;
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.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.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 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.util.*;
@Service
public class RepositoryDepositService {
private static final Logger logger = LoggerFactory.getLogger(RepositoryDepositService.class);
private final DepositProperties depositProperties;
private final Map<String, DepositRepository> clients;
private final ApiKeyCacheService apiKeyCacheService;
private final RepositoryDepositConfigurationCache repositoryDepositConfigurationCache;
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, DmpQuery dmpQuery, EntityDoiQuery doiQuery, EntityDoiService doiService, ApplicationContext applicationContext) {
this.depositProperties = depositProperties;
this.apiKeyCacheService = apiKeyCacheService;
this.repositoryDepositConfigurationCache = repositoryDepositConfigurationCache;
this.authorizationService = authorizationService;
this.conventionService = conventionService;
this.environment = environment;
this.depositMapper = depositMapper;
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;
}
public List<RepositoryConfig> getAvailableConfigurations() {
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();
repositories.forEach((client) -> {
List<RepositoryDepositConfiguration> repositoryConfigs = client.getConfiguration();
if (repositoryConfigs != null && !repositoryConfigs.isEmpty()) {
configurations.addAll(repositoryConfigs.stream().map(RepositoryConfig::toModel).toList());
}
});
configs = new RepositoryConfigs(configurations);
this.repositoryDepositConfigurationCache.put("base", configs);
}
return configs.getRepositoryConfigs();
}
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 = getRepository(dmpDepositModel.getRepositoryId());
//GK: Second get the Target Data Management Plan
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;
if (dmpEntity.getVersion() > 1) { //TODO: Will it start from 1 or 0?
previousDOI = this.getPreviousDOI(dmpEntity.getGroupId(), dmpEntity.getId(), dmpDepositModel.getRepositoryId());
}
//GK: Forth make the required files to be uploaded with the deposit
//TODO: Properly create required files
FileEnvelope docEnvelope = new FileEnvelope();
FileEnvelope pdfEnvelope = new FileEnvelope();
FileEnvelope jsonEnvelope = new FileEnvelope();
File zip = new File(environment.getProperty("temp.temp") + UUID.randomUUID() + ".zip");
try {
File documentFile = ResourceUtils.getFile(this.environment.getProperty("configuration.h2020template"));
docEnvelope.setFilename("test.docx");
docEnvelope.setFile(documentFile);
File pdfFile = PDFUtils.convertToPDF(docEnvelope, environment);
pdfEnvelope.setFilename("test.pdf");
pdfEnvelope.setFile(pdfFile);
File jsonFile = new File(this.environment.getProperty("temp.temp") + UUID.randomUUID() + ".json");
jsonEnvelope.setFilename("test.json");
jsonEnvelope.setFile(jsonFile);
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
//GK: Fifth Transform them to the DepositModel
DMPDepositModel depositModel = depositMapper.toDeposit(dmpEntity, zip, pdfEnvelope, jsonEnvelope, previousDOI);
//GK: Sixth Perform the deposit
String doi = "";
try {
doi = repository.deposit(dmpDepositModel.getRepositoryId(), depositModel, "");
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
//GK: Something has gone wrong return null
if (doi.isEmpty())
return null;
//GK: doi is fine store it in database
EntityDoiPersist doiPersist = new EntityDoiPersist();
doiPersist.setRepositoryId(dmpDepositModel.getRepositoryId());
doiPersist.setDoi(doi);
doiPersist.setEntityId(dmpEntity.getId());
FieldSet fieldSet = new BaseFieldSet();
return doiService.persist(doiPersist, fieldSet);
}
public String getLogo(String repoId) {
//GK: First get the right client
DepositRepository repository = getRepository(repoId);
if (repository != null) {
return repository.getLogo(repoId);
}
return null;
}
private String getPreviousDOI(UUID groupId, UUID currentId, String repoId) {
EntityDoiEntity doiEntity = null;
//GK: Step one get the previous version of the Data management plan
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
EntityDoiQuery doiQuery = this.applicationContext.getBean(EntityDoiQuery.class);
List<EntityDoiEntity> dois = doiQuery.entityIds(dmpIds).isActive(IsActive.Active).collect();
for(UUID uuid: dmpIds)
{
if (uuid.equals(currentId))
continue;
doiEntity = dois.stream()
.filter(entityDoiEntity -> entityDoiEntity.getEntityId().equals(uuid)).findFirst().orElse(null);
if (doiEntity != null)
break;
}
return doiEntity != null ? doiEntity.getDoi() : null;
}
}

27
dmp-backend/core/src/main/java/eu/eudat/service/description/DescriptionServiceImpl.java
View File

@ -11,6 +11,8 @@ import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.commons.types.description.FieldEntity;
import eu.eudat.commons.types.description.PropertyDefinitionEntity;
import eu.eudat.commons.types.descriptiontemplate.FieldSetEntity;
import eu.eudat.commons.types.descriptiontemplate.SectionEntity;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.*;
@ -181,11 +183,32 @@ public class DescriptionServiceImpl implements DescriptionService {
return this.builderFactory.builder(DescriptionBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(BaseFieldSet.build(fields, Description._id), data);
}
public void descriptionForce(DescriptionEntity description) throws Exception {
// public List<eu.eudat.commons.types.descriptiontemplate.FieldEntity> getFieldById(String id){
// List<eu.eudat.commons.types.descriptiontemplate.FieldEntity> fieldEntities = new ArrayList<>();
// if (id == null || id.isBlank()) return fieldEntities;
// if (this.getFieldSets() != null){
// for (FieldSetEntity fieldSetEntity: this.getFieldSets()) {
// fieldEntities.addAll(fieldSetEntity.getFieldById(id));
// }
// }
// if (this.getSections() != null){
// for (SectionEntity sectionEntity: this.getSections()) {
// fieldEntities.addAll(sectionEntity.getFieldById(id));
// }
// }
// return fieldEntities;
// }
private void descriptionForce(DescriptionEntity description) throws Exception {
List<String> datasetProfileValidators = new LinkedList<>();
DescriptionTemplateEntity descriptionTemplateEntity = this.entityManager.find(DescriptionTemplateEntity.class, description.getDescriptionTemplateId());
if (descriptionTemplateEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{description.getDescriptionTemplateId(), DescriptionTemplate.class.getSimpleName()}, LocaleContextHolder.getLocale()));
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity definition = this.xmlHandlingService.fromXml(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition());
eu.eudat.commons.types.descriptiontemplate.DefinitionEntity descriptionTemplateDefinition = this.xmlHandlingService.fromXml(eu.eudat.commons.types.descriptiontemplate.DefinitionEntity.class, descriptionTemplateEntity.getDefinition());
// DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
// DocumentBuilder builder = builderFactory.newDocumentBuilder();
// Document xmlDocument = builder.parse(new ByteArrayInputStream(profile.getDefinition().getBytes()));

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/AutoCompleteFieldDataHelperService.java
View File

@ -202,6 +202,11 @@ public class AutoCompleteFieldDataHelperService extends BaseFieldDataHelperServi
return xml;
}
@Override
protected boolean isMultiValueInternal(AutoCompleteDataEntity data) {
return data.getMultiAutoComplete();
}
private @NotNull AutoCompleteSingleData buildAutoCompleteSingleData(AutoCompleteDataEntity.AutoCompleteSingleData data){
AutoCompleteSingleData xml = new AutoCompleteSingleData();
if (data == null) return xml;

6
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/BaseFieldDataHelperService.java
View File

@ -25,6 +25,7 @@ public abstract class BaseFieldDataHelperService<M extends BaseFieldData, PM ext
protected abstract D applyPersistInternal(PM persist, D data);
protected abstract PM importExportMapDataToPersistInternal(IE data, PM persist);
protected abstract IE dataToImportExportXmlInternal(D data, IE xml);
protected abstract boolean isMultiValueInternal(D data);
@Override
public BaseFieldDataEntity<?> newDataInstance() {
return this.newDataInstanceInternal();
@ -59,6 +60,11 @@ public abstract class BaseFieldDataHelperService<M extends BaseFieldData, PM ext
xml.setLabel(data.getLabel());
return this.dataToImportExportXmlInternal((D)data, xml);
}
@Override
public boolean isMultiValue(BaseFieldDataEntity<?> data){
return this.isMultiValueInternal((D)data);
}
@Override
public BaseFieldDataEntity<?> applyPersist(BaseFieldDataPersist persist){
BaseFieldDataEntity<?> instance = this.newDataInstance();

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/BooleanDecisionFieldDataHelperService.java
View File

@ -93,4 +93,9 @@ public class BooleanDecisionFieldDataHelperService extends BaseFieldDataHelperSe
return xml;
}
@Override
protected boolean isMultiValueInternal(BooleanDecisionDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/CheckBoxFieldDataHelperService.java
View File

@ -96,4 +96,9 @@ public class CheckBoxFieldDataHelperService extends BaseFieldDataHelperService<C
protected CheckBoxDataImportExport dataToImportExportXmlInternal(CheckBoxDataEntity data, CheckBoxDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(CheckBoxDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/CurrencyFieldDataHelperService.java
View File

@ -93,4 +93,9 @@ public class CurrencyFieldDataHelperService extends BaseFieldDataHelperService<C
protected CurrencyDataImportExport dataToImportExportXmlInternal(CurrencyDataEntity data, CurrencyDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(CurrencyDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/DataRepositoryFieldDataHelperService.java
View File

@ -96,4 +96,9 @@ public class DataRepositoryFieldDataHelperService extends BaseFieldDataHelperSer
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(DataRepositoryDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/DatasetAutoCompleteFieldDataHelperService.java
View File

@ -99,4 +99,9 @@ public class DatasetAutoCompleteFieldDataHelperService extends BaseFieldDataHelp
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(DatasetAutoCompleteDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/DatasetIdentifierFieldDataHelperService.java
View File

@ -94,4 +94,9 @@ public class DatasetIdentifierFieldDataHelperService extends BaseFieldDataHelper
protected DatasetIdentifierDataImportExport dataToImportExportXmlInternal(DatasetIdentifierDataEntity data, DatasetIdentifierDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(DatasetIdentifierDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/DatePickerFieldDataHelperService.java
View File

@ -94,4 +94,9 @@ public class DatePickerFieldDataHelperService extends BaseFieldDataHelperService
protected DatePickerDataImportExport dataToImportExportXmlInternal(DatePickerDataEntity data, DatePickerDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(DatePickerDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/DmpAutoCompleteFieldDataHelperService.java
View File

@ -99,4 +99,9 @@ public class DmpAutoCompleteFieldDataHelperService extends BaseFieldDataHelperSe
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(DmpAutoCompleteDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/ExternalDatasetFieldDataHelperService.java
View File

@ -101,4 +101,9 @@ public class ExternalDatasetFieldDataHelperService extends BaseFieldDataHelperSe
xml.setType(data.getType());
return xml;
}
@Override
protected boolean isMultiValueInternal(ExternalDatasetDataEntity data) {
return data.getMultiAutoComplete();
}
}

1
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/FieldDataHelperService.java
View File

@ -27,4 +27,5 @@ public interface FieldDataHelperService {
BaseFieldDataEntity<?> applyPersist(BaseFieldDataPersist persist, BaseFieldDataEntity<?> data);
BaseFieldDataPersist importExportMapDataToPersist(BaseFieldDataImportExport xml);
BaseFieldDataImportExport dataToImportExportXml(BaseFieldDataEntity<?> data);
boolean isMultiValue(BaseFieldDataEntity<?> data);
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/FreeTextFieldDataHelperService.java
View File

@ -96,4 +96,9 @@ public class FreeTextFieldDataHelperService extends BaseFieldDataHelperService<F
protected FreeTextDataImportExport dataToImportExportXmlInternal(FreeTextDataEntity data, FreeTextDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(FreeTextDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/JournalRepositoryFieldDataHelperService.java
View File

@ -100,4 +100,9 @@ public class JournalRepositoryFieldDataHelperService extends BaseFieldDataHelper
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(JournalRepositoryDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/LicenseFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class LicenseFieldDataHelperService extends BaseFieldDataHelperService<Li
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(LicenseDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/OrganizationFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class OrganizationFieldDataHelperService extends BaseFieldDataHelperServi
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(OrganizationDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/PublicationFieldDataHelperService.java
View File

@ -76,6 +76,11 @@ public class PublicationFieldDataHelperService extends BaseFieldDataHelperServic
return PublicationDataImportExport.class;
}
@Override
protected boolean isMultiValueInternal(PublicationDataEntity data) {
return data.getMultiAutoComplete();
}
@Override
public List<PublicationData> buildInternal(FieldSet fieldSet, List<PublicationDataEntity> data, EnumSet<AuthorizationFlags> authorizationFlags){
return this.builderFactory.builder(PublicationDataBuilder.class).authorize(authorizationFlags).build(fieldSet, data);

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/PublicationRepositoryFieldDataHelperService.java
View File

@ -100,4 +100,9 @@ public class PublicationRepositoryFieldDataHelperService extends BaseFieldDataHe
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(PublicationRepositoryDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/RadioBoxFieldDataHelperService.java
View File

@ -139,6 +139,11 @@ public class RadioBoxFieldDataHelperService extends BaseFieldDataHelperService<R
return xml;
}
@Override
protected boolean isMultiValueInternal(RadioBoxDataEntity data) {
return false;
}
private @NotNull RadioBoxOption buildOption(RadioBoxDataEntity.Option data){
RadioBoxOption xml = new RadioBoxOption();
if (data == null) return xml;

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/RegistryFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class RegistryFieldDataHelperService extends BaseFieldDataHelperService<R
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(RegistryDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/ResearcherAutoCompleteFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class ResearcherAutoCompleteFieldDataHelperService extends BaseFieldDataH
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(ResearcherAutoCompleteDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/ResearcherFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class ResearcherFieldDataHelperService extends BaseFieldDataHelperService
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(ResearcherDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/RichTextAreaDataFieldDataHelperService.java
View File

@ -96,4 +96,9 @@ public class RichTextAreaDataFieldDataHelperService extends BaseFieldDataHelperS
protected RichTextAreaDataImportExport dataToImportExportXmlInternal(RichTextAreaDataEntity data, RichTextAreaDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(RichTextAreaDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/ServiceFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class ServiceFieldDataHelperService extends BaseFieldDataHelperService<Se
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(ServiceDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/TagFieldDataHelperService.java
View File

@ -96,4 +96,9 @@ public class TagFieldDataHelperService extends BaseFieldDataHelperService<TagDat
protected TagDataImportExport dataToImportExportXmlInternal(TagDataEntity data, TagDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(TagDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/TaxonomyFieldDataHelperService.java
View File

@ -98,4 +98,9 @@ public class TaxonomyFieldDataHelperService extends BaseFieldDataHelperService<T
xml.setMultiAutoComplete(data.getMultiAutoComplete());
return xml;
}
@Override
protected boolean isMultiValueInternal(TaxonomyDataEntity data) {
return data.getMultiAutoComplete();
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/TextAreaFieldDataHelperService.java
View File

@ -95,4 +95,9 @@ public class TextAreaFieldDataHelperService extends BaseFieldDataHelperService<T
protected TextAreaDataImportExport dataToImportExportXmlInternal(TextAreaDataEntity data, TextAreaDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(TextAreaDataEntity data) {
return false;
}
}

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/UploadFieldDataHelperService.java
View File

@ -140,6 +140,11 @@ public class UploadFieldDataHelperService extends BaseFieldDataHelperService<Upl
return xml;
}
@Override
protected boolean isMultiValueInternal(UploadDataEntity data) {
return false;
}
private @NotNull UploadDataOption buildOption(UploadDataEntity.Option data){
UploadDataOption xml = new UploadDataOption();
if (data == null) return xml;

5
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/ValidationFieldDataHelperService.java
View File

@ -95,4 +95,9 @@ public class ValidationFieldDataHelperService extends BaseFieldDataHelperService
protected ValidationDataImportExport dataToImportExportXmlInternal(ValidationDataEntity data, ValidationDataImportExport xml) {
return xml;
}
@Override
protected boolean isMultiValueInternal(ValidationDataEntity data) {
return false;
}
}

6
dmp-backend/core/src/main/java/eu/eudat/service/fielddatahelper/WordListFieldDataHelperService.java
View File

@ -142,6 +142,12 @@ public class WordListFieldDataHelperService extends BaseFieldDataHelperService<W
}
return xml;
}
@Override
protected boolean isMultiValueInternal(WordListDataEntity data) {
return data.getMultiList();
}
private @NotNull ComboBoxDataOptionEntity buildOption(ComboBoxDataEntity.Option data){
ComboBoxDataOptionEntity xml = new ComboBoxDataOptionEntity();
if (data == null) return xml;

104
dmp-backend/core/src/main/java/eu/eudat/utilities/pdf/PDFUtils.java
View File

@ -1,52 +1,52 @@
package eu.eudat.utilities.pdf;
import eu.eudat.model.file.FileEnvelope;
import org.apache.commons.io.IOUtils;
import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
import org.springframework.http.HttpEntity;
import org.springframework.http.HttpHeaders;
import org.springframework.http.MediaType;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.web.client.RestTemplate;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.file.Files;
import java.util.UUID;
public class PDFUtils {
public static File convertToPDF(eu.eudat.depositinterface.models.FileEnvelope file, Environment environment) throws IOException {
FileEnvelope envelope = new FileEnvelope();
envelope.setFilename(file.getFilename());
envelope.setFile(file.getFile());
return convertToPDF(envelope, environment);
}
public static File convertToPDF(FileEnvelope file, Environment environment) throws IOException {
LinkedMultiValueMap<String, Object> map = new LinkedMultiValueMap<>();
String uuid = UUID.randomUUID().toString();
map.add("files", new FileSystemResource(file.getFile()));
map.add("filename", uuid + ".pdf");
HttpHeaders headers = new HttpHeaders();
headers.setContentType(MediaType.MULTIPART_FORM_DATA);
headers.add("Content-disposition", "attachment; filename=" + uuid + ".pdf");
headers.add("Content-type", "application/pdf");
HttpEntity<LinkedMultiValueMap<String, Object>> requestEntity = new HttpEntity<LinkedMultiValueMap<String, Object>>(
map, headers);
byte[] queueResult = new RestTemplate().postForObject(environment.getProperty("pdf.converter.url") + "forms/libreoffice/convert"
, requestEntity, byte[].class);
File resultPdf = new File(environment.getProperty("temp.temp") + uuid + ".pdf");
FileOutputStream output = new FileOutputStream(resultPdf);
IOUtils.write(queueResult, output);
output.close();
Files.deleteIfExists(file.getFile().toPath());
return resultPdf;
}
}
//package eu.eudat.utilities.pdf;
//
//import eu.eudat.model.file.FileEnvelope;
//import org.apache.commons.io.IOUtils;
//import org.springframework.core.env.Environment;
//import org.springframework.core.io.FileSystemResource;
//import org.springframework.http.HttpEntity;
//import org.springframework.http.HttpHeaders;
//import org.springframework.http.MediaType;
//import org.springframework.util.LinkedMultiValueMap;
//import org.springframework.web.client.RestTemplate;
//
//import java.io.File;
//import java.io.FileOutputStream;
//import java.io.IOException;
//import java.nio.file.Files;
//import java.util.UUID;
//
//public class PDFUtils {
//
// public static File convertToPDF(eu.eudat.depositinterface.models.FileEnvelope file, Environment environment) throws IOException {
// FileEnvelope envelope = new FileEnvelope();
// envelope.setFilename(file.getFilename());
//// envelope.setFile(file.getFile());
// return convertToPDF(envelope, environment);
// }
//
// public static File convertToPDF(FileEnvelope file, Environment environment) throws IOException {
// LinkedMultiValueMap<String, Object> map = new LinkedMultiValueMap<>();
// String uuid = UUID.randomUUID().toString();
// map.add("files", new FileSystemResource(file.getFile()));
// map.add("filename", uuid + ".pdf");
// HttpHeaders headers = new HttpHeaders();
// headers.setContentType(MediaType.MULTIPART_FORM_DATA);
// headers.add("Content-disposition", "attachment; filename=" + uuid + ".pdf");
// headers.add("Content-type", "application/pdf");
//
// HttpEntity<LinkedMultiValueMap<String, Object>> requestEntity = new HttpEntity<LinkedMultiValueMap<String, Object>>(
// map, headers);
//
// byte[] queueResult = new RestTemplate().postForObject(environment.getProperty("pdf.converter.url") + "forms/libreoffice/convert"
// , requestEntity, byte[].class);
//
// File resultPdf = new File(environment.getProperty("temp.temp") + uuid + ".pdf");
// FileOutputStream output = new FileOutputStream(resultPdf);
// IOUtils.write(queueResult, output);
// output.close();
// Files.deleteIfExists(file.getFile().toPath());
//
// return resultPdf;
// }
//}

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

@ -34,7 +34,7 @@
<dependency>
<groupId>gr.cite.opendmp</groupId>
<artifactId>repositorydepositbase</artifactId>
<version>1.0.4</version>
<version>2.0.0</version>
</dependency>

3
dmp-backend/web/src/main/java/eu/eudat/controllers/DMPs.java
View File

@ -19,7 +19,6 @@ import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.model.DmpUser;
import eu.eudat.model.file.FileEnvelope;
import eu.eudat.utilities.pdf.PDFUtils;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.datasetwizard.DatasetsToBeFinalized;
import eu.eudat.models.data.dmp.DataManagementPlan;
@ -221,7 +220,7 @@ public class DMPs extends BaseController {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
FileEnvelope file = this.dataManagementPlanManager.getWordDocument(id, configLoader);
String name = file.getFilename().substring(0, file.getFilename().length() - 5).replace(" ", "_").replace(",", "_");
File pdffile = PDFUtils.convertToPDF(file, environment);
File pdffile = null; //PDFUtils.convertToPDF(file, environment); //TODO
InputStream resource = new FileInputStream(pdffile);
logger.info("Mime Type of " + name + " is " +
new MimetypesFileTypeMap().getContentType(file.getFile()));

17
dmp-backend/web/src/main/java/eu/eudat/controllers/Datasets.java
View File

@ -3,11 +3,7 @@ package eu.eudat.controllers;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.data.DescriptionEntity;
import eu.eudat.data.DescriptionTemplateEntity;
import eu.eudat.data.query.items.item.datasetprofile.DatasetProfileWizardAutocompleteRequest;
import eu.eudat.data.query.items.table.dataset.DatasetPublicTableRequest;
import eu.eudat.data.query.items.table.dataset.DatasetTableRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.exceptions.datasetwizard.DatasetWizardCannotUnlockException;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.managers.DatasetManager;
@ -19,19 +15,15 @@ import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.forms.VisibilityRuleService;
import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
import eu.eudat.model.file.FileEnvelope;
import eu.eudat.utilities.pdf.PDFUtils;
import eu.eudat.models.data.dataset.DatasetOverviewModel;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.dmp.AssociatedProfile;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.listingmodels.DataManagementPlanOverviewModel;
import eu.eudat.models.data.listingmodels.DatasetListingModel;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.types.ApiMessageCode;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.query.QueryFactory;
import jakarta.persistence.NoResultException;
import jakarta.transaction.Transactional;
import org.apache.poi.util.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -44,9 +36,6 @@ import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.multipart.MultipartFile;
import jakarta.persistence.NoResultException;
import jakarta.transaction.Transactional;
import javax.management.InvalidApplicationException;
import java.io.File;
import java.io.FileInputStream;
@ -244,7 +233,7 @@ public class Datasets extends BaseController {
if (fileName.endsWith(".docx")){
fileName = fileName.substring(0, fileName.length() - 5);
}
File pdffile = PDFUtils.convertToPDF(file, environment);
File pdffile = null; // PDFUtils.convertToPDF(file, environment); //TODO
InputStream resource = new FileInputStream(pdffile);
HttpHeaders responseHeaders = new HttpHeaders();

95
dmp-backend/web/src/main/java/eu/eudat/controllers/DepositController.java
View File

@ -1,95 +0,0 @@
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;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import java.util.List;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/deposit/"})
public class DepositController extends BaseController {
private static final Logger logger = LoggerFactory.getLogger(DepositController.class);
private final DepositManager depositManager;
private final AuthorizationService authorizationService;
private final RepositoryDepositService repositoryDepositService;
@Autowired
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"})
public @ResponseBody
ResponseEntity<ResponseItem<List<RepositoryConfig>>> getAvailableRepos() {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
List<RepositoryConfig> ids = this.repositoryDepositService.getAvailableConfigurations();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<RepositoryConfig>>().status(ApiMessageCode.NO_MESSAGE).payload(ids));
}
@RequestMapping(method = RequestMethod.POST, value = {"/getAccessToken"})
public @ResponseBody
ResponseEntity<ResponseItem<String>> getAccessToken(@RequestBody DepositCode depositCode) throws Exception {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
String accessToken = this.depositManager.authenticate(depositCode.getRepositoryId(), depositCode.getCode());
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.NO_MESSAGE).payload(accessToken));
}
@RequestMapping(method = RequestMethod.POST, value = {"/createDoi"})
public @ResponseBody
ResponseEntity<ResponseItem<EntityDoi>> createDoi(@RequestBody DepositRequest depositRequest) {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
try {
EntityDoi doi = this.repositoryDepositService.deposit(depositRequest);
if(doi != null){
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<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<EntityDoi>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to create DOI for the Data Management Plan: " + e.getMessage()));
}
}
@RequestMapping(method = RequestMethod.GET, value = {"/logo/{repositoryId}"})
public @ResponseBody
ResponseEntity<ResponseItem<String>> getLogo(@PathVariable("repositoryId") String repositoryId) {
this.authorizationService.authorizeForce(Permission.AdminRole, Permission.ManagerRole, Permission.UserRole, Permission.AnonymousRole);
try {
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));
}
else{
return ResponseEntity.status(HttpStatus.NOT_FOUND).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message(repositoryId + " has no logo").payload(null));
}
} catch (Exception e) {
logger.error(e.getMessage(), e);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message("Failed to load " + repositoryId + "'s logo: " + e.getMessage()));
}
}
}

102
dmp-backend/web/src/main/java/eu/eudat/controllers/v2/DepositController.java Normal file
View File

@ -0,0 +1,102 @@
package eu.eudat.controllers.v2;
import eu.eudat.audit.AuditableAction;
import eu.eudat.authorization.Permission;
import eu.eudat.controllers.BaseController;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.censorship.EntityDoiCensor;
import eu.eudat.model.censorship.deposit.DepositConfigurationCensor;
import eu.eudat.model.deposit.DepositConfiguration;
import eu.eudat.model.persist.deposit.DepositAuthenticateRequest;
import eu.eudat.model.persist.deposit.DepositRequest;
import eu.eudat.service.deposit.DepositService;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.auditing.AuditService;
import gr.cite.tools.data.censor.CensorFactory;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.LoggerService;
import gr.cite.tools.logging.MapLogEntry;
import gr.cite.tools.validation.MyValidate;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.*;
import java.util.AbstractMap;
import java.util.List;
import java.util.Map;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/deposit/"})
public class DepositController extends BaseController {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DepositController.class));
private final AuthorizationService authorizationService;
private final DepositService depositService;
private final CensorFactory censorFactory;
private final AuditService auditService;
@Autowired
public DepositController(ApiContext apiContext, AuthorizationService authorizationService, DepositService depositService, CensorFactory censorFactory, AuditService auditService){
super(apiContext);
this.authorizationService = authorizationService;
this.depositService = depositService;
this.censorFactory = censorFactory;
this.auditService = auditService;
}
@GetMapping("/repositories/available")
public List<eu.eudat.model.deposit.DepositConfiguration> getAvailableRepos(FieldSet fieldSet) {
logger.debug(new MapLogEntry("retrieving" + DepositConfiguration.class.getSimpleName()).And("fields", fieldSet));
this.censorFactory.censor(DepositConfigurationCensor.class).censor(fieldSet, null);
List<DepositConfiguration> model = this.depositService.getAvailableConfigurations(fieldSet);
this.auditService.track(AuditableAction.Deposit_GetAvailableRepositories, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("fields", fieldSet)
));
//this.auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
return model;
}
@PostMapping("/get-access-token")
public String getAccessToken(@MyValidate @RequestBody DepositAuthenticateRequest model) throws Exception {
logger.debug(new MapLogEntry("get access token" + DepositAuthenticateRequest.class.getSimpleName()).And("model", model));
String accessToken = this.depositService.authenticate(model);
this.auditService.track(AuditableAction.Deposit_GetAccessToken, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("model", model)
));
return accessToken;
}
@PostMapping("/deposit")
@Transactional
public EntityDoi deposit(@MyValidate @RequestBody DepositRequest model) throws Exception {
logger.debug(new MapLogEntry("persisting" + DepositRequest.class.getSimpleName()).And("model", model).And("fieldSet", model.getProject()));
this.censorFactory.censor(EntityDoiCensor.class).censor(model.getProject(), null);
EntityDoi persisted = this.depositService.deposit(model);
this.auditService.track(AuditableAction.Deposit_Deposit, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("model", model)
));
//this.auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
return persisted;
}
@GetMapping("/repositories/{repositoryId}/logo")
public String getLogo(@PathVariable("repositoryId") String repositoryId) {
logger.debug(new MapLogEntry("get logo" + DepositConfiguration.class.getSimpleName()).And("repositoryId", repositoryId));
String logo = this.depositService.getLogo(repositoryId);
this.auditService.track(AuditableAction.Deposit_GetLogo, Map.ofEntries(
new AbstractMap.SimpleEntry<String, Object>("repositoryId", repositoryId)
));
//this.auditService.trackIdentity(AuditableAction.IdentityTracking_Action);
return logo;
}
}

2
dmp-backend/web/src/main/java/eu/eudat/controllers/v2/DescriptionTemplateController.java
View File

@ -94,7 +94,7 @@ public class DescriptionTemplateController {
}
@GetMapping("{id}")
public DescriptionTemplate get(@PathVariable("id") UUID id, FieldSet fieldSet, Locale locale) throws MyApplicationException, MyForbiddenException, MyNotFoundException {
public DescriptionTemplate get(@PathVariable("id") UUID id, FieldSet fieldSet) throws MyApplicationException, MyForbiddenException, MyNotFoundException {
logger.debug(new MapLogEntry("retrieving" + DescriptionTemplate.class.getSimpleName()).And("id", id).And("fields", fieldSet));
this.censorFactory.censor(DescriptionTemplateCensor.class).censor(fieldSet, null);

44
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java
View File

@ -19,8 +19,7 @@ import eu.eudat.commons.enums.old.notification.NotifyState;
import eu.eudat.data.query.items.table.dataset.DatasetTableRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
import eu.eudat.depositinterface.models.DMPDepositModel;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.models.DmpDepositModel;
import eu.eudat.exceptions.datamanagementplan.DMPNewVersionException;
import eu.eudat.exceptions.datamanagementplan.DMPWithDatasetsDeleteException;
import eu.eudat.exceptions.security.ForbiddenException;
@ -28,20 +27,18 @@ import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.model.DmpUser;
import eu.eudat.model.mapper.deposit.DMPToDepositMapper;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.forms.VisibilityRuleService;
import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.commons.types.xml.XmlBuilder;
import eu.eudat.model.EntityDoi;
import eu.eudat.model.file.FileEnvelope;
import eu.eudat.query.*;
import eu.eudat.utilities.pdf.PDFUtils;
import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
import eu.eudat.logic.utilities.documents.word.WordBuilder;
import eu.eudat.logic.utilities.documents.xml.ExportXmlBuilder;
import eu.eudat.model.doi.DepositRequest;
import eu.eudat.model.doi.Doi;
import eu.eudat.model.persist.deposit.DepositRequest;
import eu.eudat.models.HintedModelFactory;
import eu.eudat.models.data.dataset.DatasetOverviewModel;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
@ -57,6 +54,7 @@ import eu.eudat.models.data.listingmodels.*;
import eu.eudat.models.data.project.ProjectDMPEditorModel;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.queryable.QueryableList;
import eu.eudat.service.deposit.DepositService;
import eu.eudat.service.dmpblueprint.DmpBlueprintService;
import eu.eudat.types.MetricNames;
import gr.cite.commons.web.authz.service.AuthorizationService;
@ -114,7 +112,7 @@ public class DataManagementPlanManager {
private UserManager userManager;
private final MetricsManager metricsManager;
private final ConfigLoader configLoader;
private List<RepositoryDeposit> repositoriesDeposit;
private DepositService repositoriesDeposit;
private final UserScope userScope;
private final AuthorizationService authorizationService;
private final DmpBlueprintService dmpBlueprintService;
@ -123,7 +121,7 @@ public class DataManagementPlanManager {
@Autowired
public DataManagementPlanManager(XmlHandlingService xmlHandlingService, ApiContext apiContext, DatasetManager datasetManager, Environment environment, RDAManager rdaManager, UserManager userManager,
MetricsManager metricsManager, ConfigLoader configLoader, List<RepositoryDeposit> repositoriesDeposit, UserScope userScope, AuthorizationService authorizationService, DmpBlueprintService dmpBlueprintService, QueryFactory queryFactory) {
MetricsManager metricsManager, ConfigLoader configLoader, DepositService repositoriesDeposit, UserScope userScope, AuthorizationService authorizationService, DmpBlueprintService dmpBlueprintService, QueryFactory queryFactory) {
this.xmlHandlingService = xmlHandlingService;
this.apiContext = apiContext;
this.datasetManager = datasetManager;
@ -2573,8 +2571,8 @@ public class DataManagementPlanManager {
@Transactional
public Doi createDoi(DepositRequest depositRequest) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(UUID.fromString(depositRequest.getDmpId()));
public EntityDoi createDoi(DepositRequest depositRequest) throws Exception {
DmpEntity dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(depositRequest.getDmpId());
if (!isUserOwnerOfDmp(dmp))
throw new Exception("User is not authorized to invoke this action");
if (!dmp.getStatus().equals(DmpStatus.Finalized))
@ -2582,16 +2580,16 @@ public class DataManagementPlanManager {
/*if (dmp.getDoi() != null)
throw new Exception("DMP already has a DOI");*/
FileEnvelope file = getWordDocument(depositRequest.getDmpId(), configLoader);
FileEnvelope file = getWordDocument(depositRequest.getDmpId().toString(), configLoader);
String name = file.getFilename().substring(0, file.getFilename().length() - 5).replaceAll("[^a-zA-Z0-9_+ ]", "").replace(" ", "_").replace(",", "_");
File pdfFile = PDFUtils.convertToPDF(file, environment);
byte[] pdfFile = null; //PDFUtils.convertToPDF(file, environment); //TODO
eu.eudat.depositinterface.models.FileEnvelope pdfEnvelope = new eu.eudat.depositinterface.models.FileEnvelope();
pdfEnvelope.setFile(pdfFile);
pdfEnvelope.setFilename(name + ".pdf");
eu.eudat.depositinterface.models.FileEnvelope rdaJsonFile = new eu.eudat.depositinterface.models.FileEnvelope();
try {
FileEnvelope rdaJsonDocument = getRDAJsonDocument(depositRequest.getDmpId());
rdaJsonFile.setFile(rdaJsonDocument.getFile());
FileEnvelope rdaJsonDocument = getRDAJsonDocument(depositRequest.getDmpId().toString());
//rdaJsonFile.setFile(rdaJsonDocument.getFile()); //TODO
rdaJsonFile.setFilename(rdaJsonDocument.getFilename());
} catch (Exception e) {
logger.error(e.getMessage(), e);
@ -2600,20 +2598,16 @@ public class DataManagementPlanManager {
File supportingFilesZip = this.createSupportingFilesZip(dmp);
DMPDepositModel dmpDepositModel = DMPToDepositMapper.fromDMP(dmp, pdfEnvelope, rdaJsonFile, supportingFilesZip, previousDOI);
DmpDepositModel dmpDepositModel = new DmpDepositModel(); // DMPToDepositMapper.fromDMP(dmp, pdfEnvelope, rdaJsonFile, supportingFilesZip, previousDOI);//TODO
String finalDoi = null;
for(RepositoryDeposit repo: this.repositoriesDeposit){
if(repo.getConfiguration().stream().anyMatch(x-> x.getRepositoryId().equals(depositRequest.getRepositoryId()))){
try {
finalDoi = repo.deposit(depositRequest.getRepositoryId(), dmpDepositModel, depositRequest.getAccessToken());
finalDoi = this.repositoriesDeposit.deposit(depositRequest).getDoi();
} catch (Exception e) {
logger.error(e.getMessage(), e);
return null;
}
}
}
Doi doiModel = null;
EntityDoi doiModel = null;
if (finalDoi != null) {
EntityDoiEntity doiEntity = new EntityDoiEntity();
@ -2630,15 +2624,15 @@ public class DataManagementPlanManager {
// dmp.getDois().add(doiEntity);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
doiModel = new Doi().fromDataModel(doiEntity);
doiModel = new EntityDoi();//.fromDataModel(doiEntity); //TODO
}
if(supportingFilesZip != null) {
Files.deleteIfExists(supportingFilesZip.toPath());
}
Files.deleteIfExists(rdaJsonFile.getFile().toPath());
Files.deleteIfExists(pdfFile.toPath());
Files.deleteIfExists(file.getFile().toPath());
// Files.deleteIfExists(rdaJsonFile.getFile().toPath()); //TODO
// Files.deleteIfExists(pdfFile.toPath());
// Files.deleteIfExists(file.getFile().toPath());
return doiModel;

73
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DepositManager.java
View File

@ -1,73 +0,0 @@
package eu.eudat.logic.managers;
import eu.eudat.depositinterface.repository.RepositoryDeposit;
import eu.eudat.depositinterface.repository.RepositoryDepositConfiguration;
import eu.eudat.model.doi.DepositRequest;
import eu.eudat.model.doi.Doi;
import eu.eudat.model.doi.RepositoryConfig;
import jakarta.transaction.Transactional;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.core.ParameterizedTypeReference;
import org.springframework.stereotype.Component;
import org.springframework.web.reactive.function.client.WebClient;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
@Component
public class DepositManager {
private static final Logger logger = LoggerFactory.getLogger(DepositManager.class);
//private List<RepositoryDeposit> repositories;
private DataManagementPlanManager dataManagementPlanManager;
private final List<RepositoryDeposit> depositClients;
@Autowired
public DepositManager(/*List<RepositoryDeposit> repositories,*/ DataManagementPlanManager dataManagementPlanManager, @Qualifier("depositClients") List<RepositoryDeposit> depositClients){
//this.repositories = repositories;
this.dataManagementPlanManager = dataManagementPlanManager;
this.depositClients = depositClients;
}
public List<RepositoryConfig> getAvailableRepos() {
List<RepositoryConfig> reposConfigModel = new ArrayList<>();
for (RepositoryDeposit r: this.depositClients) {
List<RepositoryDepositConfiguration> repoConf = r.getConfiguration();
if(repoConf != null) {
for(RepositoryDepositConfiguration cf: repoConf){
RepositoryConfig repoModel = new RepositoryConfig();
reposConfigModel.add(repoModel.toModel(cf));
}
}
}
return reposConfigModel;
}
public String authenticate(String id, String code) {
for(RepositoryDeposit r: this.depositClients){
if(r.getConfiguration().stream().anyMatch(x -> x.getRepositoryId().equals(id))){
return r.authenticate(id, code);
}
}
return null;
}
@Transactional
public Doi deposit(DepositRequest depositRequest) throws Exception {
return this.dataManagementPlanManager.createDoi(depositRequest);
}
public String getRepositoryLogo(String repositoryId){
for(RepositoryDeposit r: this.depositClients){
Optional<RepositoryDepositConfiguration> cf = r.getConfiguration().stream().filter(x -> x.getRepositoryId().equals(repositoryId)).findFirst();
if(cf.isPresent()){
return cf.get().isHasLogo() ? r.getLogo(repositoryId) : null;
}
}
return null;
}
}

8
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlan.java
View File

@ -2,7 +2,7 @@ package eu.eudat.models.data.dmp;
import eu.eudat.data.DmpEntity;
import eu.eudat.model.DmpUser;
import eu.eudat.model.doi.Doi;
import eu.eudat.model.EntityDoi;
import eu.eudat.models.DataModel;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.dynamicfields.DynamicFieldWithValue;
@ -33,7 +33,7 @@ public class DataManagementPlan implements DataModel<DmpEntity, DataManagementPl
private List<DynamicFieldWithValue> dynamicFields;
private Map<String, Object> properties;
private List<DmpUser> users;
private List<Doi> dois;
private List<EntityDoi> dois;
private Project project;
private Funder funder;
private Boolean isPublic;
@ -173,10 +173,10 @@ public class DataManagementPlan implements DataModel<DmpEntity, DataManagementPl
this.users = users;
}
public List<Doi> getDois() {
public List<EntityDoi> getDois() {
return dois;
}
public void setDois(List<Doi> dois) {
public void setDois(List<EntityDoi> dois) {
this.dois = dois;
}

18
dmp-backend/web/src/main/java/eu/eudat/models/data/listingmodels/DataManagementPlanOverviewModel.java
View File

@ -1,12 +1,8 @@
package eu.eudat.models.data.listingmodels;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.commons.enums.DescriptionStatus;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.data.DmpEntity;
import eu.eudat.model.DmpUser;
import eu.eudat.model.doi.Doi;
import eu.eudat.model.EntityDoi;
import eu.eudat.models.DataModel;
import eu.eudat.models.data.dataset.DatasetOverviewModel;
import eu.eudat.models.data.dmp.AssociatedProfile;
@ -14,9 +10,9 @@ import eu.eudat.models.data.dmp.Organisation;
import eu.eudat.models.data.dmp.Researcher;
import eu.eudat.models.data.grant.GrantOverviewModel;
import java.time.Instant;
import java.util.*;
import java.util.stream.Collectors;
import java.util.Date;
import java.util.List;
import java.util.UUID;
public class DataManagementPlanOverviewModel implements DataModel<DmpEntity, DataManagementPlanOverviewModel> {
private String id;
@ -37,7 +33,7 @@ public class DataManagementPlanOverviewModel implements DataModel<DmpEntity, Dat
private String description;
private boolean isPublic;
private Date publishedAt;
private List<Doi> dois;
private List<EntityDoi> dois;
public String getId() {
@ -166,10 +162,10 @@ public class DataManagementPlanOverviewModel implements DataModel<DmpEntity, Dat
this.publishedAt = publishedAt;
}
public List<Doi> getDois() {
public List<EntityDoi> getDois() {
return dois;
}
public void setDois(List<Doi> dois) {
public void setDois(List<EntityDoi> dois) {
this.dois = dois;
}

19
dmp-backend/web/src/main/resources/config/cache.yml
View File

@ -2,14 +2,6 @@ cache:
manager:
fallbackToNoOpCache: true
caffeineCaches:
- names: [ "apikey" ]
allowNullValues: true
initialCapacity: 100
maximumSize: 500
enableRecordStats: false
expireAfterWriteMinutes: 10
expireAfterAccessMinutes: 10
refreshAfterWriteMinutes: 10
- names: [ "userBySubjectId" ]
allowNullValues: true
initialCapacity: 100
@ -34,7 +26,7 @@ cache:
expireAfterWriteMinutes: 10
expireAfterAccessMinutes: 10
refreshAfterWriteMinutes: 10
- names: [ "deposit" ]
- names: [ "depositConfigById" ]
allowNullValues: true
initialCapacity: 100
maximumSize: 500
@ -51,9 +43,6 @@ cache:
expireAfterAccessMinutes: 1
refreshAfterWriteMinutes: 1
mapCaches:
apiKey:
name: apikey
keyPattern: resolve_$keyhash$:v0
userBySubjectId:
name: userBySubjectId
keyPattern: user_by_subject_$subject$:v0
@ -66,6 +55,6 @@ cache:
dashboardStatisticsByUserId:
name: dashboardStatisticsByUserId
keyPattern: dashboard_stats_by_usr_$key$:v0
deposit:
name: deposit
keyPattern: base:v0
depositConfigById:
name: depositConfigById
keyPattern: deposit_config_by_id_$repositoryId$:v0

14
dmp-backend/web/src/main/resources/config/permissions.yml
View File

@ -94,6 +94,20 @@ permissions:
allowAnonymous: false
allowAuthenticated: false
# Deposit
BrowseDeposit:
roles:
- Admin
clients: [ ]
allowAnonymous: false
allowAuthenticated: false
EditDeposit:
roles:
- Admin
clients: [ ]
allowAnonymous: false
allowAuthenticated: false
# Language
BrowseLanguage:
roles: [ ]

6
dmp-migration-tool/web/src/main/resources/config/application-devel.properties
View File

@ -1,9 +1,9 @@
dmp.domain = http://localhost:4200
####################PERSISTENCE OVERRIDES CONFIGURATIONS##########
database.url=jdbc:postgresql://dbserver02.local.cite.gr:5432/dmptool
database.username=dmtadm
database.password=t00L4DM@18!
database.url=jdbc:postgresql://dbserver05.local.cite.gr/opendmp-prod-anonym
database.username=opendmp-psql
database.password=EG$NCKq&mARNFCtFfM
spring.datasource.maxIdle=10
spring.datasource.minIdle=5
spring.datasource.maxActive=10